Biology subjects

Marin, A.

Publications and source records attributed to Marin, A..

At least 19 recordsLinked to original sources

bioRxiv2026

BATOseq-PE: A public batoid DNA library with the first molecular insights into the cryptic diversity, genetic health, and management of Peruvian marine rays

Batoids (rays, skates, and relatives) are among the most threatened cartilaginous fishes globally, yet the molecular diversity of Peruvian taxa remains poorly evaluated. Furthermore, regional barcode sequences for high-conservation-priority taxa, such as sawfish, manta, and devil rays, are often restricted to private records, hindering essential phylogeographic and population structure assessments. To bridge this gap, we developed BATOseq-PE, the first public genetic reference library for Peruvian marine batoids, covering 14 species sequenced in vitro from local specimens, complemented by a novel in silico assembled mitogenome for Notoraja martinezi. This open-access repository contributes 73 novel COI barcodes, providing robust taxonomic resolution across 15 molecular operational taxonomic units (MOTUs) and Barcode Index Numbers (BINs). Notably, we provide the first Peruvian public records for high-priority species such as Mobula munkiana, Mobula thurstoni, Myliobatis peruviana, Rostroraja velezi, and the first global public barcodes for N. martinezi and Zapteryx xyster. By coupling BATOseq-PE with global datasets, we conducted the first multi-taxa screening for delimitation and phylogeographic assessments on Peruvian batoids, revealing a cryptic lineage within R. velezi and genetic connectivity patterns suggesting female philopatry in Mobula mobular. Finally, by integrating nucleotide diversity into a Genetic Diversity Risk Indicator (GDRI) alongside ecological and fishery data, we identified an alarming trend where heavy fishing pressure overlaps with extinction risk and depleted genetic diversity, allowing us to suggest data-driven, tailored management strategies. BATOseq-PE represents a valuable resource to accelerate taxonomic and population assessments, ultimately fostering ray conservation through the integration of genetic frameworks into fishery management.

genetics↗

bioRxiv2026

Incorporation of native HCV E1E2 into a nanoparticle vaccine platform

Development of an effective HCV vaccine requires the induction of both broadly neutralizing antibodies (bnAbs) and a robust cellular response. One issue that has arisen is that HCV subunit vaccines have limited immunogenicity, thus requiring multivalent formats in order to elicit a robust anti-HCV immune response. Toward that end, nanoparticle vaccines possess the ability to facilitate a controlled multivalent presentation and trafficking to lymph nodes, where they can interact with both arms of the immune system. Here, we used a soluble, secreted form of E1E2 (sE1E2) to assemble native E1E2 into a nanoparticle platform using a post-purification coupling assembly system. Nanoparticles were assembled by purifying sE1E2 containing a C-terminal SpyTag and an mi3-SpyCatcher fusion separately and covalently coupling the components via incubation. Free sE1E2-SpyTag was removed from nanoparticle preparations via gel filtration. The sE1E2-mi3 nanoparticles are fully competent to bind conformation-dependent bnAbs, indicating retention of a native assembly in the nanoparticle format. Electron microscopy analysis showed a clear incorporation of sE1E2 on the surface of the nanoparticle. Immunogenicity of sE1E2-mi3 nanoparticles was examined relative to sE1E2 alone and membrane-bound E1E2 (mbE1E2) following inoculation of groups of CD1 mice. Assessment of the immunogenicity of the sE1E2-mi3 nanoparticles showed that the nanoparticle assembly has a similar immunogenicity profile to that of mbE1E2 after only a prime and one boost, and overall superior to sE1E2. This proof-of-principle study sets the stage for further exploration of nanoparticles and other multivalent platforms for the development of E1E2-based vaccines. ImportanceHepatitis C virus infects approximately 50 million people, and at present no effective HCV vaccine exists. Due to the high sequence variability of HCV and the resulting difficulty in developing a vaccine that elicits a broadly neutralizing response, multiple efforts are underway to enhance the immunogenicity of HCV vaccine candidates. In this study, we incorporated native soluble, secreted E1E2 (sE1E2) into a 60-mer nanoparticle via the SpyTag-SpyCatcher system and covalent isopeptide bond attachment using the purified components. These nanoparticles are antigenically intact and elicit a neutralizing antibody response at an earlier time point in the immunization regimen than the corresponding subunit vaccine. These studies show that a well-characterized sE1E2 platform compatible with multiple genotypes can be coupled to nanoparticles for use as a vaccine candidate.

