Back

Development, Growth & Differentiation

○ Wiley

Preprints posted in the last 30 days, ranked by how well they match Development, Growth & Differentiation's content profile, based on 12 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

1
A germline-specific reporter reveals conserved primordial germ cell developmental dynamics between jawless and jawed fish species

Sarasamma, S.; Chung-Davidson, Y.-W.; Buchinger, T. J.; Song, J.; Li, W.

2026-09-24 developmental biology 10.64898/2026.09.23.753524 medRxiv
Top 0.1%
0.8%
Show abstract

Primordial germ cells (PGCs) are the stem cell lineage responsible for transmitting genetic information across generations and are therefore central to studies of germline development, reproduction, and evolution. However, a lack of molecular tools in jawless vertebrates such as lampreys and hagfish has limited comparative insights into the evolutionary origins of vertebrate germline cells. Here, we report the development of the first germline-specific reporter (GSR) in the sea lamprey (Petromyzon marinus), Tg(piwil1: egfp-UTRnanos1), a piwil1-based germline reporter that is driven by the sea lamprey piwil1 regulatory region that directs Green Fluorescent Protein (GFP) expression in early PGCs. Promoter activity was validated by robust GFP expression in PGCs of zebrafish embryos co-injected with Tol2 transposase mRNA. Injection of the construct into sea lamprey embryos resulted in early, persistent, and gonad-localized GFP-positive cells. These results demonstrate stable germline-specific transgene expression in a jawless vertebrate and suggest deep evolutionary conservation of germline regulatory mechanisms between jawless and jawed vertebrates. Furthermore, the piwil1-based germline reporter line enabled lifetime visualization of zebrafish germline cells, revealing that increased PGC abundance during embryogenesis biases toward female sexual differentiation. Together, this study establishes the first GSR system in a jawless vertebrate and provides a useful platform for investigating germline biology and vertebrate germline evolution.

2
How opsins diversified after the teleost whole-genome duplication: Insights from two parietopsins of the red piranha, Pygocentrus nattereri

Sato, K.; Yamashita, T.; Sakai, K.; Ohuchi, H.; Kusakabe, T. G.; Gyoja, F.

2026-09-25 evolutionary biology 10.1101/2025.09.17.675483 medRxiv
Top 0.3%
0.4%
Show abstract

The teleost whole-genome duplication (TGD) contributed to functional diversification of opsins. Some TGD paralogs, including those of parapinopsin (PP), Vertebrate Ancient (VA) opsin, and long wavelength-sensitive (LWS) opsin, show different absorption spectra and/or expression patterns. However, our knowledge of detailed evolutionary processes and mechanisms by which TGD contributed to opsin diversification is still limited. Here, we report that TGD paralogs of parietopsin (PT1 and PT2) are retained in extant species. While most species, including the zebrafish, have only PT1, several characins, including the red piranha (Pygocentrus nattereri), retain both PT1 and PT2. The Mexican tetra (Astyanax mexicanus) and catfishes have only PT2. To assess the degree of functional diversification between PT1 and PT2, we characterized spectral properties and expression patterns. Maximum absorption spectra differ slightly among PTs. Those of red piranha PT1, PT2, Mexican tetra PT2, and Japanese catfish (Silurus asotus) PT2 were located at 517 nm, 528 nm, 517 nm, and ~535 nm, respectively. Fluorescence in situ hybridization showed that (1) piranha PT1 and PT2 are expressed in the same pineal cells, and (2) they are also co-expressed with PP1. Based on these findings, functional diversification of opsins after gene duplication is discussed.

3
Transient 5-azacytidine exposure elicits persistent myogenic-like transcriptional remodeling in zebrafish fibroblasts: implications for cultivated seafood

Ikeda, D.; Mizusawaa, N.; Watabe, S.

