Biology subjects

Navarro, A.

Publications and source records attributed to Navarro, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Multivalent ubiquitin recognition regulates multiple stages of Tau self-assembly

Liquid-liquid phase separation (LLPS) has emerged as an important intermediate in the pathological self-assembly of Tau, yet the molecular mechanisms that regulate this process remain incompletely understood. Although ubiquitin is a prominent component of pathological inclusions in tauopathies and other neurodegenerative diseases, its presence has largely been linked to targeting aberrant proteins for proteasomal or autophagic clearance. Here, we identify Tau as a ubiquitin-binding protein and demonstrate that multivalent, non-covalent ubiquitin recognition regulates multiple stages of Tau self-assembly. Biochemical, biophysical, structural, and computational analyses identified four ubiquitin-binding elements within the Tau microtubule-binding repeat region that engage the canonical hydrophobic patch of ubiquitin, providing a structural basis for multivalent recognition of mono- and poly-ubiquitin species. Functionally, mono- and poly-ubiquitin suppress Tau condensate formation while enhancing the liquid-like properties of condensates that persist. In contrast, mono-ubiquitin selectively enhances aggregation of the disease-linked Tau-P301L variant under conditions without detectable LLPS, demonstrating that ubiquitin exerts distinct effects depending on the molecular context and stage of Tau self-assembly. Together, these findings establish non-covalent ubiquitin recognition as a previously unrecognized mechanism regulating Tau phase behavior and aggregation. More broadly, they expand the role of ubiquitin beyond protein quality control, with ubiquitin architecture providing an additional layer of regulation over Tau condensate formation, dynamics, maturation, and aggregation.

biophysics↗

bioRxiv2026

Convergent Amino-Acid Substitutions Link Primate Longevity to Male-Fertility Genes

Maximum lifespan varies widely among mammals, but the genomic basis of this variation remains incompletely understood. We used body-mass-corrected longevity and a phylogenetically informed phenotype-shift framework to compare 126 primate species, selecting seven long-lived and six short-lived species for convergent amino-acid substitution analysis. Stringent pooling across species identified 1,068 recurrent phenotype-associated positions in 934 genes. These genes showed significant agreement with mammal-wide longevity candidates, with 226 genes shared compared with 120 expected by chance (1.88-fold enrichment; P = 1.16 x 10exp-22). Functional analysis detected 17 significant terms, with the strongest coherent signal involving male infertility and decreased male fertility. Our results show that focused primate sampling recovers a non-random component of the broader mammalian longevity signal and point to male reproductive biology as a promising direction for investigating the evolution of lifespan.

evolutionary biology↗

bioRxiv2026

Phenotype shift scores reveal the scale and phylogenetic structure of phenotypic differentiation in primates.

Continuous traits evolve unevenly across phylogenies, producing patterns of phenotypic differentiation shaped by both shared ancestry and lineage-specific change. Identifying exceptionally differentiated species pairs may therefore improve genome-phenome comparisons, but existing approaches rarely rank such contrasts across entire trees. Here we introduce the Phenotype Shift Score (PSS), a phylogenetic comparative framework integrating model-based trait divergence, observed trait range and patristic distance. Applying PSS to 153 continuous primate traits reveals trait-specific distributions of extreme differentiation across evolutionary depth. Body and brain mass show deeper-than-expected extremes under fitted Brownian motion or Ornstein-Uhlenbeck nulls, whereas body-size-adjusted brain mass localizes recent differentiation within cercopithecid lineages, complementing published branchwise reconstructions. PSS-informed groups produce more selective and more strongly enriched comparative-genomic signals than groups based on absolute phenotypic extremes. PSS is implemented in the open-source R package phyloPSS, with pairwise results available through the Primate Genome-Phenome Archive.

evolutionary biology↗

bioRxiv2026

Distinct DNA-binding syntax and chromatin remodeling capacities of bHLH transcription factors in cell differentiation, reprogramming and cancer

