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Mantle cell lymphoma (MCL) is a clinically aggressive and incurable form of non-Hodgkin lymphoma with very heterogeneous clinical and biological behaviors. Dysregulation of RNA splicing machinery is common in various types of cancer, including hematologic malignancies, and is associated with cancer progression. However, whether and how splicing factors, the spliceosome components responsible for pre-mRNA splicing, regulate MCL aggressive behaviors remain largely unknown. Bioinformatics analyses were employed to profile the mRNA expression of two key families of splicing factors, that are serine/arginine-rich (SR) and heterogenous nuclear ribonucleoprotein (hnRNP) families, in clinical specimens of MCL patients in comparison to normal B cells. Functional roles of splicing factors in MCL aggressive phenotypes defined as hallmarks of cancer were investigated in MCL cell lines. Kaplan–Meier survival analyses were performed to determine the clinical significance of splicing factors according to their gene expression level. Depletion of SRSF1, hnRNP F, and PTBP1, which are highly expressed in MCL clinical specimens, by CRISPR/Cas9 system significantly inhibit cell growth and proliferation, motility, and angiogenesis of MCL cells. SRSF1, hnRNP F (for Z-138 cells), and PTBP1 were found to mediate BTZ sensitivity in MCL cells, in agreement with an increase in caspase-3 activation and the occurrence of splicing events that favor the expression of pro-apoptotic isoforms of apoptosis regulatory genes. We also found that depletion of SRSF1, hnRNP F, and PTBP1 induces the expression of autophagy-related genes and the accumulation of autophagic vacuoles, which may act as one of the tumor-suppressive mechanisms. Survival analyses revealed that co-high expression of SRSF1, HNRNPF, or PTBP1 and oncogenic MYC predicts poor clinical outcomes in MCL patients. Our data describe the clinical significance of aberrant SRSF1, hnRNP F, and PTBP1 in MCL and their tumor-promoting roles via the regulation of cancer hallmarks, which could be important in understanding MCL pathogenesis and therapeutic development.

Over the past decade, significant advancements have been made in understanding the developmental mechanisms involved in human gastrointestinal formation, with organoids emerging as key experimental models. These three‐dimensional in vitro cellular structures mimic the organization and functions of various gut regions, providing a powerful tool for research. By replicating critical stages of gut development, we can now direct the differentiation of cells into specific gastrointestinal tissues. In this protocol, we outline how to generate two types of organoids derived from human pluripotent stem cells (hPSCs): human intestinal organoids (HIOs) and human colonic organoids (HCOs). First, we induce definitive endoderm formation to produce these organoids and specify midgut/hindgut tissues. Three‐dimensional spheroids form spontaneously, can be collected, embedded in an extracellular matrix, and cultured over time. During this phase, the organoid epithelium develops, supported by a mesenchymal layer that promotes maturation and differentiation. After a month of culture, HIOs and HCOs reach a developmental and maturation stage comparable to that of the human fetal intestine. These organoids can be used to study human gastrointestinal development, model diseases, and test therapeutic agents. Human pluripotent stem cells can be guided through a stepwise differentiation process to produce self‐organizing intestinal and colonic organoids. The resulting organoids recapitulate fetal‐stage epithelial and mesenchymal organization, offering a powerful model to explore human gastrointestinal development and its disorders.

Clonal hematopoiesis (CH), a prevalent and premalignant state in the elderly, has been detected in young individuals under selective pressures such as hematopoietic cell transplantation (HCT). However, the origin of CH and mutational processes underlying CH driver mutations in young blood systems remain unclear. Here, we used genome‐wide somatic mutation profiles to retrospectively trace the origin of DNMT3A‐mutant CH in three individuals, 14–41 years after childhood HCT. Both the rate and spectrum of somatic mutations in individuals with posttransplant CH were consistent with normal age‐associated mutagenesis. Phylogenetic analysis revealed that DNMT3A‐mutant HSPCs were present in the donor before 6.8 years of age, including during fetal development, despite being undetectable with a limit of detection of variant allele frequency of 0.001 at the time of transplantation. These findings were validated by comparing the observed mutations to expected age‐dependent mutational signatures. Our results reveal that undetectable DNMT3A‐mutant clones in young donors can expand into significant CH clones within decades upon transplantation. The rapid expansion of these clones in this context indicates that specific environmental pressures, rather than solely mutation acquisition, drive the development of CH.

