Citations

Importance Elevated low-density lipoprotein cholesterol (LDL-C) is a modifiable risk factor for cardiovascular disease, the leading cause of premature death worldwide. Assessing the LDL-C–related burden is critical for guiding prevention and treatment strategies. Objectives To estimate the global, regional, and national burden of ischemic heart disease and ischemic stroke attributable to elevated LDL-C (relative to 35-54 mg/dL) from 1990 to 2023 and to quantify the contributions of population growth, aging, risk-deleted burden, and exposure changes to burden trends. Design, Setting, and Population This comparative risk assessment, part of the Global Burden of Disease Study 2023, estimated population-level LDL-C exposure and associated health loss in 204 countries and territories. Mean LDL-C levels were estimated using spatiotemporal gaussian process regression based on 806 studies across 161 countries. Relative risks were derived from meta-analyses of 38 randomized clinical trials. Population-attributable fractions for deaths and disability-adjusted life-years (DALYs) were estimated by age and sex for adults aged 25 years or older from 1990 to 2023, with 95% uncertainty intervals. Exposure Population-level LDL-C concentrations. Main Outcomes and Measures Population-attributable fractions, counts, and rates (all ages and age standardized per 100 000) of LDL-C–attributable deaths and DALYs from ischemic heart disease and ischemic stroke, with uncertainty intervals. Results In 2023, elevated LDL-C accounted for 3.6 million deaths (95% uncertainty interval, 2.2-5.4 million; 6.0% of global mortality) and 90.7 million DALYs (95% uncertainty interval, 58.9-123.3 million; 3.2% of DALYs). Although global all-ages rates remained stable, age-standardized death and DALY rates decreased by 45.6% and 39.5%, respectively, since 1990. In 2023, age-standardized LDL-C–attributable DALY rates were highest in Eastern Europe and lowest in high-income Asia-Pacific. One-third of the global LDL-C burden occurred in India and China. Population growth and aging drove the increasing burden, with notable regional disparities in LDL-C exposure and risk-deleted DALY rates shifting toward middle-sociodemographic settings. Conclusions and Relevance Despite declining age-standardized rates, the absolute LDL-C burden has increased since 1990 due to demographic changes and has shifted toward middle-sociodemographic countries. Measurement and surveillance gaps persist. Strengthened prevention, diagnosis, and treatment access strategies are essential to mitigate the health burden of LDL-C.

Most genetic variants associated with complex traits are hypothesized to regulate gene expression. To understand the genetics underlying gene expression variability, we characterized 14,324 RNA-sequencing samples from the Trans-Omics for Precision Medicine program and performed expression and splicing quantitative trait locus (e/sQTL) analyses in six tissues and cell types, including whole blood ( n = 6454) and lung ( n = 1291). We detected tens of thousands of secondary cis-e/sQTLs, showing that secondary cis-e/sQTL discovery remains unsaturated. We fine-mapped UK Biobank–derived genome-wide association study (GWAS) signals from 164 traits and identified e/sQTL colocalizations for 10,611 GWAS signals, including 7096 that colocalize with secondary e/sQTLs. Our results suggest that even larger e/sQTL analyses will uncover additional secondary e/sQTLs, further benefiting GWAS interpretation.

Enteroblastic, hepatoid, and clear cell carcinomas are rare subtypes of colorectal carcinoma (CRC) with histologic and immunohistochemical (IHC) overlap. We assessed 37 CRCs that possibly represent these subtypes. Provisional criteria for each subtype, along with case photomicrographs and IHC data, were circulated among the authors to provide diagnostic interpretations. Based on plurality consensus, the carcinomas were classified as enteroblastic (n=13), hepatoid (n=6), and clear cell (n=18). Unanimous agreement was reached in 18% (3 clear cell, 3 hepatoid). Interobserver analysis revealed a mean pairwise Cohen κ of 0.63 (range: 0.32 to 0.91), with the hepatoid subtype eliciting the greatest consensus. Clear cell areas were the most likely to intermix with areas of conventional CRC ( P <0.001). Seven patients (20%) had inflammatory bowel disease (mostly linked to enteroblastic CRC). Twenty-three of 34 patients (68%) had nodal metastasis, and 12 (32%) had distant metastasis (mostly to the liver) at presentation. Median recurrence-free survival was 17 months, with enteroblastic cases the most likely to recur (54%, P =0.015). Median follow-up length was 27 months, with 14 patients (40%) dying of disease (representing 7 enteroblastic, 4 hepatoid, and 3 clear cell CRC). Mutations were identified in TP53 (n=8) , APC (n=3) , FBXW7 (n=2), and KRAS (n=1). Inflammatory bowel disease significantly worsened recurrence-free survival on multivariate analysis, while distant metastasis significantly worsened both recurrence-free and overall survival on multivariate analysis. Enteroblastic, hepatoid, and clear cell CRC demonstrate morphologic and IHC overlap, leading to interobserver variability in diagnosis. Given potential differences in clinical correlations and outcomes, more refined criteria are likely necessary.

