Thierry Voet

CRISPR-Cas9 has become a key genome imaging tool, because of its sequence-specific binding to genomic DNA. To achieve signal amplification or multiplexing, various complex CRISPR-Cas9 modifications were introduced, primarily relying on expression-based delivery. However, these engineering strategies often invoke structural perturbations and their performance remained dictated by vector design and in vivo CRISPR ribonucleoprotein (RNP) assembly. To date, research mainly focused on optimizing the expression-based delivery mechanisms of CRISPR components rather than addressing the engineering itself. Here, we developed a modular SPAAC (bio-orthogonal strain-promoted azide-alkyne cycloaddition) click-chemistry-based strategy for engineering the CRISPR RNP that is completely dissociated from its assembly. We demonstrated that CRISPR can be modified (with fluorophores and DNA) at all stages of RNP in vitro assembly and subsequently validated the technology for genome imaging. Importantly, we also revealed that engineering native CRISPR RNP only after it is being formed, minimizes structural perturbations to the complex and yields a two-fold enhanced accessibility of 'clicked' DNA. Finally, we utilized SPAAC to conjugate non-native RNA-DNA hybrids, regardless of 5'-3' directionality, to develop a covalently-attached rolling-circle signal amplification approach. The modularity and universal nature of our approach holds the potential to deliver significant advances to both CRISPR imaging and prime-editing fields.

Understanding the spatial and temporal dynamics of tumour evolution is crucial for determining the drivers of cancer progression. Linking genotype to phenotype across a tumour remains challenging, however. Here, we use single-cell and spatial multi-omics to comprehensively profile a primary malignant peripheral nerve sheath tumour (MPNST) and its multifocal recurrence. Combining the native barcoding system from extensive heterogeneity in copy number alterations with mutation data, we resolve the evolutionary tree of this tumour, revealing a branching structure suggestive of ongoing chromosomal instability. We show that gene dosage effects contribute to phenotypic diversity and scale predominantly linearly with copy number. Using spatial genomics assisted by laser capture microdissection and spatial transcriptomics, we performed in situ lineage tracing in this human tumour, elucidating the relationship between local expansions and interactions between tumour cells and the microenvironment. These findings demonstrate the potential of combined bulk, single-cell and spatial techniques to dissect cancer evolution in time and space and link genotype to phenotype in detail.

Lipids constitute one of the largest and most diverse classes of cellular molecules, sustaining membrane architecture, energy storage, and signaling. Consequently, their dysregulation underlies a broad spectrum of human disease. However, the genetic mechanisms governing lipid homeostasis have remained largely inaccessible, owing to the lack of approaches capable of systematically linking defined genetic perturbations to large-scale changes in cellular lipidome composition. Here we introduce LipoGrid, a spatial mass spectrometry platform that resolves the genetic architecture of lipid metabolism at single-cell resolution. LipoGrid arrays CRISPR/Cas9-perturbed cells on a micropatterned grid and sequentially captures lipidomic and gRNA identity from the same cells, complemented by single-cell RNA sequencing of matched cell populations subjected to the same perturbations. Using this approach, we quantified the relative abundance of 158 distinct lipid species across 143 target genes in a rigorously controlled experimental framework. We find that most gene knockouts produced measurable alterations in lipid composition, often affecting specific lipid classes and molecular subspecies. The screen accurately recapitulated established gene-lipid relationships, including enzyme-substrate specificities, lipid pathway regulators, and disease-associated loss-of-function phenotypes, thereby demonstrating the sensitivity and accuracy of LipoGrid. By jointly profiling transcriptomic and lipidomic responses, we further uncover compensatory feedback mechanisms that buffer the impact of genetic perturbations on the cellular lipidome. Collectively, these findings establish LipoGrid as a scalable multimodal platform for systematically mapping gene-lipid interactions and reveal the regulatory networks linking gene perturbation, transcriptional adaptation, and lipidome remodeling. Highlights: Micropatterned single-cell growth enables spatial lipidomic perturbation screens LipoGrid maps 143 gene knockouts to 158 lipid species and transcriptomic states Perturbed lipidomes reveal compensatory feedback and lipid-class-specific uptake Recovers enzyme substrate specificities and disease-linked lipid signatures

Figure S3 showing a comparison between identified mutational signatures from the samples and the COSMIC database.

Figure S2 showing DBS and indel count in the cord blood DNA.

FigureS1 showing the assessment of possible maternal contamination in the cord blood samples.

Figure S4 showing the identified indel signatures in the cord blood samples.

Figure S5 showing a comparison between the in vitro generated mutational signatures and the COSMIC database.

Supplementary tables listing demographic, oncological and obstetrical data per patient (Table S1), statistical comparisons (Table S2) and annotated variants (Table S3).

Chemotherapy is included in the standard-of-care for cancer treatment during pregnancy. However, whether prenatal exposure to maternal chemotherapy treatment has a mutagenic impact on the fetal genome remains unexplored. Therefore, we investigated mutation accumulation in hematopoietic stem and progenitor cells from neonates born to pregnant patients with cancer treated with chemotherapy, as well as healthy pregnant women and untreated pregnant patients with cancer. The mutational burden in hematopoietic stem and progenitor cells from neonates born to untreated pregnant patients with cancer and to healthy controls was similar but increased after prenatal exposure to varying types of chemotherapy regimens. Mutational signature analyses attributed the excess mutations to clock-like processes, which are active during normal cellular aging, or to direct mutagenesis by platinum-based drugs in neonates prenatally exposed to platinum-containing regimens. Our findings in the neonatal hematopoietic compartment are consistent with mutational signatures previously identified in cells of cancer survivors directly exposed to these chemotherapeutic drugs.Significance:This study demonstrates that environmental mutagenic exposure during pregnancy can increase somatic mutation accumulation in the fetus. Given that detrimental early life exposures can adversely affect health outcomes later in life, our study highlights the need for further research into the impact of environmentally induced genomic insults during the perinatal period.See related commentary by Furudate and Takahashi, p. 870