We evaluate the effect of most FDA-approved drugs (>7,000 conditions) on double-strand DNA break repair pathways by analyzing mutational outcomes in human induced pluripotent stem cells. We identify drugs that can be repurposed as inhibitors and enhancers of repair outcomes attributed to non-homologous and microhomology-mediated end joining (NHEJ, MMEJ), and homology-directed repair (HDR). We also identify functions of the proteins estrogen receptor 2 (ESR2) and aldehyde oxidase 1 (AOX1), affecting several key DNA repair proteins, such as ATM and 53BP1. Silencing of ESR2 can have a synergistic effect on increasing HDR when combined with NHEJ inhibition (mean 4.6-fold increase). We further identify drugs that induce synthetic lethality when NHEJ or HDR is blocked and may therefore be candidates for precision medicine. We anticipate that the ability to modulate the DNA repair outcomes with clinically safe drugs will help disease modeling, gene therapy, chimeric antigen receptor immunotherapy, and cancer treatment. DNA repair pathways shape CRISPR editing outcomes. Here, authors identified FDA approved drugs that can be repurposed as repair modulators or to induce synthetic lethality, and uncovered new roles for ESR2 and AOX1 in DNA repair, enhancing editing and offering potential therapeutic applications.

Despite the progressive extension of CFTR variant eligibility to the triple combination of elexacaftor/tezacaftor/ivacaftor (ETI), most rare CFTR pathogenic variants remain ineligible for CFTR modulators. It is crucial to determine whether unexplored variants are rescuable by clinical modulators and to identify innovative therapeutic strategies for rescuing non-responder variants. The approach known as “theratyping” (in vitro testing of genotypes) has been accepted by the Food and Drug Administration (FDA) for the extension of clinical modulators’ approval for in vitro responding genotypes. We used one of the most advanced models for theratyping: organoids derived from nasal epithelia of people with cystic fibrosis (pwCF). We optimized the forskolin-induced swelling (FIS) of organoids to assess CFTR basal or modulator-restored function. Nasal organoids mimicked the original epithelial tissue, CFTR residual activity, and modulator response. We set up the FIS assay using nasal organoids with reference genotypes and theratyped 38 rare (non-F508del) CFTR genotypes, either eligible or non-eligible for FDA approval, for treatment with ETI or ivacaftor. We found strong correspondence between the in vitro response of CFTR variants to modulators and their FDA approval status. Additionally, some previously uncharacterized CFTR variants have proven responsive to clinical modulators, with significant therapeutic implications. These results suggest that the nasal organoid FIS assay, pending confirmation of the prediction in the corresponding pwCF, might be considered as a powerful in vitro tool to predict modulator efficacy in each pwCF, guiding out-of-label prescription in CF, and to identify uncharacterized variants responsive to modulators. This approach may allow comparison of the efficacy of different therapeutics or the identification of innovative strategies for non-responding genotypes, improving personalized therapy and quality of life for pwCF.

Background: Lung cancer is a leading cause of cancer-related mortality worldwide, with heterogeneity and acquired resistance posing major challenges to treatment. Advances in next-generation sequencing (NGS) have enabled comprehensive genomic profiling, yet there remains a need for robust patient-derived models to study tumor biology and inform precision medicine. This study aims to establish and characterize patient-derived lung cancer organoids (LCOs) using whole-genome sequencing (WGS) to explore their genomic landscape and therapeutic potential. Methods: We established a panel of LCOs from resected tumors and malignant pleural effusions (MPEs) of 14 non-small cell lung cancer (NSCLC) patients. Organoids were authenticated and subjected to WGS to profile somatic single nucleotide variants (SNVs), insertions/deletions (InDels), copy number variations (CNVs), structural variants (SVs), and microsatellite instability (MSI). Bioinformatic analyses were performed to annotate mutations, assess tumor mutation burden (TMB), and explore mutational signatures. Furthermore, deep learning-based drug response prediction and in vitro drug sensitivity assays were conducted to evaluate therapeutic potentials in the established LCOs. Results: In the established LCOs, WGS revealed recurrent mutations in TP53, TTN, MUC16, and FLG, with approximately 80% of somatic variants located in non-coding regions, highlighting the potential role of regulatory elements in lung cancer pathogenesis. Early and locally advanced-stage tumor-derived LCOs exhibited higher TMB and MSI compared to those from advanced-stage disease, suggesting greater clonal diversity prior to therapeutic intervention. Drug screening demonstrated the feasibility of using genomic data for drug prediction, but requires more advanced models to fully utilize the WGS data. Conclusions: Our comprehensive genomic characterization of patient-derived LCOs provides valuable insights into the mutational landscape and evolutionary dynamics of lung cancer. These well-annotated organoid models serve as a powerful resource for investigating tumor biology and developing genomically informed therapeutic strategies.