TPS277 Background: Recent advances in genomic sequencing have deepened our understanding of the molecular complexity of metastatic castration-resistant prostate cancer (mCRPC), revealing multiple actionable alterations that now inform biomarker-driven treatment strategies. Accordingly, germline and somatic tumor profiling is recommended for all patients with mCRPC. Beyond DNA aberrations, gene expression profiling can uncover additional therapeutic targets and pathway activations. The phase 2 PREDICT trial is leveraging both DNA and RNA alterations to guide rationally designed, biomarker-based therapeutic approaches for patients with mCRPC. Methods: This multi-center, multi-arm, biomarker-driven phase 2 umbrella trial is evaluating rationally selected therapies for patients with metastatic castration-resistant prostate cancer (mCRPC). The primary endpoint is objective response rate in patients with measurable disease, with secondary endpoints including radiographic progression-free survival, PSA response, time to first symptomatic skeletal event, overall survival, safety, and correlative biomarker analyses. Eligible patients must have progressive mCRPC of any histology, prior treatment with an androgen receptor pathway inhibitor (ARPI), and either prior or declined taxane chemotherapy, with both measurable and non-measurable disease permitted. Enrollment requires standard-of-care next-generation DNA sequencing from tissue or circulating tumor DNA performed in a CLIA-certified laboratory, and RNA-based allocation will use the CLIA-certified Caris MI Tumor Seek assay (whole exome and whole transcriptome sequencing) on tissue obtained within 12 months of study entry, with a real-time molecular tumor board reviewing results to confirm arm assignment. Patients with RB1 loss (DNA), an RB functional loss signature (RNA), or an NEPC signature (RNA) will receive the EZH1/2 inhibitor valemetostat; those with ≥2 of 3 tumor suppressor gene alterations (TP53, RB1, PTEN), FANC alterations (DNA), or SLFN11 overexpression (RNA) will receive cabazitaxel plus carboplatin; and those without study-defined alterations will receive physician’s choice of cabazitaxel, ARPI, or 177Lu-PSMA-617. The design permits incorporation of additional biomarker-defined arms, and up to 158 patients per arm (64 with measurable and 94 with non-measurable disease) will be accrued under a Simon two-stage minimax design, providing a one-sided type I error of 0.05 if the true response rate is 0.20 and 90% power if the response rate is 0.37 (Clinical trial information: NCT06632977). Clinical trial information: NCT06632977 .

ABSTRACT Tumorigenesis and metastasis are frequently attributed to the intricate interplay between cancer cells and the tumor microenvironment (TME). Comprehending the mechanisms and key regulators of cancer‐immune crosstalk in the TME is imperative for developing efficacious immunotherapy. Through a series of in vivo CRISPR screens, we identified tumor‐intrinsic ITGB1 as a critical regulator of triple‐negative breast cancer (TNBC) development and deciphered its underlying mechanisms. Tumoral ITGB1 facilitated the establishment of pro‐tumorigenic TME by orchestrating tumor‐associated myeloid populations. Suppressing ITGB1 favored the enrichment of anti‐tumorigenic myeloid cells and enhanced infiltration of CD4 and CD8 T cells, culminating in superior antitumor effects. CRISPR scanning pinpointed a previously unrecognized functional domain essential for ITGB1's pro‐tumorigenic activity. This domain is distinct from all known ligand‐binding sites in ITGB1. An antibody capable of sterically blocking this domain significantly impaired TNBC progression. These findings position tumoral ITGB1 as a promising therapeutic target for reprogramming the TME from a pro‐ to an anti‐tumorigenic state, thereby effectively inhibiting TNBC development. Our study uncovers a novel mechanism of TNBC development and provides a unique therapeutic strategy for targeting ITGB1 in TNBC treatment.