2026-10-05 cell biology 10.64898/2026.10.01.756133 medRxiv
Top 0.3%
0.3%
Show abstract

Fibroblasts are readily obtained and expanded and may provide an alternative cell source for cultivated seafood if their latent myogenic potential can be accessed. We examined whether transient exposure to 5-azacytidine (AZA), a cytidine analogue known to convert mouse embryonic fibroblasts into myoblasts, elicits a persistent muscle gene program in embryo-derived zebrafish (Danio rerio) Z3 fibroblasts. Cells were exposed to 0, 2.5, 5 or 10 M AZA for 48 h and maintained in drug-free medium for 3 weeks. RNA-seq identified 744 genes that increased and 670 that decreased consistently across the concentration series. Increased genes encompassed myogenic regulators, fusion factors, sarcomeric components and excitation-contraction machinery, whereas decreased genes were enriched for extracellular-matrix and adhesion functions. In a separate six-dose RT-qPCR experiment (0-20 M AZA) with three biological replicates per concentration, all 19 selected muscle genes were significantly increased at 1.25 M, the lowest concentration tested, whereas 9 of 12 extracellular-matrix/fibroblast genes were significantly decreased. Several muscle genes plateaued or declined at higher concentrations, and multinucleated myotubes were not observed. A separate 5-aza-2'-deoxycytidine (decitabine) series showed a comparable muscle-associated response at 0.25 M. These findings indicate that zebrafish fibroblasts retain access to a myogenic-like transcriptional program, and they provide a model for identifying food-compatible approaches to control fish-cell lineage plasticity for cultivated seafood.

4
Cell Position-Associated Division Orders and Cell Cycle Durations Shape Asymmetric Trajectories of Cell Fates and Morphological Events in Pre- and Peri-implantation Mouse Embryos

Yang, H.

2026-09-29 developmental biology 10.64898/2026.09.24.754028 medRxiv
Top 0.4%
0.3%
Show abstract

A central question in developmental biology is how spatiotemporal embryo morphological events and cell differentiation are precisely coordinated to eventually develop into a mature organism. Previous research has shown cell positions and asymmetric division stages are related to cell lineage specification since morula stage. However, the detailed spatiotemporal dynamics and histories of embryonic cells and their relations with cell lineage specification remain incompletely understood from the onset of embryo development onward. My study on in-vitro embryos showed that continuous live cell tracking mapped community-like patterns in cell origin and differentiation. Cell positions, cell temporal factors (such as cell division order and cell cycle) and their histories intricately interacted over pre- and peri-implantation stages. These interactions of spatiotemporal cellular activities directed embryo morphological events and asymmetric cell lineage origin and differentiation throughout 2-cell to around 100-cell stage. In conclusion, this study provides comprehensive insights into the cellular spatiotemporal dynamics of cell inheritance and differentiation during pre- and peri-implantation morphological events and cell lineage specification. By longitudinally integrating spatial and temporal parameters relating to early embryogenesis, the findings not only bridge divergent explanations stemmed from different studies in the field but also offers a refined foundation for evaluating embryo potential and improving outcomes in assisted reproductive technologies, stem cell research, and regenerative medicine.

5
Generation of a transgenic cephalopod

Montague, T. G.; Gibbons, C. J.; Barlow, G. T.; Bashkirova, E. V.; Xu, Y.; Castagna, E. C.; Mungioli, T. J.; Patrick, K. A.; Nemes, A.; Varma, A.; Looger, L. L.; Albertin, C. B.; Lomvardas, S.; Axel, R.

2026-09-28 genetics 10.64898/2026.09.23.753964 medRxiv
Top 0.5%
0.2%
Show abstract

Coleoid cephalopods (cuttlefish, octopus, and squid) are marine mollusks with elaborate nervous systems that support a diverse repertoire of complex behaviors. These include the neural control of the color, pattern, and texture of the skin, facilitating both adaptive camouflage and innate patterning that may reflect internal state. The development of transgenic cephalopods expressing fluorescent proteins, optogenetic actuators, and reporters of neural activity would contribute a new and important technology to cephalopod biology. The generation of transgenic cephalopods, however, has remained a major challenge. Here, we report the development of stable transgenic dwarf cuttlefish (Ascarosepion bandense) expressing ubiquitous nuclear-localized mScarlet, a red fluorescent protein. We evaluated multiple strategies for transgenesis, and established cuttlefish lines using both CRISPR and the transposons Sleeping Beauty and Minos. The stable expression of transgenes enabled live imaging of cell dynamics during embryonic development. The Minos transposon emerged as the most efficient transgenesis strategy and is adaptable to promoters and transgenes of choice. These strategies now enable the generation of diverse genetic tools for mechanistic studies of cephalopod biology.

