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Biology subjects

Ramirez, R.

Publications and source records attributed to Ramirez, R..

14 recordsLinked to original sources

Seasonal Light and Temperature Timing in a Stoichiometric Food Web

Seasonal food-web interactions can depend on whether consumer performance is high when food quantity and elemental quality are favorable. We extend a closed-phosphorus model containing pelagic and benthic producers, variable producer phosphorus quotas, and a shared Daphnia grazer by allowing annual light and temperature cycles to have an adjustable phase difference. The previous light-seasonality preprint has a nonisolated grazer-free boundary. We parameterize its annual periodic extension by the fraction of producer phosphorus in phytoplankton and derive the unique positive annual producer orbit for every fixed allocation. Linearization in the rare-grazer direction then gives an exact conditional Floquet exponent. Its decomposition into a mean-rate term and a covariance term identifies the effect of seasonal timing. A reconstructed descriptive thermal proxy uses quasi-acclimated filtration-capacity means from the official Muller et al. dataset; it supplies only a relative response shape over 15-25 degrees C, not an absolute ingestion calibration. In a representative configuration, changing phase while preserving the annual light and temperature distributions changes the invasion exponent from -0.00382 to 0.01486 day^-1, with annual multipliers 0.248 and 227, respectively. The constant-mean-ingestion exponent is positive, so the negative case is generated by adverse timing covariance. Sign reversal persists across a range of phosphorus allocations, but not across the entire boundary family. The result is a local invasion criterion for specified grazer-free cycles, not a theorem of global persistence or extinction. Within this parameterized boundary problem, relative seasonal timing can change the sign of infinitesimal consumer growth.

ecology↗

Stoichiometric Aquatic Food-Web Models Coupling Pelagic and Benthic Zones

Ecological stoichiometry allows us to investigate how food quality affects food-web population dynamics. We consider periphyton, phytoplankton, and a shared Daphnia consumer in a closed system with separate benthic and pelagic phosphate pools. The producers have variable phosphorus-to-carbon ratios, while the consumer maintains a constant ratio. We construct the model, establish boundedness under stated conditions, characterize its grazer-free equilibrium families and their local spectra, derive conditions for positive consumer growth, and examine its numerical bifurcation structure as light-dependent carrying capacity varies. The bifurcation diagrams contain stable and unstable equilibrium branches together with a stable periodic family, revealing a more complex response to light enrichment than a single sequence of steady states and oscillations. A descending consumer equilibrium branch illustrates that greater light availability need not increase consumer biomass. We then introduce periodically varying carrying capacities and compare weak and strong seasonal forcing. Stronger forcing produces brief consumer rebounds in the high-light example, although the peaks diminish over the displayed interval. Together, the growth conditions and branch diagrams provide a framework for interpreting population dynamics in terms of food quantity and food quality. Independent numerical continuation identifies a Hopf crossing and a fold; the termination mechanism of the periodic branch remains unresolved.

ecology↗

Synergistic anti-tumor activity of EGFR inhibition and C/EBPβ antagonism in GBM.

Glioblastoma (GBM) is the most prevalent primary brain cancer, with poor prognosis and limited therapeutic options available. The genetic and cellular heterogeneity characteristic of GBM contributes to poor response rates. Activating mutations of the epidermal growth factor receptor (EGFR) gene are among the most frequent alterations in GBM, occurring in roughly half of cases. Despite the prevalence of EGFR mutations, EGFR inhibition has shown limited success in GBM. The transcription factor C/EBP{beta} is a master regulator of the mesenchymal transformation in GBM, an aggressive state characterized by increased invasiveness and resistance to chemotherapy. Lucicebtide is a C/EBP{beta} antagonist peptide with demonstrated single agent activity in patients with recurrent GBM that is currently being evaluated in a clinical trial in combination with radiation and temozolomide in patients with newly-diagnosed GBM (NCT04478279), with emerging data supporting clinical activity in that setting. Here we show that in the TCGA-GBM dataset, patients with EGFR mutations display significant enrichment of a high C/EBP{beta} activity signature. Functionally, genetic inactivation of EGFR by CRISPR results in synthetic lethality in the presence of lucicebtide in GBM cell lines, and synergistic in vitro cytotoxicity and suppression of C/EBP{beta} target gene expression was observed in combination experiments with lucicebtide and EGFR inhibitors. Finally, enhanced anti-tumor activity was demonstrated in vivo in the combination setting, as combined subpharmacologic dose levels of lucicebtide and the EGFR inhibitor osimertinib potently suppressed GBM xenograft growth. These data identify EGFR and C/EBP{beta} dependencies in GBM and support lucicebtide combination with EGFR inhibitors as a potential therapeutic option for a sizable fraction of GBM patients.