Abstract PAX5 is genetically altered in over 30% of B-ALL cases, with point mutations representing the second most common type of alteration. These point mutations are highly enriched in the DNA binding (paired) domain and have been recognized as founder events in PAX5 P80R and PAX5alt B-ALL subtypes, which account for over 12% of B-ALL. However, the molecular features and underlying mechanisms of these mutations in B-ALL remain largely undefined, limiting the development of targeted therapies and resulting in poor outcomes, especially in adult patients. We systematically investigated the functional roles and oncogenic mechanisms of PAX5 paired domain mutations. Integrated CRISPR screening and genomic profiling revealed that the paired domain is critical for PAX5 function. Disruptions in this region significantly reduced cell viability in B-ALL cell lines, and analysis of 2,955 B-ALL samples showed that recurrent PAX5 missense mutations are highly enriched in this domain, further underscoring its functional importance. Functional analysis of knock-in mice with PAX5 mutations revealed that R38H and R140L severely impair DNA binding and block B-cell differentiation, while P34L and P80R retain binding ability but alter binding specificity and gene regulation. Mice carrying homozygous (P34L, R38H, P80R, R140L) or heterozygous (R38H, P80R) mutations developed spontaneous B-ALL within one year. To model co-occurring mutations observed in patients, Pax5 R38H/P34L and R38H/R140L mice were generated. These compound mutations exhibited greater leukemogenic potential than single mutants. Transcriptomic analysis of leukemia samples showed consistent up-regulation of metabolic pathways and Myc target genes. Notably, biallelic PAX5 alterations and additional genetic lesions in signaling pathways were detected in all PAX5R38H/+ and PAX5P80R/+ leukemias, faithfully recapitulating the genetic alteration features of patient B-ALL driven by PAX5 mutations. Among Pax5-mutant mouse strains, Pax5P80R/+ mice develop B-ALL with short latency and complete penetrance, making them an ideal model to study the mutational evolution and leukemogenesis of B-ALL. To characterize the stepwise leukemogenesis process, we performed serial bone marrow aspirations in the same Pax5P80R/+ mice. In all 17 mice analyzed, we identified early preleukemic clones with only Pax5 WT deletions, followed by the emergence of leukemic clones harboring Jak1/3 mutations. Single-cell RNA/BCR-seq revealed that Pax5 WT allele deletions relieve metabolic constraints, thereby promoting clonal expansion of preleukemic B cells blocked at the pre-B stage. These changes coincide with downregulation of metabolic checkpoint genes and upregulation of glycolytic enzymes, promoting genetic instability and facilitating malignant transformation. Clinically, PAX5 P80R patients have better outcomes than PAX5alt cases. Using our mouse models, we observed that leukemic cells driven by the PAX5 P80R mutation exhibit greater sensitivity to dexamethasone compared to the ones carrying other PAX5 mutations in PAX5alt subtype, potentially due to their heightened dependence on glucose uptake and glycolysis, suggesting that metabolic rewiring driven by PAX5 mutants may influence therapeutic response. Interestingly, we found that an aberrant isoform of MEGF10 (aMEGF10) is highly and specifically expressed in PAX5 P80R B-ALL. This N-terminal truncated isoform encodes a protein that retains the intracellular immunoreceptor tyrosine-based activation motifs (ITAMs). Using CUT&Tag, we showed that PAX5 P80R directly binds to the aMEGF10 promoter. By engineering human CD34⁺ cells, we established a humanized PAX5 P80R leukemia model that recapitulates the gene expression profile of patient samples, including robust activation of aMEGF10. Functionally, aMEGF10 binds to and activates SYK, thereby promoting leukemic cell proliferation. Importantly, this oncogenic effect depends on intact ITAM motifs and SYK signaling, revealing a novel targetable vulnerability in PAX5 P80R leukemias. Overall, the study establishes that PAX5 DNA binding domain mutations contribute to leukemogenesis through stepwise loss of PAX5 WT alleles and acquisition of signaling pathway mutations, involving impaired differentiation, metabolic deregulation, and novel oncogene activation. These findings not only deepen the understanding of PAX5-driven leukemias but also highlight aMEGF10–SYK signaling as a promising therapeutic target.

