The research, published in Frontiers in Aging, analyzed autophagy flux in primary skin fibroblasts from apparently healthy male donors aged 20, 38, 74, and 96 years. Fibroblasts are a widely adopted aging cell system because they retain the cellular and molecular signatures of their donors: the skin is directly exposed to ultraviolet radiation, pollutants, and genotoxic agents over a lifetime, so fibroblasts from older individuals carry the in vivo wear of their chronological age into a controlled culture dish. By comparing cells across this age range, the team could trace how each phase of autophagy changes as human cells grow old.

Autophagy is a multi-step assembly line. Under starvation signaling, inhibition of mTOR activates the ULK1/2 kinase complex, which nucleates a phagophore. Two ubiquitin-like conjugation systems, ATG12/ATG5/ATG16L and LC3, elongate and seal the membrane into an autophagosome. The SNARE protein syntaxin 17 is then recruited to mature autophagosomes, licensing their fusion with lysosomes to form autolysosomes, where hydrolases degrade the luminal content. Because each step can fail independently, measuring flux across the whole pathway is essential for designing therapies that reactivate the specific phase that is actually broken.

The master switch of this pathway is transcription factor EB, or TFEB, which controls the expression of autophagy and lysosomal genes. Under nutrient-rich conditions, phosphorylated TFEB sits inert in the cytoplasm; during stress, calcineurin-mediated dephosphorylation drives it into the nucleus. When the researchers examined fibroblasts by confocal microscopy, TFEB activation looked surprisingly intact, even enhanced, in aging. Starvation pushed TFEB into the nuclei of cells from all donors, and the 96-year-old fibroblasts showed the strongest nuclear signal, even accumulating TFEB in the nucleus under normal, non-starved conditions.

That nuclear buildup translated into transcription. Quantitative RT-PCR showed that the TFEB target genes LAMP1, SQSTM1, and MAP1LC3B responded to starvation in cells from all ages, with SQSTM1 and MAP1LC3B transcripts rising markedly higher in the 96-year-old fibroblasts than in the 20-year-old controls. The authors interpret this premature nuclear accumulation of TFEB in old cells as a compensatory alarm: a signaling mechanism mobilized to counteract the impaired flux and lysosomal dysfunction discovered downstream. Alternative explanations, such as altered mTORC1- or ERK-mediated phosphorylation trapping TFEB in the nucleus, or an age-dependent decline in CRM1-mediated nuclear export, remain to be tested.

Autophagosome formation also held up. Treating cells with chloroquine, which blocks autophagosome-lysosome fusion, revealed LC3-positive puncta in fibroblasts from all donors, and Western blotting of the LC3-I to LC3-II conversion showed that autophagosomes formed with similar efficiency across the age spectrum. Flow cytometry with Cyto-ID dye even found a greater accumulation of autophagic vacuoles in the older cultures, implying that the early machinery operates at least as vigorously in old cells, likely as an active coping mechanism against age-related cellular stress.

The picture changed when the team probed the end of the line. The selective autophagy receptor p62, which is itself degraded in autolysosomes, normally accumulates when flux is blocked. Yet when fibroblasts were starved and treated with the lysosomal inhibitors E64D and pepstatin A, young and middle-aged cells accumulated LC3-II and p62 robustly, while cells from the 74- and 96-year-old donors showed no significant accumulation at all. The lysosome-dependent turnover of the canonical autophagy markers had decayed with age, a result the authors confirmed with bafilomycin A1, an inhibitor of the V-ATPase pump that arrests autophagosome-lysosome fusion.

Confocal colocalization assays pinpointed where the assembly line jams. In young fibroblasts, starvation significantly increased the overlap between LC3 and syntaxin 17, indicating enhanced autophagosome maturation, with Pearson correlation coefficients rising from 0.35 to 0.63. In old fibroblasts, starvation produced no such increase, with coefficients of 0.42 versus 0.39. Similarly, the colocalization of LC3 with the lysosomal membrane protein LAMP1, an indicator of autophagosome-lysosome fusion, rose sharply in young cells under starvation but only marginally in aged cells. The final two steps of autophagy, maturation and fusion, had quietly failed.

The culprit appears to be the lysosome itself. LysoBrite staining revealed that fibroblasts from the oldest donor carried a significantly increased abundance of lysosomes, and starvation enlarged lysosomes in all cultures, with the most expanded organelles in the 74- and 96-year-old cells. These enlarged lysosomes were unresponsive to autophagy induction: the 96-year-old fibroblasts showed the greatest basal lysosomal activity but failed to activate it further under starvation, unlike cells from younger donors. Consistent with overloaded, dysfunctional organelles, lipofuscin, the non-degradable autofluorescent pigment formed by incomplete lysosomal digestion, accumulated heavily in the oldest fibroblasts, and starvation could clear it in young cells but not in old ones.