cancer biology↗

A minimal transcriptomic signature predicts intravascular tumor extension in renal cell carcinoma

Renal cell carcinoma (RCC) with venous tumor thrombus, termed renal intravascular tumor extension (RITE), is associated with aggressive behavior and poor clinical outcomes. Yet, its underlying molecular determinants remain incompletely defined. We analyzed RNA sequencing data from three independent RCC cohorts comprising 721 samples. Two cohorts included matched samples of index tumor, tumor thrombus, and normal adjacent kidney tissue. Analyses integrated dimensionality reduction, differential gene expression, interpretable machine learning, and gene ontology approaches. Principal component analysis revealed that only these two cohorts exhibited a coherent RITE-associated transcriptional structure. Their sequencing depth was sufficient to delineate 6,317 differentially expressed genes that distinguish RITE from non-RITE tumors. SHAP-based feature attribution across logistic regression, random forest, and XGBoost yielded a robust 29-gene consensus signature, which was further distilled into a compact 13-gene panel that preserved maximal classification performance. These genes converged on biological themes, including loss of distal epithelial identity, dysregulation of ion transport pathways, and consistent enrichment of mitochondrial processes such as oxidative phosphorylation. Together, these findings define a newly discovered and uniquely refined molecular signature of venous tumor extension in RCC and highlight mechanistically relevant pathways that may inform biomarker development and future translational strategies for predicting or mitigating RITE progression.

cancer biology↗

Lung progenitors exhaustion in response to microenvironment stress during aging

Progenitor cells in aged tissues undergo changes in their microenvironment that may impact their functionality during regeneration. Despite recent advances in understanding the role of adult lung progenitors, the impact of aging on these cells remains unclear. To analyze aging modifications, we used aged wild-type mice of 18-24 months old, and Zmpste24-/- deficient mice, which exhibit an accelerated aging phenotype. A three-dimensional organoid culture system was employed to assess the lung regeneration capacity. Additionally, mouse epithelial cells and fibroblasts were isolated and characterized with senescence and autophagy markers. Our findings revealed that lung epithelial cells from aged mice and Zmpste24-/- mice hold their regeneration capacity, maintaining their phenotype and a healthy cellular state through an increase in autophagy, particularly when co-cultured with healthy fibroblasts. Conversely, cultured fibroblasts from Zmpste24-/- mice show nuclear defects and acquire a senescent phenotype, characterized by mTORC1 activation and reduced autophagy, which in turn impairs organoid formation. Moreover, these progenitor cells become increasingly susceptible to mechanical stress with aging due to reduced nuclear lamins and the Zmpste24 defect. This vulnerability is illustrated by FACS sorting, which can further compromise their regenerative potential. Our results indicate that, in aging, progenitor cells and their fibroblast niche integrate microenvironmental signals that shape cell-cell interactions essential for lung regeneration.

cell biology↗

Multi-omics integrative approach of senescent endothelial cells and derived extracellular vesicles in a replicative senescence model

Aging is a major unmodifiable risk factor for cardiovascular disease (CVD). Replicative endothelial senescence (RES), characterized by permanent cell-cycle arrest and a senescence-associated secretory phenotype (SASP), is a hallmark of vascular aging. However, the molecular mechanisms underlying RES, particularly the role of extracellular vesicles (EVs), remain poorly understood. To this aim, an integrated multi-omics approach (proteomics, mRNA, and miRNA profiling) was applied to characterize senescent and early-passage human umbilical vein endothelial cells (HUVECs) and their secreted EVs. Senescent HUVECs and EVs displayed a canonical senescence profile, including cell-cycle arrest, DDR activation, NF-{kappa}B signaling, and SASP induction, alongside marked suppression of RNA metabolism, ribosome biogenesis, and DNA repair. Multi-omics integration has linked endothelial senescence to vascular aging, maladaptive angiogenesis, and ECM remodeling, which are key processes in CVD development. Moreover, senescent EVs propagate senescence by exporting fewer reparative and antioxidant factors while carrying pro-fibrotic, adipogenic, and angiogenic mediators. Multi-omics profiling revealed consistent transcript-protein changes in senescent cells and EVs, defining a robust molecular signature of RES, including endothelial cell-specific markers and post-transcriptional regulators (lncRNAs and miRNAs). Among these, miR-22-3p and miR-126-5p emerged as key modulators in both cells and EVs, with miR-22-3p demonstrating compartment-specific regulation. Integration further uncovered a coordinated regulatory network involving miRNAs (miR-23, miR-335-3p, miR-29 family, miR-590-3p, and miR-126-5p) that were inversely correlated with transcription factors (e.g., REST, KLFs, and ZNFs) and downstream targets, collectively driving endothelial senescence through impaired PI3K-Akt signaling. Although further validation is needed, these findings provide new insights into the molecular mechanisms of RES and open perspectives for modulating secondary senescence and age-related vascular diseases.

