Center for Human Genetics

BackgroundThe integration of multimodal single-cell data enables comprehensive organ reference atlases, yet its impact remains largely unexplored, particularly in complex tissues. Using the kidney as an emblematic example of a complex organ, we perform a systematic evaluation of multimodal single-cell integration strategies, with heart tissue used for additional methodological validation.ResultsWe generate a benchmarking dataset for the renal cortex by integrating 3' and 5' scRNA-seq with joint snRNA-seq and snATAC-seq, profiling 119,744 high-quality nuclei/cells from 19 donors. To align cell identities and enable consistent comparisons, we develop the interpretable machine learning tool scOMM (single-cell Omics Multimodal Mapping) and systematically assess integration strategies. "Horizontal" integration of scRNA and snRNA-seq improves cell-type identification, while "vertical" integration of snRNA-seq and snATAC-seq has an additive effect, enhancing resolution in homogeneous populations and difficult-to-identify states. Global integration is especially effective in identifying adaptive states and rare cell types, including WFDC2-expressing Thick Ascending Limb and Norn cells, previously undetected in kidney atlases.ConclusionsOur work establishes a robust framework for multimodal reference atlas generation, advancing single-cell analysis and extending its applicability to diverse tissues.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13059-026-04002-4.

Deleterious mutations in the CYBB gene encoding NOX2 typically cause X-linked recessive chronic granulomatous disease (XR-CGD) by affecting NADPH oxidase-dependent respiratory burst in phagocytes. However, two missense variants (T178P, Q231P) were previously shown to cause isolated Mendelian susceptibility to mycobacterial disease (MSMD) in otherwise healthy males. We describe a novel, private variant in CYBB (c.998C > A, p.S333Y) identified in a male patient with adult-onset disseminated Mycobacterium avium infection. Despite preserved transcript levels, NOX2 protein expression was reduced in the patient's cells. Functionally, an intermediate phenotype was observed, characterized by reduced but not abolished ROS production, with a cell-type specific degree of impairment. This case represents the second report of isolated X-linked recessive MSMD caused by a missense CYBB variant, and the first case presenting in adulthood. Our findings indicate a hypomorphic variant that impairs respiratory burst in a cell type-specific manner, extending previous observations in two kindreds with CYBB-associated MSMD.

Bismuth selenide (Bi2Se3) is a promising semiconductor material, with applications ranging from thermoelectric devices and topological insulators (TIs) to photocatalysis. Here, Bi2Se3 films were grown on fluorine-doped tin oxide (FTO) substrates using electrodeposition under controlled parameters, such as the electrodeposited charge and electrolyte temperature for solar-driven water splitting, resulting in films with different crystalline phases, morphologies, and PEC performances. Heating the electrolyte promotes the formation of uniform and compact films as well as the coexistence of orthorhombic (O–Bi2Se3) and rhombohedral (R–Bi2Se3) structures. Notably, PEC measurements demonstrated a significant increase in photocurrent density (up to 0.52 mA/cm2 at 0.6 VAg/AgCl) and lower charge transfer resistance in films deposited with a heated electrolyte. Absorbance and Fourier transform infrared (FTIR) analyses indicate that interactions between the crystalline phases can alter their spectra, possibly due to the formation of an R/O–Bi2Se3 heterophase junction, which contributes to the improvements noted in the PEC performance. Density functional theory (DFT) calculations indicate that R–Bi2Se3 is a TI, while the temperature of O–Bi2Se3 is normal, suggesting that grown films can host electronically active R/O heterophase. These findings highlight the impact of changes in surface morphology, crystal structure, and surface chemistry on enhancing PEC performance, offering a straightforward and scalable approach for optimizing nonoxide semiconductors through electrochemical strategies for solar-driven water splitting.

The recycling of fossil-based plastic waste remains a key challenge in reducing environmental pollution and greenhouse gas emissions. An innovative approach is the biotechnological conversion of the n-alkane mixture obtained from thermal pyrolysis of plastic waste. This study focuses on the use of the oleaginous yeast Yarrowia lipolytica for the valorization of polyethylene (PE)-derived pyrolysis oil. From a screening of 50 Y. lipolytica strains, the most promising candidate was selected, and its single-cell phenotype was stabilized by MHY1 deletion. In shake flask experiments, this strain grew similarly on 5-20 vol% of n-hexadecane, revealing no inhibitory effects. Subsequently, a high cell density fermentation was established in a 4 L bioreactor using a pulsed fed-batch approach, resulting in biomass concentrations of up to 145.6 g·L-1, which contained 22.0% triacylglycerols. In addition, cultivation at pH 2.5, compared to pH 4.0, reduced citrate formation from 95.6 to 0.8 g·L-1, while biomass and TAG titers remained similar. Overall, these results highlight the potential of integrating plastic waste-derived pyrolysis oil into future bioprocesses using Y. lipolytica as an effective platform for high cell density production.