Basic helix-loop-helix (bHLH) transcription factors orchestrate cell differentiation, reprogramming, and oncogenic transformation, yet the molecular determinants that govern their DNA-binding specificity and capacity to remodel chromatin remain incompletely understood. Here, we assemble and unify all available bHLH induction ChIP-seq datasets (74 experiments covering 17 factors) and integrate them with matched chromatin accessibility, nucleosome positioning, CpG methylation, transcriptomic profiling, methyl-HT-SELEX, and structural modeling. Using an exact hexanucleotide-based approach, we define the sequence grammar that shapes bHLH-DNA interactions and identify distinct motif architectures associated with binding to accessible versus inaccessible chromatin. CAT- and CAG-preferring bHLH factors--including proneural and myogenic regulators--display robust pioneer-like behavior, characterized by preferential engagement of closed chromatin through specific E-box variants, cooperative motif clustering, and characteristic spacing patterns. TWIST factors exhibit a unique 5-bp E-box periodicity linked to dedifferentiation programs, whereas CAC-preferring oncogenic bHLHs remain largely restricted to open chromatin. By integrating methylation and SELEX data, we reveal that CpG methylation drives a systematic shift from the canonical CAC-CAC motif toward CAT-CAC E-boxes, providing a mechanistic explanation for MYC enhancer invasion in cancer and uncovering parallel behavior in the HEY family. Nucleosome chemical mapping and structural predictions further show that nearly all bHLH factors bind preferentially at nucleosome flanks, independent of -helix length, challenging prior models of nucleosomal engagement. Together, these results establish a unified framework linking sequence syntax, chromatin state, and transcriptional outcome across the bHLH family, providing mechanistic principles for understanding lineage specification, reprogramming, and oncogenic enhancer remodeling.

molecular biology↗

bioRxiv2025

Cross-competition shapes CD8+ T cell hierarchies and differentiation after RNA vaccination

Short SummaryImmunodominance is a universal feature of adaptive immunity that constrains T cell expansion, clonal diversity and breadth resulting in a narrowly focused T cell response. While observed across diverse priming settings and vaccine platforms, the influence of immunodominance on T cell phenotype remains unclear. Using an mRNA lipoplex vaccine encoding multiple antigens to study how immunodominance influences CD8+ T cell fate, we found that dominant CD8+ T cell responses alter the magnitude and phenotype of subdominant responses through peptide-MHC-I stability-mediated T cell cross-competition. Dominant CD8+ T cell responses preferentially acquired markers associated with terminal differentiation and cytotoxic function, while sub-dominant responses adopted memory-precursor and stem-like features. Removal of dominant responses allowed increased expansion of sub-dominant T cell responses and adoption of terminally differentiated effector phenotypes. These findings reveal that immunodominance dynamically shapes the magnitude, breadth and differentiation of CD8+ T cell responses and highlights opportunities to fine-tune T cell responses for therapeutic vaccination.

immunology↗

bioRxiv2025

A phylogenetic protein-coding genome-phenome map of complex traits across 224 primate species.

Complex traits arise from networks of coding and regulatory loci, making it difficult to resolve their genetic basis. Macroevolutionary studies leverage tens of millions of years of divergence across species to uncover fixed genomic changes invisible to within-species approaches, such as GWAS, offering a complementary framework for generating hypotheses in biomedical research. Here, we present the first phylogenetic protein-coding primate-wide genome-phenome map (P3GMap), spanning 200 curated traits across 224 primate species, which we release through the Primate Genome-Phenome Archive (PGA, https://pgarchive.github.io). Using two complementary approaches, convergent amino acid substitutions and relative evolutionary rates, we linked protein-coding variation to complex phenotypes and identified thousands of candidate gene-trait associations, including lineage-specific signals related to diet, immunity, and lifespan. One sentence summaryCross-species genome-phenome mapping in primates reveals thousands of protein-coding variants linked to the evolution of complex traits.

evolutionary biology↗

bioRxiv2025

Modeling acquired TKI resistance and effective combination therapeutic strategies in murine RET+ lung adenocarcinoma

