The ubiquitin-proteasome system (UPS) is a fundamental regulatory mechanism maintaining cellular proteostasis through the targeted degradation of proteins. Beyond its canonical role in protein turnover, the UPS governs diverse biological processes, including cell cycle control, DNA repair, immune responses, and stress adaptation. Dysregulation of UPS components is increasingly recognized as a driving force in the pathogenesis of numerous diseases, such as cancer, neurodegenerative disorders, metabolic dysfunctions, and infections. In plants, the UPS also plays a pivotal role in environmental stress responses and hormone signaling, offering promising avenues for crop improvement. This review presents a comprehensive overview of the molecular architecture and functions of the UPS, explores its role in maintaining cellular and systemic homeostasis, and critically examines the consequences of UPS dysfunction across various disease contexts. We further highlight emerging technologies, including ubiquitinomics, CRISPR-based screens, and targeted protein degradation platforms, that are accelerating UPS research. Finally, we discuss current challenges and future opportunities for translating UPS insights into therapeutic and biotechnological innovations. A deeper understanding of the UPS across biological systems is essential for developing next-generation strategies to combat human diseases and enhance agricultural resilience.

ABSTRACT Over the past decade, Immuno-Oncology has largely focused on blocking inhibitory surface receptors like PD-1 to enhance T cell anti-tumor activity. However, intracellular immune checkpoints such as CISH, which function independently of tumor-expressed ligands, offer powerful and previously untapped therapeutic potential. As a downstream regulator of TCR signaling, CISH controls T cell activation, expansion, and neoantigen reactivity. Though historically considered undruggable, recent advances in CRISPR engineering have enabled functional interrogation of these targets. We demonstrate that CISH deletion enhances T cell activation and anti-cancer functions more effectively than other emerging intracellular checkpoints. In CAR-T cells, CISH inactivation significantly increased sensitivity to tumor antigen, enabling robust recognition and killing even at low antigen levels, conditions that often lead to treatment failure with conventional T cell therapies, mirroring antigen escape scenarios seen in solid tumors. Our findings further validate CISH as a potent and druggable intracellular checkpoint capable of boosting anti-tumor T cell responses across diverse cancer types, independent of PD-L1 status. The underlying mechanisms of CISH inhibition may help explain the positive outcomes reported in recent clinical studies of this approach in solid tumor immunotherapy.

Glandular trichomes are specialized epidermal structures that play an essential role in plant defense by synthesizing, storing, and secreting specialized metabolites. This study investigates the function of NtAGL66 , an AGAMOUS-like gene in Nicotiana tabacum , uncovering its role in the development of secretory heads in long glandular trichomes. Expression profiling reveals that NtAGL66 is specifically expressed in the developing secretory glands. Functional analyses show that NtAGL66 overexpression promotes the differentiation of the secretory structure, while CRISPR-Cas9-mediated knockout significantly reduces the capacity of trichomes to form functional secretory glands, highlighting its essential role in trichome specialization. Transcriptomic (RNA-seq) and functional genomic (DAP-seq) analyses indicate that NtAGL66 regulates also secondary metabolic pathways and is likely involved in broader transcriptional networks, including floral development. Notably, this includes genes such as NtTOE1, previously shown to control both floral organogenesis and glandular trichome formation in tomato. Moreover, NtAGL66 directly regulates the transcription factor NtGL2 through promoter binding. By identifying an AGAMOUS-like gene as a key regulator of secretory gland development, this study offers novel insights into the genetic mechanisms underlying glandular trichome differentiation and specialized metabolite biosynthesis in Solanaceae .

Summary CRISPR-Cas systems provide adaptive immunity against phage infection in prokaryotes using an RNA-guided complex that recognizes complementary foreign nucleic acids. Different types of CRISPR-Cas systems have been identified that differ in their mechanism of defense. Upon infection, Type III CRISPR-Cas systems employ the Cas10 complex to find phage transcripts and synthesize cyclic oligo-adenylate (cOA) messengers. These ligands bind and activate CARF immune effectors that cause cell toxicity to prevent the completion of the viral lytic cycle. Here we investigated two proteins containing an N-terminal haloacid dehalogenase (HAD) phosphatase domain followed by four predicted transmembrane helices and a C-terminal CARF domain, which we named Chp. We show that, in vivo, Chp localizes to the bacterial membrane and that its activation induces a growth arrest, leads to a depletion of ATP and IMP and prevents phage propagation during the type III CRISPR-Cas response. In vitro, the CARF domain of Chp binds cyclic tetra-adenylates and the HAD phosphatase domain dephosphorylates dATP, ATP and IMP. Our findings extend the range of molecular mechanisms employed by CARF effectors to defend prokaryotes against phage infection.