6
Lasp family proteins generated by teleost-specific genome duplication

XIE, Y.; Morimoto, K.; Tsunakawa, R.; Mori, Y.; Awaya, H.; Haruta, S.; Fujita, Y.; Chokki, T.; Nakayama, A.; Usui, Y.; Katsuyama, Y.; TERASAKI, A. G.

2026-10-09 evolutionary biology 10.64898/2026.10.05.756842 medRxiv
Top 0.8%
0.1%
Show abstract

Two rounds of whole-genome duplication (2R-WGD) in the vertebrate lineage are thought to have driven gene diversification. Mammals have four genes encoding five nebulin superfamily proteins (LASP1, LASP2/NEBL, NEB, and NRAP) hypothesised to have arisen from invertebrate LASP via WGD. Here, we examined the evolutionary fate of the nebulin superfamily after an additional WGD, teleost-specific genome duplication (TGD). Genome and transcriptome analysis of zebrafish (Danio rerio) and medaka (Oryzias latipes), of which the complete genomes were recently determined, showed only lasp family genes retained duplicate copies. Zebrafish retained two LASP2/NEBL-derived ohnologs; one (LASP2L) had been misidentified as a nebulette gene in the Zebrafish Information Network (ZFIN) despite lacking nebulette-specific exons. Another (LASP2/NEBL) is newly identified in this study because it lies in a newly determined region of the latest genome assembly. Contrastingly, medaka retained two LASP1 ohnologs and one LASP2/NEBL. The duplicated lasp family proteins showed overlapping and specific tissue expression patterns. We confirmed all three zebrafish lasp proteins bound actin and co-localized with actin-rich structures when ectopically expressed in cultured fibroblasts. This supports that TGD-derived lasp duplicates underwent lineage-specific retention and expression divergence in teleosts whilst conserving core actin-binding properties.

7
Brief Communication: Differential degradation of exogenous DNA in microalgal cell lysates

Kumari, E.; Baiden, N.; Verruto, J.; Marsden, O.; Waite, J.; Hu, I.

2026-09-24 molecular biology 10.64898/2026.09.23.753703 medRxiv
Top 1%
0.1%
Show abstract

Chlorella sorokiniana is an industrially important microalga, but its genetic manipulation remains limited by poor transformation efficiency. Although several barriers have been proposed, the role of intracellular nuclease activity has received little attention. Here, we compared the degradation of exogenous double-stranded DNA in whole-cell lysates from transformation-recalcitrant (Chlorella sorokiniana and Tetradesmus obliquus) and transformation-proficient (Phaeodactylum tricornutum, Microchloropsis gaditana, and Nannochloropsis oceanica) microalgae. C. sorokiniana rapidly degraded both linear and plasmid DNA, while T. obliquus exhibited intermediate activity. In contrast, no detectable degradation was observed in the transformation-proficient species. DNA degradation in C. sorokiniana occurred within minutes, and nuclease activity in both recalcitrant species was inhibited by EDTA and Zn2+, consistent with a metal ion-dependent endonuclease. These findings suggest that intracellular nuclease activity may represent an underexplored barrier to exogenous DNA stability during transformation and provide a potential target for improving genetic transformation of recalcitrant microalgae.

8
β-catenin Dynamics in Regenerating Hydra

Garion, L.; Ascoli-Abbina, Y.; Dori, N.; Pasvinter, I.; Keren, K.

2026-09-24 biophysics 10.64898/2026.09.21.752673 medRxiv
Top 1%
0.1%
Show abstract

Body axis specification is essential for morphogenesis, yet how axial patterning is dynamically coordinated remains unclear. In Hydra, Wnt/{beta}-catenin signaling is central to axial patterning, but its spatiotemporal dynamics are not well understood. Since nuclear {beta}-catenin mediates Wnt-dependent transcription, its localization provides a relevant readout for pathway dynamics. Here, we track {beta}-catenin abundance and nuclear localization in vivo during regeneration from bisected Hydra, tissue rings, and small tissue fragments. Following bisection, nuclear {beta}-catenin is detected exclusively at the regenerating oral end, where a broad signal appears and then declines before focusing at the future head. Tissue rings, lacking both head and foot, exhibit similar oral-aboral asymmetry. In regenerating fragments, the initial response often spans nearly the entire tissue, including the future foot region, followed by an additional peak before stabilizing at the future head. Overall, our results show that the spatial restriction of nuclear {beta}-catenin correlates with the divergence of regenerative dynamics toward head or foot formation, while the trajectories leading to these outcomes vary across different initial tissue configurations.

