Alexander van Oudenaarden

Intestinal homeostasis requires tight regulation of stem cell maintenance and differentiation to absorptive and secretory cell types, two major intestinal lineages. Key signaling pathways have been identified, but how they balance cell type composition remains unclear. We uncovered oscillatory expression of the Notch-target protein Hes1 (hairy and enhancer of split 1) that controls cell fate specification in a frequency-dependent manner. An endogenous fluorescent Hes1 reporter revealed distinct, cell type–specific oscillation frequencies forming a gradient along the crypt-villus axis, which was modulated by cell cycle phase as well as Wnt (wingless-related integration site)–signaling and Notch-signaling activity. We developed a microfluidic system to modulate Notch-signaling oscillations in organoids and found the oscillation frequency to regulate the balance of cell type composition. This study provides evidence that information for cell fate specification is encoded in the frequency of an oscillatory signal.

Mitochondrial DNA (mtDNA) mutations cause inherited disease, accumulate with age, and recur in tumors, yet their effects remain unresolved because existing models interrogate one engineered allele at a time. We developed mtDIVE, a random C→T mutagenesis platform for pooled mitochondrial forward genetics in human epithelial cells and zebrafish embryos. mtDIVE generates genotypes ranging from single substitutions to >100 mutations per molecule, impairs respiration, and causes lineage-specific developmental delay. Coupling single-cell transcriptomics with mtDNA genotyping revealed that selection on mutant genomes and their transcriptional consequences depend on metabolic state and developmental lineage. Obligate OXPHOS eliminates highly mutated cells by apoptosis, whereas glycolytic conditions promote their competitive displacement. Individual loci exert modest but non-redundant effects that predict cell state beyond aggregate mutation burden, and cancer-recurrent variants are enriched among mutations linked to reduced mitochondrial transcription. Thus, mtDIVE links mtDNA genotypes to cellular phenotypes, separating the consequences of mutation identity from mutational load.

How tumors generate a cryptic “dark” proteome absent from healthy tissues, and whether it can be reversibly activated, remains unclear. In Ewing sarcoma, all tumors are driven by EWSR1::ETS fusions, making it a tractable model to study dark proteome activation. Integrating matched transcriptomes, translatomes and proteomes from 48 patient tumors with long-read RNA sequencing, single-cell Ribo-seq, proteomics and immunopeptidomics in cell line models, we show that EWSR1::FLI1 acts as a reversible switch recurrently inducing hundreds of cancer-specific neoproteins. Many arise from canonical coding regions via intragenic transcription start sites, generating truncated or out-of-frame neoproteins. We uncover a fusion-dependent increase in ribosomal readthrough into poly(A) tails, generating a stable 80-amino-acid TRPM4 neoprotein that, despite lacking a stop codon, is the most abundant tumor-specific microprotein across patients. Proteomic, immunopeptidomic, and immunofluorescence analyses validate neoproteins as tumor-restricted antigens, revealing a therapeutically actionable cancer dark proteome controlled by one oncogenic fusion. Highlights: Fusion proteins activate in- and out-of-frame neoproteins through intragenic transcription. Neoproteins exhibit distinct protein structures and localizations compared to their host genes. Mass spectrometry detects 911 cryptic proteins, including 29 EwS neoproteins, 15 HLA-I presented. TRPM4-dORF is a stop-less 80-aa neoprotein with abundant peptide evidence exclusively in EwS.

Protein synthesis is dynamically regulated to control cell growth, differentiation, and stress responses. Recent single-cell sequencing methods can map ribosome positions on individual transcripts ^1–4 , but cannot capture the global translational states that coordinate protein synthesis across the transcriptome. In contrast, methods that measure the global translational landscape, such as polysome profiling and cryogenic electron tomography ⁵ , lack either single-cell resolution or throughput. Here we introduce SCISSOR (Single-Cell Inference of Structural States of Ribosomes), a strategy that infers global translation activity in individual cells from the differential protection of ribosomal RNA (rRNA) against nuclease digestion. By integrating these protection signatures with the structure of the ribosome, SCISSOR resolves multiple ribosomal states and quantifies their abundance across thousands of individual cells. Applying SCISSOR reveals systematic variation in global translation across the cell cycle in human cells, as well as during the differentiation of murine intestinal stem cells into distinct epithelial lineages. These findings uncover principles of global translational regulation that are invisible to transcriptomic or ribosome-profiling assays, establishing a framework for studying global translation control at single-cell resolution.