The findings carry a clear therapeutic message. Rather than simply switching autophagy on, interventions in aging may need to target the final steps of the pathway: TFEB activators to stimulate lysosomal biogenesis through the CLEAR gene network, mTOR inhibitors such as rapamycin to restore flux, and lysosomal acidification enhancers, from small molecules to acidic nanoparticles, to boost enzymatic activity. The authors acknowledge that a single donor per age group limits generalizability, and future studies with additional donors will be needed to confirm whether late-stage autophagy impairment is a universal hallmark of fibroblast aging. But the core conclusion stands: in old human cells, the recycling plant’s opening hours are fine; it is the crusher at the end of the line that has broken down.

Subject of Research: Impaired autophagy flux and lysosome dysfunction in aged human fibroblasts

Article Title: Impaired autophagy and lysosome function in human fibroblast aging

Article References: Unzueta-Mendoza, J. J., García-Aguirre, I., Königsberg, M., Arrieta-Cruz, I., Lizcano-Meneses, S., Magaña, J. J., Alarcón-Aguilar, A., & Cisneros, B. (2026). Impaired autophagy and lysosome function in human fibroblast aging. Frontiers in Aging, 7, Article 1971981. https://doi.org/10.3389/fragi.2026.1971981

Image Credits: AI Generated

DOI: 10.3389/fragi.2026.1971981

Keywords: autophagy, lysosomes, TFEB, fibroblast aging, lipofuscin, autophagosome-lysosome fusion, LC3, p62, cellular recycling, aging biology, Impaired, lysosome

Autophagy is the cell’s housekeeping system, a process in which damaged proteins and organelles are engulfed in double-membraned vesicles called autophagosomes and delivered to lysosomes for destruction. Two molecular markers define this pathway: LC3, a protein that decorates the autophagosomal membrane, and p62, an adaptor that ferries ubiquitinated cargo to the growing autophagosome. The AAA-ATPase p97/VCP, meanwhile, is a hexameric molecular motor best known for extracting ubiquitinated proteins from cellular structures and handing them off to the proteasome or the autophagy machinery. Previous work by the same group had shown that blocking p97/VCP function in mouse Sertoli cells causes defective autophagosome maturation, cell cycle arrest, and apoptosis, making the protein a plausible candidate for regulating hormone-related protein turnover in these cells.

To test this idea, the researchers used the Sertoli 15P-1 cell line, a well-established mouse model derived through transmeiotic differentiation of male germ cells in culture. They exposed the cells to three pharmacological agents chosen for their opposing effects on autophagic flux. Testosterone served as the physiological ligand relevant to ABP regulation. Chloroquine, a lysosomotropic agent, blocks the fusion of autophagosomes with lysosomes, causing LC3 and p62 to accumulate because cargo can no longer be degraded. Rapamycin, by contrast, inhibits the mTOR signaling pathway and stimulates autophagy, accelerating the clearance of cellular components. Comparing the effects of these treatments allowed the team to infer whether ABP and p97/VCP travel together through the autophagic pipeline.

The experimental design combined three complementary techniques. Western blotting quantified protein expression levels across treatment groups, providing a biochemical readout of pathway activity. Single and double immunofluorescence staining revealed where p97/VCP, ABP, LC3, and p62 reside within the cells and, crucially, whether their locations overlap, a phenomenon called colocalization that suggests functional interaction. Finally, small interfering RNA (siRNA) transfection was used to specifically silence the gene encoding p97/VCP, creating a loss-of-function condition against which the drug treatments could be compared. This triangulation of methods strengthens the interpretation, because each approach has distinct limitations that the others can compensate for.

The Western blot results painted a picture consistent with autophagic involvement. p62 expression was highest in the group treated with both chloroquine and testosterone compared with the control siRNA condition, although the difference did not reach statistical significance. LC3 expression peaked in the chloroquine-treated group, again without reaching significance, which is the expected pattern when autophagic flux is blocked at the lysosomal step: autophagosomes accumulate because they cannot be cleared. As anticipated, the lowest expression of p97/VCP was detected in the VCPsi group, confirming that the siRNA transfection successfully knocked down the target protein and validating the loss-of-function arm of the study.

The immunofluorescence analyses delivered the study’s most striking findings. Significant differences in protein colocalization patterns emerged across all treatment groups, with one notable exception: p62 in rapamycin-treated samples showed no significant change. This pattern suggests that the physical association between p97/VCP and ABP shifts depending on the state of the autophagic machinery. When chloroquine jams the lysosomal bottleneck, proteins destined for degradation pile up and their colocalization with p97/VCP changes; when rapamycin revs up autophagy, the dynamics of interaction shift again. The authors report that these data provide the first evidence in the literature of a direct relationship between p97/VCP and ABP within Sertoli cells, a finding that reframes how scientists think about hormonal regulation in the testis.

Why does this matter for fertility? ABP’s job is to bind testosterone and maintain the extraordinarily high intratesticular concentrations that developing germ cells require. Disrupting ABP levels has measurable consequences: transgenic mice overexpressing ABP show meiotic arrest and germ cell apoptosis, and altered ABP expression has been linked to impaired sperm function in multiple models. If p97/VCP governs how quickly ABP is degraded, then the recycling motor effectively acts as a dial controlling how much ABP, and by extension how much bioavailable testosterone, is present in the seminiferous tubule environment at any given time. The data suggest a novel regulatory mechanism by which p97/VCP may influence spermatogenesis and male fertility through ABP degradation, offering a potential explanation for some forms of testicular dysfunction that currently lack a molecular diagnosis.