9
NANOG is dispensable for hypoblast but essential for embryonic disc development during conceptus elongation in sheep

Martinez de los Reyes, N.; Carvajal-Serna, M.; Marigorta, P.; Toledano-Diaz, A.; Santiago-Moreno, J.; Bermejo-Alvarez, P.; Ramos-Ibeas, P.

2026-09-25 developmental biology 10.64898/2026.09.24.754098 medRxiv
Top 1%
0.1%
Show abstract

NANOG is a conserved regulator of epiblast identity and is essential for hypoblast development and embryo survival after the blastocyst stage in mice. However, its role during post-blastocyst development remains poorly understood in non-rodent mammals. Here, we investigated the function of NANOG during ovine embryogenesis using CRISPR/Cas9-mediated gene ablation. NANOG ablation did not affect blastocyst formation or the initial development of the epiblast. However, NANOG-deficient blastocysts contained significantly fewer SOX17+ hypoblast cells by day (D) 8, followed by reduced hypoblast migration during early post-hatching stages in D12 in vitro embryos. These defects were transient, as hypoblast development was comparable between NANOG-deficient and wild-type conceptuses during subsequent in vivo conceptus elongation from embryonic day (E) 11 onwards. In contrast, although extraembryonic membranes development and conceptus elongation proceeded normally, NANOG-deficient conceptuses lacked SOX2+ epiblast cells and failed to form an embryonic disc (ED) from E11 onwards. These findings demonstrate that NANOG is dispensable for hypoblast development but is required for epiblast maintenance and ED formation during conceptus elongation in sheep.

10
The molecular basis of hard cornification in the keratinized jaw sheaths and keratodonts of anuran tadpoles

Dias, P. H. d. S.; Hsiung, K.; Stallard, N.; Jones, J.; Capitosti, A.; Harrington, S.; Lukas, P.; Chrysostomakis, I.; Vera Candioti, F.; Hawlitschek, O.; Haas, A.; Bohne, A.; Paluh, D. J.

2026-10-02 evolutionary biology 10.64898/2026.09.30.755311 medRxiv
Top 2%
0.1%
Show abstract

Hard cornification is the developmental process that produces the hardened epidermal structures that characterize tetrapod diversity, including scales, feathers, hair, and claws. This process relies on keratin proteins and additional reinforcing proteins that assemble, cross-link, and strengthen tissues to become mechanically resilient. Although the molecular composition of hard cornified tissues is known to vary among tetrapods, the program is least understood in amphibians. Within frogs, hard cornification occurs in the mouthparts of most tadpoles and in the nuptial pads, hindfoot claws, and foot tubercles of some adults. We characterized transcriptomic profiles of Bombina orientalis tadpoles at three developmental stages before, during, and after mouthpart cornification. We identified 25 keratin genes orthologous to amniote hard keratins in the B. bombina genome, 18 of which are upregulated in cornifying larval mouthparts. Furthermore, two of these hard keratin paralogs and an amphibian epidermal differentiation gene exhibit distinct spatial expression patterns within the jaw sheaths and keratodonts evidenced by in situ hybridization, suggesting they have discrete functional roles. The newly discovered diversity of the hard keratin repertoire in Bombina , and the concurrent expression of many of these paralogs in tadpole mouthparts, suggests that anuran hard cornification is much more complex than adult cornified traits thus far characterized in Xenopus frogs. Our results also challenge the notion that the diversification of keratins in Amphibia is primarily associated with the transition to more terrestrial habits, and may instead be shaped, in part, by the novel feeding apparatus of aquatic tadpoles.

11
4D confocal microscopy of time dependent cell and nuclear osmotic response reveals differential osmoregulation and transport kinetics

Azam, I.; Olver, D. J.; Benson, J. D.