All genomes have mobile genetic segments called transposable elements (TEs)1. Here we describe a system, which we term SOS splicing, that protects Caenorhabditis elegans and human genes against DNA-transposon-mediated disruption by excising these TEs from host mRNAs. SOS splicing, which seems to operate independently of the spliceosome, is a pattern-recognition system triggered by the base-pairing of inverted terminal repeat elements, which are a defining feature of DNA transposons. We identify three factors required for SOS splicing in both C. elegans and human cells: AKAP17A, which binds TE-containing mRNAs; the RNA ligase RTCB; and CAAP1, which bridges RTCB and AKAP17A to allow RTCB to ligate mRNA fragments generated by TE excision. We propose that SOS splicing is a previously undescribed conserved and RNA-structure-directed mode of mRNA splicing, and that an identified function of SOS splicing is to genetically buffer animals from the deleterious effects of DNA-transposon-mediated gene perturbation.

The rapid and sustained proliferation of cancer cells necessitates increased protein production, which, along with their disrupted metabolism, elevates the likelihood of translation errors. Ribosome-associated quality control (RQC), a recently identified mechanism, mitigates ribosome collisions resulting from frequent translation stalls. However, the precise pathophysiological role of the RQC pathway in oncogenesis remains ambiguous. Our research centered on the pathogenic implications of mitochondrial stress-induced protein carboxyl-terminal alanine and threonine tailing (msiCAT-tailing), a specific RQC response to translational arrest on the outer mitochondrial membrane, in glioblastoma (GBM). The presence of msiCAT-tailed mitochondrial proteins was observed commonly in glioblastoma stem cells (GSCs). The exogenous introduction of the mitochondrial ATP synthase F1 subunit alpha (ATP5α) protein, accompanied by artificial CAT-tail mimicking sequences, enhanced mitochondrial membrane potential (ΔΨm) and inhibited the formation of the mitochondrial permeability transition pore (MPTP). These alterations in mitochondrial characteristics provided resistance to staurosporine (STS)-induced apoptosis in GBM cells. Consequently, msiCAT-tailing can foster cell survival and migration, whereas blocking msiCAT-tailing via genetic or pharmacological intervention can impede GBM cell overgrowth.

Human pluripotent stem cells (hPSC) are increasingly used in clinical trials, with retinal pigment epithelium (RPE) being among the most transplanted cell types. However, hPSC frequently acquire chromosomal abnormalities, whose impact on differentiation and transplant safety is incompletely understood. In this work, we investigate how aneuploidy influences the progression of hPSC through undirected RPE differentiation. Large-scale omics analysis of genetically normal hPSC cultures reveals pervasive low-grade mosaicism, with 3–6% of cells carrying different aneuploidies. During undirected differentiation, all aneuploid cells are lost except those with a gain of chromosome arm 1q. These cells differentiate efficiently only when co-cultured with wild-type cells, which promote neural differentiation through paracrine signals that 1q-gain cells are uniquely receptive to. This interaction enables 1q-gain cells not only to persist but to eventually dominate the culture, owing to their competitive advantage.

Background: Decoding the genetic code to unveil its genome functionality is a monumental task which would greatly advance the understanding of disease mechanisms and development of targeted treatment approaches. Although large language models (LLMs) have transformed natural language processing across diverse domains, translating the complex language of DNA into human-readable form remains challenging due to genomic data complexity and unexplored regions of the human genome. Current (genomic) language models either have a solid understanding of natural language or of the genomic code. Models fusing both aspects are largely lacking. Results: Here we present Genolator, a multimodal large language model that integrates embeddings from DNA sequences, amino acid sequences, and protein structures with natural language queries. Fine-tuned on over 370,000 question-answer pairs generated using abstracted Gene-Ontology (GO) terms, Genolator effectively answers queries regarding protein subcellular localization, molecular function, and biological processes. Evaluation demonstrates high accuracy in confirming or denying protein function associations, outperforming baseline models such as openly available allrounder LLMs like GPT 4.1 as well as smaller domain specific models integrating knowledge from foundation models like Evo2 and ESM-2. Explorations of the Genolator's hidden states unveil a biologically and linguistically plausible organization of its learned representations. Conclusion: Genolator enhances accessibility to genomic information by enabling natural language interaction with protein data, facilitating biological discovery, and clinical research. It represents a step towards bridging genomic code and human language through the integration of a multimodal LLM.

Despite extensive genetic heterogeneity, 72% of pathogenic alleles for Hirschsprung disease (HSCR) arise from coding and regulatory variants in genes of the RET and EDNRB gene regulatory network (GRN) in the enteric nervous system (ENS). To elucidate the mechanisms leading to enteric neuronal loss from these genetic defects, we generated four strains of mice carrying reduced function alleles at Ret or Ednrb or both, along with their wild-type alleles. ENS tissue- and single-cell gene expression profiling of the developing and postnatal gastrointestinal tract in these five mouse models revealed three major insights: i) Ret and Ednrb deficiency, rather than complete loss, is sufficient to induce HSCR, ii) Ret and Ednrb demonstrate strong trans interactions, and iii) disruption of this interaction leads to cellular fate changes to compensate for neuronal loss. Critically, we show the combined reduction of signaling of these two receptors below a threshold in enteric neural crest-derived cells (ENCDCs) leads to a molecular tipping point at which otherwise lesser cellular defects result in aganglionosis. This study of targeted mouse models of a multifactorial disorder reveals how increasing dosage of genetic defects within a GRN leads to quantifiably increasing dysregulation from genotype to gene expression to cellular identity to function. Importantly, our studies establish that aganglionosis results only with severely reduced gene expression at both receptor genes and their consequent disruption of normal and compensatory cell fate trajectories.