Acute kidney injury (AKI) remains a major clinical challenge, characterized by a rapid decline in glomerular filtration rate, accumulation of metabolic waste, and disruption of fluid and electrolyte homeostasis. Worldwide, AKI affects up to 20% of hospitalized patients and carries a high mortality rate in its most severe forms (Susantitaphong et al., 2013; Kellum et al., 2021). Even when patients survive the initial injury, AKI is known to result in incomplete recovery with respect to renal function. Even a single episode of AKI predisposes many and accelerates the progression of chronic kidney disease (CKD), resulting in diminished quality of life for patients (Ishani et al., 2009; Zuk and Bonventure, 2019; Kurzhagen et al., 2020). This creates a pressing need for interventions that foster true renal regeneration rather than merely mitigating acute damage.

Mammalian kidneys, including those of humans and mice, often possess a limited capacity for regeneration/healing post-injury. After AKI, repair mechanisms in these systems predominantly involve proliferation of surviving tubular epithelial cells and activation of fibrotic pathways, rather than the de novo nephron formation, or neonephrogenesis (Yang et al., 2010; Jin et al., 2020; Yu and Bonventre, 2020). As a result, traditional mammalian models, while invaluable for understanding injury pathways and development of novel therapeutics, fall short in revealing the molecular programs that underpin full structural and functional restoration of renal tissue.

In contrast to these traditional mammalian models, the spiny mouse (Acomys) has the unique ability to regenerate renal tissue among others, without developing fibrotic/scarred tissue in comparison to traditional laboratory mice (Jiang et al., 2019; Okamura et al., 2021). Upon injury via unilateral ureter obstruction, the spiny mouse downregulates profibrotic cytokines in comparison to C57/BL6 counterparts (Okamura et al., 2021).

Other, non-mammalian models such as the zebrafish (Danio rerio) and the axolotl (Ambystoma mexicanum) have also provided crucial insights into regeneration. Zebrafish have greatly emerged as a powerful, high-throughput model for studying kidney regeneration as adult zebrafish are capable of robust epithelial repair within individual nephrons which occurs concomitantly with neonephrogenesis (Zhou et al., 2010; Diep et al., 2011; McCampbell et al., 2015; Brilli et al., 2019; Liu et al., 2023). These parallel processes ensure rapid recovery from catastrophic organ damage. While there have been a number of advances in understanding the underlying molecular mechanisms that accomplish neonephrogenesis, the process is still not completely understood (Chiba et al., 2016; Brilli et al., 2019; Liu et al., 2023; He et al., 2025).

Research using the axolotl, a neotenic salamander, is in its infancy (Chen et al., 2023). However, theaxolotl model has a long history of utility for studying mechanisms of vertebrate regeneration due to their ability to replace complex body parts such as their limbs, tail, spinal cord, lenes and brain, with recent studies exacting cellular niches with differential expression patterns (Wigmore and Holder, 1985; Lust et al., 2022).

As a whole, high-throughput transcriptomic profiling has greatly enhanced our understanding of the transcriptional networks driving injury response, repair, and development in the kidney (Lindström et al., 2021; Luft, 2021; Hinze et al., 2022; Creed et al., 2024). Notably, the recent meta-analysis conducted by Abdank et al. systematically compared transcriptomic signatures across multiple human and mouse AKI studies, uncovering conserved and species-specific injury markers (Abdank et al., 2024).

Despite these advances, comparative studies have yet to incorporate zebrafish, spiny mouse, and axolotl into a unified cross-species meta-analysis. To address this gap, our study builds upon the foundational work of Abdank et al. by integrating recently published RNA-seq datasets of zebrafish, spiny mouse, and axolotl kidney regeneration with two human and two murine AKI datasets (Okamura et al., 2021; Chen et al., 2023; He et al., 2025). While we were unable to match injury methodologies across all species, due to species specific limitations when using aquatic-based animal models, we hope to highlight conserved transcriptional patterns found in regenerating tissues (with some commentary at the single cell level) as well as explore the transcriptional landscape across species in AKI and its subsequent recovery process across species and notable injury models.

This study expands the cross-species analysis of acute kidney injury (AKI) by incorporating transcriptomic data from three species capable of renal regeneration: zebrafish, axolotl, and spiny mouse, into a comparative framework that previously centered on human and murine models (Abdank et al., 2024). Through this expanded analysis, we reveal patterns of both conserved and divergent gene expression across species in response to kidney injury and recovery, underscoring the complexity and heterogeneity of renal repair programs across species/models used in AKI studies.

