Biology subjects

Fuentes, F.

Publications and source records attributed to Fuentes, F..

9 recordsLinked to original sources

bioRxiv2026

Development of a microbiome based health score for non-invasive monitoring of farmed Atlantic salmon (Salmo salar)

The sustainability of Atlantic salmon (Salmo salar) farming is threatened by infectious diseases, environmental stressors, feed limitations, and regulatory or economic constraints. Although current health monitoring is improving with AI-powered camera systems that analyze behavior and nutrition, these tools typically identify stress responses rather than early signs of disease states. Because the microbial community undergoes successional reassembly in response to physiological disruptions before host barriers are breached, the microbiome offers a proactive early warning approach. In this study, a comparative cohort design was employed using a total of 171 individuals (n= 85 "healthy"; n=86 "lesioned") collected from a commercial marine facility and classified based on external clinical signs. The microbiome of multiple body sites (gills, skin, urogenital pore, and mucosa) from healthy and lesioned salmon were profiled using 16S rRNA amplicon sequencing. No differences in alpha diversity were observed between tissues and conditions. However, beta diversity was significantly different in clinical status, and the interaction of tissue with the status. Conversely, the mucosa and urogenital microbiomes were compositionally similar to each other, as were the gill and skin microbiomes, suggesting that urogenital swabs could serve as a non-invasive proxy for gut microbiome profiling, and skin for gill microbiomes. Several supervised models were trained on these profiles and used to classify salmon status with high accuracy. Based on these data, two Salmon Microbiome Health Score were developed that accurately differentiated the two cohorts. These scores are proposed as a novel biomarker, enabling proactive health management in aquaculture and complementing emerging technological monitoring systems.

genomics↗

bioRxiv2025

Lipid-mediated GPR32 signaling reprograms macrophage metabolism to impair anti-tuberculous immunity

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), has evolved strategies to evade innate immunity and establish persistent infection. However, the mechanisms by which M. tuberculosis reprograms human macrophage metabolism remain incompletely defined. Tuberculous pleural effusion (TB-PE), a common extrapulmonary manifestation that frequently coexists with pulmonary TB, offers a unique, clinically relevant immunometabolic window into the TB microenvironment. Here, using patient-derived TB-PE samples, we demonstrate that this microenvironment induces a metabolic state in human macrophages that compromises their antimicrobial function. Lipidomic analysis identified an enrichment of the specialized pro-resolving mediator Resolvin D5 (RvD5), which signals through GPR32 to suppress macrophage microbicidal activity. The acellular fraction of TB-PE was sufficient to induce RvD5 secretion by monocytes, correlating with increased expression of RvD5 biosynthetic enzymes in pleural monocytes from TB patients. Mechanistically, RvD5-GPR32 signaling inhibited glycolysis without promoting oxidative phosphorylation, reducing HIF-1 activity and impairing intracellular M. tuberculosis control. HIF-1 stabilization restored antimicrobial function. These findings uncover the RvD5-GPR32-HIF-1 axis as a mechanism of metabolic immune suppression and a potential target for host-directed TB therapy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/663524v3_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@64feceorg.highwire.dtl.DTLVardef@948ab0org.highwire.dtl.DTLVardef@1d387forg.highwire.dtl.DTLVardef@682f72_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Major antigenic differences in Aeromonas salmonicida isolates correlate with the emergence of a new strain causing furunculosis in Chilean salmon farms

Aeromonas salmonicida is the etiological agent of furunculosis, a septicemic disease with high mortality rates affecting salmonids and other teleost species worldwide. Reviewing molecular diagnostic protocols for routine diagnostics, we realized that the amplification of the vapA target gene failed in some cases of furunculosis. Therefore, we hypothesized that the emergence of a new strain may be involved in recent outbreaks. In this work, we demonstrate that the vapA locus is absent in the new strain, which explains why it lacks the major membrane component VapA protein, a critical virulence factor. In addition, we found that the vapA-absent strain differs from its counterparts in outer membrane protein and lipopolysaccharide profiles, suggesting profound changes at the membrane structure level and in antigenic properties. These features along with sequence analysis information allowed us to infer that a complex genomic rearrangement, probably an indel encompassing the entire vapA locus, gave rise to this membrane phenotype. Although the causes for pathogen evolution and emergence were not fully elucidated, our results strongly suggest that the vapA-absent strain is responsible for a raising proportion of recent furunculosis cases, and that it may be related to a less virulent disease and a low serological response upon vaccination with the A. salmonicida antigen formulation currently used in Chile.

