Hui Liu

In the published article, there was an error in Figure 2D as published. During the revision process, Figure 2 was updated; however, an earlier version of panel 2D was inadvertently reinserted during the final production stage after revision. This error originated from a version mix-up at the time of revised submission and was carried over to the final proof. The corrected Figure 2 and its caption appear below.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated. PAGE \* Arabic \* MERGEFORMAT 3 Figure 6. TANK expression is positively correlated with CD163, CD11b, PD-1, PD-L1, CD40, STAT3 and HIF1A expression in glioma. As surface markers of M2 macrophages and neutrophils, IHC shows that CD163 and CD11b are positively correlated with the expression of TANK (CD163, Spearman r = 0.342, P < 0.05; CD11b, Spearman r = 0.360, P < 0.05). As important immunosuppressive molecules, PD-1, PD-L1 and CD40 expression increased with the increase of TANK expression (PD-1, Spearman r = 0.293, P < 0.05; PD-L1, Spearman r = 0.316, P < 0.05; CD40, Spearman r = 0.338, P < 0.05). TANK was found to be positively related to HIF1A expression (Spearman r = 0.450, P < 0.05), a core molecule of the hypoxiainduced signaling pathway, and STAT3 (Spearman r = 0.503, P < 0.05), a key molecule of IL6/STAT3 signaling pathway.

Pigmentation varies widely across humans and is shaped by melanin quantity, type, and spatial distribution. Retinal pigmentation protects against light-induced damage, yet its genetic and evolutionary bases remain unclear. We developed a deep learning framework (DeepGRP) to quantify retinal pigmentation from high-resolution fundus images and conducted a genome-wide association study (GWAS), identifying 42 signals, including 26 previously unidentified loci, with single-nucleotide polymorphism–based heritability of 21.4%. Single-nucleus assay for transposase-accessible chromatin by sequencing and RNA sequencing of human fetal retinal tissues revealed key cellular contributors, including retinal pigment epithelium and photoreceptor cells. Among candidate genes, ARHGAP18 emerged as a previously unrecognized regulator of melanogenesis. Evidence of polygenic adaptation in Europeans suggests selection driven by snow-reflected light at high latitudes. A polygenic risk score for retinal pigmentation correlated with a 4.8-fold higher risk of myopia and a 1.5-fold lower risk of skin cancer. These findings demonstrate the power of deep learning for large-scale ocular phenotyping and reveal insights into the genetic and evolutionary architecture of retinal pigmentation.

Restoring retinal pigment epithelium (RPE) cells is crucial for treating retinal degenerative (RD) diseases, with chemical reprogramming offering a transformative, scalable solution. However, identifying key chemical compounds for generating functional RPE cells from somatic cells remains challenging. Here, we present a two-step chemical reprogramming strategy to convert fibroblasts into functional chemical induced RPE (ciRPE) cells. Leveraging the Single-Cell Reprogramming Compound Finder (scRCF), which integrates transcriptomics-guided predictions with advanced screening, we identified chemical cocktails that precisely reprogram fibroblasts through an intermediate state into ciRPE cells. These ciRPE cells closely mimic the structure and function of native RPE cells, and upon transplantation into RD rats, they seamlessly integrate into host tissue, protect photoreceptors, and restore visual function. Omics and mechanistic analyses revealed that the identified compounds synergistically activate core transcription factors, including Ascl1 and Olig2, orchestrating the reprogramming process. This study provides a scalable, non-integrative approach for generating functional RPE cells, offering a promising strategy for cell replacement therapies targeting RD diseases.

Human retinal stem cells hold great promise in regenerative medicine, yet their existence and characteristics remain elusive. Here, we performed single-cell multiomics and spatial transcriptomics of human fetal retinas and uncovered a cell subpopulation, human neural retinal stem-like cells (hNRSCs), distinct from retinal pigment epithelium stem-like cells and traditional retinal progenitor cells. We found that these hNRSCs reside in the peripheral retina in the ciliary marginal zone, exhibiting substantial self-renewal and differentiation potential. We conducted single-cell and spatial transcriptomic analyses of human retinal organoids (hROs) and revealed that hROs contain a population of hNRSCs with similar transcriptional profiles and developmental trajectories to hNRSCs in the fetal retina potentially capable of regenerating all retinal cells. Furthermore, we identified crucial transcription factors, such as MECOM , governing hNRSC commitment to neural retinogenesis and regulating repair processes in hROs. hRO-derived hNRSCs transplanted into the rd10 mouse model of retinitis pigmentosa differentiated and were integrated into the retina, alleviated retinal degeneration, and improved visual function. Overall, our work identifies and characterizes a distinct category of retinal stem cells from human retinas, underscoring their regenerative potential and promise for transplantation therapy.