Our findings reinforce the notion that regenerative species employ transcriptional programs that are distinct from those observed in traditional mammalian models. Notably, zebrafish, axolotl, and spiny mouse share a set of 19 genes that are differentially expressed during AKI, two of which are associated with apolipoproteins, items necessary for cholesterol maintenance (APOA1 and APOB). Subsequent GO enrichment of these 19 genes suggests that modulation of lipid handling and membrane repair may play a pivotal role in enabling regeneration. This comes as apolipoprotein-L1 (APOL1) has become of great interest in the nephrology community as genetic mutations in APOL1 are associated with CKD progression in humans, especially in individuals of African descent (Genovese et al., 2010; Privratsky et al., 2020). With respect to APOA1 and CKD, patients with higher serum levels of APOA1 have been associated with lower prevalence of CKD (Goek et al., 2012). In zebrafish, apoa1a has been investigated in larvae as a regulator or renal function, where loss of apoa1 was associated with limited renal clearance of a sugar-fluorophore conjugate (Kotb et al., 2016). In axolotl, apolipoproteins (notably apoeb), have been shown to be upregulated in (primarily) cells with hematopoietic lineages during the wound repair process in limb amputation, a similar trend to which we present, where apoeb is upregulated in the axolotl AKI response (Leigh et al., 2018). In contrast, both zebrafish and spiny mouse show downregulation of APOB and APOA1 in the AKI context.

In our analysis of transcripts that are uniquely shared between recovery in the spiny mouse and recovery in zebrafish, we find the cell cycle regulator CDKN1A to be downregulated in both species. In the (human) AKI setting, we also found CDKN1A to be upregulated in fenestrated endothelium, suggesting a role of the kinase in the vasculature-based injury response in mammals (Basile et al., 2001; Maringer and Sims-Lucas, 2016). In a cross-species cisplatin induced AKI model, CDKN1A downregulation was found to be associated with increased cell viability and decreased presence of ferroptosis markers (Gao et al., 2024). In a mouse IRI (ischemia reperfusion injury) based transcriptomic analysis, Cdkn1a expression was found to be upregulated post injury (He et al., 2022). This suggests a potential for innate responses to injury in these species allowing for suppression of canonical injury responses to aid in the process of regeneration, albeit in a species-specific manner. Notably, in the adult axolotl pancreas, Cdkn1a is naturally downregulated in comparison to human CDKN1A, but shares a similar differential expression pattern to the mouse (Mus) Cdkn1a (Ma et al., 2025). Also interestingly, we found that LEFTY1/2 were both downregulated in spiny mouse and zebrafish in the ‘recovery’ stage. Supplementation of Lefty-1 in mice has been associated with a decrease in sustained injury post AKI, and has been postulated to be modulator of the immune response after injury (Xu et al., 2016; Zhang et al., 2018). With respect to GO terms associated with genes associated with both spiny mouse/zebrafish AKI, we find that, perhaps unsurprisingly, immune responses to injury, are common, with varied leukocyte properties being highlighted. Of note in immune related responses to injury, CCL2 was found to be downregulated in the spiny mouse while upregulated in zebrafish. In a skin-based spiny mouse study, Acomys Ccl2 was found to have no differential expression in comparison to other Mus species, which had upregulated Ccl2 in response to injury of the outer-ear skin (Gawriluk et al., 2020). In our analysis of human single-cell resolution data, we found that CCL2 was upregulated in endothelial populations post-injury, an idea consistent with Kirita et al., where they demonstrated endothelial cells play a role in early injury repair via CCL2 secretion (Kirita et al., 2020).

