Biology subjects

Gomez, A.

Publications and source records attributed to Gomez, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Multiple FGFR1 mutations modulate tumorigenic mechanisms in glioneuronal tumors.

FGFR1 genetic alterations are associated with human diseases, including brain tumors. We reported multiple FGFR1 mutations in familial and sporadic cases of low-grade glioneuronal tumors, suggesting intrinsic mechanisms of selective pressure toward FGFR1 multiple events arising in the context of a quiet genome. To decipher the molecular mechanisms triggered by multiple FGFR1 mutations, we have mapped the proximal interactome of wild-type, single-and double-mutant FGFR1 proteins through a BioID-MS approach. Our data reveals novel oncogenic functionality for the two hotspots N546K and K656E, linked to evasion of lysosomal degradation. We identified a modulatory role played by the susceptibility variant R661P, which hampers the oncogenic potential of both hotspot mutations by rescuing receptor degradation and reducing N546K affinity for the downstream effector PLC{gamma}. The R661P variant alone abolished the self-renewal capacity of oligodendroglioma cells and showed downregulation of genes involved in neurodevelopment and neuro-glial cell fate decisions, both aspects overcome in the double mutants. This study sheds light on the oncogenic effects associated with FGFR1 alterations and their recurrence in low-mutation burden and therapy naive tumors.

cancer biology↗

bioRxiv2025

Time-course Transcriptomics Reveals the Impact of Treponema pallidum on Microvascular Endothelial Cell Function and Phenotype

Syphilis, caused by Treponema pallidum subsp. pallidum, is an urgent global public health threat. Syphilis vaccine development has been impeded by limited understanding of the molecular mechanisms that enable T. pallidum to establish and maintain infection. The vascular endothelium is critical for T. pallidum attachment, dissemination, and host immune response initiation; however, the molecular details of T. pallidum-endothelial interactions are incompletely understood. To enhance understanding, we performed time-course transcriptomic profiling on T. pallidum-exposed brain microvascular endothelial cells. These analyses showed T. pallidum exposure altered pathways related to extracellular matrix, growth factors, integrins, and Rho GTPases. The induced transcriptional response was consistent with endothelial to mesenchymal transition, a process involved in fetal development and vascular dysfunction. This study provides a comprehensive understanding of the molecular responses of endothelial cells to T. pallidum and identified the host pathways that might cause syphilis disease symptoms, information that could aid in syphilis vaccine design. Highlights{square} Exposure of microvascular endothelial cells to Treponema pallidum subsp. Pallidum significantly alters the endothelial cell transcriptome {square}Signaling pathways related to extracellular matrix organization, growth factors, integrins, and Rho GTPases were overrepresented for genes differentially expressed in T. pallidum-exposed endothelial cells {square}Exposure to T. pallidum induces pathways and factors consistent with endothelial to mesenchymal transition, a host process central to development that may explain the devastating effects of congenital infection {square}T. pallidum exposure induces expression of Snail, the main transcription factor associated with the process of endothelial to mesenchymal transition O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/651946v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@e121beorg.highwire.dtl.DTLVardef@6e4caeorg.highwire.dtl.DTLVardef@16c3f03org.highwire.dtl.DTLVardef@19cf020_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Imaging-based screen identifies novel natural compounds that perturb cell and chloroplast division in Chlamydomonas reinhardtii

