Biology subjects

Klein, M.

Publications and source records attributed to Klein, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

A multisensory, bidirectional, valence encoder guides behavioral decisions

A key function of the brain is to categorize sensory cues as repulsive or attractive and respond accordingly. While we have some understanding of how sensory information is processed in the sensory periphery, the classification of cues according to valence in central brain circuits is less well understood. Here, we addressed this question in the Drosophila larva, where we could leverage the synaptic resolution connectome to determine where innate and learnt information from distinct aversive and appetitive sensory modalities converges; and combine this with imaging and manipulation of neural activity to determine how valence information is encoded and used to guide navigation. We found that information from multiple innately aversive and attractive sensory modalities converges onto a common output neuron of the learning circuit, specifically the Mushroom Body output neuron, MBON-m1. We discovered that this neuron is required for navigating both attractive odor and aversive temperature cues and is activated by attractive cues, such as food odour and sugar, and inhibited by different aversive cues, such as cooling, salt, or non-food odors. Together, our study reveals a neuron that bi-directionally encodes valence and controls actions.

neuroscience↗

bioRxiv2025

Characterization of the TREM-1 Signaling Landscape in Human Neutrophils

The Triggering Receptor Expressed on Myeloid Cells (TREM)-1 is a member of the Immunoglobulin superfamily, and an activating receptor mainly expressed on myeloid cells. Beyond its role in acute and chronic inflammatory processes, TREM-1 is also involved in cancer emergence and progression probably by alteration of the tumor-associated neutrophils (TAN) and macrophages (TAM). Advanced information about the TREM-1 signaling cascade may reveal novel targets for treating inflammatory and cancer diseases. As many specific kinase inhibitors are approved for treating various diseases, targeting kinases being active after TREM-1 ligation serves as a promising approach. Therefore, we investigated the protein tyrosine kinome (PTK) and serine threonine kinome (STK) by kinome activity profiling of purified human neutrophils after TREM-1 activation. As TREM-1 interacts with Toll-like receptor (TLR) 4 signaling, we used TLR4-activation by LPS to define TREM-1 specific pathways. We found an increased kinome activity after receptor ligation and could predict individual kinases. To gain further insights into the signaling cascade, we additionally investigated the transcriptomic profile that made us available to link the kinome activity to the resulting transcriptomic profile. In sum, we revealed several signaling pathways being active after TREM-1 ligation that are associated with various biological processed and diseases. This study facilitates selecting kinase inhibitors for further validation with the aim of targeting TREM-1 signaling in various inflammatory or cancer disease conditions.

immunology↗

bioRxiv2025

OmniPath: integrated knowledgebase for multi-omics analysis

Analysis and interpretation of omics data largely benefit from the use of prior knowledge. However, this knowledge is fragmented across resources and often is not directly accessible for analytical methods. We developed OmniPath (https://omnipathdb.org/), a database combining diverse molecular knowledge from 168 resources. It covers causal protein-protein, gene regulatory, miRNA, and enzyme-PTM (post-translational modification) interactions, cell-cell communication, protein complexes, and information about the function, localization, structure, and many other aspects of biomolecules. It prioritizes literature curated data, and complements it with predictions and large scale databases. To enable interactive browsing of this large corpus of knowledge, we developed OmniPath Explorer, which also includes a large language model (LLM) agent that has direct access to the database. Python and R/Bioconductor client packages and a Cytoscape plugin create easy access to customized prior knowledge for omics analysis environments, such as scverse. OmniPath can be broadly used for the analysis of bulk, single-cell and spatial multi-omics data, especially for mechanistic and causal modeling. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/675512v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@17c2b6borg.highwire.dtl.DTLVardef@1069835org.highwire.dtl.DTLVardef@1f2ce76org.highwire.dtl.DTLVardef@1d0b34f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Single-cell chromatin landscape and DNA methylation patterns reveal shared molecular programs in human tumor and non-tumor tissue CCR8+ Treg cells

Regulatory T (Treg) cells, a subset of CD4+ T cells, play a crucial role in immunoregulation. Notably, CCR8-expressing Treg cells in tissues also contribute to organ homeostasis and repair. To determine whether these tissue-regenerative programs are active in the tumor microenvironment, we employed single-cell chromatin accessibility and genome-wide DNA methylation analyses to investigate CCR8+ tissue Treg cells isolated from human tumor and adjacent tumor-free tissues. Our findings indicate that CCR8+ tissue Treg cells from tumor and corresponding tumor-free tissues exhibit a high degree of similarity, suggesting that the tumor microenvironment may harbor highly activated tissue Treg cells. This observation was consistent across various tumor types and origins, including primary tumors and metastases. Using quantitative proteomics, we identified several candidate factors associated with the regenerative and suppressive programs of Treg cells, which may serve as potential reservoir of druggable targets for future therapeutic interventions.

immunology↗

bioRxiv2025

B cells maintain the homeostasis of splenic marginal zone antigen-presenting cells to promote the anti-viral CD8+ T cell response