The selection of cells that have acquired a desired gene edit is often done by the introduction of additional genes that confer drug resistance or encode fluorophores. However, such marker genes can have unintended physiological effects and are not compatible with editing of single nucleotides. Here, we present SNIPE, a method that allows the marker-free selection of edited cells based on single nucleotide differences to unedited cells. SNIPE drastically enriches for cells, which have been precisely edited (median 7-fold). We validate the approach for 42 different edits using Cas9 or Cas12a in different cell types and species. We use it to enrich for combinations of substitutions that change missense mutations carried by all people today back to the ancestral state seen in Neandertals and Denisovans. We also show that it can be used to kill cultured tumor cells with aberrant genotypes and to repair heterozygous tumorigenic mutations. Genome editing often requires marker genes for selection of edited cells. Here, the authors present SNIPE, a marker-free method that selects cells based on DNA sequence, enabling precise enrichment of edited cells and applications from evolutionary research to the elimination of cancer cells.

Older adults have decreased vaccine efficacy, but the adjuvanted recombinant VZV-gE zoster vaccine (RZV) is highly efficacious. We investigated memory-like innate immune responses after RZV and after the zoster vaccine live (ZVL), which is much less efficacious. RZV increased NK, monocyte, and DC activation in response to in vitro VZV-gE stimulation for up to 5 years post-vaccination, while ZVL increased only DC responses to VZV for up to 90 days. In purified monocyte and NK cell cocultures, RZV recipients showed increased responses to VZV-gE, HCMV and HSV antigenic stimulation post-vaccination. ATAC-seq analysis of purified monocytes revealed decreased accessibility in areas of the TGFβ1 gene. scRNA-seq and immunoproteomics confirmed decreased TGFβ1 transcription and translation, respectively. Exogenous supplementation and inhibition of TGFβ1 modulated in vitro monocyte responses to VZV-gE. In conclusion, RZV generated homologous (VZV-gE) and heterologous (HCMV, HSV) trained immunity in monocytes through genomic repression of the regulatory cytokine TGFβ-1. Cytokine modulation may represent a novel mechanism of generating trained immunity in myeloid cells. Author summaryOlder adults have decreased vaccine efficacy, but the adjuvanted recombinant varicella zoster virus (VZV)-gE zoster vaccine (RZV; Shingrix™) is highly efficacious. We investigated memory-like innate immune responses after RZV and after the zoster vaccine live (ZVL; Zostavax™), which is much less efficacious than RZV. We found that RZV increased the functionality of several innate immune cell subsets against VZV-gE other herpesviruses. The increase in functionality was associated with decreased production of the inhibitory cytokine TGFβ1, which may have resulted from decreased ability to use the TGFβ1 gene as a template for the synthesis of its product. We concluded that RZV generated homologous (VZV-gE) and heterologous (other herpesviruses) memory-like responses in innate immune cell subsets through genomic repression of the regulatory cytokine TGFβ-1.

Background: Natural killer (NK) cells are key effector lymphoid cells involved in both innate and adaptive immunity and are capable of clearing abnormally aggregated α-synuclein (αSyn). In preclinical Parkinson’s disease (PD) models, NK cell depletion worsens motor deficits and increases insoluble αSyn accumulation, suggesting a neuroprotective role. However, the therapeutic potential of NK cell transfer in modulating αSyn pathology and neurodegeneration remains unexplored. Methods: To assess the efficacy of NK cell therapy, we administered biweekly systemic injections of untouched NK cells isolated from B6C3H donor mice into 2-month-old presymptomatic homozygous M83 transgenic mice injected with human αSyn preformed fibrils. Neurological function was assessed via clasping behavior and clinical scoring. αSyn pathology and dopaminergic neurodegeneration were evaluated via immunohistochemistry. CyTOF-based immune profiling and multiplex ELISA were performed to characterize central and peripheral immune responses. Results: Adoptive NK cell transfers improved motor function and reduced αSyn pathology in a region- and dose-dependent manner, with significant reductions in phosphorylated-αSyn inclusions and tyrosine hydroxylase-positive neuronal loss in the substantia nigra. NK cell transfer modulated the CNS immune landscape by reducing CD11b+CD45high and MHCII+ activated microglial, CD4⁺ T cells, and neutrophil infiltration, while promoting CD19+ B and CD8+ T cells. Similar immunomodulatory effects were observed in the periphery, including restoration of follicular B cells and reduced neutrophil frequencies. Mechanistically, αSyn exposure downregulated activating NK ligands and upregulated inhibitory receptor ligand mQa1b, along with p21 induction in microglia, suggesting a senescence-associated, immune-evasive phenotype that may contribute to reduced therapeutic efficacy at later disease stages. Conclusions: Our study provides direct evidence of NK cells exerting neuroprotective and immunomodulatory effects in a preclinical model of synucleinopathy. These findings support NK cell transfer as a novel therapeutic strategy for PD and related neurodegenerative disorders.