Successful cell division requires faithful division and segregation of organelles into daughter cells. The unicellular alga Chlamydomonas reinhardtii has a single, large chloroplast whose division is spatiotemporally coordinated with furrowing. Cytoskeletal structures form in the same plane at the midzone of the dividing chloroplast (FtsZ) and the cell (microtubules), but how these structures are coordinated is not understood. Previous work showed that loss of F-actin blocks chloroplast division but not furrow ingression, suggesting that pharmacological perturbations can disorganize these events. In this study, we developed an imaging platform to screen natural compounds that perturb cell division while monitoring FtsZ and microtubules and identified 70 unique compounds. One compound, curcumin, has been proposed to bind to both FtsZ and tubulin proteins in bacteria and eukaryotes, respectively. In C. reinhardtii, where both targets coexist and are involved in cell division, curcumin at a specific dose range caused a severe disruption of the FtsZ ring in chloroplast while leaving the furrow-associated microtubule structures largely intact. Time-lapse imaging showed that loss of FtsZ and chloroplast division failure delayed the completion of furrowing but not the initiation, suggesting that the chloroplast-division checkpoint proposed in other algae requires FtsZ or is absent altogether in C. reinhardtii. SIGNIFICANCE STATEMENTO_LISuccessful cell division requires the coordination of both organelle inheritance and cytokinesis. The unicellular alga Chlamydomonas reinhardtii, which spatiotemporally coordinates the division of its chloroplast with cytokinesis, is an excellent model to study the regulation. C_LIO_LIWe screened libraries of natural compounds for perturbations of cell and/or chloroplast division, identifying 70 unique chemicals. By time-lapse microscopy using one of the hits, curcumin, we demonstrate that although chloroplast division failures delay the completion of cytokinesis, it does not impair initiation. C_LIO_LIThese findings suggest that the chloroplast-division checkpoint proposed in other algae requires FtsZ or is absent altogether in C. reinhardtii. C_LI

cell biology↗

bioRxiv2024

A brain-body feedback loop driving HPA-axis dysfunction in breast cancer

Breast cancer patients often exhibit disrupted circadian rhythms in circulating glucocorticoids (GCs), such as cortisol. This disruption correlates with reduced quality of life and higher cancer mortality1-3. The exact cause of this phenomenon -- whether due to treatments, stress, age, co-morbidities, lifestyle factors, or the cancer itself remains unclear. Here, we demonstrate that primary breast cancer alone blunts host GC rhythms by disinhibiting neurons in the hypothalamus, and that circadian phase-specific neuromodulation of these neurons can attenuate tumor growth by enhancing anti-tumor immunity. We find that mice with mammary tumors exhibit blunted GC rhythms before tumors are palpable, alongside increased activity in paraventricular hypothalamic neurons expressing corticotropin-releasing hormone (i.e., PVNCRH neurons). Tumor-bearing mice have fewer inhibitory synapses contacting PVNCRH neurons and reduced miniature inhibitory post-synaptic current (mIPSC) frequency, leading to net excitation. Tumor-bearing mice experience impaired negative feedback on GC production, but adrenal and pituitary gland functions are largely unaffected, indicating that alterations in PVNCRH neuronal activity are likely a primary cause of hypothalamic-pituitary-adrenal (HPA) axis dysfunction in breast cancer. Using chemogenetics (hM3Dq) to stimulate PVNCRH neurons at different circadian phases, we show that stimulation just before the light-to-dark transition restores normal GC rhythms and reduces tumor progression. These mice have significantly more effector T cells (CD8+) within the tumor than non-stimulated controls, and the anti-tumor effect of PVNCRH neuronal stimulation is absent in mice lacking CD8+ T cells. Our findings demonstrate that breast cancer distally regulates neurons in the hypothalamus that control output of the HPA axis and provide evidence that therapeutic targeting of these neurons could mitigate tumor progression.

neuroscience↗

bioRxiv2024

Population genomics of Macrophomina spp. reveals cryptic host specialization and evidence for meiotic recombination

Knowledge of the factors structuring populations of pathogenic fungi is fundamental to disease management efforts and basic biology. High-quality short-read sequence data were obtained for 463 Macrophomina spp. isolates collected from 91 host plant species and soil in 23 countries. Analyses revealed high diversity, admixture, and equal mating type ratios suggesting on-going recombination. Although most tested isolates could asymptomatically colonize strawberry, only isolates from a single phylogroup caused disease. In addition to strawberry, evidence for host specialization was discovered for soybean, demonstrating this broad host range pathogen contains phylogroups with cryptic specialization. Geography x isolate genotype associations were weak, suggesting these species were frequently trafficked between regions. Re-analysis using genomic data supported current species boundaries, and new molecular markers were designed to specifically identify each species. Contrary to expectations, M. phaseolina should be considered a species with both specialist and generalist populations for which meiosis can increase genetic diversity.

genomics↗

bioRxiv2024

Microphysiological system modeling pericyte-induced temozolomide resistance in glioblastoma