microbiology↗

bioRxiv2026

Castration-resistant prostate cancer cells are addicted to the high activity of cyclin-dependent kinase 2

BackgroundCyclin-dependent kinases drive the progression through the cell cycle and thereby form classical targets for cancer therapy. In prostate cancer (PC), the first line of therapy typically targets androgen receptor (AR), but it frequently leads to development of incurable form of the disease, castration-resistant PC (CRPC). Here, we sought to understand if CRPC cells are selectively addicted to a specific cell cycle kinase. MethodsWe used PC and CRPC patient data to evaluate transcriptional changes and modeled the responses in vitro using multiple models of PC, CRPC and normal cells. Development of a CDK2 inhibitor-resistant CRPC cell line, and a compound screen were used to identify chronic and acute vulnerabilities to augment the efficacy of our candidate therapy in multiple PC, CRPC and also normal cells, to assure selectivity. ResultsWe show that the emergence of CRPC is associated with significant upregulation of cyclins that positively regulate cyclin-dependent kinase 2 (CDK2) and downregulation of CDK4 cyclins. Accordingly, CDK2-specific inhibitors and its knock down efficiently reduce proliferation of PC and CRPC cells. CDK2 inhibitor-resistant CRPC model displayed transcriptional rewiring of cell cycle regulators, characterized by a shift towards CDK4/6-dependency and increased AR-signaling. Combinatorial drug screen discovered both antagonistic and additive combinations, and we show that AR inhibitors selectively augment the efficacy of CDK2 inhibitors against PC and CRPC cells, but the combination is not toxic to normal cells. ConclusionWe discovered that CRPC cells are addicted to high CDK2 activity and show that combination of CDK2 inhibitors with the currently used anti-CRPC therapies selectively augment their efficacy.

cancer biology↗

bioRxiv2026

Hypanus brevis: a newly resurrected Eastern South Pacific stingray lineage revealed by integrative taxonomy

Hypanus brevis (Garman, 1880) and Hypanus dipterurus (Jordan & Gilbert, 1880) are currently considered as a conspecific lineage of the Eastern Pacific "diamond stingray". This group has been the subject of nomenclatural disputes for about 145 years, with H. brevis accepted as the junior synonym. To clarify the historical confusion surrounding this lineage, we employed an integrative taxonomic approach using specimens from the Eastern North and Eastern South Pacific (ENP and ESP). Both single (COI) and multilocus (COI - 16S rRNA) genetic analyses revealed a distinct evolutionary unit in the ESP. While morphological analyses detected subtle differences between ENP and ESP specimens (e.g., disc length and internostril width), most characters exhibited significant overlap, suggesting low evolutionary divergence. A Bayesian molecular clock analysis estimated this divergence at approximately 5.6 Ma. In accordance with Garmans (1880) original description based on specimens from Paita (northern Peru), we formally resurrect H. brevis from synonymy with H. dipterurus. Our findings suggest an anti-tropical speciation pathway, with core populations of H. brevis and H. dipterurus restricted to the temperate waters of the ESP and ENP, respectively. Notably, a single, fixed COI haplotype was detected in all H. brevis specimens from the north-central Peruvian coast. This result may indicate a severe bottleneck event, raising concerns about the genetic health and long-term viability of this vulnerable species. Finally, we analyzed historical fishery data of H. brevis to infer its current population status, suggesting targeted conservation measures and precautionary management to prevent further loss of genetic diversity.

genetics↗

bioRxiv2025

Tracing the illicit Peruvian delicacy: proof-of-concept multiplex-PCR for the simultaneous detection of seven commercial Macrobrachium prawn species

