Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 811 records · Page 45Linked to original sources

bioRxiv2023

Spatial Transcriptomics Analysis of Gene Expression Prediction using Exemplar Guided Graph Neural Network

Spatial transcriptomics (ST) is essential for understanding diseases and developing novel treatments. It measures the gene expression of each fine-grained area (i.e., different windows) in the tissue slide with low throughput. This paper proposes an exemplar guided graph network dubbed EGGN to accurately and efficiently predict gene expression from each window of a tissue slide image. We apply exemplar learning to dynamically boost gene expression prediction from nearest/similar exemplars of a given tissue slide image window. Our framework has three main components connected in a sequence: i) an extractor to structure a feature space for exemplar retrievals; ii) a graph construction strategy to connect windows and exemplars as a graph; iii) a graph convolutional network backbone to process window and exemplar features, and a graph exemplar bridging block to adaptively revise the window features using its exemplars. Finally, we complete the gene expression prediction task with a simple attention-based prediction block. Experiments on standard benchmark datasets indicate the superiority of our approach when compared with past state-of-the-art methods. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/534914v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@6507f5org.highwire.dtl.DTLVardef@ed7ea5org.highwire.dtl.DTLVardef@159fd5org.highwire.dtl.DTLVardef@1b09270_HPS_FORMAT_FIGEXP M_FIG C_FIG In this paper, we aim to predict gene expression of each window in a tissue slide image. Given a tissue slide image, we encode the windows to feature space, retrieve its exemplars from the reference dataset, construct a graph, and then dynamically predict gene expression of each window with our exemplar guided graph network. HighlightsO_LIWe propose an exemplar guided graph network to accurately predict gene expression from a slide image window. C_LIO_LIWe design a graph construction strategy to connect windows and exemplars for performing exemplar learning of gene expression prediction. C_LIO_LIWe propose a graph exemplar bridging block to revise the window feature by using its nearest exemplars. C_LIO_LIExperiments on two standard benchmark datasets demonstrate our superiority when compared with state-of-the-art approaches. C_LI

bioinformatics↗

bioRxiv2023

Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities

Two distinct fates, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common progenitor cells, the inner cell mass (ICM), in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonic ENdoderm (XEN) stem cells - in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. The dominant PrE transcriptional program, safeguarded by Gata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mapping in vitro trajectories to embryos revealed reprogramming in either direction tracked along, and toggled between, EPI and PrE in vivo states without transitioning through the ICM.

developmental biology↗

bioRxiv2023

Mammalian Esophageal Stratified Tissue Homeostasis is Maintained Distinctively by the Epithelial Pluripotent p63+Sox2+ and p63-Sox2+ Cell Populations

Self-renewing, damage-repair and differentiation of mammalian stratified squamous epithelia are subject to tissue homeostasis, but the regulation mechanisms remain elusive. Here, we investigate the esophageal squamous epithelial tissue homeostasis in vitro and in vivo. We establish a rat esophageal organoid (rEO) in vitro system and show that the landscapes of rEO formation, development and maturation trajectories can mimic those of rat esophageal epithelia in vivo. Single-cell RNA sequencing (scRNA-seq), snap-shot immunostaining and functional analyses of stratified "matured" rEOs define that the epithelial pluripotent stem-cell determinants, p63 and Sox2, play crucial but distinctive roles for regulating mammalian esophageal tissue homeostasis. We identify two cell populations, p63+Sox2+ and p63-Sox2+, of which the p63+Sox2+ population presented at the basal layer is the cells of origin required for esophageal epithelial stemness maintenance and proliferation whereas the p63-Sox2+ population presented at the suprabasal layers is the cells of origin having a dual role for esophageal epithelial differentiation (differentiation-prone fate) and rapid tissue damage-repair responses (proliferation-prone fate). Given the fact that p63 and Sox2 are developmental lineage oncogenes and commonly overexpressed in ESCC tissues, p63-Sox2+ population could not be detected in organoids formed by esophageal squamous cell carcinoma (ESCC) cell lines. Taken together, these findings reveal that the tissue homeostasis is maintained distinctively by p63 and/or Sox2 dependent cell lineage populations required for the tissue renewing, damage-repair and protection of carcinogenesis in mammalian esophagi.

