Biology subjects

Jimenez, I.

Publications and source records attributed to Jimenez, I..

6 recordsLinked to original sources

bioRxiv2024

The role of inflammation in a humanized mouse model of transthyretin cardiac amyloidosis

BackgroundSystemic amyloidosis represents a group of protein-misfolding diseases that confer significant morbidity and mortality for millions of patients worldwide. Transthyretin cardiac amyloidosis (ATTR) is a particularly devastating amyloid disease that affects middle-aged and elderly individuals and leads to cardiomyopathy (ATTR-CM), which has a median survival of 2.5 to 3.5 years [1, 2]. ATTR-CM can be hereditary, leading to a more aggressive disease course in younger patients. The most prevalent TTR variant in the United States is V122I, which is found in 3-4 % of African Americans [3]. Despite the significant healthcare burden, ATTR-CM remains underdiagnosed due to a lack of disease awareness and limited diagnostic techniques [4]. Informative in vivo models have proven elusive during the past decade [5]. Moreover, there is no available treatment to reverse cardiac dysfunction due to amyloid fibril deposition [1, 6, 7]. Therefore, a better understanding of the molecular mechanisms of ATTR-CM is imperative to developing novel, effective therapies. Method and ResultsTo explore the pathogenesis of ATTR, we created a murine TTR knockout (TTR-KO) model expressing the human V122I TTR variant. To study the gender differences, both male and female TTR-KO mice were utilized in this study. Significant elevations of human TTR were observed in both male and female ATTR murine plasma post-injection 3 months (human TTR level (ng/ml) Male ATTR: 109.9 {+/-} 5.568; Male control: 28.17 {+/-} 7.010; p=0.0008, N=3 mice/group; Female ATTR: 127.5 {+/-} 32.43; Female control: 20.08 {+/-} 8.351; p=0.0327, N=3 mice/group) with preserved cardiac function (FS% Male ATTR: 26.07 {+/-} 3.667; Male control: 22.69 {+/-} 1.585; p=0.3712, N=6-8 mice/group; Female ATTR: 26.62 {+/-} 1.980; Female control: 31.25 {+/-} 4.482;p=0.3397, N=5-6 mice/group). Notably, the mouse model exhibited cardiac amyloid deposits confirmed by amyloidotic-specific Congo Red staining and Thioflavin T Staining. Transmission electron microscopy revealed both immature and mature amyloid fibrils in the extracellular matrix. RNA-sequencing of the ATTR mouse heart identified distinct transcriptomic patterns and conserved inflammation pathways similar to those seen in a cohort of human ATTR heart samples, including leukocyte transendothelial migration, T-cell receptor signaling, and apoptosis, along with upregulation of inflammatory markers CXCL-1/2/3 and CCL20, were observed in ATTR murine hearts. At the posttranslational level, we confirmed an increased level of CCL5 (MFI ATTR: 801 {+/-} 105; Control: 426{+/-} 64; p=0.0061, N=3 mice/group) in murine plasma post-injection 3 months by a luminance-based immunoassay. The CXCL- and CCL-chemokines family are critical for directing leukocytes to inflammation sites. ConclusionIn this study, we developed a humanized V122I ATTR mouse model with elevated circulating human TTR level and Congophilic amyloid deposits in the murine heart and kidneys. Our transcriptomic study suggested that inflammation may contribute to the ATTR-CM pathogenesis. Further studies are needed to decipher the precise interactions between inflammation and ATTR-CM. Highlights/Whats new/Clinical relevanceO_LIWe developed a humanized mouse model to replicate the multisystem complexity and clinical diversity associated with V122I ATTR-CM. C_LIO_LIOur study unveiled the pathogenic molecular mechanisms of amyloid deposition in ATTR-CM via a novel mouse model. C_LIO_LIWe identified signature inflammatory pathways that uncover potential therapeutic targets for ATTR-CM. C_LIO_LIOur ATTR mouse model allows for preclinical pharmacogenomic assessments of novel therapeutics, which will undoubtedly improve outcomes for ATTR-CM patients. C_LI

pathology↗

bioRxiv2022

COMBINATION THERAPIES TARGETING ALK-ABERRANT NEUROBLASTOMA IN PRECLINICAL MODELS.