Glioblastoma (GBM) is a malignancy with poor survival and high rates of chemoresistance. Temozolomide (TMZ), the standard-of-care chemotherapy for GBM patients, but GBM cells can be resistant to TMZ, resulting in limited clinical efficacy. Elucidating the complex mechanisms of TMZ chemoresistance in GBM requires novel in vitro models replicating the complex tumor microenvironment (TME). We present an multicellular 3D GBM model recapitulating the biomechanical characteristics of brain tissues and pericyte-mediated TMZ resistance. The composite hydrogel used to encapsulate GBM spheroids (U87, LN229, and PDM140), pericytes, or GBM spheroids with pericytes, mimics the rheological properties of brain tissues (G[~]800Pa and G"[~]100Pa). When untreated, the GBM models remain viable and proliferative for 14 days. PDM140 spheroids were most sensitive to TMZ (IC50=73M), followed by LN229 (IC50=278M) and U87 (IC50=446M). With pericytes, the viability of TMZ-treated GBM spheroids significantly increases by 22.7% for PDM140, 32.5% for LN229, and 22.1% for U87, confirming pericyte-induced GBM chemoresistance responses. The upregulation (380-fold) of C-C motif chemokine ligand 5 (CCL5) in pericytes upon TMZ treatment could explain the chemoresistance responses. This innovative brain-mimicking 3D GBM model represents a novel in vitro platform for testing the efficacy of TMZ and novel drugs targeting CCL5-mediated chemoresistance pathways in GBM.

bioengineering↗

bioRxiv2024

A high-throughput method for quantifying Drosophila fecundity

Measurements of Drosophila fecundity are used in a wide variety of studies, such as investigations of stem cell biology, nutrition, behavior, and toxicology. In addition, because fecundity assays are performed on live flies, they are suitable for longitudinal studies such as investigations of aging or prolonged chemical exposure. However, standard Drosophila fecundity assays have been difficult to perform in a high-throughput manner because experimental factors such as the physiological state of the flies and environmental cues must be carefully controlled to achieve consistent results. In addition, exposing flies to a large number of different experimental conditions (such as chemical additives in the diet) and manually counting the number of eggs laid to determine the impact on fecundity is time-consuming. We have overcome these challenges by combining a new multiwell fly culture strategy with a novel 3D-printed fly transfer device to rapidly and accurately transfer flies from one plate to another; the RoboCam, a low-cost, custom built robotic camera to capture images of the wells automatically; and an image segmentation pipeline to automatically identify and quantify eggs. We show that this method is compatible with robust and consistent egg laying throughout the assay period; and demonstrate that the automated pipeline for quantifying fecundity is very accurate (r2 = 0.98 for the correlation between the automated egg counts and the ground truth) In addition, we show that this method can be used to efficiently detect the effects on fecundity induced by dietary exposure to chemicals. Taken together, this strategy substantially increases the efficiency and reproducibility of high throughput egg laying assays that require exposing flies to multiple different media conditions.

genetics↗

bioRxiv2024

An efficient inducible model for the control of gene expression in renin cells

BackgroundFate mapping and genetic manipulation of renin cells have relied on either non-inducible Cre lines that can introduce developmental effects of gene deletion or BAC transgene-based inducible models that may be prone to spurious and/or ectopic gene expression. MethodsWe generated an inducible mouse model in which CreERT2 is under the control of the endogenous Akr1b7 gene, an independent marker of renin cells. ResultsWe evaluated the pattern of Cre expression in Akr1b7CreERT2/+;R26RmTmG/+ mice in which Akr1b7+/renin+ cells become GFP+ upon tamoxifen administration. At E18.5 and P5, GFP was found in Juxtaglomerular cells, along the arterioles, and in the glomerular mesangium. In adult kidneys, GFP was present mainly in Juxtaglomerular cells. In mice treated with captopril and a low sodium diet to induce recruitment of renin cells, GFP extended along the afferent arterioles and in the mesangium. In addition, we deleted renin in adult mice and found a marked reduction in kidney renin expression and mean arterial pressure in mutant animals. When subjected to a homeostatic threat, mutant mice were unable to recruit renin+ cells. Most importantly, mice with renin deletion induced in the adult developed concentric vascular hypertrophy ruling out potential developmental effects on the vasculature due to the lack of renin. ConclusionsRenin can be efficiently and specifically deleted in renin cells in adult life using our conditional model. Akr1b7CreERT2 mice constitute an excellent model for the fate mapping of renin cells and for the spatial and temporal control of gene expression in renin cells.