cell biology↗

bioRxiv2023

Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)

Tissue biology involves an intricate balance between cell-intrinsic processes and interactions between cells organized in specific spatial patterns, which can be respectively captured by single cell profiling methods, such as single cell RNA-seq (scRNA-seq) and spatial transcriptomics, and histology imaging data, such as Hematoxylin-and-Eosin (H&E) stains. While single cell profiles provide rich molecular information, they can be challenging to collect routinely in the clinic and either lack spatial resolution or high gene throughput. Conversely, histological H&E assays have been a cornerstone of tissue pathology for decades, but do not directly report on molecular details, although the observed structure they capture arises from molecules and cells. Here, we leverage vision transformers and adversarial deep learning to develop the Single Cell omics from Histology Analysis Framework (SCHAF), which generates a tissue samples spatially-resolved whole transcriptome single cell omics dataset from its H&E histology image. We demonstrate SCHAF on a variety of tissues-- including lung cancer, metastatic breast cancer, placentae, and whole mouse pups--training with matched samples analyzed by sc/snRNA-seq, H&E staining, and, when available, spatial transcriptomics. SCHAF generated appropriate single cell profiles from histology images in test data, related them spatially, and compared well to ground-truth scRNA-Seq, expert pathologist annotations, or direct spatial transcriptomic measurements, with some limitations. SCHAF opens the way to next-generation H&E analyses and an integrated understanding of cell and tissue biology in health and disease.

bioinformatics↗

bioRxiv2023

Effect of cell membrane tension on the lifetime and size of mature clathrin-coated pits and their spatial distribution

Clathrin-mediated endocytosis is the most characterized pathway for cells to internalize diverse receptor-bound cargo, such as proteins, nanoparticles, and viruses. However, the effect of membrane tension on clathrin-coated pit (CCP) maturation remains inadequately characterized. This study aimed to determine the effect of membrane tension on CCP maturation both spatially and temporarily, which remains a controversial and elusive issue. We obtained the sizes and spatial distributions of CCPs by the structured illumination microscopy of fixed cells and observed CCP lifetimes in live cells by total internal reflection fluorescence microscopy. The processes of CCP maturation and abortion were reproduced numerically through Monte Carlo simulation. The results showed that the growth time of CCP was more reasonably proportional to its volume rather than its surface area. We further investigated the spatial distribution of the membrane tension and size of CCPs, finding a significant positive correlation between the membrane tension and the size of mature CCPs spatially. This indicates that the CCPs tend to enrich in the highest-tension region, especially the mature ones. These results agreed with our numerical prediction that the CCP structure grew larger to overcome a higher energy barrier caused by higher background cell membrane tension. Our findings enhance the understanding of CCP maturation dynamics and underscore the importance of membrane tension in regulating CCP development.

biophysics↗

bioRxiv2023

Curved adhesions mediate cell attachment to soft matrix fibres in 3D

Mammalian cells adhere to the extracellular matrix (ECM) and sense mechanical cues through integrin-mediated adhesions1, 2. Focal adhesions and related structures are the primary architectures that transmit forces between the ECM and the actin cytoskeleton. Although focal adhesions are abundant when cells are cultured on rigid substrates, they are sparse in soft environments that cannot support high mechanical tensions3. Here, we report a new class of integrin-mediated adhesions, curved adhesions, whose formation is regulated by membrane curvature instead of mechanical tension. In soft matrices made of protein fibres, curved adhesions are induced by membrane curvatures imposed by the fibre geometry. Curved adhesions are mediated by integrin [a]V{beta}5 and are molecularly distinct from focal adhesions and clathrin lattices. The molecular mechanism involves a previously unknown interaction between integrin {beta}5 and a curvature-sensing protein FCHo2. We find that curved adhesions are prevalent in physiologically relevant environments. Disruption of curved adhesions by knocking down integrin {beta}5 or FCHo2 abolishes the migration of multiple cancer cell lines in 3D matrices. These findings provide a mechanism of cell anchorage to natural protein fibres that are too soft to support the formation of focal adhesions. Given their functional importance for 3D cell migration, curved adhesions may serve as a therapeutic target for future development.