The natural context in which CRISPR-Cas systems are active in Enterobacteriaceae has remained enigmatic. Here, we find that the Citrobacter rodentium Type I-E CRISPR-Cas system is activated by the oxygen-responsive transcriptional regulator Fnr in the anoxic mouse intestine. Since Fnr-dependent regulation is predicted in ~41% of Enterobacteriaceae cas3 orthologs, we propose that anoxic regulation of CRISPR-Cas immunity is an adaptation that protects Enterobacteriaceae against threats arising from the intestinal microbiome.

Many taxa have independently evolved genetic sex determination where a single gene located on a sex chromosome controls gonadal differentiation. The gene anti-Mullerian hormone ( amh ) has convergently evolved as a sex determination gene in numerous vertebrate species, but how this gene has repeatedly evolved this novel function is not well understood. In the threespine stickleback ( Gasterosteus aculeatus ), amh was duplicated onto the Y chromosome ( amhy ) ∼22 million years ago. To determine whether amhy is the primary sex determination gene, we used CRISPR/Cas9 and transgenesis to show that amhy is necessary and sufficient for male sex determination, consistent with the function of a primary sex determination gene. Despite being indispensable for sex determination, we detected low levels of amhy expression throughout early development. This indicates the mechanism of sex determination is likely unrelated to overall dosage of amhy and its autosomal paralog, amha . Threespine stickleback have striking differences in behavior and morphology between sexes. The creation of sex reversed lines allow us to investigate the genetic basis of secondary sex characteristics. Here we show one of the classic traits important for reproductive success, male nuptial coloration, is controlled by both Y-linked genetic factors as well as hormonal factors independent of sex chromosome genotype. This research establishes stickleback as a model to investigate how amh regulates gonadal development and how this gene repeatedly evolves novel function in sex determination. Analogous to the four core genotypes model in house mice, sex-reversed threespine stickleback offer a new vertebrate model for investigating the separate contributions of gonadal sex and sex chromosomes to sexual dimorphism.

The typhoid toxin is a secreted virulence factor of typhoidal serovars of the bacterial pathogen Salmonella enterica implicated in typhoid fever and chronic infections. The toxin causes a DNA damage response in human cells, characterised by cell-cycle arrest and cellular distension, resulting in cellular senescence and increased bacterial burden. To better understand host responses to typhoid toxin, we performed a transcriptomic analysis of intoxicated host cells and found that the toxin induced expression of genes relating to the type-I interferon response, including the ubiquitin-like protein ISG15. ISG15 was upregulated in a STING-dependent manner, reduced bacterial burden, and was found to be critical to host cell survival in response to the typhoid toxin and purified interferon. This highlights ISG15 as an important component of the host cell defence to the typhoid toxin.

Genome alterations arise from inaccurate DNA repair, accumulating into distinct mutational signatures. Here, we investigate the role of every genomically encoded gene in double-strand break (DSB) repair by generating high-resolution outcome profiles following gene knockouts. Using a CRISPR/Cas9-based, massive-parallel bulk library approach, we construct a comprehensive, user-explorable mutational signature catalogue (MUSIC), mapping the full repertoire of DSB repair factors. Our analysis identifies and validates gene clusters – including nearly all known and several novel genes – linked to non-homologous end-joining, 53BP1 sub-pathways, homology-directed repair, and polymerase Theta (POLQ)-mediated end-joining. By focusing on pathway-specific repair outcomes, we uncover a previously unrecognized role for the WRN helicase in suppressing inverted templated insertions, a poorly understood POLQ-associated mutational signature also found in human disease alleles. Furthermore, in-depth analysis of MUSIC’s scar features reveals unexpected distinctions among genes within the same pathway, providing mechanistic insight and opening multiple new avenues for investigation into chromosomal break repair.

