Biology subjects

Rivera, R.

Publications and source records attributed to Rivera, R..

10 recordsLinked to original sources

bioRxiv2026

METTL14-dependent m6A modification restrains interferon signaling to prevent myocarditis and dilated Cardiomyopathy

The impact of inflammation on heart failure is increasingly recognized; but how cardiomyocyte restrains innate immune activation remains poorly defined, and nor does the role of N-methyladenosine (mA) modification in maintaining cardiac immune homeostasis. Here, we demonstrate that cardiomyocyte-specific deletion of the mA methyltransferase METTL14 triggers myocarditis, dilated cardiomyopathy, and premature lethality. Meanwhile, widespread hypomethylation and upregulation of innate immune and necroptosis-related transcripts in Mettl14-deficient hearts exemplified by IFN-1 and STAT1. Mechanistically, METTL14 deficiency promotes RIPK1 accumulation thereby priming cardiomyocytes for necroptosis and inflammatory cell death. Genetic ablation of IFN-I receptor Ifnar1 can largely rescue the processes and improve cardiac function and survival. Furthermore, METTL14 loss disrupts mitochondrial integrity and autophagy/mitophagy flux, suggesting mitochondrial dysfunction-driven innate immune activation upstream of IFN-I signaling. Collectively, these findings identify METTL14-mediated mA modification as a critical safeguard against cardiomyocyte-intrinsic IFN-I signaling and necroptosis and establish an epitranscriptomic-innate immune axis that drives inflammatory heart failure.

pathology↗

bioRxiv2026

Loss of Sun2 ablates nuclear mechanosensing-driven extracellular matrix production and mitigates lung fibrosis

Fibrosis and pathological stiffening of tissue are driven by mechanical and biochemical signaling pathways. Here, we find that Sun2, an integral inner nuclear membrane component of Linker of Nucleoskeleton and Cytoskeleton (LINC) complexes, is up-regulated in the lung of patients suffering from fibrotic conditions and in fibroblasts during an injury-induced mouse model of lung fibrosis. Sun2 protein levels also increase in primary lung fibroblasts in a substrate stiffness-dependent manner. Sun2-/- primary lung fibroblasts respond to TGF{beta}, become contractile, and express a key marker of extracellular matrix-producing fibroblasts, Cthrc1. Consistent with this, Sun2 is dispensable for myofibroblast formation and repairing the alveolar barrier after bleomycin injury. Remarkably, however, fibrosis does not develop in bleomycin-treated Sun2-/- mouse lungs. This is explained by the requirement for Sun2 to up-regulate genes encoding extracellular matrix proteins. We therefore suggest that Sun2-containing LINC complexes contribute to a mechanical coincidence detection mechanism that acts in concert with canonical TGF{beta} signaling necessary for pathologic extracellular matrix protein production, representing a nuclear mechanosensing node for intervention in fibrotic diseases of the lung.

cell biology↗

bioRxiv2026

SUN2 mediates epigenetic remodeling to drive mechanotransduction during skin fibrosis

Fibrosis involves sustained changes in fibroblast gene expression, leading to excessive extracellular matrix (ECM) deposition and progressive tissue stiffening. Although matrix stiffness is a potent regulator of cell fate and transcription, it is not clear how nuclear mechanosensing contributes to fibrosis. Here, we define a central role for SUN2, a component of linker of nucleoskeleton and cytoskeleton (LINC) complexes, as a mediator of stiffness-dependent nuclear and chromatin responses during skin fibrosis. SUN2 transcripts are upregulated in dermal fibroblasts of patients with systemic sclerosis and Sun2 protein is elevated in fibrotic mouse skin. Nuclear size, A-type lamins and Sun2 are elevated in dermal fibroblasts plated on stiff substrates. Loss of Sun2 protects against bleomycin-induced skin fibrosis in vivo and abolishes stiffness-induced changes in nuclear size and fibrotic gene expression in vitro. Mechanistically, we identify three Sun2-dependent mechanosensitive chromatin states and show that mechanical induction of the histone methyltransferase Ezh2 requires Sun2. These findings define SUN2 as a nuclear mechanosensor that couples matrix stiffness to chromatin regulation and transcriptional programs that drive fibrosis, identifying it as a potential therapeutic target pathway in fibrotic disease.

cell biology↗

bioRxiv2022

Molecular and mineral responses of corals grown under artificial Calcite Sea conditions