The genus Macrobrachium (Decapoda, Palaemonidae) comprises nearly 300 prawn species distributed worldwide. At least nine of these species naturally inhabit the Pacific slope river systems of Peru, where most sustain significant artisanal fisheries and are highly prized as a luxury delicacy in the nations traditional cuisine. Here, we developed and validated a multiplex PCR assay with species-specific primers to identify seven Macrobrachium species of economic importance to Peru. Through robust validation, our assays achieved high specificity and efficiency, enabling fast and simultaneous identification of the seven target species. The utility of our novel multiplex PCR assay was evaluated as a proof-of-concept tool for conducting the first molecular monitoring of species diversity and illegal trade in Peruvian prawns across different commercial sectors. Among the 51 analyzed commercial prawn samples, a total of four species were detected, including M. caementarius (82.4%), M. rosenbergii (11.8%), M. americanum (3.9%), and M. gallus (1.9%). Notably, our molecular monitoring in restaurants revealed the first evidence of illegal trade in native wild-caught prawns in La Libertad region occurring during the reproductive closed season, when only the market of the exotic farmed prawn M. rosenbergii is permitted. These findings underscore the urgent need for enhanced monitoring programs in prawn fisheries in northern Peru, as current efforts are mainly focused on more productive central and southern regions. Our multiplex PCR assay provides a robust and efficient tool that can assist authorities and researchers in monitoring efforts, combating illegal trade, conducting diversity research, and supporting conservation.

genetics↗

bioRxiv2025

Viral transport in evaporating sessile model respiratory droplets

Viral particles, or virions, may remain infectious in the dry residue of respiratory droplets for times as long as hours. This is counterintuitive, since salt concentration increases dramatically as the drops water evaporates, making the drop a harsh environment for virions. It has been hypothesized that the drop components (mainly salt and the glycoprotein mucin) segregate during the evaporation process, with virions being transported away from salt deposits. This would protect them from the salts damaging effects. Thus, understanding where virions reside in a drop residue is essential to disentangle the physico-chemical mechanisms that drive their inactivation. However, determining the virion location in an environment as heterogeneous and complex as a respiratory drop is challenging. Here we show experimentally that virions in the drops dry residue are found mainly forming aggregates in protein-rich regions, outside salt crystals. The mechanism yielding the observed viral spatial distribution can be found in the internal flow phenomena within the droplet, which are described using numerical simulations. We anticipate our results to be relevant to explain the discrepancies in the infectivity decay rates measured in respiratory drops between previous reported studies.

biophysics↗

bioRxiv2025

Single-Cell Network Analysis Identifies CLEC4E as a Key Mediator of Proinflammatory mDC Responses in Influenza Infection

The severity of influenza is often driven by an excessive host immune response rather than the virus itself, yet the key molecular drivers within specific immune cells remain poorly understood. While recent single-cell RNA sequencing studies have successfully identified immune populations involved, they have largely not identified the upstream drivers modulating their pro-inflammatory functions. Here we employed an integrated single-cell co-expression network to address this gap. Our analysis identified myeloid dendritic cells (mDCs) as central to pro-inflammatory response during infection. Through a multi-layered key driver analysis, we pinpointed C-type lectin, CLEC4E as a top candidate modulating this pathological inflammatory response. The role of CLEC4E was confirmed in an independent single-cell dataset from influenza-infected patients and further validated in vivo. Pharmacological inhibition of CLEC4E in a murine influenza model significantly reduced disease severity and lower viral titers in the lungs. This study not only clarifies that CLEC4E overexpression in mDCs contributes to pro-inflammatory signaling pathways influencing influenza severity but also shows the power of single-cell network approaches to uncover novel and robust therapeutic targets hidden within complex immune responses.

systems biology↗

bioRxiv2025

From berries to brain: Assessing the impact of (poly)phenols in the MPTP mouse model of Parkinson's disease

The growing burden of chronic neurodegenerative diseases (NDs), particularly Parkinsons disease (PD), prompts the need for effective preventive strategies and treatments. Dietary (poly)phenols have emerged for their neuroprotective potential. This study investigated a (poly)phenol-enriched diet, comprising a berry mixture, to counteract key PD hallmarks in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-intoxicated mice and elucidate the phenolic metabolic fingerprint underlying these effects. The berry-enriched diet prevented motor deficits in the MPTP mice model, preserved dopaminergic neurons in the midbrain, reduced glial activation and gene expression of inflammatory cytokines. Notably, berries also attenuated macrophage infiltration observed in the substantia nigra 7 days post-MPTP. Metabolomic analysis revealed distinct phenolic signatures in plasma and brain tissue between standard- and berry-fed mice. Overall, this pioneering study provides compelling evidence that a (poly)phenol-enriched diet may play a protective role in neurodegenerative disorders, highlighting its potential for future strategies to prevent or slow PD progression.