Abstract Before human genome sequencing, a genome-wide study of sibling centenarian pairs identified a longevity-associated locus on chromosome 4. Here, we mapped the genes in this locus and identified a collagen gene, COL25A1. Introducing an SNP linked to longevity that changes a serine predicted to be phosphorylated to leucine in COL25A1 , into col-99 , the C. elegans ortholog, extended lifespan. These col-99(gk694263 [S106L] ) SNP-mutants exhibited enhanced innate immune-related transcriptional responses, and their lifespan extension was abolished by inhibiting the p38 MAPK pathway. YAP-1, a transcriptional co-activator responsive to extracellular matrix changes, was essential for this longevity. Mechanistically, we propose that this SNP modifies furin-mediated cleavage of this transmembrane collagen in vitro, and expressing the cleaved extracellular domain of COL-99 alone was sufficient to prolong lifespan. These findings reveal a potential mechanism by which a human centenarian-associated SNP in COL25A1 influences furin cleavage and shedding of the collagen ectodomain to promote healthy longevity.

Basement membranes (BMs) are specialized extracellular matrices (ECMs) essential for tissue structure and function. In non-vertebrates, ECM components can be produced both locally and by distant tissues. In contrast, mammalian ECM has traditionally been considered to originate predominantly from adjacent or tissue-resident cells. The kidney glomerular basement membrane (GBM), composed of laminin-α5β2γ1 and collagen-α3α4α5(IV), is produced by neighboring epithelial cells and functions as a filtration barrier. Alport syndrome, a genetic kidney disease in children, is characterized by GBM structural defects and ectopic laminin-α2 deposition, but the source of this laminin remains unknown. Here, using CRISPR/Cas9 transgenic models, we demonstrated that ectopic laminin-α2 originates not from local kidney cells but from the circulation. Furthermore, laminin-α2 in the mesangium partially derives from circulating sources even under healthy conditions. Our findings uncover a non-cell-autonomous mechanism whereby GBM integrity regulates circulating protein incorporation, revealing a previously unrecognized trans-tissue regulation of BM composition in mammals.

When cells divide, the newly replicated sister chromatids must be segregated evenly to the daughter cells. During mitosis, mechanical force is applied by spindle microtubules in 2 ways: first by pushing on chromosome arms to promote chromosome congression to the cell equator in metaphase, and then by pulling on kinetochores to promote sister chromatid disjunction during anaphase. For segregation to proceed faithfully, the pliable interphase chromatin must be transformed into stiff mitotic chromosomes able to withstand these forces. However, it is unclear how the cell establishes chromosome stiffness and what the consequences are for dividing cells if this stiffness is disrupted. Many of the structural changes imposed on chromosomes in mitosis are driven by Condensin complexes, in conjunction with Topoisomerase IIα. Here, we have combined rapid protein depletion and live cell imaging with in-depth mechanical characterization of purified mitotic chromosomes to probe the roles of Condensins I and II in the establishment and maintenance of the mechanical strength of mitotic chromosomes. We show that Condensin I, but not Condensin II, is required to establish chromosome stiffness and chromatin elasticity, and yet ceases to be required for the maintenance of these properties once chromosome formation has been completed. Nevertheless, depletion of Condensin I from already formed chromosomes still impacts centromeric chromatin and leads to a loss of sister centromere cohesion. We propose that the extensive chromatin loop network established by Condensin I is locked in place by Topoisomerase IIα mediated DNA catenation.

The biopharmaceutical sector relies on CHO cells to investigate biological processes and as the preferred host for production of biotherapeutics. Simultaneously, advancements in CHO cell genome assembly have provided insights for developing sophisticated genetic engineering strategies. While the majority of these efforts have focused on coding genes, with some interest in transcribed non-coding RNAs (e.g., microRNAs and lncRNAs), there remains a lack of genome-wide systematic studies that precisely examine the remaining 90% of the genome. This unannotated “dark matter” includes regulatory elements and other, poorly understood or characterized functionality of the genome that may be potentially critical for cell survival. In this study, we deployed a genome-scale CRISPR screening platform with 112,272 paired guide RNAs targeting 14,034 genomic regions for complete deletion of 150 kb long sections. This platform enabled the execution of a negative screen that selectively identified dying cells to determine regions essential for cell survival. By using paired gRNAs, we overcame the intrinsic limitations of traditional frameshift strategies, which will likely have little or no effect on the non-coding genome. This study revealed 427 regions essential for CHO survival, many of which currently lack gene annotation or known function. For these regions we present annotation status, transcriptional activity as well as annotated chromatin states such as enhancers. Selected regions, specifically those that were negative for all the above, were individually deleted for confirmation. This work sheds a novel light on a substantial part of the mammalian genome which is traditionally difficult to investigate and therefore, neglected.