BackgroundALK activating mutations are identified in approximately 10% of newly diagnosed neuroblastomas and ALK amplifications in a further 1-2% of cases. Lorlatinib, a third generation ALK inhibitor, will soon be given alongside induction chemotherapy for children with ALK-aberrant neuroblastoma. However, resistance to single agent treatment has been reported and therapies that improve the response duration are urgently required. We studied the preclinical combination of lorlatinib with chemotherapy, or with the MDM2 inhibitor, idasanutlin, as recent data has suggested that ALK inhibitor resistance can be overcome through activation of the p53-MDM2 pathway. AimsTo study the preclinical activity of ALK inhibitors alone and in combination with chemotherapy or idasanutlin. MethodsWe compared different ALK inhibitors in preclinical models prior to evaluating lorlatinib in combination with chemotherapy or idasanutlin. We developed a triple chemotherapy (CAV: cyclophosphamide, doxorubicin and vincristine) in vivo dosing schedule and applied this to both neuroblastoma genetically engineered mouse models (GEMM) and patient derived xenografts (PDX). ResultsLorlatinib in combination with chemotherapy was synergistic in immunocompetent neuroblastoma GEMM. Significant growth inhibition in response to lorlatinib was only observed in the ALK-amplified PDX model with the highest ALK expression. In this PDX lorlatinib combined with idasanutlin resulted in complete tumor regression and significantly delayed tumor regrowth. ConclusionOur study suggests that in neuroblastoma, high ALK expression could be associated with response to lorlatinib and either chemotherapy or idasanutlin. The synergy between MDM2 inhibition and ALK inhibition warrants further evaluation of this combination as a potential clinical approach for children with neuroblastoma. STATEMENT OF TRANSLATIONAL RELEVANCENeuroblastoma is a pediatric tumor of the developing sympathetic nervous system. Around 50% of high-risk neuroblastoma patients are curable. Mutations or amplification of Anaplastic Lymphoma Kinase (ALK) have emerged as a marker with which to further risk-stratify patients. The ALK inhibitor lorlatinib will soon be used alongside chemotherapy in upfront treatment of high-risk patients with ALK-aberrant disease. In this preclinical study, we used a panel of ALK aberrant neuroblastoma models to evaluate ALK inhibitors focusing on lorlatinib in combination with conventional chemotherapy and the small molecule MDM2 inhibitor idasanutlin. In both approaches we found synergy in models with high basal ALK expression without MAPK pathway alterations. We conclude that in neuroblastoma the level of ALK expression could be an additional biomarker predictive of clinical response to ALK inhibitors.

cancer biology↗

bioRxiv2021

Interplay between intrinsic reprogramming potential and microenvironment controls neuroblastoma cell plasticity and identity

Two cell identities, noradrenergic and mesenchymal, have been characterized in neuroblastoma cell lines according to their epigenetic landscapes relying on specific circuitries of transcription factors. Yet, their relationship and relative contribution in patient tumors remain poorly defined. Here, we demonstrate that the knock-out of GATA3, but not of PHOX2A or PHOX2B, in noradrenergic cells induces a mesenchymal phenotype. Our results document spontaneous plasticity in several models between both identities and show that plasticity relies on epigenetic reprogramming. We demonstrate that an in vivo microenvironment provides a powerful pressure towards a noradrenergic identity for these models. Consistently, tumor cells with a mesenchymal identity are not detected in a series of PDX models. Further study of the intra-tumor noradrenergic heterogeneity reveals two distinct cell populations exhibiting features of chromaffin-like or sympathoblast-like cells. This work emphasizes that both external cues of the environment and intrinsic factors control plasticity and cell identity in neuroblastoma.