RET gene rearrangements yield oncogenic fusion proteins that drive a subset of lung adenocarcinomas (LUAD). The tyrosine kinase inhibitors (TKIs) selpercatinib and pralsetinib are approved therapies for RET+ lung cancers and have markedly improved clinical outcomes in these patients, but acquired resistance remains a hurdle to their durable management. Using a recently developed murine model of RET+ lung cancer driven by a Trim24-Ret fusion protein, two Trim24-Ret cell lines (TR.1 and TR.2) were established. Orthotopic lung tumors generated by transplantation of these cell lines initially respond to selpercatinib followed by prompt progression within [~]3 weeks of initiating TKI treatment. Cell lines derived from the selpercatinib-resistant TR.1 and TR.2 tumors exhibited in vitro sensitivity to MET and ERBB-targeted TKIs, indicating acquired bypass signaling through these receptor tyrosine kinases. Moreover, the selpercatinib-resistant TR.1 and TR.2 cell lines exhibited increased sensitivity to MEK and PTPN11 inhibitors relative to the parental cell lines, indicating a greater dependence on MAPK pathway signaling. The TKI-resistant cell lines showed no evidence for MET gene amplification, but exhibited varied induction of multiple genes that function within MET and ERBB2:ERBB4 interaction networks including ligands (HGF, NRG1), adaptors (GAB1) and co-receptors (NRP1). Consistent with an important role for MET signaling in driving acquired selpercatinib resistance, mice bearing orthotopic lung tumors derived from TR.1 or TR.2 cells that had progressed on selpercatinib treatment underwent significant re-shrinkage upon co-treatment with the MET inhibitor, crizotinib, although progression re-occurred. By contrast, upfront treatment with selpercatinib and crizotinib in orthotopic tumors yielded complete elimination of 78% of TR.1 tumors and a prolonged duration of response in TR.2 tumors. The findings highlight the failings inherent in treating acquired resistance mechanisms at progression and the potential therapeutic impact of predicting and targeting dominant mechanisms of resistance prior to or early after initiating oncogene-targeting TKI treatment in RTK-driven LUAD.

cancer biology↗

bioRxiv2024

The Mitochondrial Ubiquitin Ligase MARCHF5 Cooperates with MCL1 to Inhibit Apoptosis in KSHV-Transformed Primary Effusion Lymphoma Cell Lines

Kaposis sarcoma-associated herpesvirus (KSHV) causes several malignancies in people with HIV including Kaposis sarcoma and primary effusion lymphoma (PEL). We have previously shown that PEL cell lines require myeloid cell leukemia-1 (MCL1) to inhibit apoptosis. MCL1 is an oncogene that is amplified in cancers and causes resistance to chemotherapy regimens. MCL1 is thus an attractive target for drug development. The emerging clinical relevance and therapeutic potential of MCL1 motivated us to study the roles of this oncogene in PEL in depth. Using a systems biology approach, we uncovered an unexpected genetic interaction between MCL1 and MARCHF5 indicating that they function in the same pathway. MARCHF5 is an E3 ubiquitin ligase most known for regulating mitochondrial homeostasis and antiviral signaling, but not apoptosis. We thus investigated how MCL1 and MARCHF5 cooperate to promote PEL cell survival. CRISPR knockout (KO) of MARCHF5 in PEL cell lines resulted in a significant increase in apoptosis despite the presence of MCL1. The anti-apoptotic function of MARCHF5 was dependent on its E3 ligase and dimerization activities. Loss of MARCHF5 or inhibition of the 26S proteasome furthermore stabilized the MCL1 antagonist NOXA without affecting levels of MCL1. Interestingly, NOXA KO provides a fitness advantage to PEL cells suggesting that NOXA is the pro-apoptotic signal that necessitates the anti-apoptotic activities of MCL1 and MARCHF5. Finally, endogenous reciprocal co-immunoprecipitation experiments show that MARCHF5 and NOXA are found in the same protein complex. Our findings thus provide the mechanistic link that underlies the genetic interaction between MCL1 and MARCHF5. We propose that MARCHF5 induces the degradation of the MCL1 antagonist NOXA thus reinforcing the pro-survival role of MCL1 in these tumor cells. This newly appreciated interaction of the MCL1 and MARCHF5 oncogenes may be useful to improve the design of combination therapies for KSHV malignancies.