SUMMARY Metabolites are essential substrates for epigenetic modifications. Although nuclear acetyl-CoA constitutes a small fraction of the whole cell pool, it regulates cell fate by locally providing histone acetylation substrate. Here, we combined phenotypic chemical screen and genome-wide CRISPR screen to demonstrate a nucleus-specific acetyl-CoA regulatory mechanism that can be modulated to achieve therapeutic cancer cell reprogramming. While previously thought that nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively active, we found that nPDC is constitutively inhibited by the nuclear protein ELMSAN1 through direct interaction. Pharmacologic inhibition of the ELMSAN1-nPDC interaction derepressed nPDC activity, enhancing nuclear acetyl-CoA generation and reprogramming cancer cells to a postmitotic state with diminished cell-of-origin signatures. Reprogramming was synergistically enhanced by histone deacetylase 1/2 inhibition, resulting in inhibited tumor growth, durably suppressed tumor-initiating ability, and improved survival in multiple cancer types in vivo , including therapy-resistant sarcoma patient-derived xenografts and carcinoma cell line xenografts. Our findings highlight the potential of targeting ELMSAN1-nPDC as epigenetic cancer therapy.

Despite the availability of numerous methods for controlling gene expression, there remains a strong need for technologies that maximize two key properties: selectivity and reversibility. To this end, we have developed a novel approach that exploits the highly sequence-specific nature of CRISPR-associated endoribonucleases (Cas RNases), which recognize and cleave short RNA sequences known as direct repeats (DRs). In this approach, referred to as DREDGE (direct repeat-enabled downregulation of gene expression), selective control of gene expression is enabled by introducing one or more DRs into the untranslated regions (UTRs) of target mRNAs, which will then be cleaved upon expression of the cognate Cas RNase. We previously demonstrated that the expression of target genes with DRs in their 3' UTRs are efficiently controlled by the DNase-dead version of Cas12a (dCas12a) with a high degree of selectivity and complete reversibility. Here we assess the feasibility of using DREDGE to regulate the expression of genes with DRs inserted within their 5' UTRs. Among five different Cas RNases tested, Csy4 was found to be the most efficient in this format, yielding robust downregulation with rapid onset in doxycycline-regulatable systems targeting either a stably expressed fluorescent protein or an endogenous gene, notably in a fully reversible manner. Unexpectedly, dCas12a was also found to be modestly effective despite binding essentially irreversibly to the cut mRNA on its 5' end and boosting mRNA levels. Our results expand the utility of DREDGE as an attractive method for regulating gene expression in a targeted, highly selective, and fully reversible manner.

ABSTRACT Type III CRISPR systems detect non-self RNA and activate the enzymatic Cas10 subunit, which generates nucleotide second messengers for activation of ancillary effectors. Although most signal via cyclic oligoadenylate (cOA), an alternative class of signalling molecule SAM-AMP, formed by conjugating ATP and S-adenosyl methionine, was described recently. SAM-AMP activates a trans-membrane effector of the CorA magnesium transporter family to provide anti-phage defence. Intriguingly, immunity also requires SAM-AMP degradation by means of a specialised CRISPR-encoded NrN family phosphodiesterase in Bacteroides fragilis . In Clostridium botulinum , the nrn gene is replaced by a gene encoding a SAM-AMP lyase. Here, we investigate the structure and activity of C. botulinum SAM-AMP lyase, which can substitute for the nrn gene to provide CorA-mediated immunity in Escherichia coli . The structure of SAM-AMP lyase bound to its reaction product methylthioadenosine-AMP (MTA-AMP) reveals key details of substrate binding and turnover by this PII superfamily protein. Bioinformatic analyses reveal candidate phage-encoded SAM-AMP lyases and we demonstrate that one, hereafter named AcrIIIB4, degrades SAM-AMP efficiently in vitro .