cell biology↗

Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon

Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv & 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs & Pf: 28 SNPs) and MS panels (Pv: 16 MS & Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He) was similar across the subpopulations for both makers: HeMS = 0.68 - 0.78 (p = 0.23) and HeSNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, FST) was also comparable: FST-MS = 0.04 - 0.14 and FST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends (HeMS = 0 - 0.48 p = 0.03 - 1; HeSNP = 0 - 0.09, p = 0.03 - 1) and pairwise FST comparisons (FST-MS= 0.14 - 0.65, FST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.

genomics↗

Acylation of MLKL impacts its function in necroptosis

Mixed lineage kinase domain-like (MLKL) is a key signaling protein of necroptosis. Upon activation by phosphorylation, MLKL translocates to the plasma membrane and induces membrane permeabilization which contributes to the necroptosis-associated inflammation. Membrane binding of MLKL is initially initiated by the electrostatic interactions between the protein and membrane phospholipids. We previously showed that MLKL and its phosphorylated form (pMLKL) are S-acylated during necroptosis. Here, we characterize acylation sites of MLKL and identify multiple cysteines that can undergo acylation with an interesting promiscuity at play. Our results show that MLKL and pMLKL undergo acylation at a single cysteine, C184, C269 and C286 are the possible acylation sites. Using all atom molecular dynamic simulations, we identify differences that the acylation of MLKL causes at the protein and membrane level. Through systematic investigations of the S-palmitoyltransferases that might acylate MLKL in necroptosis, we showed that zDHHC21 activity has the strongest effect on pMLKL acylation, inactivation of which profoundly reduced the pMLKL levels in cells and improved membrane integrity. These results suggest that blocking the acylation of pMLKL destabilizes the protein at the membrane interface and causes its degradation, ameliorating necroptotic activity. At a broader level, our findings shed light on the effect of S-acylation on MLKL functioning in necroptosis and MLKL-membrane interactions mediated by its acylation.

biochemistry↗

Characterization of a KDM5 Small Molecule Inhibitor with Antiviral Activity against Hepatitis B Virus

Chronic hepatitis B (CHB) is a global health care challenge and a major cause of liver disease. To find new therapeutic avenues with a potential to functionally cure chronic Hepatitis B virus (HBV) infection, we performed a focused screen of epigenetic modifiers to identify replication inhibitors. From this work we identified isonicotinic acid inhibitors of the histone lysine demethylase 5 (KDM5) with potent anti-HBV activity. To enhance the cellular permeability and liver accumulation of the most potent KDM5 inhibitor identified (GS-080) an ester prodrug was developed (GS-5801) that resulted in improved bioavailability and liver exposure as well as an increased H3K4me3:H3 ratio on chromatin. GS-5801 treatment of HBV-infected primary human hepatocytes inhibited HBV replication and antigen levels. Evaluation of GS-5801 antiviral activity in a humanized mouse model of HBV infection, however, did not result in antiviral efficacy, despite achieving pharmacodynamic levels of H3K4me3:H3 predicted to be efficacious from the in vitro model. Here we discuss potential reasons for the disconnect between in vitro and in vivo efficacy, which highlight the translational difficulties of epigenetic targets for viral diseases.

pharmacology and toxicology↗

FoxP3 can fold into two distinct dimerization states with divergent functional implications for T cell homeostasis

FoxP3 is an essential transcription factor (TF) for immunologic homeostasis, but how it utilizes the common forkhead DNA-binding domain (DBD) to perform its unique function remains poorly understood. We here demonstrate that, unlike other known forkhead TFs, FoxP3 forms a head-to-head dimer using a unique linker (Runx1-binding region, RBR) preceding the forkhead domain. Head-to-head dimerization confers distinct DNA-binding specificity and creates a docking site for the cofactor Runx1. RBR is also important for proper folding of the forkhead domain, as truncation of RBR induces domain-swap dimerization of forkhead, which was previously considered the physiological form of FoxP3. Rather, swap-dimerization impairs FoxP3 function, as demonstrated with the disease-causing mutation R337Q, while a swap-suppressive mutation largely rescues R337Q-mediated functional impairment. Altogether, our findings suggest that FoxP3 can fold into two distinct dimerization states: head-to-head dimerization representing functional specialization of an ancient DBD and swap-dimerization with impaired functions.

immunology↗

Comparative Multiomic Analysis Reveals Low T Cell Infiltration as the Primary Feature of Tobacco Use in HPV(+) Oropharyngeal Cancer