2026-10-06 biophysics 10.64898/2026.09.30.755591 medRxiv
Top 2%
0.1%
Show abstract

A cell's ability to maintain its volume is a prerequisite for its essential physiological functions. Changes in extracellular osmolarity induce the flux of water and solutes across the cell and nuclear membrane and, therefore, alters cell and nuclear volumes. Here, we investigated the equilibrium and dynamic volumetric responses of cells and nuclei in adherent human hepatoma (HepG2) cell monolayers using live three-dimensional imaging. Through image segmentation, 3D reconstruction, and volume rendering, precise cell and nuclear volumes were quantified. We found that during hypoosmotic stress, cells swell and lose osmolytes through active volume regulation, and nuclei undergo greater relative expansion than cells. During hyperosmotic stress, we found that both cells and nuclei shrink rapidly, develop irregular morphologies and undergo passive volume regulation. Furthermore, we explored the osmotic responses in these cells by restoring isosmotic conditions following osmotic stress and found that nuclei returned to volumes greater than their initial isosmotic volume, whereas cytoplasmic volume returned to a value below its initial isosmotic volume following swelling. By fitting coupled transport models water and solute permeability estimates for both cells and nuclei were made from their dynamic responses to different anisosmotic media with and without the presence of permeating solutes dimethyl sulfoxide and ethylene glycol. Together, these quantitative measurements of cell, cytoplasm, and nuclear volumetric responses and associated transport parameters have important implications for understanding cell physiology and the mechanism of osmoregulation.

12
Revisiting Hydractiniidae (Hydrozoa): Mitogenomic Insights into the Diversity, Systematics and Life-Cycle Evolution of North Atlantic and Arctic Species

Beckmann, L. M.; Hosia, A.; Ronowicz, M.; Martell, L.; Soto-Angel, J. J.

2026-10-12 evolutionary biology 10.64898/2026.10.09.757902 medRxiv
Top 2%
0.0%
Show abstract

Hydractiniidae is a diverse family of colonial hydrozoans exhibiting substantial variation in colony organization, reproduction and life-cycle strategies, including species with and without a medusa stage. Several hydractiniids are also established model organisms, yet species boundaries and distributions remain incompletely resolved, limiting comparisons of reproductive and developmental traits across taxa. Here, we combine morphological and molecular data to reassess hydractiniid diversity, species identities, and life-cycle variation in material from the North Atlantic and Arctic Ocean. We integrate detailed observations of colonies and reproductive structures with DNA barcoding and mitochondrial genomes to evaluate species boundaries and provide molecular support for taxonomic identifications. Our results confirm 10 species in the study area, occurring from shallow waters to 2600 m depth and from coastal fjords to deep-sea hydrothermal vents. We further show that some historical species identifications and distribution records require reassessment. We establish a new genus for Arctic hydractiniid species (Bonneviactinia gen. nov.) and reassign two species to Schuchertinia. Mapping reproductive strategies onto the phylogeny reveals a broad pattern of increasing retention of medusa characters, from fixed sporosacs through reduced and fixed medusoids and non-liberated eumedusoids to fully developed, free-swimming feeding medusae, suggesting a progressive evolutionary trajectory in life-cycle complexity across Hydractiniidae. Furthermore, we clarify the identity of Podocoryna carnea and, through rearing experiments from polyp stage to medusae, characterize its morphological variation and developmental stages. By linking morphologically documented specimens and vouchers to genetic data, we establish reference resources that will facilitate future taxonomic, phylogenetic and biodiversity studies, including molecular surveys of marine communities. Together, these results demonstrate the value of integrative taxonomy for resolving hydractiniid diversity and provide a comparative foundation for investigating the evolution of reproductive strategies and life-cycle complexity in Medusozoa.

13
Unraveling APA dynamics during quiescence transitions reveals Pabp modulation of sod2 expression via APA to regulate cellular quiescence

Deng, X.; Zhang, L.; Du, Z.; Zhao, X.; Sarker, B.; Jabeen, Y.; Guan, L.; Zhou, T.; Huang, S.; Zhou, Y.; Liang, L.; Xu, C.

2026-09-28 cell biology 10.64898/2026.09.27.754748 medRxiv
Top 2%
0.0%
Show abstract