cancer biology↗

bioRxiv2020

The Nature of Espeletia Species

Species are often regarded as basic units of study in biology, following the presumption that they are real and discrete natural entities. But several biologists wonder if species are arbitrary divisions that do not correspond to discrete natural groups of organisms. Two issues must be addressed to solve this controversy, but few studies seem to do so. The first is whether organisms form sympatric and synchronic groups that are distinct in terms of phenotypes and genome-wide allele frequencies, often called "good species." Alternatives to "good species" include "cryptic species," syngameons and, more generally, cases in which phenotypes and genome-wide allele frequencies reflect contrasting evolutionary histories. The second issue is the degree to which species taxa (i.e., taxonomic classification at the species level) reflect natural groups of organisms or constitute arbitrary divisions of biological diversity. Here, we empirically addressed both issues by studying plants of the Andean genus Espeletia (Asteraceae). We collected a geographically dense sample of 538 specimens from the paramo de Sumapaz, in the Cordillera Oriental of Colombia. Additionally, we examined 165 herbarium specimens previously collected by other researchers in this region, or from taxa known to occur there. We tested for the existence of phenotypic groups using normal mixture models and data on 13 quantitative characters. Among 307 specimens with all 13 measurements, we found six distinct phenotypic groups in sympatry. We also tested for the existence of groups defined by genome-wide allele frequencies, using ancestry models and data on 2,098 single nucleotide polymorphisms. Among 77 specimens with complete genomic data, we found three groups in sympatry, with high levels of admixture. Concordance between groups defined by phenotype and genome-wide allele frequencies was low, suggesting that phenotypes and genome-wide allele frequencies reflect contrasting evolutionary histories. Moreover, the high levels of admixture suggest that Espeletia plants form a syngameon in the paramo de Sumapaz. To determine the extent to which species taxa corresponded to phenotypic and genomic groups, we used data on 12 phenotypic characters to assign 307 specimens to species taxa, according to descriptions of species taxa in the most recent monograph of Espeletia. This sample included 27 specimens cited in the monograph. Remarkably, only one out of 307 specimens in our sample fell inside any of the phenotypic ranges reported in the monograph for the species taxa known to occur in the paramo de Sumapaz. These results show that species taxa in Espeletia are delineations of largely empty phenotypic space that miss biological diversity.

evolutionary biology↗

bioRxiv2017

Can net diversification rates account for spatial patterns of species richness?

The diversification rate hypothesis (DRH) proposes that spatial patterns of species richness result from spatial variation in net diversification rates. We developed an approach using a time-calibrated phylogeny and distributional data to estimate the maximum explanatory power of the DRH, over a given time period, to current species richness in an area. We used this approach to study species richness patterns of a large family of suboscine birds across South America. The maximum explanatory power of the DRH increased with the duration of the time period considered and grain size; it ranged from 13 - 37 fold local increases in species richness for T = 33 Ma to less than 2-fold increases for T [≤] 10 Ma. For large grain sizes ([≤] 8{degrees} x 8{degrees}) diversification rate over the last 10 Ma could account for all the spatial variance in species richness, but for smaller grain sizes commonly used in biogeographical studies (1{degrees} x 1{degrees}), it could only explain < 16% of this variance. Thus, diversification since the Late Miocene, often thought to be a major determinant of Neotropical diversity, had a limited imprint on spatial richness patterns at small grain sizes. Further application of our approach will help determine the role of the DRH in explaining current spatial patterns of species richness.\n\nNote to readersThis manuscript has been seen by a few researchers, some of whom suggested that before publishing our work in a peer-reviewed journal we should conduct simulations to demonstrate that our methods properly estimate the contribution of variance in diversification rates to spatial variation in species richness. Although we believe that our approach derives logically from theory and statistics and is therefore valid, we understand that it is rather unique and see why some readers would think that an independent validation is necessary. Unable to complete such validation in the near future, however, we decided to make this manuscript available as a preprint to share our ideas and hopefully stimulate discussion on what we believe is a most interesting topic. We also hope to receive feedback that may enable us to improve our work for publication in a journal at a later date.

evolutionary biology↗

bioRxiv2017

Atlantean Evolution in Darwin’s Finches—Issues and Perspectives in Species Delimitation using Phenotypic Data

Progress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species. In light of this model, we show that analytical approaches employed in taxonomic studies using phenotypic data are often compromised by three issues: (1) reliance on graphical analyses of phenotypic space that do not consider the frequency of phenotypes; (2)exclusion of characters potentially important for species delimitation following reduction of data dimensionality; and (3) use of measures of central tendencies to evaluate phenotypic distinctiveness. We outline approaches to overcome these issues based on statistical developments related to normal mixture models and illustrate them empirically with a reanalysis of morphological data recently used to claim that there are no morphologically distinct species of Darwins ground-finches (Geospiza). We found negligible support for this claim relative to taxonomic hypotheses recognizing multiple species. Although species limits among ground-finches merit further assessments using additional sources of information, our results bear implications for other areas of inquiry including speciation research: because ground-finches have likely speciated and are not trapped in a process of \"Sisyphean\" evolution as recently argued, they remain useful models to understand the evolutionary forces involved in speciation. Our work underscores the importance of statistical approaches grounded on appropriate evolutionary models for species delimitation. Approaches allowing one to fit normal mixture models without a priori information about species limits offer new perspectives in the kind of inferences available to systematists, with significant repercusions on ideas about the structure of biological biodiversity. [morphology; normal mixture model; phenotype; principal components analysis; species limits; variable selection.]

evolutionary biology↗