Summary Transcriptional complexes with a common composition regulate the production of flavonoid pigments, trichomes, root hairs and other epidermal traits in seed plants. These complexes are composed of transcription factors from the MYB and basic helix-loop-helix (bHLH) families along with a tryptophan-aspartate repeat (WDR) scaffold protein (MBW complexes). The MYB member has been found to be the most pathway-specific component of the complex and modifications to these MYB genes are overrepresented in studies investigating the genetic basis of changes in pigmentation phenotypes across flowering plants. Here we investigated the orthologues of the MBW complex in a divergent lineage to understand its origin and evolution. We found evidence that these transcriptional complexes also form in the liverwort Marchantia polymorpha , indicating, together with an analysis of published gene family phylogenies, that they are ancestral to land plants. The functions of each of the two orthologous MYB genes, Mp MYB14 and Mp MYB02 , both depend on the single orthologous bHLH gene, Mp bHLH12 . We could not assess the functional role of the WDR genes in M. polymorpha , due to low mutant recovery suspected to be caused by pleiotropic effects on viability. We propose that the two transcriptional complexes with alternative MYB paralogues in M. polymorpha represent an ancestral function, regulation of the flavonoid pathway, and a derived function, maturation of liverwort-specific oil bodies. Our findings imply a replicated pattern by which new complexes have evolved in independent land plant lineages, through duplication of the evolutionarily labile MYB member and co-option of its interaction partners.

Abstract Background: The CD247 chain of the T-cell receptor (TCR) is essential for normal T cell development and function. Reported CD247-deficient patients showed severe immunodeficiency despite the presence of two populations of peripheral T cells, most with low TCR levels carrying the germline variant and a few with higher TCR levels due to somatic reversion. However, the revertant T cells remained a minority and did not improve the patients’ clinical status. Purpose: To compare the capability of somatic reversions of CD247 germline changes (p.M1T and p.Q70X) to restore TCR expression and function. Methods: CD247 wild-type (WT) and p.Q70L/W/Y somatic revertants were individually introduced in CD247-deficient mouse (MA5.8), human mutant (PM1T), and CRISPR/Cas9-generated Jurkat (ZKO) T cell lines by nucleofection or transduction. Results: MA5.8 mouse T cells do not accurately model human CD247 deficiencies, as Q70X restores TCR expression in MA5.8 but not in human cells. In human cell models, all somatic revertant variants restored TCR expression with varying degrees (WT=Q70L>Q70W>Q70Y). However, rescue of TCR-induced activation events, including ZAP-70 phosphorylation and CD69/CD25 upregulation, did not match such hierarchy (WT=Q70W>Q70L=Q70Y). Conclusion: Somatic reversions, such as those detected in patients with pathogenic CD247 germinal changes, display a discordant capability to rescue TCR expression versus function. These findings shed light on the role of CD247 in TCR expression and function during human T cell development, with implications for immunodeficiencies, as well as for the biological consequences of CD247 somatic mosaicism.

Abstract Uropathogenic Escherichia coli (UPEC) is the leading cause of urinary tract infections (UTIs), driven by virulence factors such as iron acquisition systems and adhesive pili. In this study, we employed CRISPR-Cas9-mediated genome editing to functionally inactivate two critical virulence genes— iucD , involved in aerobactin-mediated iron uptake, and papC , encoding the outer membrane usher protein essential for P pilus assembly. Using a clinical UPEC isolate, we introduced premature stop codons via homologous repair templates guided by gene-specific single-guide RNAs. Colony PCR and Sanger sequencing confirmed precise site-specific editing, leading to truncated protein variants. In silico analyses using InterPro and Swiss-Model revealed a complete loss of essential domains in both proteins. Molecular docking studies demonstrated a marked reduction in binding affinities of truncated IucD for NAD(P)H and impaired protein-protein interaction between truncated PapC and PapG. This study highlights the utility of CRISPR-Cas9 as a powerful tool for dissecting bacterial pathogenesis and supports the potential of targeting virulence determinants like iucD and papC as part of an antivirulence strategy for managing UPEC infections.