The implications extend well beyond the testis. ABP is not exclusive to Sertoli cells; it is also expressed in the brain, the liver, and the placenta, tissues where steroid hormone handling is equally critical. The authors propose that their work lays a foundational framework for future investigations in these ABP-expressing tissues, potentially linking p97/VCP expression to endocrine and pathophysiological disorders far removed from reproduction. Notably, p97/VCP has already been implicated in preeclamptic placenta, where altered expression coincides with impaired autophagy, and in testicular ischemia-reperfusion injury. Mutations in the VCP gene also cause multisystem proteinopathy, a devastating condition combining muscle, bone, and neurodegenerative disease, underscoring how central this protein is to cellular protein quality control across organ systems.

Technically, the study sits at the intersection of two major protein degradation systems. p97/VCP was originally identified as an ATPase co-purified with the inhibitor of NF-kappaB and the 26S proteasome, and it remains a linchpin of ubiquitin-proteasome-mediated degradation. But accumulating evidence shows that p97/VCP also cooperates with autophagy: in yeast, the orthologous Cdc48 protein regulates autophagosome biogenesis in concert with the ubiquitin-like protein Atg8, and in mammalian cells p97 inhibitors impair both ubiquitin-dependent and autophagic protein clearance. The p62 adaptor itself bridges the two systems, linking the autophagy pathway to the ubiquitin-proteasome system during the degradation of ubiquitinated proteins. The new findings place ABP squarely within this dual-disposal network in Sertoli cells.

As with any cell-line study, caveats apply. The statistical comparisons for p62 and LC3 did not reach significance, so the biochemical trends should be treated as suggestive rather than definitive, and the colocalization data, while significant, demonstrate proximity rather than direct biochemical binding. Follow-up work in primary Sertoli cells, intact seminiferous tubules, and animal models will be needed to confirm that the p97/VCP-ABP axis operates in vivo and to determine whether manipulating it can rescue fertility in disease settings. Nevertheless, by connecting a master regulator of protein homeostasis to a keystone hormone-binding protein, the study opens a concrete new avenue for research into male infertility, and it hints that therapies targeting autophagy, a strategy already being explored in fields from neurodegeneration to cancer, may one day find applications in reproductive medicine as well.

Subject of Research: Autophagic degradation of androgen-binding protein by p97/VCP in Sertoli cells and its implications for male fertility

Article Title: The Autophagic Interaction Between p97/VCP and ABP Protein Expressions in Sertoli Cell Line: the Effects of Chloroquine and Rapamycin

Article References: Corumluoglu, I., & Cayli, S. (2026). The Autophagic Interaction Between p97/VCP and ABP Protein Expressions in Sertoli Cell Line: the Effects of Chloroquine and Rapamycin. Reproductive Sciences. https://doi.org/10.1007/s43032-026-02231-3

Image Credits: AI Generated

DOI: 10.1007/s43032-026-02231-3

Keywords: p97/VCP, androgen-binding protein, autophagy, Sertoli cells, spermatogenesis, testosterone, chloroquine, rapamycin, male infertility, siRNA, LC3, p62

The research, led by Junrui Luo and Zhiqiang Liu at Henan Polytechnic University in Jiaozuo, China, focused on TRIM37, a member of the tripartite motif family of E3 ubiquitin ligases. These enzymes act as molecular quality-control agents, attaching small ubiquitin protein tags to specific target molecules, which then marks those targets for destruction or alters their behavior. TRIM37 had already been implicated in cancer development and in maintaining the health of centrioles, the barrel-shaped structures from which cilia are built. But its precise role in the assembly of primary cilia, a process biologists call ciliogenesis, had remained murky until now.

To probe that role, the team worked with two widely used laboratory cell lines: human retinal pigment epithelial cells, known as RPE1 cells, which are a standard model for studying cilia, and HK2 cells, a human kidney cell line. Both of these cell types normally grow prominent primary cilia when they exit the active cell cycle and settle into a quiescent state. When the researchers used RNA interference to knock down TRIM37 expression, they observed a striking effect: the fraction of cells that managed to grow cilia dropped significantly, and the cilia that did form were noticeably shorter than normal. Importantly, the team verified that this defect was not simply a side effect of altered cell cycle progression, ruling out one obvious alternative explanation.

A key clue to the mechanism came from the location of the protein itself. Using fluorescence microscopy, the researchers found that TRIM37 accumulates at the basal body, the modified centriole that anchors the cilium to the cell and serves as the gateway through which building blocks are ferried into the growing organelle. This strategic positioning suggested that TRIM37 might be doing more than just housekeeping at the cilium’s foundation. It hinted that the protein could be actively managing the local environment needed for ciliary assembly, possibly by coordinating the delivery or removal of materials at the base of the structure.