microbiology↗

bioRxiv2024

CD4+ T cells drive corneal nerve damage but are dispensable for corneal epitheliopathy development in dry eye disease

Dry eye disease (DED) is characterized by a dysfunctional tear film in which the cornea epithelium and its abundant nerves are affected by ocular desiccation and inflammation. Although adaptive immunity and specifically CD4+ T cells play a role in DED pathogenesis, the exact contribution of these cells to corneal epithelial and neural damage remains undetermined. To address this, we explored the progression of a surgical DED model in wild-type (WT) and T cell-deficient mice. We observed that adaptive immune-deficient mice developed all aspects of DED comparably to WT mice except for the absence of functional and morphological corneal nerve changes, nerve damage-associated transcriptomic signature in the trigeminal ganglia, and sustained tear cytokine levels. Adoptive transfer of CD4+ T cells from WT DED mice to T cell-deficient mice reproduced corneal nerve damage but not epitheliopathy. Conversely, T cell-deficient mice reconstituted solely with naive CD4+ T cells developed corneal nerve impairment and epitheliopathy upon DED induction, thus replicating the WT DED phenotype. Collectively, our data show that while corneal neuropathy is driven by CD4+ T cells in DED, corneal epithelia damage develops independently of the adaptive immune response. These findings have implications for T cell-targeting therapies currently in use for DED. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/586336v2_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1138e85org.highwire.dtl.DTLVardef@f1d0c7org.highwire.dtl.DTLVardef@1c1cccaorg.highwire.dtl.DTLVardef@6c09a7_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementDry eye is a frequent ocular disorder in which damage to the corneal epithelium and nerves is triggered by inadequate lubrication. The local CD4+ T cell-predominant immune response aggravates ocular surface impairment but the exact contribution of these cells to corneal epithelial and neural disease remains undetermined. Using adoptive transfer of T cells into T cell-deficient mice, trigeminal transcriptomics, and tear cytokine analysis, we delineate the pathogenic role of CD4+ T cells, revealing that they drive corneal nerve damage but are dispensable for epithelial disease to develop in response to desiccation. CD4+ T cells promote corneal neuropathy possibly by releasing proinflammatory cytokines onto the ocular surface. These findings have implications for T cell-targeting therapies currently used for dry eye.

immunology↗

bioRxiv2023

Ocular TRPV1 deficiency protects from dry eye-induced corneal nerve damage

BackgroundCorneal nerve damage causes the most clinically significant symptoms in dry eye disease (DED) yet its pathophysiology remains poorly understood. Transient receptor potential vanilloid-1 (TRPV1) channels abound in corneal nerve fibers and respond to inflammation-derived ligands, which increase in DED. TRPV1 overactivation promotes axonal degeneration in vitro but whether it contributes to corneal neuropathy is unknown. Therefore, here we explored the role of TRPV1 in DED-associated corneal nerve damage. MethodsSurgical DED was induced in TRPV1-deficient (TRPV1KO) and wild-type (wt) mice. Corneal nerve function was measured on days 0, 5, and 10 by mechanical and capsaicin sensitivity and eye-closing ratio as an indicator of non-evoked pain. Nerve and epithelial morphology was evaluated by confocal microscopy of corneal wholemounts. Pharmacological TRPV1 inhibition in wild-type mice was also evaluated. Resultswt and TRPV1KO mice developed comparable ocular desiccation and corneal epithelial damage. Contrasting with wt mice, corneal mechanosensitivity in TRPV1KO mice did not decrease with disease progression. Capsaicin sensitivity increased in wt mice with DED, and consistently, wt but not TRPV1KO mice with DED displayed signs of non-evoked pain. Wt mice with DED exhibited nerve degeneration throughout the corneal epithelium whereas TRPV1KO mice only developed a reduction in the most superficial nerve endings that failed to propagate to the deeper subbasal corneal nerves. Pharmacological blockade of ocular TRPV1 activity reproduced these findings in wt mice with DED. Although TRPV1KO mice with DED had fewer pathogenic Th1 and Th17 CD4+ T cells in the lymph nodes, conjunctival immune infiltration was comparable between strains. Moreover, CD4+ T cells from wt and TRPV1KO mice with DED were equally pathogenic when transferred into T cell-deficient mice, confirming that TRPV1 activity in T cells is not involved in corneal neuropathy. ConclusionsAlthough ocular desiccation is sufficient to trigger superficial corneal nerve damage in DED, proximal propagation of axonal degeneration requires TRPV1 signaling. Conversely, local inflammation sensitizes ocular TRPV1 channels, which are also involved in ocular pain, a key symptom of the disease. Thus, our findings suggest that ocular TRPV1 overactivation is a driving force in DED-associated corneal neuropathy and a potential therapeutic target. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=63 SRC="FIGDIR/small/554143v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@12d43d7org.highwire.dtl.DTLVardef@c11354org.highwire.dtl.DTLVardef@1dc0098org.highwire.dtl.DTLVardef@ab2e60_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Glycolytic imprinting of monocytes impairs HIF1α-driven migration of dendritic cells in tuberculosis