Abstract The efficacy of chimeric antig en receptor (CAR) T cell therapy in solid tumors is limited by immunosuppression and antigen heterogeneity. To overcome these barriers, “armored” CAR T cells, which secrete proinflammatory cytokines, have been developed. However, their clinical application has been limited due to toxicities related to peripheral expression of the armoring transgene. Here, we developed a novel CRISPR knock-in strategy that uses endogenous gene regulatory mechanisms to drive transgene expression in a tumor-localized manner. By screening endogenous genes with tumor-restricted expression, the NR4A2 and RGS16 promoters were identified to support the delivery of cytokines such as IL-12 and IL-2 directly to the tumor site, leading to enhanced anti-tumor efficacy and long-term survival of mice in both syngeneic and xenogeneic models. This was concomitant with improved CAR T cell polyfunctionality, activation of endogenous anti-tumor immunity, a favorable safety profile, and was applicable using CAR T cells from patients.

Deconvolving the substrates of hundreds of kinases linked to phosphorylation networks driving cellular behavior is a fundamental, unresolved biological challenge, largely due to the poorly understood interplay of kinase selectivity and substrate proximity. We introduce KolossuS, a deep learning framework leveraging protein language models to decode kinase-substrate specificity. KolossuS achieves superior prediction accuracy and sensitivity across mammalian kinomes, enabling proteome-wide predictions and evolutionary insights. By integrating KolossuS with CRISPR-based proximity proteomics in vivo, we capture kinase-substrate recognition and spatial context, obviating prior limitations. We show this combined framework identifies kinase substrates associated with physiological states such as sleep, revealing both known and novel Sik3 substrates during sleep deprivation. This novel integrated computational-experimental approach promises to transform systematic investigations of kinase signaling in health and disease.

Biological membranes often feature an unequal and actively maintained concentration gradients of lipids between bilayer leaflets, termed lipid asymmetry. 1–3 Lipid asymmetry has been linked to many cellular processes 4,5 , but the mechanisms that connect lipid trans-bilayer concentration gradients to cellular functions are poorly understood. Here we systematically map the cellular processes affected by dysregulation of lipid asymmetry by knocking out flippases, floppases, and scramblases in mammalian cells. We identify broad alterations to core metabolic pathways including nutrient uptake, neutral lipid turnover, pentose phosphate pathway and glycolysis. Lipidomics, respirometry, lipid and metabolic imaging, and live-cell calorimetry revealed elevated neutral lipid and ATP consumption rates which are coupled with increased heat loss per unit of biomass synthesized despite slower growth. This suggests that compensatory maintenance of lipid asymmetry strains the cellular energy budget, inducing a shift from a growth-promoting anabolic to a more energy-using catabolic state. Our data indicate that lipid asymmetry and its active maintenance is key for proper cell energetics, highlighting its putative role as a cellular store of potential energy akin to proton and ion transmembrane gradients.

A typical cell therapy product comprises engineered cells that detect disease-related molecular cues in their surrounding or on a surface of a target cell, and activate a response that alleviates disease symptoms or eradicates diseased cells. mRNA as a therapeutic substrate has become prevalent in the last decade across multiple therapeutic areas, and it has also been evaluated as a building block of cell therapies. However, compared to DNA-based building blocks, it is much more challenging to use mRNA in a programmable manner to engineer complex multi-input/multi-output processes that can fully support the next generation of cell and gene therapies. Addressing this challenge requires the exploration of novel post-transcriptional control mechanisms that bridge mRNA regulation with extracellular surroundings. Here, we engineer a family of s ynthetic m RNA s plicing (SMS) receptors by redesigning the Inositol-requiring enzyme 1 (IRE1) to regulate protein synthesis from a precursor mRNA. We design SMS-based receptors that sense diverse intracellular and extracellular inputs, highlighting the versatility and modularity of this platform. We apply this approach to design a ‘cytokine-converter’ receptor that detects inflammatory cytokines and produces an anti-inflammatory output in response. That receptor is successfully validated in cell lines and primary T cells upon mRNA delivery. These cells generate anti-inflammatory IL-10 upon stimulation by physiological levels of either TNF-α or IL-1β secreted by macrophage-like cells, highlighting their potential as a cell therapy for inflammatory diseases. With its modular and programmable architecture, the SMS platform is poised to become an important enabling tool for sophisticated programmable mRNA therapeutics.