Abstract Pseudouridine (Ψ) is the most prevalent RNA modification in human cells. Although Ψ was among the first post-transcriptional modifications discovered (1951), its biological functions remain poorly understood. More recently, Ψ was incorporated into COVID-19 mRNA vaccine, where it enhances RNA stability and reduces innate immune sensing. However, the precise roles of RNA Ψ in cancer, including leukemia, are largely unknown. Here, we identify RNA Pseudouridine Synthase D4 (RPUSD4) as a novel vulnerability in acute myeloid leukemia (AML) via directly catalyzing mitochondrial RNA (mt-RNA) Ψ formation. We further provide proof-of-concept evidence that targeting RPUSD4 suppresses leukemogenesis and stimulates anti-leukemia immunity. To investigate whether RNA Ψ dysregulation is involved in leukemia, we first compared RNA Ψ levels between primitive CD34+ cells (LSC-enriched) and CD34- bulk cells from multiple primary AML specimens. CD34+ AML cells exhibited significantly elevated RNA Ψ levels. We also examined Ψ levels across various RNA types in AML cells, identifying that mt-RNA contained much higher Ψ levels than other RNA types. These findings imply that RNA Ψ, particularly mt-RNA Ψ, may play a role in LSC biology and leukemogenesis. Further unbiased CRISPR screening revealed RPUSD4 as the most critical Ψ synthase for LSC maintenance. Large-scale transcriptomic and patient data analyses showed that RPUSD4 is highly expressed in AML specimens (P = 3.5 × 10-9), particularly within LSCs (P = 1.4 × 10-18). RPUSD4 knockout (KO) significantly suppressed AML proliferation, reduced mitochondrial OxPhos, and decreased LSC frequency in vitro and substantially delayed AML progression in vivo (MLL-r and FLT3ITD models). Of note, RPUSD4 KO-mediated anti-leukemia effects could be fully rescued by wild-type but not catalytically inactive RPUSD4 both in vitro and in vivo, demonstrating that Ψ synthase activity is essential for its function in leukemia. To profile RPUSD4-dependent Ψ sites, we applied two orthogonal technologies, direct nanopore sequencing and PRAISE sequencing (PMID: 36997645), both capable of detecting Ψ at single-base resolution. These approaches converged on a single RPUSD4-dependent Ψ at position 3,067 on mt-16S rRNA. This Ψ site is essential for maintaining rRNA stability. RPUSD4 KO induced mt-16S rRNA decay, thereby suppressing mitochondrial translation. This led to OxPhos inhibition, growth suppression, and LSC eradication in AML. Mechanistically, RPUSD4 is exclusively localized in mitochondria, where it directly interacts with the mt-RNA exonuclease PNPase. Under physiological conditions, PNPase resides within mitochondria and degrades mt-RNA to prevent accumulation of mitochondrial double-stranded RNA (mt-dsRNA). Upon RPUSD4 depletion, PNPase translocates from mitochondria to the cytosol, resulting in two major consequences: (i) mRNA decay:Cytosolic PNPase degrades mRNAs, particularly the nuclear-encoded mitochondrial mRNAs, such as DHODH(Dihydroorotate dehydrogenase). By retrogradely upregulating DHODH, RPUSD4 promotes de novo pyrimidine synthesis in AML. (ii) Aberrant mt-dsRNA accumulation: The buildup and cytoplasmic release of mt-dsRNA activates “viral mimicry” response that sensitizes AML cells to T cell cytotoxicity. Finally, to therapeutically target RPUSD4, we developed an RNA-based inhibitor, CpG-siRNARPUSD4, by conjugating a specific RPUSD4 siRNA to a Toll-like receptor (TLR9) ligand. CpG-siRNARPUSD4 is specifically internalized by TLR9+ cells, including AML cells, thereby maximizing selectivity and minimizing toxicity. Preclinical studies demonstrate that pharmacologically targeting RPUSD4 significantly prolonged survival across multiple AML models, including patient-derived xenograft (PDX) models, and rendered AML cells more susceptible to T cell–mediated cytotoxicity. Furthermore, the RPUSD4 inhibitor exhibited a promising synergistic effect with DHODH inhibitor in treating relapsed AML in vivo. For instance, in a representative relapsed PDX model, median survival times (in days) were: Ctrl – 28, RPUSD4 inhibitor – 36, DHODH inhibitor – 39, and combination – over 60. In conclusion, our findings uncover a previously unrecognized role of RPUSD4 and mt-RNA Ψ in leukemic metabolism, anti-leukemia immunity, and LSC maintenance. This study also bridges a critical knowledge gap regarding the role of RNA Ψ in leukemogenesis.