neuroscience↗

bioRxiv2025

Distinct and Combined Interferon-α/β-receptor-1 Loss in Neurons and Astrocytes Disrupt Brain Energy Metabolism and Drive Parkinsonian Dementia

Dysregulated interferon-alpha/beta-receptor 1 (IFNAR1) signaling was recently identified to contribute to the development of sporadic Parkinsons Disease (PD) into PD with Dementia (PDD). The molecular, cellular, and phenotypic impacts of brain IFNAR1 loss in aging have not been explored in vivo, which may reveal novel disease mechanisms and therapeutic targets. Here it is shown that baseline IFNAR1 expression varies in the major brain cell types, including neurons and astrocytes, and is differentially affected in PD and Lewy Body Dementia patients compared to unaffected controls. Neuron- and astrocyte-specific transcriptomic and proteomic alterations in Ifnar1-/- mice implicate mitochondrial defects and synergistic dysfunctional neurotransmission upon IFNAR1 loss, leading to glucose hypermetabolism measured by functional metabolic analysis. Consequently, Ifnar1-/- mice exhibited PDD-like pathogenesis, including dopaminergic cell loss in the substantia nigra, cortical neurodegeneration, Lewy-body-like inclusions, neuroinflammation, and progressive PDD-like behavior deficits. Brain cell-specific IFNAR1 loss examined in vivo revealed delayed but distinct development of PDD-like phenotypes, where neuropathology, motor, and cognitive behavior deficits were specifically recapitulated only in mice lacking neuronal IFNAR1, and behavior resembling neuropsychiatric abnormalities recapitulated only in mice lacking astrocytic IFNAR1. This work supports a crucial role of IFNAR1 in brain homeostasis and emphasizes a need for understanding neurodegenerative pathophysiology in cell-specific contexts. HighlightsO_LIIFNAR1 and related type-I IFN genes are differentially expressed among major brain cell types in Parkinsons Disease, Lewy Body Dementia, and unaffected controls C_LIO_LIEarly molecular alterations in Ifnar1-/- mice show lack of immunomodulation contributing to neuroinflammation, mitochondrial defects, and dysregulated energy metabolism C_LIO_LIIfnar1-/- mice develop a progressive Parkinsonian-like disease phenotype, including dopaminergic cell loss in substantia nigra, cortical neurodegeneration, phosphorylated (p)alpha-synuclein+ and pTau+ Lewy-body-like inclusions, neuroinflammation, and progressive motor, cognitive, and neuropsychiatric disturbance-like behavior deficits C_LIO_LINeuropathologies, motor, and cognitive deficits are recapitulated in mice lacking neuronal IFNAR1 (Syn1Cre;Ifnar1fl/fl) whereas neuropsychiatric abnormalities are recapitulated in mice lacking astrocytic IFNAR1 (GFAPCre;Ifnar1fl/fl) C_LI

neuroscience↗

bioRxiv2025

A meta-review of DNA-based identification methods and mislabeling analysis of Eastern South Pacific seafood

The Eastern South Pacific Ocean is a nutrient-rich and highly diverse region that plays a pivotal role in the global seafood trade. Despite its importance, the seafood industry in this region is hindered by complex supply chains and insufficient regulation frameworks, which facilitate illegal practices, including mislabeling. DNA-based methods have emerged as essential tools for seafood authentication, helping to mitigate mislabeling and supporting conservation strategies. This study provides the first comprehensive review of DNA-based methods used globally to identify seafood species from the Eastern South Pacific Ocean. Historical and current techniques were systematically examined, with a focus on emerging technologies that offer promising applications in the field. Nearly three decades of research have enabled the successful identification of over 200 commercially valuable species using more than ten distinct DNA-based methods. Fish and mollusks constituted the most extensively studied seafood groups, with DNA sequencing emerging as the predominant technique. Furthermore, a global mislabeling meta-analysis, encompassing 1,806 seafood products from the Eastern South Pacific Ocean, revealed an estimated mislabeling rate of 24.8% (95% CI [22.9-26.9]). Notably, a substantial proportion of mislabeled and substituted products corresponds to highly threatened shark species. This raises serious conservation concerns, particularly given that nations bordering the Eastern South Pacific Ocean are major players in the global shark trade. Overall, the findings of this review underscore the urgent need to integrate advanced DNA-based techniques into existing regulatory frameworks. They also establish a solid foundation for developing targeted policies and encouraging collaborative efforts among nations in this region.