Quiescence is a reversible proliferation arrest enabling cells to adapt to environmental changes, yet the post-transcriptional mechanisms governing its transitions remain poorly understood. Here, we map genome-wide alternative polyadenylation (APA) dynamics across 15 time points of quiescence transitions in fission yeast using 3'-end RNA sequencing. We reveal that APA undergoes extensive remodeling: driving global 3'UTR lengthening during early quiescence entry, 3' UTR shortening upon quiescence establishment, and progressive reversal to proliferative-state lengths during quiescence exit. Integrating 3' UTR dynamics with differential expression analysis, we identify candidate genes potentially regulated through APA-mediated 3' UTR mechanisms. We demonstrate that sod2, encoding mitochondrial superoxide dismutase, autoregulates its mRNA and protein levels via APA-dependent 3' UTR changes. Disrupting proximal APA site of sod2 in a mitophagy-deficient (atg43{Delta}) background exacerbates quiescence maintenance defects and mitochondrial dysfunction. We further identify Pabp as an upstream regulator of sod2 APA. This study establishes the temporal APA remodeling during quiescence transitions and reveals a Pabp-APA-sod2 regulatory axis governing post-transcriptional control of cellular quiescence.

14
A Large-Scale Deep Normative Modeling of Primary Sulcal Patterns Reveals Deviations in a Spectrum of Disorders

Kwon, H.; Morton, S. U.; Newburger, J. W.; Feldman, H. A.; Lee, J.-M.; Grant, P. E.; Im, K.

2026-09-28 neuroscience 10.64898/2026.09.24.754179 medRxiv
Top 2%
0.0%
Show abstract

Primary sulcal patterns, the spatial arrangement of the earliest cortical folds, emerge prenatally and remain essentially stable after birth. Alterations are associated with cognitive outcomes and hold promise as clinical biomarkers. However, detecting abnormalities is challenging due to the high topological variability and complexity of normal individual sulcal patterns. Here, we introduce an unsupervised generative model that quantifies individual sulcal pattern deviations against a normative baseline learned from 10,349 typically developing subjects spanning early childhood through adulthood. We combine a generative reconstruction error with a discriminator trained on diffusion-generated pseudo-atypical graphs to leverage their complementary strengths in sensitivity and robustness. The discriminator captures subtle anomalies and is robust to demographic and data quality variations, whereas the generative model enables severity stratification and demonstrates cross-site generalizability. Across two clinical cohorts spanning subtle to overt sulcal abnormalities (congenital heart disease and polymicrogyria), our model captured global and localized condition-related deviations and linked them to neurodevelopmental outcomes. By enabling population-scale, individualized quantification of sulcal deviations, this framework provides a foundation for future clinical risk stratification.

15
Plasma Extracellular Vesicle Lipidomics Reveals an SMPD1-Driven Sphingomyelin Salvage Pathway Collapse in Parkinson's Disease

Rai, S.; Chaubey, A.; Paul, S.; Zehra, S.; Ananya, ; Rajan, R.; Shekhar, S.; Reddy T, J.; Jain, S.; Gupta, S.; Inampudi, K. K.; Rani, N.; Mahadevan, A.; Modi, G. P.; Kumar, S.

2026-09-28 neuroscience 10.64898/2026.09.25.754317 medRxiv
Top 2%
0.0%
Show abstract

While lysosomal lipid dysregulation is implicated in Parkinsons disease (PD), identifying the precise enzymatic drivers remains limited by the lack of subcellularly resolved metabolic mapping. Leveraging endosome-origin plasma extracellular vesicle (PsEV) lipidomics, we identified a profound bidirectional disruption of the ceramide-sphingomyelin (SM) axis in PD, driven by asymmetric upregulation of sphingomyelin phosphodiesterase 1 (SMPD1) and sphingomyelin synthase 1 (SGMS1). BODIPY-C5 SM tracking revealed that SMPD1 perturbation severely impairs lysosomal SM turnover. Crucially, this SMPD1-driven hydrolysis forces a salvage pathway collapse, bottlenecked by SPHK1/SGPL1 downregulation, which precipitates oxidative membrane damage and PINK1/Parkin-dependent mitophagy failure. We robustly validated this multi-pathway dysfunction across orthogonal in vitro, in vivo mouse, and postmortem human brain models. Furthermore, SMPD1/SGMS1 expression distinctly stratifies clinical phenotypes, marking the aggressive Postural Instability/Gait Difficulty (PIGD) subtype. Our findings establish SMPD1-mediated lysosomal impairment and ceramide-SM imbalance as a core biochemical axis in PD pathophysiology.

16
Highly inducible transcription is impaired in cells lacking Cyclin T1 (CycT1) of the positive transcription factor b (P-TEFb).

Kajitani, T.; Huang, F.; Nishiura, K.; Irwin, D.; Chein, A.; Fujinaga, K.