physiology↗

bioRxiv2024

Treponema pallidum periplasmic and membrane proteins are recognized by circulating and skin CD4+ T cells

BackgroundHistologic and serologic studies suggest the induction of local and systemic Treponema pallidum (Tp)-specific CD4+ T cell responses to Tp infection. We hypothesized that Tp-specific CD4+ T cells are detectable in blood and in the skin rash of secondary syphilis and persist in both compartments after treatment. MethodsPBMC collected from 67 participants were screened by IFN{gamma} ELISPOT response to Tp sonicate. Tp-reactive T cell lines from blood and skin were probed for responses to 88 recombinant Tp antigens. Peptide epitopes and HLA class II restriction were defined for selected antigens. ResultsWe detected CD4+ T cell responses to Tp sonicate ex vivo. Using Tp-reactive T cell lines we observed recognition of 14 discrete proteins, 13 of which localize to bacterial membranes or the periplasmic space. After therapy, Tp-specific T cells persisted for at least 6 months in skin and 10 years in blood. ConclusionsTp infection elicits an antigen-specific CD4+ T cell response in blood and skin. Tp-specific CD4+ T cells persist as memory in both compartments long after curative therapy. The Tp antigenic targets we identified may be high priority vaccine candidates.

immunology↗

bioRxiv2024

Endocrine disruptor-induced epimutagenesis in vitro: Insight into molecular mechanisms

Endocrine disrupting chemicals (EDCs) such as bisphenol S (BPS) are xenobiotic compounds that can disrupt endocrine signaling following exposure due to steric similarities to endogenous hormones within the body. EDCs have been shown to induce disruptions in normal epigenetic programming (epimutations) that accompany dysregulation of normal gene expression patterns that appear to predispose disease states. Most interestingly, the prevalence of epimutations following exposure to many different EDCs often persists over multiple subsequent generations, even with no further exposure to the causative EDC. Many previous studies have described both the direct and prolonged effects of EDC exposure in animal models, but many questions remain about molecular mechanisms by which EDCs initially induce epimutations or contribute to the propagation of EDC-induced epimutations either within the exposed generation or to subsequent generations. Additional questions remain regarding the extent to which there may be differences in cell-type specific susceptibilities to various EDCs, and whether this susceptibility is correlative with expression of relevant hormone receptors and/or the location of relevant hormone response elements (HREs) in the genome. To address these questions, we exposed cultured mouse pluripotent (induced pluripotent stem [iPS]), somatic (Sertoli and granulosa), and germ (primordial germ cell like [PGCLC]) cells to BPS and measured changes in DNA methylation levels at the epigenomic level and gene expression at the transcriptomic level. We found that there was indeed a difference in cell-type specific susceptibility to EDC-induced epimutagenesis and that this susceptibility correlated with differential expression of relevant hormone receptors and, in many cases, tended to generate epimutations near relevant HREs within the genome. Additionally, however, we also found that BPS can induce epimutations in a cell type that does not express relevant receptors and in genomic regions that do not contain relevant HREs, suggesting that both canonical and non-canonical signaling mechanisms can be disrupted by BPS exposure. Most interestingly, we found that when iPS cells were exposed to BPS and then induced to differentiate into PGCLCs, the prevalence of epimutations and differentially expressed genes (DEGs) initially induced in the iPSCs was largely retained in the resulting PGCLCs, however, >90% of the specific epimutations and DEGs were not conserved but were rather replaced by novel epimutations and DEGs following the iPSC to PGCLC transition. These results are consistent with a unique concept that many EDC-induced epimutations may normally be corrected by germline and/or embryonic epigenetic reprogramming but that due to disruption of the underlying chromatin architecture induced by the EDC exposure, many novel epimutations may emerge during the reprogramming process as well. Thus, it appears that following exposure to a disruptive agent such as an EDC, a prevalence of epimutations may transcend epigenetic reprogramming even though most individual epimutations are not conserved during this process.

molecular biology↗

bioRxiv2023

Sediment source and dose influence the larval performance of the threatened coral Orbicella faveolata

