Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.09.12.675858

Transcriptomic and proteomic dynamics of ovarian follicle group culture resemble in vivo folliculogenesis

Jones, A. S. K.·Hannum, D. F.·Schissel, T.·Machlin, J. H.·Padmanabhan, V.·Li, J. Z.·Shikanov, A.
View original source ↗Export metadata ↓

Abstract

The prohibitively low yield of fertilizable oocytes obtained from cultured ovarian follicles limits clinical translation of in vitro follicle maturation for fertility preservation. This is in part due to an incomplete understanding of the process of follicle development. Previous work has demonstrated that group culture of primary murine follicles had a synergistic effect on growth and maturation in contrast to single follicles, but mechanisms remained unknown. Here, we cultured primary follicles in groups of 5 (5X) or 10 (10x) for twelve days, separated the somatic cells from oocytes, and analyzed the temporal transcriptional signatures every two days. In total, 13,461 genes in somatic cells and 10,091 genes in oocytes were computationally sorted into ten temporally distinct gene expression patterns. The somatic cell temporal gene expression patterns showed strong concordance with the granulosa and theca cell markers reported in a recent single-cell whole ovary RNA sequencing study. Importantly, canonical markers of steroidogenesis in cultured follicles followed expected trajectories of decreasing Amh expression and increasing Inhba, Inhbb, Cyp11a1, Cyp17a1, Cyp19a1, Lhcgr, and Fshr over the culture period. Furthermore, when comparing the 10X and 5X culture groups, we identified 306 and 14 differentially expressed genes in somatic cells and oocytes, respectively. Shotgun proteomics data was aligned with the somatic cell transcriptomic data and identified four L-R pairs that were differentially expressed between the two conditions. These comprehensive datasets uncovered temporal dynamics of in vitro folliculogenesis in a compartment-specific manner, serving as a valuable resource for optimizing future follicle culture systems for fertility preservation.

Explore related subjects

cell biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Jones, A. S. K., Hannum, D. F., Schissel, T., Machlin, J. H., Padmanabhan, V., Li, J. Z., Shikanov, A.. 2025-09-15. Transcriptomic and proteomic dynamics of ovarian follicle group culture resemble in vivo folliculogenesis. https://doi.org/10.1101/2025.09.12.675858

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Unraveling the metabolic landscape of alkaptonuria through a human-relevant in vitro liver disease model

Alkaptonuria (AKU) is a rare inherited metabolic disorder of tyrosine catabolism caused by a deficient homogentisate 1,2-dioxygenase (HGD) enzyme. This results in the accumulation of homogentisic acid (HGA), driving a progressive multisystem pathology characterized by debilitating early-onset osteoarthritis due to connective tissue degeneration. While previous in vitro studies have primarily relied on exogenous HGA exposure in osteoarticular cell models, the direct metabolic consequences of endogenous HGD deficiency within its native hepatic context remain poorly understood. Here, we established the first human-relevant HGD knockout hepatic in vitro model using a universal in-house-developed homology-directed repair approach. Integrative multi-omic analysis revealed that HGD deficiency induces widespread metabolic rewiring extending beyond disrupted tyrosine catabolism. HGD-deficient hepatocytes exhibited elevated oxidative stress accompanied by impaired mitochondrial respiration and a pseudohypoxic metabolic adaptation toward increased glycolytic dependency. Despite this glycolytic shift, the cells displayed reduced anabolic and translational activity alongside attenuated proliferation, consistent with a chronic stress-adaptive survival state rather than a proliferative metabolic phenotype. This study provides systems-level insights into the pathophysiology of AKU and establishes a versatile platform for mechanistic and therapeutic investigation.

cell biology↗
bioRxiv2026

P-body sequestration of clock transcripts delays repressor synthesis to set circadian period in Drosophila

Negative-feedback oscillators require a delay between the accumulation of a repressor's mRNA and the action of its protein. In the circadian clock, this delay has been attributed largely to post-translational control of PERIOD (PER) stability and nuclear entry. The RNA-binding proteins shown to regulate per translation, ATAXIN2 and its partners, promote it, leaving open whether any step holds clock transcripts back before they are translated. Here, using time-resolved miniTurbo proximity labeling of endogenous PER across four phases of the circadian cycle in Drosophila clock neurons, we define a 252-protein PER proximitome that partitions into a nuclear arm and a cytoplasmic RNA-metabolism arm. A behavioral RNAi screen identified two P-body components, the DEAD-box helicase Me31B (DDX6) and the 5'-3' exonuclease Pacman (Pcm; XRN1), as strong regulators of circadian rhythms. Using single-molecule RNA-FISH, proximity RNA editing and ribosome profiling, we show that as per and tim transcripts accumulate, they localize to Me31B-labeled P-bodies and are poorly translated, most prominently at ZT12. Me31B knockdown disrupts P-bodies and releases per mRNA from them, causing PER to accumulate earlier and to ~2-fold higher levels, whereas Me31B overexpression delays PER accumulation and lengthens the free-running period by ~2 h. Knockdown of Pcm, in contrast, impairs clearance of per mRNA, sustaining PER and TIM accumulation, prolonging the repression phase and abolishing cycling of ~89% of rhythmic transcripts. Together, these findings identify P-body sequestration as a repressive step that delays repressor synthesis, and Pcm-dependent decay as required to end repression on time. Given the deep conservation of DDX6 and XRN1, RNP compartments may provide a conserved means of generating delay in circadian and other negative-feedback circuits.

cell biology↗
bioRxiv2026

Defining redundancy in the stickers and spacers of the cell-cell junction protein Canoe's intrinsically disordered region

Cell-cell adherens junctions (AJs) and their dynamic cytoskeletal linkage power morphogenesis. AJs are enormous complexes with hundreds of proteins linked by multivalent interactions. Like other biomolecular condensates, intrinsically disordered regions (IDRs) in junctional proteins play important roles in AJ assembly and function, using spacer elements to span distances, and stickers to engage targets. To define molecular mechanisms, we need to define the functional units within IDRs. Drosophila Canoe, homolog of human Afadin, is our model. Canoe mediates morphogenesis and has an extensive IDR, with two conserved F-actin-binding stickers and two poorly conserved spacers. We combined biochemical, genetic and cell biological approaches to define the function of these IDR elements. While no single element is essential, deleting the full IDR essentially eliminates Canoe function. By scrambling the amino acid sequence of the spacers, we find that length and composition are more important than amino acid sequences, though sequences in the C-terminal spacer affect Canoe localization. Finally, we test redundancy of the F-actin-binding stickers. Deleting both reduces but does not eliminate viability, and sensitized assays reveal their redundant roles. These data reveal the robustness of IDRs.

cell biology↗