cell biology↗

bioRxiv2023

Coupling of Slack and NaV1.6 sensitizes Slack to quinidine blockade and guides anti-seizure strategy development

Quinidine has been used as an anticonvulsant to treat patients with KCNT1-related epilepsy by targeting gain-of-function KCNT1 pathogenic mutant variants. However, the detailed mechanism underlying quinidines blockade against KCNT1 (Slack) remains elusive. Here, we report a functional and physical coupling of the voltage-gated sodium channel NaV1.6 and Slack. NaV1.6 binds to and highly sensitizes Slack to quinidine blockade. Homozygous knockout of NaV1.6 reduces the sensitivity of native sodium-activated potassium currents to quinidine blockade. NaV1.6-mediated sensitization requires the involvement of NaV1.6s N-and C-termini binding to Slacks C-terminus, and is enhanced by transient sodium influx through NaV1.6. Moreover, disrupting the Slack-NaV1.6 interaction by viral expression of Slacks C-terminus can protect against SlackG269S-induced seizures in mice. These insights about a Slack-NaV1.6 complex challenge the traditional view of "Slack as an isolated target" for anti-epileptic drug discovery efforts, and can guide the development of innovative therapeutic strategies for KCNT1-related epilepsy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/532982v3_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1127858org.highwire.dtl.DTLVardef@19ad9f4org.highwire.dtl.DTLVardef@15b5542org.highwire.dtl.DTLVardef@13a86b4_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Hierarchy and networks in the transcriptional response of Mycobacterium abscessus to antibiotics

Mycobacterium abscessus causes acute and chronic pulmonary infection in patients with chronic lung damage. It is intrinsically resistance to antibiotics effective against other pathogenic mycobacteria largely due to the drug-induced expression of genes that confer resistance. Induction of genes upon exposure to ribosome targeting antibiotics proceeds via WhiB7-dependent and -independent pathways. WhiB7 controls the expression of >100 genes, a few of which are known determinants of drug resistance. The function of the vast majority of genes within the regulon is unknown, but some conceivably encode additional mechanisms of resistance. Furthermore, the hierarchy of gene expression within the regulon, if any, is poorly understood. In the present work we have identified 56 WhiB7 binding sites using chromatin immunoprecipitation sequencing (CHIP-Seq) which accounts for the WhiB7-dependent upregulation of 70 genes, and find that M. abscessus WhiB7 functions exclusively as a transcriptional activator at promoters recognized by {sigma}A/{sigma}B We have investigated the role of 18 WhiB7 regulated genes in drug resistance and demonstrated the role of MAB_1409c and MAB_4324c in aminoglycoside resistance. Further, we identify a {sigma}H-dependent pathway in aminoglycoside and tigecycline resistance which is induced upon drug exposure and is further activated by WhiB7 demonstrating the existence of a crosstalk between components of the WhiB7-dependent and -independent circuits. Abstract ImportanceThe induction of multiple genes that confer resistance to structurally diverse ribosome-targeting antibiotics is funneled through the induction of a single transcriptional activator, WhiB7, by antibiotic-stalled ribosomes. This poses a severe restriction in M. abscessus therapy as treatment with one ribosome-targeting antibiotic confers resistance to all other ribosome-targeting antibiotics. Here we uncover the intricacies of the WhiB7 regulatory circuit, identify three previously unknown determinants of aminoglycoside resistance and unveil a communication between WhiB7 dependent and independent components. This not only expands our understanding of the antibiotic resistance potential of M. abscessus but can also inform the development of much needed therapeutic options.