The effects of turbidity and sedimentation stress on early life stages of corals are poorly understood, particularly in Atlantic species. Dredging operations, beach nourishment, and other coastal construction activities can increase sedimentation and turbidity in nearby coral reef habitats and have the potential to negatively affect coral larval development and metamorphosis, reducing sexual reproduction success. In this study, we investigated the performance of larvae of the threatened Caribbean coral species Orbicella faveolata exposed to sediments collected from a reef site in southeast Florida recently impacted by dredging (Port Miami), and compared it to the performance of larvae exposed to sediments collected from the offshore, natal reef of the parent colonies. In a laboratory experiment, we tested whether low and high doses of each of these sediment types affected the survival, settlement, and respiration of coral larvae compared to a no-sediment control treatment. In addition, we analyzed the sediments used in the experiments with 16S rRNA gene amplicon sequencing to assess differences in the microbial communities present in the Port versus Reef sediments, and their potential impact on coral performance. Overall, O. faveolata larvae exposed to high doses of either sediment type (Port or Reef) exhibited reduced survival and settlement rates, but only the Port sediments resulted in adverse effects in the low-dose treatment. Sediments collected near the Port also contained different microbiomes than Reef sediments, and higher relative abundances of the bacteria Desulfobacterales, which has been associated with coral disease. We hypothesize that differences in microbiomes between the two sediments may be a contributing factor in explaining the observed differences in larval performance. Together, these results suggest that the settlement success and survival of O. faveolata larvae are more readily compromised by encountering port inlet sediments compared to reef sediments, with potentially important consequences for the recruitment success of this species in affected areas.

ecology↗

bioRxiv2023

Pathogenic Leptospira are widespread in the urban wildlife of southern California

Leptospirosis is the most widespread zoonotic disease in the world, yet it is broadly understudied in multi-host wildlife systems. Knowledge gaps regarding Leptospira circulation in wildlife, particularly in densely populated areas, contribute to frequent misdiagnoses in humans and domestic animals. We assessed Leptospira prevalence levels and risk factors in five target wildlife species across the greater Los Angeles region: striped skunks (Mephitis mephitis), Northern raccoons (Procyon lotor), coyotes (Canis latrans), Virginia opossums (Didelphis virginiana), and fox squirrels (Sciurus niger). We sampled more than 960 individual animals, including over 700 from target species in the greater Los Angeles region, and an additional 260 sampled opportunistically from other regions and species. In the five target species, seroprevalences ranged from 5-60% and active infection prevalences ranged from 0.8-15.2% in all except fox squirrels (0%). Patterns of serologic reactivity suggest that mainland terrestrial wildlife, particularly mesocarnivores, could be the source of repeated observed introductions of Leptospira into local marine and island ecosystems. Overall, we found evidence of widespread Leptospira exposure in wildlife across Los Angeles and surrounding regions. This indicates exposure risk for humans and domestic animals and highlights that this pathogen can circulate endemically in many wildlife species even in densely populated urban areas.

ecology↗

bioRxiv2022

Antibiotic resistance genes in sewages from hospitals and the urban setting in a Peruvian city in the highlands

BackgroundThe establishment of metagenomics seems a suitable approach to assess the abundance and diversity of antibiotic resistance genes (ARG) MethodsMetagenomics study in a Peruvian city from the highlands, where samples were derived from sewage waters from two hospitals and the urban setting. DNA extraction was performed in 250 mL and then 16S rRNA gene amplification and shotgun sequencing were carried out. The bioinformatics pipeline was performed following recommendations for metagenomics analysis. Alpha diversity was evaluated with the Shannon and Simpsons indices; whereas beta diversity was evaluated through the Bray-Curtis index, and using the principal coordinate analysis (PCoA) to explore and visualize the differences. ResultsWe found a high abundance of bacteria related to resistance to beta-lactams, macrolides, aminoglycosides, fluoroquinolones, and tetracyclines. The urban sample did not differ significantly from the wastewater ARG presence from the hospitals in Huanuco. ConclusionMetagenomics analysis through sewage strategies seems to help to monitor the AMR to establish local public health policies, especially in cities or countries with limited resources to establish large projects conceiving the One Health approach.

molecular biology↗

bioRxiv2022

Mink on the brink: Comparing survey methods for detecting a Critically Endangered carnivore, the European mink Mustela lutreola