During tuberculosis, migration of dendritic cells (DCs) from the site of infection to the draining lymph nodes is known to be impaired, hindering the rapid development of protective T-cell mediated immunity. However, the mechanisms involved in the delayed migration of DCs during tuberculosis (TB) are still poorly defined. Here, we found that infection of DCs with Mycobacterium tuberculosis (Mtb) triggers HIF-1-mediated aerobic glycolysis in a TLR2-dependent manner, and that this metabolic profile is essential for DC migration. In particular, the lactate dehydrogenase (LDH) inhibitor oxamate and the HIF-1 inhibitor PX-478 abrogated Mtb-induced DC migration in vitro to the lymphoid tissue-specific chemokine CCL21, and in vivo to lymph nodes in mice. Strikingly, we found that although monocytes from TB patients are inherently biased toward glycolysis metabolism, they differentiate into poorly glycolytic and poorly migratory DCs, compared with healthy subjects. Taken together, these data suggest that because of their preexisting glycolytic state, circulating monocytes from TB patients are refractory to differentiation into migratory DCs, which may explain the delayed migration of these cells during the disease and opens avenues for host-directed therapies for TB. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/535400v6_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@9c6849org.highwire.dtl.DTLVardef@82981dorg.highwire.dtl.DTLVardef@1d0b7faorg.highwire.dtl.DTLVardef@1deb76f_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2021

Humoral immune responses against seasonal coronaviruses predict efficiency of SARS-CoV-2 spike targeting, FcγR activation, and corresponding COVID-19 disease severity

Despite SARS-CoV-2 being a "novel" coronavirus, several studies suggest that detection of anti-spike IgG early in infection may be attributable to the amplification of humoral memory responses against seasonal hCoVs in severe COVID-19 patients. In this study, we examined this concept by characterizing anti-spike IgG from a cohort of non-hospitalized convalescent individuals with a spectrum of COVID-19 severity. We observed that anti-spike IgG levels positively correlated with disease severity, higher IgG cross-reactivity against betacoronaviruses (SARS-CoV-1 and OC43), and higher levels of proinflammatory Fc gamma receptor 2a and 3a (Fc{gamma}R2a & Fc{gamma}R3a) activation. In examining the levels of IgG targeting betacoronavirus conserved and immunodominant epitopes versus disease severity, we observed a positive correlation with the levels of IgG targeting the conserved S2FP region, and an inverse correlation with two conserved epitopes around the heptad repeat (HR) 2 region. In comparing the levels of IgG targeting non-conserved epitopes, we observed that only one of three non-conserved immunodominant epitopes correlated with disease severity. Notably, the levels of IgG targeting the receptor binding domain (RBD) were inversely correlated with severity. Importantly, targeting of the RBD and HR2 regions have both been shown to mediate SARS-CoV-2 neutralization. These findings show that, aside from antibody (Ab) targeting of the RBD region, humoral memory responses against seasonal betacoronaviruses are potentially an important factor in dictating COVID-19 severity, with anti-HR2-dominant Ab profiles representing protective memory responses, while an anti-S2FP dominant Ab profiles indicate deleterious recall responses. Though these profiles are masked in whole antigen profiling, these analyses suggest that distinct Ab memory responses are detectable with epitope targeting analysis. These findings have important implications for predicting severity of SARS-CoV-2 infections (primary and reinfections), and may predict vaccine efficacy in subpopulations with different dominant antibody epitope profiles.