microbiology↗

bioRxiv2023

Remote neuronal activity drives glioma infiltration via Sema4f

The tumor microenvironment (TME) plays an essential role in malignancy and neurons have emerged as a key component of the TME that promotes tumorigenesis across a host of cancers. Recent studies on glioblastoma (GBM) highlight bi-directional signaling between tumors and neurons that propagates a vicious cycle of proliferation, synaptic integration, and brain hyperactivity; however, the identity of neuronal subtypes and tumor subpopulations driving this phenomenon are incompletely understood. Here we show that callosal projection neurons located in the hemisphere contralateral to primary GBM tumors promote progression and widespread infiltration. Using this platform to examine GBM infiltration, we identified an activity dependent infiltrating population present at the leading edge of mouse and human tumors that is enriched for axon guidance genes. High-throughput, in vivo screening of these genes identified Sema4F as a key regulator of tumorigenesis and activity-dependent infiltration. Furthermore, Sema4F promotes the activity-dependent infiltrating population and propagates bi-directional signaling with neurons by remodeling tumor adjacent synapses towards brain network hyperactivity. Collectively, our studies demonstrate that subsets of neurons in locations remote to primary GBM promote malignant progression, while revealing new mechanisms of tumor infiltration that are regulated by neuronal activity.

cancer biology↗

bioRxiv2023

MRE11A: a novel negative regulator of human DNA mismatch repair

DNA mismatch repair (MMR) is a highly conserved pathway that corrects DNA replication errors. Although well characterized, MMR factors remain to be identified. As a 3-5 exonuclease and endonuclease, meiotic recombination 11 homolog A (MRE11A) is implicated in multiple DNA repair pathways. However, the role of MRE11A in MMR is unclear. Here, we show that MRE11A deficiency increased the sensitivity of HeLa cells to N-methyl-N nitro-N nitrosoguanidine (MNNG) treatment, implying a potential role of MRE11 in MMR. Moreover, we found MRE11A was largely recruited to chromatin and negatively regulated the DNA damage signals within the first cell cycle after MNNG treatment. We also showed that knockdown of MRE11A increased, while overexpressing MRE11A decreased, MMR activity in HeLa cells, suggesting that MRE11A negatively regulates MMR activity. Furthermore, we show that the recruitment of MRE11A to chromatin requires MLH1 and that MRE11A competes with PMS2 for binding to MLH1. This decreases PMS2 levels in whole cell and on chromatin, and consequently comprises MMR activity. Collectively, our findings reveal that MRE11A is a negative regulator of human MMR.

molecular biology↗

bioRxiv2023

The Role of Terminal Uridyl Transferases in the Circadian Rhythm

The 3 terminal oligo-uridylation, a post-transcriptional mRNA modification, is conserved among eukaryotes and drives mRNA degradation, thereby affecting several key biological processes such as animal development and viral infection. Our TAIL-seq experiment of mouse liver mRNA collected from six zeitgeber times reveals transcripts with rhythmic poly(A) tail lengths and demonstrates that overall 3 terminal uridylation frequencies at mRNA poly(A) tail very-ends undergo rhythmic change. Consistently, major terminal uridylyl transferases, TUT4 and TUT7, have cycling protein expression in mouse liver corresponding to 3 terminal uridylation rhythms, indicating that the cycling expression of TUTases correlates with the rhythmic pattern of uridylation. Furthermore, the double knockdown of TUT4 and TUT7 in U2OS cells lengthens the circadian period and decreases the rhythmic amplitude of clock gene expression. Our work thoroughly profiles the dynamic changes in poly(A) tail lengths and terminal modifications and uncovers uridylation as a post-transcriptional modulator in the mammalian circadian clock.

molecular biology↗

bioRxiv2023

Deciphering the gut microbiome of grass carp through multi-omics approach

BackgroundAquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in the metabolism and immunity of fish, and has the potential to give rise to novel green inputs for fish culture. However, our understanding of fish gut microbiome is still lacking. ResultsWe identified 575,856 non-redundant genes by metagenomic sequencing of the intestinal content samples of grass carp. Taxonomic and functional annotation of the gene catalogue revealed specificity of the gut microbiome of grass carp compared with mammals. Co-occurrence analysis indicated exclusive relations between the genera belonging to Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes, suggesting two independent ecological groups of the microbiota. The association pattern of Proteobacteria with the gene expression modules of fish gut and liver was consistently opposite to that of Fusobacteria, Firmicutes and Bacteroidetes, implying differential functionality of Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes. Therefore, the two ecological groups were divided into two functional groups, i.e., Functional Group 1: Proteobacteria; Functional Group 2: Fusobacteria/Firmicutes/Bacteroidetes. Further analysis revealed that the two functional groups differ in genetic capacity for carbohydrate utilization, virulence factors and antibiotic resistance. Finally, we proposed that the ratio of "Functional Group 2/Functional Group 1" can be used as a biomarker that efficiently reflects the structural and functional characteristics of the microbiota of grass carp. ConclusionsThe gene catalogue is an important resource for investigating the gut microbiome of grass carp. Multi-omics analysis provides insights into functional implications of the main phyla that comprise the fish microbiota, and shed lights on targets for microbiota regulation.