Abstract A systematic approach to identifying novel therapeutic strategies is essential for expanding curative options in hematopoietic malignancies such as acute myeloid leukemia (AML). We have recently established a high-resolution genetic platform that enables de novo therapeutic development through the CRISPR-Tiling Instructed Computer-Aided (CRISPR-TICA) workflow (Nat Struct Mol Biol 2024, PMID: 38316881). Using this approach, we further identified a new therapeutic pocket and its lead compound for AML treatment (Sci Adv 2024, PMID: 38394203). Here, we present an integrative pipeline, CRISPR-TICA.ai, which combines CRISPR-based functional genomics with generative artificial intelligence (GenAI)-driven ligand modeling to perform high-throughput evaluation of the top 100 leukemia-essential genes and their therapeutic potential in AML. We first used the CRISPR screen dataset published by Novartis (Cancer Discov 2016, PMID: 27260157), which tile-scanned 68 genes in three cancer cell lines, as the initial training dataset to establish the CRISPR-TICA.ai pipeline. Structurally, ligandable protein surface pockets were identified by employing the P2Rank algorithm (J Cheminform 2018, PMID: 30109435). For each pocket, we used the structure-guided diffusion model DiffSBDD (Nat Comput Sci 2024, PMID: 39653846) to generate previously unseen chemical structures that differ substantially from existing drugs, thereby enabling the exploration of novel chemical space. The model was further fine-tuned using direct preference optimization (NeurIPS 2023) against a curated dataset of known inhibitors to enrich for favorable binding profiles (low binding free energy, ΔG) and calibrated against drug-likeness (QED), synthetic accessibility (SA), lipophilicity (logP), and Lipinski's rule compliance. Additionally, our pipeline integrates ligand–protein contact maps with CRISPR-hypersensitive positions to assess spatial interactions, prioritizing ligands that effectively mask biologically essential residues with high affinity. The utility of CRISPR-TICA.ai in AML drug discovery was evaluated- we selected the top 100 leukemia-essential genes from the DepMap database (https://depmap.org/portal/) and generated custom CRISPR libraries for high-resolution gene tiling screens. These libraries comprised 20,233 sgRNAs to tile-scan all 100 genes (47,901 amino acid residues) in Molm13 AML cells at an average resolution of 2.4 amino acids per sgRNA. This dataset provided in-depth structural and functional input for CRISPR-TICA.ai to examine AI-enabled ligand design for over 300 high-confidence druggable pockets in AML. We further developed a user-friendly, web-based 3D visualization platform that interactively maps functional CRISPR hotspots alongside predicted pockets and ligands to enhance accessibility and reproducibility. This tool allows visualization of CRISPR tiling scores, predicted binding pockets, and ligand prioritization, enabling interactive exploration and application. To annotate therapeutically relevant sites, we incorporated data from multiple genomic and proteomic resources, including AlphaFold protein models, Pfam domain annotations, post-translational modification (PTM) sites, and COSMIC leukemia mutational data. Exportable files and GitHub integration are also provided for advanced users to deploy CRISPR-TICA.ai within their facilities.In summary, our study introduces a scalable, leukemia-focused framework for de novo therapeutic discovery. By integrating high-density CRISPR mutagenesis with diffusion-based GenAI modeling, CRISPR-TICA.ai provides a rational roadmap for compound design targeting residues essential for leukemia maintenance. Importantly, the CRISPR-TICA.ai pipeline is adaptable to CRISPR tiling datasets from solid tumors (e.g., the Novartis dataset), highlighting its versatility across diverse cancer types. This approach is especially promising for addressing historically undruggable and resistance-prone targets in AML and beyond.