That suspicion led the investigators to autophagy, the cell’s internal recycling program. During autophagy, the cell engulfs damaged proteins and organelles in double-membraned vesicles called autophagosomes, which then fuse with lysosomes, the acidic compartments where the cargo is broken down and its components are returned for reuse. Autophagy has a complicated, two-sided relationship with cilia: at moderate levels it can help clear inhibitors of ciliary assembly, but excessive or insufficient autophagic activity can disrupt cilium formation. The researchers discovered that when TRIM37 was depleted, cells accumulated LC3-II, a lipidated form of a protein that decorates autophagosomal membranes, along with p62, also known as SQSTM1, a cargo receptor that shuttles tagged material into autophagosomes. At the same time, levels of Beclin1 and WIPI2, two proteins essential for launching the autophagy program, declined, indicating that the initiation of autophagy itself was being suppressed.

To determine whether the accumulated autophagic machinery was actually working, the team deployed bafilomycin A1, a toxin that blocks the final step of autophagy by preventing the acidification of lysosomes and the fusion of autophagosomes with them. By comparing autophagic flux, the complete throughput of the recycling pipeline, in the presence and absence of this blocker, the researchers confirmed that TRIM37-deficient cells suffered from genuine flux impairment. An independent immunofluorescence assay measuring the colocalization of LC3 with LAMP2, a lysosomal membrane protein, painted the same picture: autophagosome formation was reduced, and the fusion of autophagosomes with lysosomes was defective. In other words, losing TRIM37 did not merely slow the recycling line at one checkpoint; it jammed the entire conveyor belt.

The next question was whether TRIM37’s enzymatic activity, its ability to transfer ubiquitin tags, was required for these effects. The researchers performed functional complementation experiments, re-introducing TRIM37 variants into depleted cells and testing whether the protein could rescue normal cilium growth and autophagic balance. The results were unambiguous: only a version of TRIM37 with intact E3 ubiquitin ligase activity could restore normal ciliogenesis and autophagic homeostasis. A catalytically dead variant could not. This finding elevated TRIM37 from a passive structural component to an active enzymatic regulator whose chemical function is the linchpin of the whole process.

Having established that TRIM37’s ligase activity was essential, the team searched for the critical substrate and found it in p62, the very cargo receptor that had piled up in TRIM37-depleted cells. The experiments showed that TRIM37 directly mediates the ubiquitination of SQSTM1/p62, promoting its turnover and thereby keeping autophagic activity within the proper range. When TRIM37 is absent, p62 accumulates unchecked, and the resulting imbalance disrupts both the initiation of autophagy and the maturation of autophagosomes, which in turn sabotages the carefully choreographed process of cilium construction.

The most convincing demonstration of this regulatory axis came from a double-knockdown experiment. When the researchers simultaneously depleted both TRIM37 and SQSTM1/p62, the ciliogenesis defects and autophagic abnormalities caused by losing TRIM37 alone were substantially alleviated. This genetic epistasis experiment, a classic strategy for ordering genes into a pathway, showed that p62 acts downstream of TRIM37 and that removing the problematic accumulation of p62 can compensate for the loss of its regulator. Together, the findings define a novel TRIM37–SQSTM1/p62–autophagy signaling axis that modulates mammalian ciliogenesis, adding a new branch to the molecular regulatory network that biologists have been mapping for decades.

The implications of this work extend beyond basic cell biology. TRIM37 is already known as the gene mutated in mulibrey nanism, a rare inherited growth disorder, and its involvement in centriole maintenance and tumorigenesis has made it a subject of intense interest. By connecting this ubiquitin ligase to the autophagy machinery and to ciliary assembly, the study offers a mechanistic framework that could eventually inform research into ciliopathies, kidney disease, and cancers in which autophagy and ciliary signaling go awry. It also underscores a growing theme in modern cell biology: organelle construction is not an isolated program but an integrated process that depends on the cell’s recycling systems running at exactly the right tempo. As researchers continue to untangle the connections between ubiquitination, autophagy, and cilia, the TRIM37–p62 axis identified here provides a clear example of how a single enzymatic regulator can coordinate two fundamental cellular systems to build one of the cell’s most important sensory structures.

Subject of Research: Regulation of primary ciliogenesis by the E3 ubiquitin ligase TRIM37 through p62 ubiquitination and autophagy control

Article Title: Ciliogenesis is regulated by TRIM37 through ubiquitinating p62 and controlling the autophagy pathway

Article References: Luo, J., Zhang, X., Zhao, C., Zhang, Y., Chen, W., Wang, Z., Li, S., & Liu, Z. (2026). Ciliogenesis is regulated by TRIM37 through ubiquitinating p62 and controlling the autophagy pathway. Cellular and Molecular Life Sciences. https://doi.org/10.1007/s00018-026-06454-0

Image Credits: AI Generated

DOI: 10.1007/s00018-026-06454-0

Keywords: TRIM37, ciliogenesis, primary cilia, autophagy, p62, SQSTM1, ubiquitination, E3 ubiquitin ligase, basal body, autophagic flux, ciliopathies, cell biology

Noncoding RNAs have emerged over the past two decades as master regulators of gene expression. Unlike messenger RNAs, they do not encode proteins, yet they exert profound influence over which genes are switched on, silenced, or fine-tuned. Among them, circular RNAs, or circRNAs, form closed loop structures that resist degradation and often act as molecular sponges that sequester microRNAs. Long noncoding RNAs, or lncRNAs, participate in chromatin remodeling, transcriptional control, and scaffolding of regulatory complexes. Through the competing endogenous RNA, or ceRNA, hypothesis, circRNAs and lncRNAs can indirectly modulate protein output by titrating away miRNAs that would otherwise suppress target messenger RNAs. When those targets happen to be autophagy-related genes, the result is a potential regulatory network capable of dialing cellular self-digestion up or down during development. Precisely how such a network operates in the human fetal intestine had never been systematically explored.