genetics↗

bioRxiv2025

Glycoengineering of the hepatitis C virus E2 glycoprotein leads to improved biochemical properties and enhanced immunogenicity

An effective vaccine against hepatitis C virus (HCV) must elicit the production of broadly neutralizing antibodies (bnAbs) reproducibly against the E1E2 glycoprotein complex. Little is known about how glycan content affects this process. Ideally, glycans would maximize epitope exposure without compromising antigen stability or exposing new epitopes. However, typical recombinant vaccines contain considerable heterogeneity in glycan content, which can affect the antibody response and neutralization potency. Here we employed glycoengineered Chinese hamster ovary (geCHO) cell lines that impart nearly homogeneous glycosylation as a means to test how specific glycan features influence antigenicity and immunogenicity for the secreted HCV E2 ectodomain (sE2). Specific geCHO antigens exhibited a modest but reproducible increase in affinity for some mAbs relative to CHO- and HEK293-produced sE2. Surprisingly, one geCHO sE2 antigen failed to bind the CD81 receptor, indicating the potential for significant glycan effects on biochemical properties. We immunized mice with the four antigens and found the total antibody response to be the same for all groups. However, sera from one geCHO group exhibited a 7-fold improvement in neutralization against the homologous HCV pseudovirus and had the most mice whose sera exhibited neutralization activity against genotypes 1b, 2a, 2b, and 3. Further analysis identified beneficial and deleterious glycan features, and the glycan that correlated the most with decreased potency was relatively small. However, size was not the sole determinant of glycan-driven effects on the antibody response. In summary, glycan content impacts biochemical properties of antigens to varying degrees and such effects can influence immune response quality and uniformity.

immunology↗

bioRxiv2025

Complete mitochondrial genome assembly of two searobin species (genus Prionotus) and their phylogenetic relationships (Triglidae: Prionotinae)

Species from the genera Bellator and Prionotus, commonly known as searobins, are marine ray-finned fish that belong to the subfamily Prionotinae. These fish have evolved distinctive morphological features and specialized behaviors that enable them to walk along the seafloor while detecting buried prey. This unique adaptation makes them ideal candidates for studies in evolutionary genetics. However, their phylogenetic relationships remain poorly understood. In this study, we utilized publicly available genomic reads from the GenBank database to assemble the first complete mitochondrial genomes of three searobin species: Bellator militaris, Prionotus alatus, and P. stephanophrys. We conducted a comparative analysis of these mitochondrial genomes, including the first phylogenetic analysis of the Prionotinae based on complete mitogenomic data. The resulting circular contigs measured 16,765 base pairs for B. militaris, 16,602 base pairs for P. alatus, and 16,896 base pairs for P. stephanophrys. The three mitogenomes exhibited a typical vertebrate organization, which includes 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a putative control region. Notably, P. stephanophrys contained an additional tRNA-Leu and an extra non-coding region. A Bayesian phylogenetic analysis grouped all Bellator species into a monophyletic clade within Prionotinae, while the sister taxon Prionotus formed a separate monophyletic subclade. The findings of this research provide valuable insights into the phylogenetic relationships and evolutionary history of the genera Bellator and Prionotus. Clarifying the taxonomy of these species may also support future management and conservation efforts for these economically valuable species.

genomics↗

bioRxiv2025

The first complete mitochondrial genome of the endangered spotted eagle ray Aetobatus ocellatus

The complete mitochondrial genome of the endangered spotted eagle ray, Aetobatus ocellatus, was determined for the first time using Next Generation Sequencing (NGS) reads mined from the Sequence Read Archive (SRA) of the GenBank database (BioSample SAMN31811701, collection site: Bohol Island, Philippines). The mitogenome of the spotted eagle ray (GenBank accession BK072016) is 20,217 bp in length and exhibits a typical vertebrate mitogenome organization, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. A phylogenetic analysis based on the nucleotide sequences of 13 protein-coding genes from different related species confirmed the species status and classification of A. ocellatus as an Indo-West Pacific species. This species was formerly described as A. narinari, which is now recognized as being restricted to the Atlantic Ocean. The findings of this study provide significant insights into the complex taxonomic and phylogenetic relationships of Aetobatidae. They may further assist in conservation strategies and help resolve taxonomic uncertainties concerning the classification of species within Aetobatidae, which remains under debate.