The immunosuppressive tumor microenvironment (TME) remains a central barrier to effective immunotherapy in solid tumors. To address this, we developed a novel gene therapeutic strategy that enables localized remodeling of the TME via tumor-intrinsic cytokine expression. Central to this approach is CancerPAM, a multi-omics bioinformatics pipeline that identifies and ranks patient-specific, tumor-exclusive CRISPR-Cas9 knock-in sites with high specificity and integration efficiency. Using neuroblastoma—a pediatric solid tumor with a suppressive TME—as a model, we applied CancerPAM to sequencing data from cell lines and patients to identify optimal integration sites for pro-inflammatory cytokines (CXCL10, CXCL11, IFNG). CRISPR-mediated CXCL10 knock-in into tumor cells significantly enhanced CAR T cell infiltration and antitumor efficacy both in vitro and in vivo. In vivo, CXCL10-expressing tumors showed significantly increased early CAR T cell infiltration and prolonged survival compared to controls. CancerPAM rankings correlated strongly with target-site specificity and knock-in efficiency, validating its predictive performance. Our findings establish CancerPAM as a powerful tool for safe and effective CRISPR-based interventions and provide a conceptual framework for integrating cytokine-driven TME remodeling with cellular immunotherapies. This personalized strategy holds promise for enhancing CAR T cells and other immunotherapies across immune-refractory solid tumors.

The single crossover occurring via homologous recombination is a common phenomenon exited among most microbes like Escherichia, Clostridium, Streptococcus, Lactobacillus , and cyanobacteria, threatening the stability of engineered strains. Among them, fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) is an attractive photosynthetic chassis for CO 2 bioconversion. To address the challenge of homologous recombination, we constructed two endogenous plasmid-based shuttle vectors, pSES and pSEL, enabling stable DNA delivery without reliance on homologous recombination. In parallel, two robust counter-selection systems were developed based on sepT 2 and rpsL , which, in combination with positive selection markers, significantly improved the screening efficiency of double-crossover mutants. Building upon these tools, we established three marker-free platforms: (i) T4CROSS, which employs two plasmids and four rounds of single crossover; (ii) TRIPLEARM, which uses a single plasmid containing three homologous arms for three rounds of single crossover; and (iii) CRISPRARM, which integrates CRISPR/Cpf1-mediated genome editing with homologous recombination. All three methods successfully repaired mutations in the pilMNOQ pilus gene cluster in Syn2973, restoring natural competence with high efficiency and positive selection rates. As proof of concept, we employed the CRISPRARM platform for a three-step sequential engineering of the sucrose biosynthetic pathway. The final engineered strain produced 7.12 g·L -1 of sucrose within four days.

SUMMARY Despite progress in understanding pre-mRNA splicing, the regulatory mechanisms controlling most alternative splicing events remain unclear. We developed CRASP-Seq, a method that integrates pooled CRISPR-based genetic perturbations with deep sequencing of splicing reporters, to quantitively assess the impact of all human genes on alternative splicing from a single RNA sample. CRASP-Seq identifies both known and novel regulators, enriched for proteins involved in RNA splicing and metabolism. As proof-of-concept, CRASP-Seq analysis of an LMNA cryptic splicing event linked to progeria uncovered Z NF 207, primarily known for mitotic spindle assembly, as a regulator of progerin splicing. ZNF207 depletion enhances canonical LMNA splicing and decreases progerin levels in patient-derived cells. High-throughput mutagenesis further showed that ZNF207’s zinc finger domain broadly impacts alternative splicing through interactions with U1 snRNP factors. These findings position ZNF207 as a U1 snRNP auxiliary factor and demonstrate the power of CRASP-Seq to uncover key regulators and domains of alternative splicing. Main Points CRASP-Seq: RNA-coupled CRISPR screen quantifying gene and domain impact on splicing Profiling of five events identified 370 genes influencing alternative splicing ZNF207 regulates splicing by interacting with U1 snRNP via its zinc-finger domains ZNF207 depletion corrects LMNA aberrant splicing causing progeria