cancer biology↗

bioRxiv2024

A murine experimental model of the unique pulmonary thrombotic effect induced by the venom of the snake Bothrops lanceolatus

BackgroundThe venom of Bothrops lanceolatus, a viperid species endemic to the Lesser Antillean Island of Martinique, induces a unique clinical manifestation, i.e., thrombosis. Previous clinical observations indicate that thromboses are more common in patients bitten by juvenile specimens. There is a need to develop an experimental model of this effect in order to study the mechanisms involved. Methodology/principal findingsThe venoms of juvenile and adult specimens of B. lanceolatus were compared by (a) describing their proteome, (b) assessing their ability to induced thrombosis in a mouse model, and (c) evaluating their in vitro procoagulant activity and in vivo hemostasis alterations. Venom proteomes of juvenile and adult specimens were highly similar. When injected by the intraperitoneal (i.p.) route, the venom of juvenile specimens induced the formation of abundant thrombi in the pulmonary vasculature, whereas this effect was less frequent in the case of adult venom. Thrombosis was not abrogated by the metalloproteinase inhibitor Batimastat. Both venoms showed a weak in vitro procoagulant effect on citrated mouse plasma and bovine fibrinogen. When administered intravenously (i.v.) venoms did not affect classical clotting tests (prothrombin time and activated partial thromboplastin time) but caused a partial drop in fibrinogen concentration. The venom of juvenile specimens induced partial alterations in some rotational thromboelastometry parameters after i.v. injection. No alterations in coagulation tests were observed when venoms were administered i.p., but juvenile and adult venoms induced a marked thrombocytopenia. Conclusions/significanceAn experimental model of the thrombotic effect induced by B. lanceolatus venom was developed. This effect is more pronounced in the case of venom of juvenile specimens, despite the observation that juvenile and adult venom proteomes are similar. Adult and juvenile venoms do not induce a consumption coagulopathy characteristic of other Bothrops sp venoms. Both venoms induce a conspicuous thrombocytopenia. This experimental model reproduces the main clinical findings described in these envenomings and should be useful to understand the mechanisms of this thrombotic effect. Author summaryEnvenomings by the viperid species Bothrops lanceolatus, endemic of the Caribbean Island of Martinique, are characterized by a unique thrombotic effect responsible for infarcts in various organs. Until now, no experimental in vivo models of this effect have been described. In this study, we developed a mouse model of thrombosis by using the intraperitoneal route of venom injection. The venom of juvenile specimens of B. lanceolatus induced the formation of abundant thrombi in the lungs, whereas the effect was much less pronounced with the venom of adult specimens. This difference in the ability of juvenile and adult venoms occurs despite both venoms having highly similar proteomic profiles. Both adult and juvenile venoms showed a weak in vitro procoagulant effect on plasma and fibrinogen, underscoring a thrombin-like (pseudo-procoagulant) activity. In vivo, the venoms did not affect the classical clotting tests (prothrombin time and activated partial thromboplastin time) but induced a partial drop in fibrinogen concentration and limited alterations in rotational thromboelastometry parameters when injected by the i.v. route. In contrast, few alterations of these parameters were observed after i.p. injection of venoms, in conditions in which thrombosis occurred, hence evidencing the lack of a consumption coagulopathy. After i.p. injection both venoms induced a pronounced thrombocytopenia. This experimental model reproduces some of the main clinical manifestations of envenoming by this species. This model can be used to identify the toxins responsible for the thrombotic effect, to study the mechanism(s) of thrombosis and to assess the preclinical efficacy of antivenoms.

pharmacology and toxicology↗

bioRxiv2024

Soil carbon in the world's tidal marshes

Tidal marshes are threatened coastal ecosystems known for their capacity to store large amounts of carbon in their water-logged soils. Accurate quantification and mapping of global tidal marshes soil organic carbon (SOC) stocks is of considerable value to conservation efforts. Here, we used training data from 3,710 unique locations, landscape-level environmental drivers and a newly developed global tidal marsh extent map to produce the first global, spatially-explicit map of SOC storage in tidal marshes at 30 m resolution. We estimate the total global SOC stock to 1 m to be 1.44 Pg C, with a third of this value stored in the United States of America. On average, SOC in tidal marshes 0-30 and 30-100 cm soil layers are estimated at 83.1 Mg C ha-1 (average predicted error 44.8 Mg C ha-1) and 185.3 Mg C ha-1 (average predicted error 105.7 Mg C ha-1), respectively. Our spatially-explicit model is able to capture 59% of the variability in SOC density, with elevation being the strongest driver aside from soil depth. Our study reveals regions with high prediction uncertainty and therefore highlights the need for more targeted sampling to fully capture SOC spatial variability.