genomics↗

bioRxiv2024

Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species

Molecular identification assays provide crucial support in the research and regulation of aquatic resources. Among them, species-specific primers provide strong discriminatory power for fast and simultaneous differentiation between closely related species. In this study, we used interspecific variations detected in two mitochondrial genes to develop species-specific primers for eDNA monitoring and identifying 10 fish and shellfish species commercially available within the Peruvian seafood sector. To ensure versatility and high specificity, our primers were subjected to PCR, qPCR, and sequencing methods, coupled with robust validation assays that included a) an in-silico stage using self-generated and public DNA sequences, b) an in-vitro stage using target species belonging to vouchered specimens, fresh and cooked commercial samples, early life stages, and broad taxa of non-target species, and c) an in-situ stage using eDNA samples from different Peruvian marine ecosystems. Our novel species-specific primers successfully passed the validation process with high efficiency and specificity in unequivocally identifying all target species with 100% accuracy and without cross-species amplifications, thereby making them valuable tools for eDNA monitoring, seafood authentication, and to identify and combat illegal, unreported and unregulated fishing. The identification assays presented herein can be used to support effective fishery management and conservation efforts not only in the Peruvian fishery sector but also in other countries where our target species also occur or are available as imported commodities.

genetics↗

bioRxiv2024

Somy evolution in the honey bee infecting trypanosomatid parasite, Lotmaria passim

Lotmaria passim is a ubiquitous trypanosomatid parasite of honey bees nestled within the medically important subfamily Leishmaniinae. Although this parasite is associated with honey bee colony losses, the original draft genome--which was completed before its differentiation from the closely related Crithidia mellificae--has remained the reference for this species despite lacking improvements from newer methodologies. Here we report the updated sequencing, assembly, and annotation of the BRL type strain (ATCC PRA-422) of Lotmaria passim. The nuclear genome assembly has been resolved into 31 complete chromosomes and is paired with an assembled kinetoplast genome consisting of a maxicircle and 30 minicircle sequences. The assembly spans 33.7 Mb and contains very little repetitive content, from which our annotation of both the nuclear assembly and kinetoplast predicted 10,288 protein-coding genes. Analyses of the assembly revealed evidence of a recent chromosomal duplication event within chromosomes 5 and 6 and provides evidence for a high level of aneuploidy in this species, mirroring the genomic flexibility employed by other trypanosomatids as a means of adaptation to different environments. This high-quality reference can therefore provide insights into adaptations of trypanosomatids to the thermally regulated, acidic, and phytochemically rich honey bee hindgut niche, which offers parallels to the challenges faced by other Leishmaniinae during the challenges they undergo within insect vectors, during infection of mammals, and exposure to antiparasitic drugs throughout their multi-host life cycles. This reference will also facilitate investigations of strain-specific genomic polymorphisms, their role in pathogenicity, and the development of treatments for pollinator infection.

genomics↗

bioRxiv2023

Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer

The nutrient status of the tumor microenvironment has major impacts on cell growth. Under nutrient depletion, asparagine synthetase (ASNS)-mediated asparagine production increases to sustain cell survival. G protein-coupled estrogen receptor-1 (GPER1) signaling converges via cAMP/PI3K/AKT with KRAS signaling to regulate ASNS expression. However, the role of GPER1 in CRC progression is still debated, and the effect of nutrient supply on both ASNS and GPER1 relative to KRAS genotype is not well understood. Here, we modeled a restricted nutrient supply by eliminating glutamine from growing cancer cells in a 3D spheroid model of human female SW48 KRAS wild-type (WT) and KRAS G12A mutant (MT) CRC cells, to examine effects on ASNS and GPER1 expression. Glutamine depletion significantly inhibited cell growth in both KRAS MT and WT cells; however, ASNS and GPER1 were upregulated in KRAS MT compared to WT cells. When nutrient supply was adequate, ASNS and GPER1 were not altered between cell lines. The impact of estradiol, a ligand for GPER1, was examined for any additional effects on cell growth. Under glutamine deplete conditions, estradiol decreased the growth of KRAS WT cells but had no effect on KRAS MT cells; estradiol had no additive or diminutive effect on the upregulation of ASNS or GPER1 between the cell lines. We further examined the association of GPER1 and ASNS levels with overall survival in a clinical colon cancer cohort of The Cancer Genome Atlas. Both high GPER1 and ASNS expression associated with poorer overall survival for females only in advanced stage tumors. These findings suggest that KRAS MT cells have mechanisms in place that respond to decreased nutrient supply, typically observed in advanced tumors, by increasing the expression of ASNS and GPER1 to drive cell growth. Furthermore, KRAS MT cells are resistant to the protective effects of estradiol under nutrient deplete conditions. ASNS and GPER1 may therefore be potential therapeutic targets that can be exploited to manage and control KRAS MT CRC.

cancer biology↗

bioRxiv2022

Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.