PurposeTobacco use is an independent adverse prognostic feature in human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC). Despite this, the biologic features associated with tobacco use have not been systematically investigated in this population. We sought to characterize the genomic and immunologic features of HPV(+) OPSCC associated with tobacco use and adverse oncologic outcomes. Experimental DesignWhole exome sequencing of 47 primary HPV(+) OPSCC tumors was performed to investigate mutational differences associated with tobacco exposure. To characterize the tumor immune microenvironment (TIME), targeted mRNA hybridization was performed and immunohistochemical (IHC) staining was used to validate these findings. ResultsLow expression of transcripts in a T cell-inflamed gene expression profile (TGEP) was associated with tobacco use at the time of diagnosis and lower overall and disease-free survival. Tobacco use was associated with an increased proportion of T>C substitutions and a lower proportion of mutational signatures typically observed in HPV(+) OPSCC tumors, but was not associated with increases in mutational burden or the rate of recurrent oncogenic mutations. ConclusionsIn HPV(+) OPSCC, low T cell infiltration of primary tumors is associated with current tobacco use and worse oncologic outcomes. Rather than an increased mutational burden, tobaccos primary and clinically relevant association is immunosuppression of the primary TIME. An objective clinical assay like the TGEP, which quantifies immune infiltration of the primary TIME, may have value for HPV(+) OPSCC risk stratification in future clinical trials.

cancer biology↗

Learning immune cell differentiation

The mammalian genome contains several million cis-regulatory elements, whose differential activity marked by open chromatin determines organogenesis and differentiation. This activity is itself embedded in the DNA sequence, decoded by sequence-specific transcription factors. Leveraging a granular ATAC-seq atlas of chromatin activity across 81 immune cell-types we show that a convolutional neural network ("AI-TAC") can learn to infer cell-type-specific chromatin activity solely from the DNA sequence. AI-TAC does so by rediscovering, with astonishing precision, binding motifs for known regulators, and some unknown ones, mapping them with high concordance to positions validated by ChIP-seq data. AI-TAC also uncovers combinatorial influences, establishing a hierarchy of transcription factors (TFs) and their interactions involved in immunocyte specification, with intriguingly different strategies between lineages. Mouse-trained AI-TAC can parse human DNA, revealing a strikingly similar ranking of influential TFs. Thus, Deep Learning can reveal the regulatory syntax that drives the full differentiative complexity of the immune system.

genomics↗

Persistent Elevation of Electrical Pain Threshold following Continuous Theta Burst Stimulation over Primary Somatosensory Cortex in Humans

BackgroundPrimary somatosensory cortex (S1) is involved in pain processing and thus its suppression using neuromodulatory techniques such as continuous theta burst stimulation (cTBS) might be a potential pain management strategy in patients with neuropathic pain. S1 cTBS is known to elevate pain threshold in young adults. However, the persistence of this effect is unknown.\n\nObjective/HypothesisWe hypothesized persistent elevation of pain threshold following cTBS over S1 in healthy, young adults.\n\nMethodsWe recruited ten subjects in a sham-controlled crossover design and recorded their electrical pain threshold (EPT) for 40 min following cTBS over S1. We assessed corticospinal excitability (CSE) to rule out the involvement of primary motor cortex due to spread of current.\n\nResultscTBS over S1 elevated EPT without modulating CSE compared to sham stimulation. EPT was elevated for 40 min post-cTBS.\n\nConclusionsS1 can be focally targeted using cTBS for a longer lasting pain relief in patients.

neuroscience↗

Building gene regulatory networks from single-cell ATAC-seq and RNA-seq using Linked Self-Organizing Maps

Rapid advances in single-cell assays have outpaced methods for analysis of those data types. Different single-cell assays show extensive variation in sensitivity and signal to noise levels. In particular, scATAC-seq generates extremely sparse and noisy datasets. Existing methods developed to analyze this data require cells amenable to pseudo-time analysis or require datasets with drastically different cell-types. We describe a novel approach using self-organizing maps (SOM) to link scATAC-seq and scRNA-seq data that overcomes these challenges and can generate draft regulatory networks. Our SOMatic package generates chromatin and gene expression SOMs separately and combines them using a linking function. We applied SOMatic on a mouse pre-B cell differentiation time-course using controlled Ikaros over-expression to recover gene ontology enrichments, identify motifs in genomic regions showing similar single-cell profiles, and generate a gene regulatory network that both recovers known interactions and predicts new Ikaros targets during the differentiation process. The ability of linked SOMs to detect emergent properties from multiple types of highly-dimensional genomic data with very different signal properties opens new avenues for integrative analysis of single-cells.

genomics↗