microbiology↗

bioRxiv2020

Host-derived lipids from tuberculous pleurisy impair macrophage microbicidal-associated metabolic activity

Mycobacterium tuberculosis (Mtb) regulates the macrophage metabolic state to thrive in the host. Yet, the responsible mechanisms remain elusive. Macrophage activation towards the microbicidal (M1) program depends on the HIF-1 -mediated metabolic shift from oxidative phosphorylation towards glycolysis. Here, we asked whether a tuberculosis (TB) microenvironment changes the M1 macrophage metabolic state. We exposed M1 macrophages to the acellular fraction of tuberculous pleural effusions (TB-PE), and found lower glycolytic activity, accompanied by elevated levels of oxidative phosphorylation and bacillary load, compared to controls. The host-derived lipid fraction of TB-PE drove these metabolic alterations. HIF-1 stabilization reverted the effect of TB-PE by restoring M1 metabolism. As a proof-of-concept, Mtb-infected mice with stabilized HIF-1 displayed lower bacillary loads and a pronounced M1-like metabolic profile in alveolar macrophages. Collectively, we demonstrate that host-derived lipids from a TB-associated microenvironment alter the M1 macrophage metabolic reprogramming by hampering HIF-1 functions, thereby impairing control of Mtb infection.

immunology↗

bioRxiv2019

Mycobacterium tuberculosis Modulates the Metabolism of Alternatively Activated Macrophages to Promote Foam Cell Formation and Intracellular Survival

The ability of Mycobacterium tuberculosis (Mtb) to persist inside host cells relies on metabolic adaptation, like the accumulation of lipid bodies (LBs) in the so-called foamy macrophages (FM). Indeed, FM are favorable to Mtb. The activation state of macrophages is tightly associated to different metabolic pathways, such as lipid metabolism, but whether differentiation towards FM differs between the macrophage activation profiles remains unclear. Here, we aimed to elucidate if distinct macrophage activation states exposed to a tuberculosis-associated microenvironment can accumulate LBs, and its impact on the control of infection. We showed that signal transducer and activator of transcription 6 (STAT6) activation in interleukin (IL)-4-activated human macrophages (M(IL-4)) prevents FM formation induced by pleural effusion from patients with tuberculosis. In these cells, LBs are disrupted by lipolysis, and the released fatty acids enter the {beta}-oxidation (FAO) pathway fueling the generation of ATP in mitochondria. We demonstrated that inhibition of the lipolytic activity or of the FAO drives M(IL-4) macrophages into FM. Also, exhibiting a predominant FAO metabolism, mouse alveolar macrophages are less prone to become FM compared to bone marrow derived-macrophages. Upon Mtb infection, M(IL-4) macrophages are metabolically re-programmed towards the aerobic glycolytic pathway and evolve towards a foamy phenotype, which could be prevented by FAO activation or inhibition of the hypoxia-inducible factor 1-alpha (HIF-1)-induced glycolytic pathway. In conclusion, our results demonstrate a role for STAT6-driven FAO in preventing FM differentiation, and reveal an extraordinary capacity by Mtb to rewire metabolic pathways in human macrophages and induce the favorable FM. IMPORTANCETuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb). While its treatment was already standardized, TB remains one of the top 10 death causes worldwide. A major problem is the efficient adaptation of Mtb to the macrophage intracellular milieu, which includes deregulation of the lipid metabolism leading to the formation of foamy macrophages (FM) which are favorable to Mtb. A critical aspect of our work is the use of tuberculous pleural effusions (TB-PE) -- human-derived biological fluid capable of mimicking the complex microenvironment of the lung cavity upon Mtb infection -- to study the FM metabolic modulation. We revealed how the STAT6 transcription factor prevents FM formation induced by PE-TB, and how Mtb counteracts it by activating another transcription factor, HIF-1, to re-establish FM. This study provides key insights in host lipid metabolism, macrophage biology and pathogen subversion strategies, to be exploited for prevention and therapeutic purposes in infectious diseases.

immunology↗