The research team, led by Si Ying Li and corresponding author Yu Zuo Bai, approached the problem with an unusually comprehensive toolkit. They performed high-throughput sequencing on ten human fetal intestinal samples spanning 7 to 20 post-conception weeks, a period during which the gut undergoes dramatic morphological and functional transformation, from initial tube formation through epithelial differentiation and the onset of digestive capacity. By profiling the expression of autophagy-related circRNAs and lncRNAs across these developmental stages, the researchers could construct predicted regulatory networks linking each noncoding RNA to microRNAs, messenger RNAs, and ultimately the autophagy machinery itself. Expression was quantified in standardized units such as FPKM, fragments per kilobase of transcript per million mapped reads, allowing rigorous comparison across samples and time points.

The sequencing data revealed clear temporal dynamics: the population of autophagy-associated noncoding RNAs was not static but changed measurably as gestational age advanced, suggesting that different regulatory circuits dominate at different phases of intestinal maturation. Notably, the analysis identified multiple previously unreported noncoding RNAs in the fetal intestine, transcripts that had simply not been cataloged in this tissue before. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, together with protein-protein interaction mapping, helped situate these transcripts within biologically meaningful networks centered on lysosomal degradation, vesicle formation, and cellular remodeling. In effect, the study produced a developmental atlas of the RNA regulators that may govern how fetal intestinal cells recycle themselves as they differentiate.

Because predicted networks alone cannot demonstrate that autophagy is actually altered, the team turned to direct structural and protein-level evidence. Using transmission electron microscopy on intestinal duplication samples, rare congenital malformations in which a duplicated segment of bowel forms alongside the normal tract, the researchers observed autophagy-related ultrastructural alterations when compared with normal postnatal intestinal controls. Electron microscopy is the gold standard for visualizing autophagosomes, the double-membraned vesicles that engulf cellular cargo before delivery to lysosomes, and their altered abundance or morphology in the duplication samples pointed to genuine perturbation of the pathway in this developmental anomaly rather than a purely theoretical regulatory link.

Immunohistochemistry reinforced this conclusion with complementary protein markers. LC3B, the lipidated form of the LC3 protein that decorates mature autophagosomal membranes, was expressed at higher levels in the intestinal duplication group, while P62, also known as SQSTM1, an adaptor protein that accumulates when autophagic flux is impaired, was lower. The combination of elevated LC3B and reduced P62 provides a characteristic signature that helps distinguish between active flux and blocked degradation, and its presence in duplication samples suggests that autophagy is dynamically engaged in these malformations. Fluorescence in situ hybridization paired with immunofluorescence double staining then allowed the researchers to visualize, in intact tissue sections, the co-expression of core noncoding RNAs and their predicted target proteins, anchoring the computational networks to spatial reality within the developing gut wall.

What makes this work particularly compelling is the convergence of scales. At the transcriptomic level, the study captures thousands of noncoding RNA species rising and falling across thirteen weeks of development. At the ultrastructural level, electron micrographs show autophagic vesicles behaving differently in malformed versus normal tissue. At the protein level, immunostaining confirms that the canonical autophagy markers shift in the predicted directions. And at the cellular level, co-localization experiments place specific regulatory RNAs in the same cells as their presumed protein targets. This multi-layer validation strategy is exactly what the ceRNA field has often been criticized for lacking, and it lends substantial credibility to the predicted networks the authors constructed.

The clinical implications extend beyond basic developmental biology. Intestinal duplications are congenital anomalies whose molecular origins remain poorly understood, and this study is among the first to implicate dysregulated autophagy, and the noncoding RNAs that may regulate it, in their pathogenesis. If specific circRNAs or lncRNAs prove to be causally involved rather than merely correlated, they could become diagnostic biomarkers identifiable in prenatal screening or, more speculatively, therapeutic targets capable of modulating autophagic flux during critical windows of organogenesis. The authors themselves frame their findings as a foundation for future studies of embryonic developmental disorders, a deliberately measured claim that reflects both the promise and the preliminary nature of the work.

There are, of course, important caveats. The sample size of ten fetal intestinal specimens, while substantial for human prenatal tissue, which is ethically and logistically difficult to obtain, still limits statistical power and generalizability. The regulatory networks are predictive, built on established miRNA-target databases and expression correlations, and ceRNA interactions in particular require functional validation through perturbation experiments before they can be considered proven mechanisms. The comparison of fetal duplication tissue with postnatal controls also introduces an age difference that the authors acknowledge through their careful design, but developmental stage remains a variable that future work will need to disentangle. Ethical oversight was rigorous, with approval from the Ethics Committee of China Medical University and written informed consent from all participants, and the study was supported by the National Natural Science Foundation of China and the Liaoning Province Science and Technology Plan Joint Project.