2026-09-28 molecular biology 10.64898/2026.09.26.754677 medRxiv
Top 2%
0.0%
Show abstract

In eukaryotic cells, the positive transcription elongation factor b (P-TEFb) plays a critical role in the transition of RNAPII from the paused state to actively transcribing mode. Although three different cyclin (Cyc) T (CycT1, T2a, and T2b) interact with CDK9 to form functional P-TEFb, a majority of P-TEFb complexes are comprised of the CycT1 and CDK9. To analyze the role of the CycT1 subunit of P-TEFb on cellular transcription, we established HEK293T cells lacking CycT1 proteins (CycT1-KO cells). While no apparent growth defects were observed with CYcT1-KO cells, the level of CDK9 was decreased and no compensatory over-expression of CycT2 was observed, suggesting that the reduced level of functional P-TEFb complexes is sufficient for the normal cell growth. Reporter gene assays indicate that NF-kappaB-dependent transcription induced by PMA was impaired in CycT1-KO cells although the function of NF-kappaB (P65) per se was not affected. On the other hand, AP1-dependent transactivation induced by PMA was unaffected in CycT1-KO cells. Moreover, transcription stimulated by JQ1, a strong P-TEFb inducer, was reduced in CycT1-KO cells. Data of biochemical analysis indicate that P-TEFb with CycT1 (P-TEFb (CDK9:CycT1)) was efficiently released from 7SKsnRNP by JQ1 while P-TEFb (CDK9:CycT2) was not affected by JQ1. Transcriptome analysis indicated that the lack of CycT1 had a minor effect on the steady-state transcription. However, expression of JQ1-dependent genes was severely reduced in CycT1-KO cells. Interestingly, referring to gene expression profiles of 33 different types of cancer revealed that 11 out of 13 top JQ1-dependent genes were also highly upregulated in Pancreatic Adenocarcinoma. From these results, we conclude that although many genes can be regulated by both P-TEFb (CDK9:CycT1) and P-TEFb (CDK9:CycT2), CycT1 plays a critical role in regulating highly inducible genes, which are also aberrantly regulated in a particular type of cancer.

17
A Modality-Invariant Measure of Neural Health

Sanchez Colon, L. A.; Niebur, E.; Kang, J.; Onyike, C.; Sarma, S.

2026-10-06 neurology 10.64898/2026.10.02.26364203 medRxiv
Top 2%
0.0%
Show abstract

Quantifying neural health with a single measure remains a major unmet challenge. Here, we report a physiological marker based on the spatial distribution of signal-derived energy correlates in the resting brain. We hypothesize that energy organization in the healthy brain approaches an entropy-maximizing, homeostatically regulated state characterized by five properties: lognormal energy distributions, balanced spatial allocation, statistical independence between regions, low energy variance, and temporal stability. Together, these properties define an energetic profile that the Neural Health Index (NHI) summarizes as a single score, computable from (scalp/intracranial) electroencephalography, magnetoencephalography, or functional magnetic resonance imaging. Across 808 participants spanning neurological, psychiatric, neurodevelopmental, and neurodegenerative disorders, NHI distinguished healthy from clinical populations with sensitivity and specificity exceeding 95% in internal and external validation, scaled with disease severity, tracked pharmacological treatment exposure, and generalized to unseen diagnoses. These findings support NHI as a disease-agnostic, modality-invariant candidate biomarker for disease stratification and treatment monitoring.

18
A Novel Open-Source CellProfiler Pipeline for Automated, User-Friendly Hierarchical and K-Means Clustering of Microglial Morphology

Landwehr, A.; Cools-Lartigue, C.; Hadera, V.; Bobotis, B.; Khakpour, M.; Gomes, F. V.; Tremblay, M.-E.

2026-09-28 cell biology 10.64898/2026.09.24.753926 medRxiv
Top 2%
0.0%
Show abstract

Microglia represent a highly dynamic and heterogeneous cell type that is critically implicated in states of health and pathology. Microglial morphological subgroups have been identified that correspond to functional characteristics determining health-related outcomes. The identification of states based on morphological characteristics will therefore provide invaluable insights into the microglia-specific functional mechanisms driving treatment effects. The application of clustering analyses enables the detection of groupings within samples reflecting differences in morphological features. Here we propose the application of three custom-created modules to be used within the open-source software CellProfiler. These modules enable the automated detection of clusters present within the sample of microglia, as well as the assessment of the abundance of these clusters across conditions. The application of the analysis is conducted in a highly user-friendly manner, with a user interface integrated into the pipeline, enabling the performance of the analysis with only minimal user input. The workflow thereby includes the conduction of an outlier assessment, followed by hierarchical clustering and k-means clustering and the generation of interactive graphs to determine the number of microglia states present in the sample. Bar plots displaying the abundance of the microglia states across conditions included in the sample will be created. This approach will facilitate faster and more comparable detection of microglial morphological clusters across studies.