microbiology↗

bioRxiv2023

A Pillar and Perfusion Plate Platform for Robust Human Organoid Culture and Analysis

Human organoids have potential to revolutionize in vitro disease modeling by providing multicellular architecture and function that are similar to those in vivo. This innovative and evolving technology, however, still suffers from assay throughput and reproducibility to enable high-throughput screening (HTS) of compounds due to cumbersome organoid differentiation processes and difficulty in scale-up and quality control. Using organoids for HTS is further challenged by lack of easy-to-use fluidic systems that are compatible with relatively large organoids. Here, we overcome these challenges by engineering "microarray three-dimensional (3D) bioprinting" technology and associated pillar and perfusion plates for human organoid culture and analysis. High-precision, high-throughput stem cell printing and encapsulation techniques were demonstrated on a pillar plate, which was coupled with a complementary deep well plate and a perfusion well plate for static and dynamic organoid culture. Bioprinted cells and spheroids in hydrogels were differentiated into liver and intestine organoids for in situ functional assays. The pillar/perfusion plates are compatible with standard 384-well plates and HTS equipment, and thus may be easily adopted in current drug discovery efforts.

bioengineering↗

bioRxiv2023

Phage administration with repeated intravenous doses leads to faster phage clearance in mammalian hosts

ObjectivesPhage therapy has shown a great promise for the treatment of multidrug-resistant bacterial infections. However, the lack of a thorough and organized understanding of phage-body interactions has limited its clinical application. MethodsHere, we administered different purified phages (Salmonella phage SE_SZW1, Acinetobacter phage AB_SZ6, and Pseudomonas phage PA_LZ7) intravenously to healthy animals (rats and monkeys) to evaluate the phage-induced host responses and phage pharmacokinetics (PK) with different intravenous (IV) doses in healthy animals. The plasma and the organs were sampled after different IV doses to determine the phage biodistribution, the phage-induced cytokines, and antibodies. The potential side effects of phages on animals were assessed. ResultsA non-compartment model revealed that the plasma phage titer gradually decreased over time following a single dose. Repeated doses caused that the plasma phage titer at 5 minutes dropped 2-3 Log10 compared to the first dose regardless of phage types in rats. Host innate immune responses were activated including the upregulated expression (>10-fold) of TNF- and splenic enlargement following repeated doses. Phage-specific neutralization antibodies in animals receiving phages were detected. Similar results were obtained from monkeys. ConclusionsThe mammalian bodies were well-tolerant to the administered phages. The animal responses to the phages and the phage biodistribution profiles could have a significant impact on the efficacy of phage therapy.

pharmacology and toxicology↗

bioRxiv2023

Brain structure-function relationships across the human lifespan based on network eigenmodes

While brain function is considered to be tightly supported by the underlying structure, the connectome-based link estimated by current models is relatively moderate, leaving the structure-function relationship an ongoing challenge in neuroscience. Here, by proposing a novel mapping method based on network eigendecomposition, we present a concise and strong correspondence between structure and function. We show that the explanation of functional connectivity can be significantly improved by incorporating interactions between different structural eigenmodes, highlighting the potential importance of collective, higher-order coupling patterns between structure and function. We also demonstrate the pronounced advantage of the present mapping in capturing individual-specific information, and apply it to assess individual differences of structure-function coupling across the lifespan. We find that structure-function liberality weakens with age, which is driven by the decreases in functional components that are less constrained by anatomy, while the magnitude of structure-aligned components is preserved. Our results contribute to a more refined understanding of structure-function coupling and how it evolves with age.

neuroscience↗

bioRxiv2023

Detection and differentiation of Xanthomonas translucens pv. translucens and pv. undulosa from wheat and barley by duplex quantitative PCR