Even with these limitations, the study marks a significant advance. It demonstrates that the noncoding RNA dimension of autophagy regulation is active and dynamic during precisely the developmental window when the human intestine acquires its structure and function, and it delivers a catalog of novel fetal intestinal transcripts that other labs can now interrogate. As single-cell sequencing and functional perturbation technologies continue to mature, this atlas provides the scaffolding on which causal studies can be built. For now, the work stands as a vivid reminder that the blueprint of human development is written not only in protein-coding genes but in the vast, looping, and still largely mysterious world of noncoding RNA, and that the cellular recycling system it governs may hold clues to some of the earliest origins of congenital intestinal disease.

Subject of Research: Autophagy-related noncoding RNA regulation during human prenatal intestinal development

Article Title: Dynamic expression of noncoding RNAs associated with autophagy-related genes in the human intestine during prenatal development

Article References: Li, S. Y., Wu, M. Y., Liu, S. T., Wang, C. Y., Tang, X. B., & Bai, Y. Z. (2026). Dynamic expression of noncoding RNAs associated with autophagy-related genes in the human intestine during prenatal development. BMC Genomics. https://doi.org/10.1186/s12864-026-13403-5

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13403-5

Keywords: autophagy, noncoding RNAs, circRNA, lncRNA, miRNA, fetal intestine, prenatal development, intestinal duplication, RNA sequencing, ceRNA, LC3B, P62

Ubiquitin is a small protein tag that cells attach to other proteins to change their fate, and the way ubiquitin molecules are linked together matters enormously. Whereas K48-linked chains typically condemn proteins to destruction by the proteasome, K63-linked chains serve a very different purpose: they orchestrate protein interactions, intracellular trafficking, and signaling activity without triggering degradation. UBE2N, also known as Ubc13, is the specialized E2 enzyme that builds these K63-linked chains, and its role in MASH had remained almost entirely unexplored until now.

The researchers began by examining liver tissue from both human patients and mouse models of MASH, and they found a consistent pattern: UBE2N was markedly downregulated in hepatocytes under metabolic stress. Digging into the mechanism, they identified THAP11 as a transcriptional repressor that binds the UBE2N promoter during disease progression, effectively silencing the enzyme as fatty acids accumulate. Single-nucleus RNA sequencing and digital spatial transcriptomics confirmed that this drop in UBE2N expression is specifically concentrated in hepatocytes rather than other liver cell types.

To establish causality, the team generated mice lacking Ube2n selectively in hepatocytes. When these animals were placed on a western diet, they developed dramatically worse MASH and liver fibrosis than their normal counterparts. Serum liver enzymes rose, inflammatory and fibrogenic genes were upregulated, and the livers showed extensive fat accumulation and scarring. Crucially, when the researchers overexpressed UBE2N in the liver, the pathological phenotypes reversed and hepatic homeostasis was largely restored, demonstrating that the enzyme is not merely a bystander but an active protector.

The mechanism underlying this protection turned out to involve two intimately connected processes: mitophagy and PANoptosis. Mitophagy is the cellular quality-control system that identifies damaged mitochondria and delivers them to lysosomes for degradation, preventing the release of inflammatory mitochondrial contents. PANoptosis, by contrast, is a recently defined form of inflammatory programmed cell death that combines features of pyroptosis, apoptosis, and necroptosis simultaneously, unleashing a potent inflammatory storm. The new study shows that when UBE2N is lost, mitophagy collapses and PANoptosis erupts, creating the destructive combination that drives MASH forward.

At the molecular level, the researchers traced how UBE2N keeps mitophagy running smoothly. Working with the PARKIN pathway, they found that UBE2N catalyzes K63-linked ubiquitination of p62, also known as SQSTM1, at a specific site, lysine 420. This modification acts as a trafficking signal, promoting the translocation of K63-tagged p62 into damaged mitochondria where it serves as an autophagy receptor, tethering the cargo to the autophagic machinery for clearance. In cells lacking UBE2N, this modification fails to occur, p62 fails to reach the mitochondria, and damaged organelles accumulate unchecked.

But the story has an unexpected twist. When p62 cannot reach mitochondria, it accumulates in the cytoplasm, and this cytoplasmic buildup has consequences of its own. The researchers found that cytoplasmic p62 aggregation drives hyperactivation of NRF2, a transcription factor normally considered protective against oxidative stress. While NRF2 activation is beneficial in moderation, the study demonstrates that excessive, sustained NRF2 signaling in this context actively promotes PANoptosis and worsens liver damage. This finding challenges the simplistic view of NRF2 as an unambiguously protective factor in liver disease.

To prove that p62 accumulation is truly the culprit, the team generated mice lacking both Ube2n and Sqstm1 in hepatocytes. Remarkably, this additional deletion substantially mitigated the severe liver pathology caused by Ube2n loss alone, confirming that the damaging effects of UBE2N deficiency flow largely through cytoplasmic p62 buildup. The result establishes p62 as a proof-of-concept therapeutic target: if its cytoplasmic accumulation can be prevented or its mitochondrial routing restored, the downstream cascade of NRF2 hyperactivation and PANoptosis might be interrupted.