ecology↗

bioRxiv2024

Inflammation promotes aging-associated oncogenesis in the lung.

BackgroundLung cancer is the leading cause of cancer death in the world. While cigarette smoking is the major preventable factor for cancers in general and lung cancer in particular, old age is also a major risk factor. Aging-related chronic, low-level inflammation, termed inflammaging, has been widely documented; however, it remains unclear how inflammaging contributes to increased lung cancer incidence. AimTo establish connections between aging-associated changes in the lungs and cancer risk. MethodsWe analyzed public databases of gene expression for normal and cancerous human lungs and used mouse models to understand which changes were dependent on inflammation, as well as to assess the impact on oncogenesis. ResultsAnalyses of GTEx and TCGA databases comparing gene expression profiles from normal lungs, lung adenocarcinoma, lung squamous cell carcinoma of subjects across age groups revealed upregulated pathways such as inflammatory response, TNFA signaling via NF{kappa}B, and interferon-gamma response. Similar pathways were identified comparing the gene expression profiles of young and old mouse lungs. Transgenic expression of alpha 1 antitrypsin (AAT) partially reverses increases in markers of aging-associated inflammation and immune deregulation. Using an orthotopic model of lung cancer using cells derived from EML4-ALK fusion-induced adenomas, we demonstrated an increased tumor outgrowth in lungs of old mice while NLRP3 knockout in old mice decreased tumor volumes, suggesting that inflammation contributes to increased lung cancer development in aging organisms. ConclusionsThese studies reveal how expression of an anti-inflammatory mediator (AAT) can reduce some but not all aging-associated changes in mRNA and protein expression in the lungs. We further show that aging is associated with increased tumor outgrowth in the lungs, which may relate to an increased inflammatory microenvironment.

cancer biology↗

bioRxiv2024

The HSFA1a is stabilized by the co-chaperone HSP70-HSP90 organizing protein HOP in Arabidopsis

Living organisms have the capacity to sense and respond to environmental stimuli, including warm conditions. Upon the increase of temperature, eukaryotic cells promote the onset of a universal transcriptional response called the heat stress response (HSR). HSR is triggered by the activation of the heat shock factor 1 (HSF1), whose activity is highly regulated in all eukaryotes. A common process of HSFA1 regulation involves its binding to HSP70 and HSP90 chaperones. However, the effect of this binding differs among eukaryotes and is not fully elucidated in plants. Moreover, the role of chaperone auxiliary proteins, such as HOP, in HSF1 regulation remains unknown. Here, we show that HOP is involved in the folding and stabilization of the HSFA1a and is required for the onset of the HSR during thermomorphogenesis in Arabidopsis. Our results demonstrate that the members of the AtHOP family bind in vivo to the HSFA1a and that the expression of multiple genes involved in the HSR, including numerous HSFA1a-responsive genes, is altered in the hop1 hop2 hop3 mutant under warm temperature. HOP is not involved in the subcellular localization of the AtHSFA1a. Instead, HSFA1a is accumulated at lower levels in the hop1 hop2 hop3 mutant while control levels are recovered in the presence of the proteasome inhibitor MG132 or the synthetic chaperone TUDCA. This uncovers the HSFA1a as a new client of HOP in plants and reveals the participation of HOP in HSFA1a stability, expanding the notorious function of the co-chaperone HOP in thermomorphogenesis.