Human retinal stem cells hold great promise in regenerative medicine, yet their existence and characteristics remain elusive. Here, we preformed single-cell multi-omics and spatial transcriptomics of human fetal retinas and uncovered a novel cell subpopulation, human neural retinal stem-like cells (hNRSCs), distinct from RPE stem-like cell and traditional retinal progenitor cells. These hNRSCs reside in the peripheral retina within the ciliary marginal zone, exhibiting substantial self-renewal and differentiation potential. We conducted single-cell and spatial transcriptomic analysis of human retinal organoids (hROs), and revealed hROs have remarkable similar hNRSCs consistent with fetal retina, capable of regenerating all retinal cells. Furthermore, we identified crucial transcription factors, notably MECOM, governing hNRSC commitment to neural retinogenesis and regulating hROs regeneration. Transplanting hRO-derived hNRSCs into the rd10 mouse of rapid retinal degeneration significantly repairs the degenerated retina and restores visual function. Together, our work identifies and characterizes a unique category of retinal stem cells from human retinas, underscoring their regenerative potential and promise for transplantation therapy.

Background: Glioma, the most prevalent malignant intracranial tumor, poses a significant threat to patients due to its high morbidity and mortality rates, but its prognostic indicators remain inaccurate. Although TRAF-associated NF-kB activator (TANK) interacts and cross-regulates with cytokines and microenvironmental immune cells, it is unclear whether TANK plays a role in the immunologically heterogeneous gliomas. Methods: TANK mRNA expression patterns in public databases were analyzed, and qPCR and IHC were performed in an in-house cohort to confirm the clinical significance of TANK. Then, we systematically evaluated the relationship between TANK expression and immune characteristics in the glioma microenvironment. Additionally, we evaluated the ability of TANK to predict treatment response in glioma. TANK-associated risk scores were developed by LASSO-Cox regression and machine learning, and their prognostic ability was tested. Results: TANK was specifically overexpressed in glioma and enriched in the malignant phenotype, and its overexpression was related to poor prognosis. The presence of a tumor microenvironment that is immunosuppressive was evident by the negative correlations between TANK expression and immunomodulators, steps in the cancer immunity cycle, and immune checkpoints. Notably, treatment for cancer may be more effective when immunotherapy is combined with anti-TANK therapy. Prognosis could be accurately predicted by the TANK-related risk score. Conclusions: High expression of TANK is associated with the malignant phenotype of glioma, as it shapes an immunosuppressive tumor microenvironment. Additionally, TANK can be used as a predictive biomarker for responses to various treatments and prognosis.

Aims: Diffuse glioma is the most frequent intracranial tumor and remains universally lethal. Prognostic biomarkers have remained a focus in diffuse glioma during the last decades. More reliable predictors to adequately characterize the prognosis of diffuse glioma are essential. Cathepsin C (CTSC), a lysosomal cysteine protease, is an essential component of the lysosomal hydrolase family, with their potential roles in diffuse glioma remaining to be characterized Objective: We aimed to investigate the performance of CTSC in predicting prognosis and therapeutic targets in diffuse glioma. Method: The expression profile of CTSC in multiple tumors and more than 2000 glioma samples with corresponding clinical data were collected through authoritative public databases. The expression level of CTSC was evaluated by qPCR and IHC. The prognostic value of CTSC was assessed using the univariate and multivariate cox regression analysis. The ESTIMATE R package was used to evaluate the immune and stromal scores based on the gene expression profile. The CIBERSORT was applied to evaluate the relative levels of 22 immune cell subtypes by using the R package 'CIBERSORT' to define the cell composition of tumor tissues. In addition, the MCP counter was used to assess the absolute abundance of neutrophils. Result: CTSC was aberrantly expressed and significantly correlated with clinical outcomes in multiple tumors. CTSC was heterogeneously expressed across histologic types and tumor grades for diffuse glioma and highly enriched in IDH or IDH1-wildtype glioma. CTSC was positively associated with immune and stromal scores and infiltrating levels of M2 macrophages and neutrophils and negatively associated with infiltrating levels of NK cells. Additionally, CTSC was closely correlated with some immune checkpoint molecules, including CD276, CD80, CD86 and PD-L2. Conclusion: Conclusion: CTSC was involved in shaping the immunosuppressive microenvironment and acted as an independent indicator of a poor prognosis in diffuse glioma. Targeting CTSC for glioma therapies might provide promising prospects.