In our investigation of genes differentially expressed across all five species analyzed in this study, we found a perhaps unsurprising lack of homology across all species, with mouse and human being the most homologous in both the AKI and Health settings. From our analysis of these top differentially expressed transcripts we find evidence of homology and heterogeneity between species with regenerative capacity and those without. In the analysis of SERPINA1, a serine protease inhibitor, we find that axolotl and humans have differing expression patterns, while the spiny mouse has a similar expression pattern to that of humans (downregulation). Differing SERPINA1 expression levels has promise as a marker in those undergoing treatment for diabetic kidney disease (Ahluwalia et al., 2024). Of the isoforms of SERPINA1, transcripts derived from latter portion of the first exon are disproportionately expressed in the kidney, with respect to upstream regions of the coding region (Matamala et al., 2015). Another example of homology across species of differing regenerative capacity can be found in LCN2, with human, mouse, and spiny mouse all showing downregulation of the transcript. In the mouse, inhibition of LCN2 can lead to exacerbation of phenotypes in unilateral ureteral obstruction models (Qiu et al., 2018). Interestingly, these same results from Qiu et al. show that Lcn2 accumulates after UUO injury, a finding at odds with the IRI injuries in which were used to generate the data analyzed within this study (Qiu et al., 2018).

In our complimentary analysis, where we surveyed highly differentially expressed transcripts in recovery across ‘injury’ and ‘health’, we find relative homology in genes such as GPX3, where GPX3 is upregulated in recovery and in the post-injury paradigm in the human, zebrafish, and mouse (Mus) models, while (slightly) downregulated in axolotl. When we refined our lens to look at cellular level expression pattern changes in the AKI model, GPX3 was found to be upregulated in proximal tubule populations, perhaps unsurprisingly, as the proximal tubule is the primary source of GPX for the body, and has been implicated as having a protective role in other ailments (Avissar et al., 1994; Tham et al., 2002; Olson et al., 2010) In rat, Gpx3 has been validated as a marker for ischemia-reperfusion injuries, the injury model used in the mouse studies analyzed in this analysis (Pei et al., 2023). In an earlier IRI study, also using rat, Gpx3 was downregulated, demonstrating further transcription level divergence across animal models (Wu et al., 2023). We also once again find a re-emergence in our analysis of SERPINA1 and SERPINA10, where the markers are downregulated in both the AKI and recovery paradigms in the spiny mouse, while being upregulated in the AKI paradigm in axolotl. Finally we look to MT1G, which was unregulated during incomplete recovery in mice (Mus) and in healthy states in both mammals but was not differentially expressed in zebrafish, suggesting a perhaps nuanced, but not mammalian specific role in renal repair or homeostasis. However, in ccRCC, MT1G has been implicated in having a potential protective role from ferroptosis via negative regulation of glutathione metabolism (Zhang et al., 2022).

In our mixed models approach at surveying global trends in transcriptional alterations in the AKI model, we found that epidermal growth factor (EGF) to be significantly downregulated. EGF has previously been indicated as a regulator of recovery in the post-AKI setting, but has also been notably characterized as a marker for CKD progression (Chen et al., 2012; Ju et al., 2015; Klein et al., 2016). With respect to recovery-associated transcripts, we found that DUSP2 was upregulated, an interesting contrast to its upregulation in the ‘injury’ model. In mice, loss of DUSP2 was associated with exacerbation of AKI phenotypes, while gain of expression lessened injury (Xiong et al., 2022). Interestingly within this recovery set, we find significant upregulation of PER1. PER1, one of the key regulators of the circadian rhythm, has only recently been appreciated, along with other circadian rhythm associated transcripts, as having a dynamic and vital role in renal health (Douma et al., 2022; Zietara et al., 2022; He et al., 2025)

To better characterize zebrafish-specific transcriptional responses, we performed GO enrichment analysis on transcripts uniquely upregulated or downregulated during zebrafish AKI. These analyses revealed involvement of pathways related to lipid metabolism, steroid processing, and prostaglandin signaling. Notably, prostaglandin signaling has been of great interest in both renal regeneration and development in zebrafish, as well as in humans (Nørregaard et al., 2015; Poureetezadi et al., 2016; Liu et al., 2023). In a follow up of these zebrafish-specific transcriptional regulators, we also find that these genes found in the AKI response can also be found to have dynamic expression patterns in development. This comes at no surprise, as previous studies have shown that transcriptional regulators of renal development can play active roles in AKI (Wingert et al., 2007; Chiba et al., 2015; Yang et al., 2023).

In conclusion, our findings emphasize the value of incorporating non-traditional model organisms into AKI studies. These regenerative species not only reveal conserved pathways that may be critical for repair but also uncover alternative strategies that can inform new approaches. Future studies integrating spatial transcriptomics and proteomics across all species will only further expand our understanding of the cellular and molecular basis of kidney regeneration.