The intestinal epithelium is continuously subjected to a variety of mechanical forces, including extrinsic peristaltic contractions and intrinsic tensile forces generated by epithelial cell migration. Yet, how these mechanical cues influence the cellular processes underlying intestinal homeostasis remains poorly understood. In this study, we examine the impact of mechanical forces on intestinal cell dynamics by applying controlled external stretch to intestinal organoids, combined with high-throughput single-cell transcriptomic profiling. Our analyses reveal that prolonged cyclic mechanical strain alters the composition of differentiated intestinal cell populations. Specifically, we identify a strain-induced shift in the absorptive lineage towards a less mature state, with expansion of the population of early-stage enterocytes at the crypt–villus interface. This shift is associated with downregulation of transcriptional programs controlling enterocyte maturation within absorptive precursor populations. Our findings indicate that mechanical strain directs the maturation of the intestinal absorptive lineage, and highlight a role for mechanical forces in shaping intestinal epithelial composition and function.

Replication stress poses a major threat to genome integrity, yet how higher-order chromatin organization contributes to replication fork protection remains unclear^1,2. Here we show that replication stress induces the formation of transient chromatin loops that enclose de novo heterochromatin-enriched stalled replication forks³. Stressed forks preferentially stall at convergent CTCF motifs, triggering stress-dependent CTCF enrichment that constrains loop extrusion and stabilizes these structures. Loop stabilization requires both CTCF anchoring and G9a-dependent heterochromatin (trimethylation of Lys9 of histone H3 (H3K9me3)) deposition on nascent DNA within the loop body. These loops function as protective scaffolds that shield stalled and reversed forks from degradation by multiple nucleases. By contrast, combined loss of stress-induced heterochromatin and CTCF enrichment destabilizes the loop scaffold, exposing multiple entry points for nucleolytic attack and resulting in extensive nascent-strand degradation through mechanisms distinct from classical fork-reversal-dependent pathways. This protective architecture is similarly critical in BRCA2-deficient cells, in which replication-stress-associated loops predominantly safeguard replication initiation zones, while nascent DNA outside these loops undergoes massive degradation and remains highly susceptible to mutations. Our study elucidates the fundamental role of replication-stress-induced three-dimensional genome reorganization in preserving replication fork stability, thereby mitigating mutagenesis and genomic instability.

Supplementary table 7: Full list of genes whose knockout was selectively toxic in the presence of LB-100 in SW-480 cells in the CRISPR-KO screen FDR smaller or equal to 0.25 and log2 fold change smaller or equal to -1 in treated/untreated comparison were criteria for hit selection.

Supplementary table 4: The composition of the stress-focused drug library Compounds comprising the stress-focused drug library with their respective targets.

Figure S3: High N-Myc levels sensitize neuroblastoma cells to LB-100, and PP2A knockdown sensitizes CRC cells to WEE1 inhibition (A) Western blots comparing N-Myc levels in isogenic neuroblastoma models. GAPDH was used as a loading control. (B) long-term viability assays compares the toxicity of LB-100 across these neuroblastoma models. LB-100 was refreshed every 2-3 days, and the cells were grown for 10 days before fixing, staining, and imaging. (C) Western blots show the knockdown of PPP2R1A in HT-29 and SW-480 cells. GAPDH was used as a loading control. (D) Dose-response assays show the effect of Adavosertib after PPP2R1A knockdown compared to a control shRNA in HT-29 and SW-480 cells. Cell viability was estimated by resazurin fluorescence after 5 days in the presence of the drug or DMSO control. The normalized values are plotted. (E) The heat map shows all “Hallmarks” and “KEGG” molecular signatures significantly enriched by LB-100 (4 µM), calyculin A (5 nM), or okadaic acid (10 nM) in HT-29 and SW-480 cells after 8 hours. Asterisks indicate significance level (* p-value <0.05, ** p-value <0.01, *** p-value <0.001).

Figure S7: Normal tissues from the orthotopic CRC PDXs are not affected by LB-100, adavosertib, or the combination. Representative Hematoxylin & Eosin (H&E) stainings of the heart, liver, lung, and spleen from the PDOX1 PDXs treated as indicated. Original magnifications are indicated.