plant biology↗

bioRxiv2023

The distribution of global tidal marshes from earth observation data

AimTidal marsh ecosystems are heavily impacted by human activities, highlighting a pressing need to address gaps in our knowledge of their distribution. To better understand the global distribution and changes in tidal marsh extent, and identify opportunities for their conservation and restoration, it is critical to develop a spatial knowledge base of their global occurrence. Here, we develop a globally consistent tidal marsh distribution map for the year 2020 at 10-m resolution. LocationGlobal Time period2020 Major taxa studiedTidal marshes MethodsTo map the location of the worlds tidal marshes we applied a random forest classification model to earth observation data from the year 2020. We trained the classification model with a reference dataset developed to support distribution mapping of coastal ecosystems, and predicted the spatial distribution of tidal marshes between 60{degrees}N to 60{degrees}S. We validated the tidal marsh map using standard accuracy assessment methods, with our final map having an overall accuracy score of 0.852. ResultsWe estimate the global extent of tidal marshes in 2020 to be 52,880 km2 (95% CI: 32,030 to 59,780 km2) distributed across 120 countries and territories. Tidal marsh distribution is centred in temperate and Arctic regions, with nearly half of the global extent of tidal marshes occurring in the temperate Northern Atlantic (45%) region. At the national scale, over a third of the global extent (18,510 km2; CI: 11,200 - 20,900) occurs within the USA. Main conclusionsOur analysis provides the most detailed spatial data on global tidal marsh distribution to date and shows that tidal marshes occur in more countries and across a greater proportion of the worlds coastline than previous mapping studies. Our map fills a major knowledge gap regarding the distribution of the worlds coastal ecosystems and provides the baseline needed for measuring changes in tidal marsh extent and estimating their value in terms of ecosystem services

ecology↗

bioRxiv2023

A Rapid, Functional sgRNA Screening Method for Generating Murine RET and NTRK1 Fusion Oncogenes

CRISPR/Cas9 gene editing technology is an indispensable and powerful tool in the field of cancer biology. To conduct successful CRISPR-based experiments, it is crucial that sgRNAs generate their designed alterations. Here, we describe a simple and efficient sgRNA screening method for validating sgRNAs that generate oncogenic gene rearrangements. We used IL3-independence in Ba/F3 cells as an assay to identify sgRNA pairs that generate fusion oncogenes involving the Ret and Ntrk1 tyrosine kinases. We confirmed these rearrangements with PCR or RT-PCR as well as sequencing. Ba/F3 cells harboring Ret or Ntrk1 rearrangements acquired sensitivity to RET and TRK inhibitors, respectively. Adenoviruses encoding Cas9 and sgRNAs that catalyze the Kif5b-Ret and Trim24-Ret rearrangements were intratracheally instilled into mice and yielded lung adenocarcinomas. A cell line (TR.1) was established from a Trim24-Ret positive tumor that exhibited high in vitro sensitivity to RET-specific TKIs. Moreover, orthotopic transplantation of TR.1 cells into the left lung yielded well-defined tumors that shrank in response to LOXO-292 treatment. The method offers an efficient means to validate sgRNAs that successfully target their intended loci for the generation of novel murine oncogene-driven tumor models.

cancer biology↗

bioRxiv2022

CAAStools, a toolbox to identify and test Convergent Amino Acid Substitutions.

BackgroundCoincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes. Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for pre-defined groups of species representing the phenotypic values targeted by the user. Implementation and availabilityCAAStools source code is available at http://github.com/linudz/caastools, along with documentation and examples. Supplementary informationSupplementary data are available.

bioinformatics↗

bioRxiv2022

Novel EGFR-Mutant Mouse Models of Lung Adenocarcinoma Reveal Adaptive Immunity Requirement for Durable Osimertinib Response