The formation of skeletal structures composed of different calcium carbonate polymorphs (aragonite and calcite) appears to be regulated both biologically and environmentally. Among environmental factors influencing aragonite and calcite precipitation, changes in seawater conditions - primarily in the molar ratio of magnesium and calcium during so-called "Calcite" (mMg:mCa below 2) or "Aragonite" seas (mMg:mCa above 2) - have had profound impacts on the distribution and performance of marine calcifiers throughout the Earths history. Nonetheless, the fossil record shows that some species appear to have counteracted such changes and kept their skeleton polymorph unaltered. Here, the aragonitic octocoral Heliopora coerulea and the aragonitic scleractinian Montipora digitata were exposed to Calcite Sea-like mMg:mCa with various levels of changes in magnesium and calcium concentration, and both mineralogical (i.e., CaCO3 polymorph) and gene expression changes were monitored. Both species maintained aragonite deposition at lower mMg:mCa ratios, while concurrent calcite presence was only detected in M. digitata. Despite a strong variability between independent experimental replicates for both species, the expression for a set of putative calcification-related genes, including known components of scleractinian skeleton organic matrix, was found to consistently change at lower mMg:mCa. These results support previously proposed involvements of the skeleton organic matrix in counteracting decreases in seawater mMg:mCa. Although no consistent changes in expression for calcium and magnesium transporters were observed, down-regulation calcium channels in H. coerulea in one experimental replicate and at an mMg:mCa of 2.5 might indicate the possibility of active calcium uptake regulation by the corals under altered mMg:mCa.

paleontology↗

bioRxiv2022

FTY720 requires vitamin B12-TCN2-CD320 signaling in astrocytes to reduce disease in an animal model of multiple sclerosis

FTY720 (fingolimod) is a sphingosine 1-phosphate (S1P) receptor modulator and sphingosine analogue approved for multiple sclerosis (MS) therapy, which can functionally antagonize the S1P receptor, S1P1. Vitamin B12 (B12) deficiency produces neurological manifestations resembling MS. Here, we report a new mechanism where FTY720 suppresses neuroinflammation by regulating B12 metabolic pathways. Nuclear RNA-seq of c-Fos-activated astrocytes (called ieAstrocytes) from experimental autoimmune encephalomyelitis (EAE) spinal cords identified up-regulation of CD320, a transcobalamin 2 (TCN2)-B12 receptor, by S1P1 inhibition. CD320 was reduced in MS plaques. Deficiency of CD320 or dietary B12 worsened EAE and eliminated FTY720s efficacy, while concomitantly down-regulating type I interferon signaling. TCN2 functioned as a chaperone for FTY720 and sphingosine, which induced astrocytic CD320 internalization. An accompanying paper identified a requirement for astrocyte sphingosine kinases in FTY720 efficacy and its altered expression in MS brains, molecularly linking MS and B12 deficiency that can be accessed by sphingolipid/fingolimod metabolic pathways.

neuroscience↗

bioRxiv2022

Single-nucleus RNA-seq of normal-appearing brain regions in relapsing-remitting vs. secondary progressive multiple sclerosis

Multiple sclerosis (MS) is an immune-mediated demyelinating disease that alters central nervous system (CNS) functions. Relapsing-remitting MS (RRMS) is the most common form, which can transform into secondary-progressive MS (SPMS) that is associated with progressive neurodegeneration. Single-nucleus RNA sequencing (snRNA-seq) of MS lesions identified disease-related transcriptomic alterations; however, their relationship to non-lesioned MS brain regions has not been reported and which could identify prodromal or other disease susceptibility signatures. Here, snRNA-seq was used to generate high-quality RRMS vs. SPMS datasets of 33,197 nuclei from 8 normal-appearing MS brains, which revealed divergent cell type-specific changes. Notably, SPMS brains downregulated astrocytic sphingosine kinases (SPHK1/2) - the enzymes required to phosphorylate and activate the MS drug, fingolimod. This reduction was modeled with astrocyte-specific Sphk1/2 null mice in which fingolimod lost activity, supporting functionality of observed transcriptomic changes. These data provide an initial resource for studies of single cells from non-lesioned RRMS and SPMS brains.

neuroscience↗

bioRxiv2021

A high throughput bispecific antibody discovery pipeline

Bispecific antibodies (BsAbs) represent an emerging class of immunotherapy but inefficiency in the current BsAb discovery paradigm has limited their broad clinical availability. Here we report a high throughput, agnostic, single-cell-based BsAb functional screening pipeline, comprising molecular and cell engineering for efficient generation of BsAb library cells, followed by functional interrogation at the single-cell level to identify and sort positive clones and downstream sequence identification with single-cell PCR and sequencing and functionality characterization. Using a CD19xCD3 bispecific T cell engager (BiTE) as a model system, we demonstrate that our single cell platform possesses a high throughput screening efficiency of up to one and half million variant library cells per run and can isolate rare functional clones at low abundance of 0.008%. Using a complex CD19xCD3 BiTE-expressing cell library with approximately 22,300 unique variants comprising combinatorially varied scFvs, connecting linkers and VL/VH orientations, we have identified 98 unique clones including extremely rare ones ([~] 0.001% abundance). We also discovered BiTEs that exhibit novel properties contradictory to conventional wisdom, including harboring rigid scFv connecting peptide linkers yet with in vitro cytotoxicity comparable to that of clinically approved Blinatumomab. Through sequencing analyses on sorted BiTE clones, we discovered multiple design variable preferences for functionality including the CD19VL-VH- CD3VH-VL and CD19VH-VL-CD3VH-VL arrangements being the most favored orientation. Sequence analysis further interrogated the sequence composition of the CDRH3 domain in scFvs and identified amino acid residues conserved for function. We expect our single cell platform to not only significantly increase the development speed of high quality of new BsAb therapeutics for cancer and other disorders, but also enable identifying generalizable design principles for new BsAbs and other immunotherapeutics based on an in-depth understanding of the inter-relationships between sequence, structure, and function.