The implications extend beyond basic biology. MASH currently affects hundreds of millions of people worldwide, and only recently did the first targeted therapy, the thyroid hormone receptor-beta agonist resmetirom, gain approval. The identification of UBE2N and the p62 trafficking pathway offers an entirely new axis for intervention, one that operates at the level of mitochondrial quality control rather than lipid metabolism alone. Hepatic targeting of Ube2n in the mouse models prevented western diet-induced MASH progression, suggesting that gene-based or small-molecule approaches aimed at restoring this pathway could be feasible.

There remain significant challenges before this biology can be translated into treatments. UBE2N participates in immune receptor signaling and skin homeostasis, so systemic manipulation carries risks of off-target effects, and the precise dose, timing, and delivery method for hepatic intervention would need careful optimization. Nonetheless, the study provides an unusually complete mechanistic arc, from a transcriptional repressor silencing a ubiquitin enzyme, through defective mitochondrial tagging and cytoplasmic protein aggregation, to inflammatory cell death and fibrosis, and it does so with consistent evidence from human tissue, mouse genetics, and cell biology. For a field desperate for new molecular handles on a growing epidemic, UBE2N and its p62-dependent pathway represent one of the most compelling new entries in years.

Subject of Research: Role of UBE2N-regulated p62 mitophagy and PANoptosis in metabolic dysfunction-associated steatohepatitis

Article Title: UBE2N deficiency contributes to MASH development via p62-regulated mitophagy and PANoptosis

Article References: Wang, F., Lee, J., Park, J.-S., Huang, M., Ma, H., Sui, G., Zhou, Z., Matsuda, M., Kim, S. Y., Tsuchiya, T., Wu, X., Lee, H., Oh, S., Park, H., Lim, K.-H., Park, C.-W., Han, S.-B., Hong, J. T., Karin, M., … Seki, E. (2026). UBE2N deficiency contributes to MASH development via p62-regulated mitophagy and PANoptosis. Nature Metabolism, 8(9), 1926-1947. https://doi.org/10.1038/s42255-026-01590-0

Image Credits: AI Generated

DOI: 10.1038/s42255-026-01590-0

Keywords: UBE2N, MASH, p62, SQSTM1, mitophagy, PANoptosis, K63-linked ubiquitination, PARKIN, NRF2, THAP11, liver fibrosis, Nature Metabolism

Mitophagy, the selective autophagic degradation of mitochondria, is a fundamentally protective process. By wrapping damaged organelles in autophagosomal membranes and delivering them to lysosomes for destruction, the cell prevents the accumulation of dysfunctional mitochondria that would otherwise poison it from within. In the liver, this process is particularly important because hepatocytes are continuously exposed to fatty acids, inflammatory cytokines and oxidative stress in conditions such as obesity and insulin resistance. Previous work has established that impaired mitochondrial homeostasis contributes to the initiation and progression of hepatic injury, and that defects in mitophagy are associated with the transition from simple steatosis to the inflammatory, fibrotic state that defines steatohepatitis. What has been missing is a clear mechanistic picture of the decision point at which a damaged mitochondrion is routed toward degradation rather than allowed to trigger cell death pathways.

Wang and colleagues addressed this question by focusing on ubiquitin signaling, the cellular language by which proteins are tagged for different fates. Ubiquitination involves the sequential action of activating enzymes, conjugating enzymes and ligases, and the identity of the ubiquitin chain, together with the substrate that carries it, encodes instructions that are read by autophagy receptors and other effector proteins. UBE2N, also known as Ubc13, is an E2 conjugating enzyme with a well-documented role in catalyzing the assembly of lysine 63-linked ubiquitin chains, a chain type classically associated with signaling rather than proteasomal degradation. Through its pairing with specialized E2 variant proteins, UBE2N builds K63-linked chains on substrate proteins that regulate inflammatory pathways, DNA damage responses and, as the new study demonstrates, autophagic cargo recognition.

The central discovery reported in the study is that UBE2N-mediated ubiquitination of p62, an autophagy receptor also known as sequestosome-1, acts as the switch between protective mitophagy and pathogenic cell death in hepatocytes. p62 is a multi-domain adaptor protein that simultaneously binds ubiquitin chains through its ubiquitin-associated domain and LC3, a core component of the autophagosomal membrane, through its LC3-interacting region. In doing so, p62 physically links ubiquitinated cargo, including damaged mitochondria, to the autophagic machinery. The canonical mitophagy pathway, which depends on the mitochondrial kinase PINK1 and the E3 ubiquitin ligase Parkin, works by ubiquitinating outer mitochondrial membrane proteins on depolarized mitochondria, after which receptors such as p62 help orchestrate the recruitment of phagophores. K63-linked chains generated by UBE2N had previously been implicated in autophagic clearance of protein aggregates and intracellular bacteria, but their role in mitochondrial quality control in the liver had not been defined.