Lung cancers bearing oncogenically-mutated EGFR represent a significant fraction of lung adenocarcinomas (LUADs) for which EGFR-targeting tyrosine kinase inhibitors (TKIs) provide a highly effective therapeutic approach. However, these lung cancers eventually acquire resistance and undergo progression within a characteristically broad treatment duration range. Our previous study of EGFR mutant lung cancer biopsies highlighted the positive association of a TKI-induced interferon {gamma} transcriptional response with increased time to treatment progression. To test the hypothesis that host immunity contributes to the TKI response, we developed novel genetically-engineered mouse models of EGFR mutant lung cancer bearing exon 19 deletions (del19) or the L860R missense mutation. Both oncogenic EGFR mouse models developed multifocal LUADs from which transplantable cancer cell lines sensitive to the EGFR-specific TKIs, gefitinib and osimertinib, were derived. When propagated orthotopically in the left lungs of syngeneic C57BL/6 mice, deep and durable shrinkage of the cell line-derived tumors was observed in response to daily treatment with osimertinib. By contrast, orthotopic tumors propagated in immune deficient nu/nu mice exhibited modest tumor shrinkage followed by rapid progression on continuous osimertinib treatment. Importantly, osimertinib treatment significantly increased intratumoral CD3+ T cell content relative to diluent treatment. The findings provide strong evidence supporting the requirement for adaptive immunity in the durable therapeutic control of EGFR mutant lung cancer.

cancer biology↗

bioRxiv2022

Adaptive immunity is required for durable responses to alectinib in murine models of EML4-ALK lung cancer

PurposeLung cancers bearing oncogenic EML4-ALK fusions respond to targeted tyrosine kinase inhibitors (TKIs; e.g. alectinib), with variation in the degree of shrinkage and duration of treatment (DOT). We previously demonstrated a positive association of a TKI-induced interferon gamma (IFN{gamma}) transcriptional response with DOT in EGFR-mutant lung cancers. Herein, we used murine models of EML4-ALK lung cancer to test a role for host immunity in the therapeutic response to alectinib. Experimental DesignThree murine EML4-ALK cell lines (EA1, EA2, EA3) were implanted orthotopically into the lungs of immunocompetent and immunodeficient mice and treated with alectinib. Tumor volumes were serially measured by CT. Immune cell content was measured by flow cytometry, multispectral immunofluorescence and CyTOF. Transcriptional responses to alectinib were assessed by RNAseq and secreted chemokines were measured by ELISA. ResultsAll cell lines were sensitive to alectinib in vitro. EA1 and EA3 tumors retained residual disease that rapidly progressed upon termination of treatment while EA2 tumors were eliminated by TKI treatment. Alectinib induced inflammatory transcriptional programs and multiple chemokines in all cell lines while untreated tumors exhibited distinct baseline chemokine expression patterns and content of CD8+ T cells and myeloid subsets. When propagated in immune-deficient mice, all three cell line-derived lung tumor models exhibited significant shrinkage followed by prompt progression despite continuous alectinib treatment. ConclusionsThe findings support an hypothesis that host and TKI-stimulated production of chemokines by tumor cells promotes functional engagement of adaptive immune cells within the tumor microenvironment that enhances the durability and depth of TKI response. Statement of Translational RelevancePatients with metastatic lung cancer harboring ALK fusions are treated with targeted tyrosine kinase inhibitors (TKI) in the first line setting. Despite bearing the same driver oncogene, patients experience a range of tumor burden reduction and variable amounts of residual disease. Residual disease burden associates with patient survival and contributes to the emergence of drug resistance yielding treatment failure. The factors mediating this differential response to TKI and residual disease are incompletely understood. Our group has developed a panel of murine ALK driven lung cancer cell lines that reproducibly show differences in the depth and duration of response when implanted into immunocompetent mice. Data using this model indicate that the presence of CD8+ T cells is a major contributor to the depth and duration of response. These models will be critical in developing rational combination therapies to augment the immune microenvironment engagement along with TKIs to improve outcomes for these patients.

cancer biology↗

bioRxiv2021

Whole-genomes from the extinct Xerces Blue butterfly reveal low diversity and long-term population decline

The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct at global scale in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. We sequenced the genomes of four 80 to 100-year-old Xerces Blue, and seven historical and one modern specimens of its closest relative, the Silvery Blue (G. lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (G. alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, both species experienced population growth during the Eemian interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity and deleterious load in the Xerces Blue were significantly greater than in the Silvery Blue, suggesting a higher incidence of inbreeding. These signals of population decline observed in Xerces Blue could be used to identify and monitor other insects threatened by human activities, whose extinction patterns are still not well known.

evolutionary biology↗