19
ST6GAL1 sialyltransferase promotes acinar cell survival and tissue regeneration during pancreatitis

Marciel, M. P.; Bhalerao, N. U.; Haldar, B.; Shinde, S. S.; Anderson, J. C.; Willey, C. D.; Iyer, S.; Dudeja, V.; Bellis, S. L.

2026-09-28 cell biology 10.64898/2026.09.26.754701 medRxiv
Top 2%
0.0%
Show abstract

The role of aberrant glycosylation in pancreatitis remains an under-investigated area of research. Here, we determined that the ST6GAL1 sialyltransferase, which adds 2-6-linked sialic acids to N-glycoproteins, was upregulated in pancreatic tissues from patients with acute (AP) and chronic (CP) pancreatitis, and in mice with experimental AP. Within these tissues, ST6GAL1 was selectively expressed in acinar cells undergoing acinar to ductal metaplasia (ADM), a process whereby injured acinar cells de-differentiate and re-enter the cell cycle to enable tissue repair. To study the functional role of ST6GAL1 in pancreatitis, we used HPNE pancreatic epithelial cells with modulated ST6GAL1 expression, along with pancreatic organoids from mice with transgenic expression of ST6GAL1 (SC mice). In these models, ST6GAL1 activity promoted the activation of EGFR (a well-known ADM-driver), ERK, and AKT. ST6GAL1-expressing cells also displayed an ERK-dependent upregulation of the anti-apoptotic proteins, Mcl-1 and Bcl-xL, and impaired apoptotic signaling by the TNFR1 and Fas death receptors. Unbiased kinomics profiling revealed that ST6GAL1 induced the activation of many receptor tyrosine kinases associated with cell survival and proliferation (e.g., EGFR, PDGFR, MET). Furthermore, ST6GAL1 enhanced the survival and proliferation of cells exposed to stress-inducing conditions such as serum withdrawal. Based on these findings, we hypothesized that the pro-survival phenotype imparted by ST6GAL1 would facilitate tissue healing following a bout of pancreatitis. Accordingly, we induced AP in wild type and SC mice via L-arginine injection and found that SC mice had more rapid and efficient tissue repair, evidenced by accelerated restoration of the acini, diminished acinar apoptosis, and reduced immune cell infiltration. Together, these findings highlight a novel glycosylation-dependent mechanism that drives cell survival, positioning ST6GAL1 as a key adaptive mediator of pancreatic regeneration.

20
Ciliary regulation of melanogenesis unveils moonlighting roles for Joubert Syndrome proteins

Magne, B.; Forsey, S.; Harper, D. C.; Zhang, J.; Snider, C. E.; Feng, Y.; Tishkoff, S. A.; Strong, A.; Drivas, T. G.; Goding, C. R.; Lee, R. J.; Marks, M. S.

2026-09-28 cell biology 10.64898/2026.09.27.754807 medRxiv
Top 2%
0.0%
Show abstract

We previously found that skin tone correlates with intronic polymorphisms influencing the expression of the Joubert Syndrome (JS) ciliopathy gene TMEM138, suggesting that primary cilia might regulate pigment production in skin melanocytes. Herein, we show that many ciliary proteins regulate basal pigmentation in wild-type mouse and human melanocytes by facilitating primary cilium-dependent Melanocortin-1 receptor signaling, and downstream activation of the Microphthalmia transcription factor and melanogenic gene expression. Additionally, we identify an extra-ciliary moonlighting role for TMEM138 and other JS proteins in endolysosomal organization required for the biogenesis of melanosomes, the pigment-producing lysosome-related organelle in melanocytes. Our results provide new mechanistic insights into the physiological regulation of pigmentation and suggest that JS-specific pathology might be mediated by ciliary-independent mechanisms.