Systemic sclerosis (SSc) is an autoimmune disease marked by fibrosis and extensive autoantibody production. Although B-cell depletion with rituximab (RTX) has shown clinical benefit, predictive biomarkers of response remain elusive. Here, we apply proteome-wide autoantibody screening using wet protein arrays covering 13,455 human antigens in serum samples from participants of the randomized trial of RTX. We identify a significant elevation in the total autoantibody levels in SSc compared to healthy controls, with greater reductions post-treatment observed in RTX high responders than in low responders. A stepwise selection highlights 88 clinically relevant autoantibodies, including those targeting G protein-coupled receptors. Among them, anti-C-C motif chemokine receptor 8 (CCR8) autoantibodies are functionally validated by cell-based assays using CCR8-overexpressing HEK293 cells. Furthermore, in a bleomycin-induced mouse model, anti-CCR8 antibody administration exacerbates dermal fibrosis and modifies immune cell infiltration. Although external validation with multiple comparison adjustment is further required, these findings reveal an autoantibody signature associated with therapeutic response and pathogenic potential in SSc, providing a foundation for precision immunotherapy and mechanistic insights into disease progression. B-cell depletion benefits systemic sclerosis, but predictive biomarkers remain limited. The authors here map autoantibody profiles using proteome-wide screening, identify C-C motif chemokine receptor 8-targeting autoantibodies with functional impact, suggesting novel pathophysiology and precision therapy targets.

Recessive dystrophic epidermolysis bullosa (RDEB) is a severe inherited skin disorder caused by mutations in COL7A1. Patient-derived induced pluripotent stem cells (iPSCs) enable the personalized study of RDEB pathogenesis and potential therapies. However, current skin cell differentiation protocols via 2D culture perform suboptimally when applied to engineered 3D skin constructs (ESC). Here, we present an approach to source fibroblasts (iFBs) and keratinocytes (iKCs) from iPSC-derived skin organoids using an optimized differentiation protocol, and utilize them to engineer ESCs modeling wild-type and RDEB phenotypes. The resulting iPSC-derived skin cells display marker expression consistent with primary counterparts and produce ESCs exhibiting significant extracellular matrix remodeling, protein deposition, and epidermal differentiation. RDEB constructs recapitulated hallmark disease features, including absence of collagen VII and reduced iFB proliferation. This work establishes a robust and scalable strategy for generating physiologically-relevant, iPSC-derived skin constructs, offering a powerful model for studying RDEB mechanisms and advancing personalized regenerative medicine.

Background: Recurrent/metastatic head and neck squamous cell carcinoma ((R/M) HNSCC) represents one of the most aggressive and immunosuppressive cancers. Despite the introduction of immune checkpoint inhibitors (ICIs), only a limited number of patients obtain long-term benefits. In (R/M) HNSCC patients, the antitumor immune response is defective, conferring resistance and promoting tumor progression. Therefore, the identification of novel biomarkers for superior clinical outcomes and easily accessible in standard clinical settings is still an unmet clinical need. Methods: Blood liquid biopsies obtained from (R/M) HNSCC patients undergoing pembrolizumab therapy (monotherapy or in combination with chemotherapy) were analyzed by flow cytometry to evaluate the levels of circulating immunosuppressive regulatory T cells (Tregs) and myeloid derived suppressor cells (MDSCs), at baseline and during therapy. Correlations between these immunosuppressive immune cell subsets and clinical parameters (clinical response rate, progression-free survival (PFS), overall survival (OS) and performance status (PS)) were performed. Results: Univariate analysis showed that before therapy, higher circulating levels of both CD137⁺Tregs and LOX-1⁺PMN-MDSCs, identified patients with significantly worse survival. Furthermore, CD137⁺Tregs resulted also positively correlated with worse PS, while high levels of LOX-1⁺PMN-MDSCs negatively affected response to pembrolizumab, with a significant increase in non-responsive patients during therapy. Interestingly, both CD137⁺Tregs as well as LOX-1⁺PMN-MDSCs exerted a higher immunosuppression on T cell proliferation than CD137−Tregs and LOX-1⁻PMN-MDSCs, respectively. Multivariate analysis revealed that the circulating LOX-1⁺PMN-MDSC subset resulted as an independent prognostic factor for survival by multivariate analysis, as confirmed in an independent validation cohort. Conclusions: The levels of blood circulating LOX-1⁺PMN-MDSCs may be proposed as non-invasive biomarkers to predict clinical outcomes of (R/M) HNSCC patients developing resistance to immunotherapy, improving patient selection and suggesting novel personalized therapies.