Two probe-based quantitative PCR (qPCR) systems, namely P-Xtt and P-Xtu, were developed for diagnosis of cereal bacterial leaf streak pathogens Xanthomonas translucens pv. translucens and pv. undulosa, respectively. P-Xtt is specific to pv. translucens. P-Xtu is specific to pv. undulosa, pv. cerealis, pv. secalis and pv. pistaciae. P-Xtt and P-Xtu worked on all accessible strains of pv. translucens and pv. undulosa, respectively. Both systems could detect 100 copies of the target gBlock DNA. The two systems could be used in both singleplex qPCR and duplex qPCR with similar efficiencies. On genomic DNA from strains of various X. translucens pathovars, both singleplex qPCR and duplex qPCR could specifically detect and differentiate pv. translucens and pv. undulosa. The duplex qPCR could detect pv. translucens and pv. undulosa from genomic DNA of 1,000 bacterial cells. On infected barley and wheat grain samples, and on one infected wheat leaf sample, the duplex qPCR showed similar efficiency compared to a previously published qPCR system but with the additional capability of pathovar differentiation. The duplex qPCR system developed in this study will be useful in studies on bacterial leaf streak and detection/differentiation of the pathogens.

plant biology↗

bioRxiv2023

Neutrophilic Inflammation in Models of Bronchopulmonary Dysplasia and Chronic Obstructive Pulmonary Disease is Rescued by a Lactobacilli Based Live Biotherapeutic

Bronchopulmonary dysplasia (BPD) is a chronic lung disease of prematurity. Exposure to noxious stimuli such as hyperoxia, volutrauma, and infection in infancy can have long-reaching impacts on lung health and predispose towards the development of conditions such as chronic obstructive pulmonary disease (COPD) in adulthood. BPD and COPD are both marked by lung tissue degradation, neutrophil influx, and decreased lung function. Both diseases also express a change in microbial signature dominated by Proteobacteria abundance and Lactobacillus scarcity. However, the relationship between pulmonary microbial dysbiosis and the mechanisms of downstream disease development has yet to be elucidated. We hypothesized that a double-hit hyperoxia and LPS murine model of BPD would show heightened Ac-PGP pathway and neutrophil activity. Through gain- and loss-of-function studies in the same model we showed that Ac-PGP plays a critical role in driving BPD development. We tested a novel inhaled live biotherapeutic using active Lactobacillus strains to counteract lung dysbiosis in in vitro and in vivo models of BPD and COPD. The Lactobacillus LBP is effective in improving lung structure and function, reducing neutrophil influx, and reducing a broad swath of pro-inflammatory markers in these models of chronic pulmonary disease. Live inhaled microbiome-based therapeutics show promise in addressing common pathways of disease progression that in the future can be targeted in a variety of chronic lung diseases.

microbiology↗

bioRxiv2023

Oncomodulin Regulates Spontaneous Calcium Signaling and Maturation of Afferent Innervation in Cochlear Outer Hair Cells

Cochlear outer hair cells (OHCs) are responsible for the exquisite frequency selectivity and sensitivity of mammalian hearing. During development, the maturation of OHC afferent connectivity is refined by coordinated spontaneous Ca2+ activity in both sensory and non-sensory cells. Calcium signaling in neonatal OHCs can be modulated by Oncomodulin (OCM, {beta}-parvalbumin), an EF-hand calcium-binding protein. Here, we investigated whether OCM regulates OHC spontaneous Ca2+ activity and afferent connectivity during development. Using a genetically encoded Ca2+ sensor (GCaMP6s) expressed in OHCs in wild-type (Ocm+/+) and Ocm knockout (Ocm-/-) littermates, we found increased spontaneous Ca2+ activity and upregulation of purinergic receptors in OHCs from GCaMP6s Ocm-/- cochlea immediately following birth. The afferent synaptic maturation of OHCs was delayed in the absence of OCM, leading to an increased number of ribbon synapses and afferent fibers on GCaMP6s Ocm-/- OHCs before hearing onset. We propose that OCM regulates the spontaneous Ca2+ signaling in the developing cochlea and the maturation of OHC afferent innervation.

developmental biology↗