Monitoring rare and elusive species is critical in guiding appropriate conservation management measures. Mammalian carnivores are challenging to monitor directly, due to their generally nocturnal and solitary lifestyle, and relatively large home ranges. The European mink Mustela lutreola is a Critically Endangered, small, semi-aquatic carnivore and is one of the most threatened mammal species in Europe. In northern Spain, the European mink population is monitored regionally using different methods and approaches, making assessment of national population status difficult. There is an urgent need to 1) assess the efficacy of survey methods, and 2) identify a standard monitoring methodology that can be deployed rapidly and inexpensively over large areas of the minks range. We deployed four methods - camera trapping, hair tubes, live trapping, and environmental DNA (eDNA) from water samples - to compare the probability of detecting European mink when present at 25 sampling sites within five 10x10km squares, and the economic cost and time required for each method. All four methods successfully detected European mink but the probability of detection varied by method. Camera trapping and hair tubes had the highest probability of detection; however, eDNA and live trapping detected mink in one 10x10km square where the latter two methods did not. For future European mink monitoring programmes, we recommend a combination of at least two methods, and suggest that camera traps or hair tubes are combined with live trapping or eDNA (depending on the scale and aims of the study), to gather critical information on distribution, occupancy and conservation status.

ecology↗

bioRxiv2022

Sniff Olfactometer (SO) Protocols

Most olfactometers used to study human olfaction have stimulus durations of more than 1 second and often lasting minutes(Dravnieks 1975; Leland et al. 2001; Schmidt and Cain 2010). During long stimulations, olfactory receptor responses and their resulting behaviors are modulated by adaptation and habituation to the stimulus(Pellegrino et al. 2017; Rankin 2009; Wilson and Linster 2008). For example, EOG results from the first deorphanized olfactory receptor tissue reached a maximum in [~]1 s, dropping to 1/2 maximum in the next second, and showing little signal reduction until the stimulation stopped after 6 seconds(Zhao et al. 1998). Longer stimulations can result in complete habituation; receptors still respond even though the behavior shows complete habituation (Barwich 2014). To minimize the effects of adaption and habituation on stimulus responses, the sniff olfactometer (SO) combined the precision of a blast olfactometer with the gentleness of a stream olfactometer by blasting a brief odorant puff (70ms duration) into a subjects self-imposed inhalation air stream(Rochelle 2017; Rochelle et al. 2017b; Wyckoff and Acree 2017). Here we describe SO protocols for threshold determinations of odorants in aqueous headspaces using odorant recognition probabilities associated with Log(odorant-concentrations(Rochelle et al. 2017a)). During a single trial a subject, preconditioned to associate a veridical name with a given odor (e.g., a pyrazine with "nuts" when the odor was detected and "not nuts" if it wasnt) was cued to "inhale" and 750ms later, a 15ml-70ms puff of odorant headspace was delivered into their inhalation airstream. A session consisted of 12 randomized double-blind trials of 3 different odorant concentrations. Additional sessions with different concentrations were conducted until the response probability to the samples ranged from below 0.2 to above 0.8. The robustness of the fitted function and the size of their confidence intervals depended on the difference between the concentrations of the odorants during a single session: small differences in sample concentration resulted in the data failing to fit a logistic function; larger concentration differences resulted in a better fit to the model. However, if one of the stimuli had no odorant at all i.e., a blank, the response to the blank was random.