bioengineering↗

bioRxiv2020

Conditional Lpar1 gene targeting identifies cell types mediating neuropathic pain

LPA1 is one of the six known receptors (LPA1-6) for lysophosphatidic acid (LPA). Constitutive Lpar1 null mutant mice have been instrumental in identifying roles for LPA-LPA1 signaling in neurobiological processes, brain development, and behavior as well as modelling human neurological diseases like neuropathic pain. Constitutive Lpar1 null mutant mice are protected from partial sciatic nerve ligation (PSNL)-induced neuropathic pain, however Lpar1 expressing cell types that are functionally responsible for mediating this protective effect are unknown. Here we report generation of a Lpar1flox/flox conditional null mutant mouse that allows cre-mediated conditional deletion combined with its use in a PSNL pain model. Lpar1flox/flox mice were crossed with cre transgenic lines driven by neural gene promoters for nestin (all neural cells), synapsin (neurons), or P0 (Schwann cells). CD11b-cre transgenic mice were also used to delete Lpar1 in microglia. PSNL-initiated pain responses were reduced following cre-mediated Lpar1 deletion with all 3 neural promoters but not the microglial promoter, supporting involvement of Schwann cells and central and/or peripheral neurons in mediating pain. Interestingly, rescue responses that were due to conditional deletion were non-identical, implicating distinct roles for Lpar1-expressing cell types. Our results with a new Lpar1 conditional mouse mutant expand an understanding of LPA1 signaling in the PSNL model of neuropathic pain.

pharmacology and toxicology↗

bioRxiv2019

Reply: Evidence that APP gene copy number changes reflect recombinant vector contamination

In the accompanying comment1, Kim et al. concluded that somatic gene recombination (SGR) and amyloid precursor protein (APP) genomic complementary DNAs (gencDNAs) in brain are contamination artifacts and do not naturally exist. We disagree. Here we address the three types of analyses used by Kim et al. to reach their conclusions: informatic contaminant identification, plasmid PCR, and single-cell sequencing. Additionally, Kim et al. requested "reads supporting novel APP insertion breakpoints," and we now provide 10 different examples that support APP gencDNA insertion within eight chromosomes beyond wildtype APP on chromosome 21 from Alzheimers disease (AD) samples. If SGR exists as experimentally supported here and previously2,3, contamination scenarios become moot. Our informatic analyses of data generated by an independent laboratory (Park et al.)4, complement and are entirely consistent with what Lee et al.2 presented via nine distinct lines of evidence, in addition to three from a prior publication3. Plasmid contamination was identified in a single pull-down dataset after publication of Lee et al.2; however subsequent analyses did not alter any of our conclusions including those of our prior publications3,5 and plasmid contamination-free replication of this approach by ourselves and others supported the original conclusions. Novel retro-insertion sites, alterations of APP gencDNA number and form with cell type from the same brain and pathogenic SNVs occurring only in AD, all support the existence of APP gencDNAs produced by SGR.

genomics↗

bioRxiv2018

Diverse Escherichia coli lineages, from domestic animals and humans in a household, carry colistin resistance gene mcr-1 in Ecuador

The aim of this study was to investigate the presence of Escherichia coli carrying mcr-1 gene in domestic animals close to a child who suffered a peritoneal infection by a mcr-1 positive E. coli. Rectal or cloacal swabs and fecal samples from domestic animals were plated on selective media to isolate colistin-resistant E. coli and isolates were submitted to detection of mcr-1 gene, pulsed field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), replicon typing and S1-PFGE. Four mcr-1 positive E. coli isolates (from chicken, turkey and dog) were recovered. No shared PFGE pattern or MLST sequence type were observed among isolates. A 60Kb IncI1{gamma} mcr-1-carrying plasmid was detected in all isolates. Our results suggest that mcr-1 gene was horizontally disseminated amongst different lineages of E. coli from domestic animals in the childs household.\n\nImportanceHorizontally transferable colistin resistance (mcr-1 gene) is thought to have originated in domestic animals and transferred to humans through meat and dairy products. In the present report we show evidence that the mcr-1 gene could be transferred to different E. coli strains colonizing different hosts (humans and pets) in the same household.

microbiology↗