We and others have previously shown that the SARS-CoV-2 accessory protein ORF6 is a powerful antagonist of the interferon (IFN) signaling pathway by directly interacting with Nup98-Rae1 at the nuclear pore complex (NPC) and disrupting bidirectional nucleo-cytoplasmic trafficking. In this study, we further assessed the role of ORF6 during infection using recombinant SARS-CoV-2 viruses carrying either a deletion or a well characterized M58R loss-of-function mutation in ORF6. We show that ORF6 plays a key role in the antagonism of IFN signaling and in viral pathogenesis by interfering with karyopherin(importin)-mediated nuclear import during SARS-CoV-2 infection both in vitro, and in the Syrian golden hamster model in vivo. In addition, we found that ORF6-Nup98 interaction also contributes to inhibition of cellular mRNA export during SARS-CoV-2 infection. As a result, ORF6 expression significantly remodels the host cell proteome upon infection. Importantly, we also unravel a previously unrecognized function of ORF6 in the modulation of viral protein expression, which is independent of its function at the nuclear pore. Lastly, we characterized the ORF6 D61L mutation that recently emerged in Omicron BA.2 and BA.4 and demonstrated that it is able to disrupt ORF6 protein functions at the NPC and to impair SARS-CoV-2 innate immune evasion strategies. Importantly, the now more abundant Omicron BA.5 lacks this loss-of-function polymorphism in ORF6. Altogether, our findings not only further highlight the key role of ORF6 in the antagonism of the antiviral innate immune response, but also emphasize the importance of studying the role of non-spike mutations to better understand the mechanisms governing differential pathogenicity and immune evasion strategies of SARS-CoV-2 and its evolving variants. ONE SENTENCE SUMMARYSARS-CoV-2 ORF6 subverts bidirectional nucleo-cytoplasmic trafficking to inhibit host gene expression and contribute to viral pathogenesis.

microbiology↗

bioRxiv2022

Bat pluripotent stem cells reveal unique entanglement between host and viruses

Bats have evolved features unique amongst mammals, including flight, laryngeal echolocation, and certain species have been shown to have a unique immune response that may enable them to tolerate viruses such as SARS-CoVs, MERS-CoVs, Nipah, and Marburg viruses. Robust cellular models have yet to be developed for bats, hindering our ability to further understand their special biology and handling of viral pathogens. To establish bats as new model study species, we generated induced pluripotent stem cells (iPSCs) from a wild greater horseshoe bat (Rhinolophus ferrumequinum) using a modified Yamanaka protocol. Rhinolophids are amongst the longest living bat species and are asymptomatic carriers of coronaviruses, including one of the viruses most closely related to SARS-CoV-2. Bat induced pluripotent stem (BiPS) cells were stable in culture, readily differentiated into all three germ layers, and formed complex embryoid bodies, including organoids. The BiPS cells were found to have a core pluripotency gene expression program similar to that of other species, but it also resembled that of cells attacked by viruses. The BiPS cells produced a rich set of diverse endogenized viral sequences and in particular retroviruses. We further validated our protocol by developing iPS cells from an evolutionary distant bat species Myotis myotis (greater mouse-eared bat) non-lethally sampled in the wild, which exhibited similar attributes to the greater horseshoe bat iPS cells, suggesting that this unique pluripotent state evolved in the ancestral bat lineage. Although previous studies have suggested that bats have developed powerful strategies to tame their inflammatory response, our results argue that they have also evolved mechanisms to accommodate a substantial load of endogenous viral sequences and suggest that the natural history of bats and viruses is more profoundly intertwined than previously thought. Further study of bat iPS cells and their differentiated progeny should advance our understanding of the role bats play as virus hosts, provide a novel method of disease surveillance, and enable the functional studies required to ascertain the molecular basis of bats unique traits.

developmental biology↗