animal behavior and cognition↗

bioRxiv2022

Functional Biomarkers of Ex-vivo Dental Caries Onset

BackgroundThe etiology of dental caries remains poorly understood. With the advent of next generation sequencing, a number of studies have focused on the microbial ecology of the disease. However, taxonomic associations with caries have not been consistent. Researchers have also pursued function-centric studies of the caries microbial communities aiming to identify consistently conserved functional pathways. A major question is whether changes in microbiome are a cause or a consequence of the disease. Thus, there is a critical need to define conserved functional biomarkers at the onset of dental caries. MethodsSince it is unethical to induce carious lesions clinically, we developed an innovative longitudinal ex-vivo model integrated with the advanced non-invasive multiphoton second harmonic generation bioimaging to spot the very early signs of dental caries, combined with 16S rRNA short amplicon sequencing and liquid chromatography-mass spectrometry-based targeted metabolomics. FindingsFor the first time, we induced longitudinally-monitored caries lesions validated with the scanning electron microscope. Consequently, we spotted the caries onset and, associated to it, distinguished five differentiating metabolites - Lactate, Pyruvate, Dihydroxyacetone phosphate, Glyceraldehyde 3-phosphate (upregulated) and Fumarate (downregulated). Those metabolites co-occurred with certain bacterial taxa; Streptococcus, Veillonella, Actinomyces, Porphyromonas, Fusobacterium, and Granulicatella, regardless of the abundance of other taxa. InterpretationThese findings are crucial for understanding the etiology and dynamics of dental caries, and devising targeted interventions to prevent disease progression. FundingThe study was funded by the National Institute for Dental and Craniofacial Research of the National Institutes of Health and the University of Minnesota. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSStudies have shown that dental caries, tooth decay, occurs as a result of disruptive imbalance in the oral ecosystem. Excessive dietary intake of fermentable carbohydrates is a critical contributor to disease progression by promoting bacterial production of acids, which shifts the microbial community to an imbalanced and a less diverse one. Studies have also shown that microbial associations with caries have not been consistent while their functions are relatively conserved across individuals. Still, the specific microbial functions associated with the dental caries onset is still unknown due to its infeasible clinical diagnosis. Added value of this studyThis study applied a novel longitudinal ex-vivo model, integrated with advanced non-invasive bioimaging, for experimental dental caries induction. This model enabled the detection of the exact onset of the disease, which is undetected clinically. Then, the microbial communities accompanying the caries onset were analyzed for their microbial composition and metabolic functions in comparison to normal conditions. Our study identified five metabolites differentiating the caries onset. Further, we investigated the co-occurrence of these metabolic biomarkers with certain oral bacteria. Implications of all the available evidenceOur study provides carefully validated evidence for biomarkers of the dental caries onset. These data are critical for early diagnostics and development of timely intervention strategies to interfere with the disease progression that otherwise requires invasive and costly health care expenses. Moreover, our data open new avenues for developing therapeutics to neutralize the identified metabolic biomarkers or target the accountable bacteria for caries prevention.

microbiology↗

bioRxiv2021

BCN057, a Modulator of GSK3b Induces KRAS G12D Mutant Pancreatic Cancer Cell Death

Effective treatment for Pancreatic Cancer remains a major challenge due to its resistance to radiation/chemotherapy and poor drug permeability. Moreover, treatment induced normal tissue toxicity, mainly to the duodenum and gastrointestinal epithelium, is common and is a dose limiting event, while toxicity to the pancreas is relatively rare1-3. Gastrointestinal toxicity, however, often results in interruption, reduction or premature withdrawal of anti-cancer therapy which is a very significant factor impacting the overall survival of patients being treated. Therefore, development of a therapeutic strategy to selectively sensitize tumor tissue without inducing normal tissue toxicity is important. In this manuscript, we show that the novel small molecule BCN057 can modulate chemo-sensitivity of oncogenic RAS pancreatic cancer cells while conversely protecting normal intestinal epithelium from off target toxicity. In particular, BCN 057 protects Lgr5 positive intestinal stem cells, thereby preserving barrier function. Further, it is demonstrated that BCN057 inhibits GSK3{beta} and thereby induces a pro-apoptotic phosphorylation pattern on c-Jun in KRAS G12D mutant pancreatic cancer cells (Panc-1) leading to the restoration of PTEN expression and consequent apoptosis. This appears to be a new mechanistic observation for the oncogenic RAS phenotype. Lastly, concurrent with its GSK3{beta} inhibition, BCN057 is a small molecule inhibitor of PD-1 expression on human T-lymphocytes co-cultured with human pancreatic cancer cells. In summary, BCN057 can promote synthetic lethality specifically to malignant cells and therefore should be considered to improve the therapeutic ratio in pancreatic and epithelial cancer treatment in conjunction with chemotherapy and radiation.

cancer biology↗

bioRxiv2021

High efficacy of therapeutic equine hyperimmune antibodies against SARS CoV-2 variants of concern

SARS-CoV-2 variants of concern (VoC) show reduced neutralization by vaccine-induced and therapeutic monoclonal antibodies. We tested therapeutic equine polyclonal antibodies (pAbs) against four VoC (alpha, beta, epsilon and gamma). We show that equine pAbs efficiently neutralize VoC, suggesting they are an effective, broad coverage, low-cost and a scalable COVID-19 treatment.

microbiology↗