By demonstrating that UBE2N directly modifies p62 with K63-linked ubiquitin chains, the study reveals an unexpected regulatory layer upstream of receptor-mediated cargo recognition. When UBE2N is active, ubiquitinated p62 is competent to engage damaged mitochondria and shepherd them into autophagosomes, preserving mitochondrial integrity and hepatocyte survival. When UBE2N activity is lost or suppressed, this routing fails: damaged mitochondria persist, their dysfunction amplifies, and the balance of cellular decision-making tips away from autophagic repair and toward cell death programs. In the context of MASH, where hepatocytes are chronically assaulted by lipotoxic stress and inflammatory signaling, this tipping point is the difference between adaptation and injury. The study’s framing of UBE2N as a molecular switch is therefore not merely metaphorical; it reflects a mechanistic bifurcation in which a single enzymatic activity determines the fate of both the organelle and the cell.

The pathological consequences of losing this switch were made evident in experimental models of metabolic dysfunction-associated steatohepatitis. MASH is characterized histologically by hepatic steatosis, lobular inflammation, hepatocyte ballooning and, in advanced stages, fibrosis. It is the progressive, inflammatory form of metabolic dysfunction-associated steatosis, formerly known as nonalcoholic fatty liver disease, and it affects a substantial and growing fraction of the global population in parallel with rising rates of obesity and type 2 diabetes. Current therapeutic options remain limited, and there is intense interest in identifying the intracellular quality-control pathways whose failure drives disease progression. The new findings place mitochondrial quality control, and specifically the ubiquitin code that governs it, at the center of that pathology, suggesting that defects in UBE2N-dependent signaling could contribute to why some patients progress from fatty liver to inflammatory, fibrotic disease while others do not.

Beyond the immediate findings, the study connects to a rich literature on mitophagy receptors and their regulation. p62 was first characterized as a scaffold in NF-kappaB signaling and later recognized as a prototypical selective autophagy receptor, with roles in the clearance of ubiquitinated protein aggregates, peroxisomes and mitochondria. The PINK1-Parkin pathway, whose discovery grew out of genetic studies of familial Parkinson’s disease, relies heavily on ubiquitin chain amplification on the mitochondrial surface, and adaptor proteins such as p62, NDP52 and OPTN translate that ubiquitin signal into autophagosome engagement. What Wang and colleagues add is the identification of the enzyme that licenses p62 itself, effectively placing UBE2N upstream of the receptor that all downstream mitophagy depends upon. This is conceptually significant because it suggests that modulating a single E2 enzyme could, in principle, tune the entire receptor-mediated mitophagy apparatus in hepatocytes.

The therapeutic implications are worth considering carefully. Pharmacological activation of mitophagy has long been proposed as a strategy for neurodegenerative disease, and the same logic applies to the liver, where boosting the clearance of dysfunctional mitochondria could interrupt the feed-forward loop of oxidative stress, inflammation and cell death that drives MASH progression. If UBE2N activity, or the K63-linked ubiquitination of p62 that it catalyzes, can be selectively enhanced, it may be possible to restore mitochondrial quality control in diseased livers without broadly suppressing inflammation or interfering with other ubiquitin-dependent processes. Conversely, the study serves as a caution: because UBE2N participates in innate immune signaling pathways, including the assembly of signaling complexes downstream of pattern-recognition receptors, any therapeutic manipulation would need to be calibrated to avoid unintended immunological consequences. The specificity of the p62-UBE2N interaction identified in the study may offer a route to such targeted intervention.

From a basic science perspective, the work also raises questions that will likely shape the field in the coming years. Which E3 ubiquitin ligase partners with UBE2N to decorate p62 with K63-linked chains? Is this modification reversible by deubiquitinating enzymes, and if so, do those enzymes represent additional nodes of regulation? How is the UBE2N-p62 axis coordinated with PINK1-Parkin activity at the mitochondrial surface, and does lipotoxic stress directly modulate UBE2N expression or localization in hepatocytes? Answering these questions will require the kind of integrated biochemical, cell biological and in vivo approach that the current study exemplifies, and the answers will determine how quickly the switch concept can be translated into clinical practice.

For now, the message of the new Nature Metabolism study is clear and consequential: hepatocyte survival in metabolic liver disease hinges on a ubiquitin-driven decision, and UBE2N sits at the fulcrum. By flipping that switch toward mitophagy, cells protect themselves; when the switch fails, the same mitochondria that once powered the cell become instruments of its destruction. As rates of MASH continue to climb worldwide, understanding and ultimately manipulating this switch may prove to be one of the more promising avenues for protecting the livers of millions of patients.

Subject of Research: The role of UBE2N-mediated ubiquitination of p62 in regulating mitophagy versus cell death in metabolic dysfunction-associated steatohepatitis (MASH).

Article Title: UBE2N flips the switch on for mitophagy and off for MASH

Article References: Madigan, E. D., Matos, S. L., & Jurczak, M. J. (2026). UBE2N flips the switch on for mitophagy and off for MASH. Nature Metabolism. https://doi.org/10.1038/s42255-026-01604-x

Image Credits: AI Generated

DOI: 10.1038/s42255-026-01604-x

Keywords: UBE2N, mitophagy, MASH, p62, ubiquitination, hepatocytes, liver disease, mitochondria, autophagy, K63-linked ubiquitin chains, metabolic dysfunction-associated steatohepatitis, PINK1-Parkin