Abstract Nucleophosmin mutations are among the most common aberrations in acute myeloid leukemia (AML). We previously uncovered a novel pivotal role for mutant NPM1 (NPM1c) in the nucleus, where it binds chromatin at key self-renewal gene loci, such as HOXA/B and MEIS1, directly regulating oncogenic transcription. How NPM1c regulates the transcriptional activity of its chromatin targets remains unclear. To identify potential nuclear cooperating partners of NPM1c, we employed TurboID proximity labeling of NPM1c and wild-type NPM1 (NPM1wt). Mass spectrometric analysis revealed an enrichment of nucleoporins in the NPM1c interactome, with Nucleoporin 98 (NUP98) emerging as a top candidate. NUP98, a key component of the nuclear pore complex (NPC), has been established as a critical oncogenic player in AML as part of oncogenic fusion proteins. In these oncofusions the N-terminal FG (phenylalanine-glycine) repeat domain of NUP98 is preserved and fused to a diverse set of partner genes. NUP98-fusion partners are believed to mediate the chromatin binding specificity of the oncoprotein while the NUP98 FG repeats have been shown to form biomolecular condensates that enhance transcriptional output. Interestingly, wild-type NUP98 (NUP98wt) itself has been linked to gene regulatory functions during embryonic development and normal hematopoiesis. However, the role of NUP98wt in transcriptional regulation in the context of leukemia remains unresolved. To explore a potential cooperation between NUP98wt and NPM1c we first validated their interaction by co-immunoprecipitation assays. We next wanted to determine whether NUP98 and NPM1c are recruited to the same chromatin sites. To this end, we performed ChIP-seq in an NPM1c endogenous degrader cell line. These experiments revealed co-occupancy of NUP98 at NPM1c target genes and a significant reduction of NUP98 binding upon degradation of NPM1c. These findings suggest that NPM1c is required for the recruitment of NUP98 to key oncogenic target loci. To dissect the functional role of NUP98wt in NPM1c AML, we performed loss of function studies. CRISPR mediated knock-out of NUP98 in NPM1 mutant (OCI-AML3) cells resulted in a significant repression of NPM1c target genes, including HOXA/B and MEIS1. Given the essential nature of NUP98, we also engineered an endogenous NUP98 degrader system in OCI-AML3 and NPM1wt (MV4-11) cells to allow for the study of the effects of rapid protein depletion. Upon degradation of NUP98, OCI-AML3 cells exhibited robust myeloid differentiation (~70% increase in CD11b) and increased apoptosis (~50% increase in Annexin V+). MV411 cells on the other hand did not show the same differentiation phenotype. To characterize the immediate transcriptional consequences of NUP98 depletion, we performed nascent RNAseq after 1 and 3 hours of degradation. In the first hours of degradation we observed a rapid and significant repression of NPM1c target genes such as HOXA/B cluster genes, MEIS1, SMC4, TNRC18, SATB1/2 and UNCX, thus demonstrating the strong dependency of the NPM1c-driven transcriptional program on the presence of NUP98. In contrast, in MV4-11 cells, NUP98 loss had no effect on HOXA/MEIS1 expression, suggesting a leukemia subtype-specific role of NUP98wt. To delineate the domains of NUP98 required for its chromatin function, we performed a CRISPR gene tiling screen of full-length NUP98 (635 sgRNAs) and based on this we generated several domain-deletion mutants for rescue experiments in the NUP98-degrader cell lines. Retroviral overexpression of the N-terminal FG-repeat containing domains of NUP98 was sufficient to rescue cell viability and prevent the differentiation phenotype typically observed upon NUP98 degradation. Strikingly, gene expression analysis showed that the NUP98 FG-repeats were sufficient to restore the expression of HOXA10, MEIS1, and HOXB9 expression. Overall, our study identifies NUP98wt as a critical cofactor for NPM1c-driven oncogenic transcription. NPM1c recruits NUP98 to its chromatin targets, functionally substituting for an oncogenic fusion partner to concentrate transcriptional condensates at oncogenic loci. This establishes a previously unrecognized, subtype-specific dependency on NUP98wt in leukemogenesis.