Natural killer and CD8+ T cells are critical in the elimination of blood-borne viruses such as cytomegalovirus (CMV); however, the role of B cells in this process is less clear. Here, using the murine CMV (MCMV) infection model, we demonstrated that the B cell-deficient mice mounted a weaker primary virus-specific CD8+ T cell response than their wild-type counterparts, which was associated with increased viral transcription. Notably, we found that the contribution of B cells to the CD8+ T-cell-mediated anti-viral response was not associated with their ability to generate antibodies but with their ability to sustain Langerin+ type 1 conventional dendritic cells (cDC1s), a dendritic cells (DC) subset known for being involved in viral and bacterial clearance in the marginal zone of the spleen. Furthermore, we found that the presence of Langerin+ cDC1s is dependent on B cells expressing lymphotoxin (LT{beta}) to maintain CD169+ marginal metallophilic macrophages (MMMs). We further discovered, using ligand-receptor interaction analyses, that the communication between MMMs and Langerin+ cDC1s was mediated via VCAM1 - ITGA4/ITGB1 interaction. Thus, our data reveals that B cell regulate the development of MMMs in the spleen via LT{beta} expression and consequently sustain Langerin+ cDC1s homeostasis for effective initiation of an anti-viral CD8+ T cell response. Overall, our study offers a new perspective on how B cells maintain the homeostasis of antigen-presenting cells in the splenic marginal zone and thus indirectly affect the virus-specific CD8+ T cell response, which could potentially be extended to other infectious and autoimmune diseases as well as tumors.

immunology↗

bioRxiv2025

Temperature-regulated FLOWERING LOCUS T homologs make distinct contributions to the floral transition in vernalization-dependent and vernalization-independent Taraxacum koksaghyz plants

Flowering that requires a period of cold (vernalization) is a key trait in many crops, but the underlying regulatory pathways are often poorly understood. Taraxacum koksaghyz is a rubber-producing dandelion of the family Asteraceae, which also includes other economically important crops such as chicory and lettuce. Most T. koksaghyz plants require cold exposure to induce flowering, but plants that have lost the dependence on vernalization are more suitable for domestication and breeding. To provide insight into the molecular basis of mandatory vernalization in T. koskaghyz, we identified three FLOWERING LOCUS T (FT) homologs (TkFT1-3) that are differentially expressed under varying environmental conditions. TkFT1 and TkFT2 are expressed under long-day conditions at ambient temperatures whereas only TkFT1 is weakly expressed under short-day conditions. Exposure to cold was shown to repress TkFT1 but induce TkFT3. Overexpression experiments revealed that TkFT1-3 bypass the vernalization requirement in T. koksaghyz and its close relative T. officinale, and promote early flowering in vernalization-independent T. brevicorniculatum. We also identified two FRUITFULL homologs (TkFUL1 and TkFUL2) as downstream targets, which were upregulated in TkFT overexpression lines. Our findings suggest that TkFT1 promotes vernalization-independent flowering, whereas TkFT3 expression during the cold period is needed to promote vernalization-dependent flowering. This study explicates the regulatory network controlling flowering time in T. koksaghyz, contributing to a broader understanding of flowering in the family Asteraceae and providing knowledge that can be used in the future to facilitate domestication and breeding. Key messageIn Taraxacum koksaghyz, FT homologs function as floral inducers that upregulate FRUITFULL homologs, with TkFT1 linked to vernalization-independent flowering and TkFT3 associated with the acquisition of flowering competence during vernalization.

developmental biology↗

bioRxiv2025

Cerebellar transcranial alternating current stimulation in the theta band facilitates extinction of learned fear responses

Fear extinction is a major component of exposure therapy for anxiety disorders. There is initial evidence that the cerebellum contributes to fear extinction learning, i.e., the ability to learn that certain stimuli are no longer associated with an aversive outcome. So far, however, knowledge of the cerebellums role in extinction is scarce. In the present study, 6 Hz cerebellar transcranial alternating current stimulation (ctACS) was used to modulate cerebellar function during extinction learning in young and healthy human participants in an MRI study. A two- day differential fear conditioning paradigm was used with acquisition and extinction training being performed on day 1, and fear extinction recall being tested on day 2. 6 Hz ctACS reduced spontaneous recovery of the initial fear association during recall, stabilizing extinction effects compared to sham ctACS. fMRI data during recall revealed significantly reduced activation in cortical areas involved in initial fear acquisition, such as the anterior cingulate and insula, in the verum ctACS group compared to the sham group. During extinction training, on the other hand, the verum group exhibited more widespread cerebral activation compared to the sham group. Group differences were significant in occipital cortical areas. Although direct stimulation effects cannot be excluded, increased activation in the visual cortex may reflect enhanced encoding and processing of visual information during fear extinction learning. The findings suggest that theta-range oscillatory interactions between the cerebellum and cortical areas support extinction processes and provide causal evidence of the cerebellar role in the human fear extinction network. Significance StatementWhile the cerebellum is well known for its role in associative learning, its contribution to fear extinction learning remains underexplored. This study used 6 Hz cerebellar transcranial alternating current stimulation (ctACS) to modulate cerebellar function during extinction training in healthy participants. The present data demonstrate that ctACS enhances cerebral cortical activation during extinction training which is followed by enhanced recall of the extinction memory and subsequently reduced activation of cerebral cortical areas associated to spontaneous recovery of fear memory. These findings provide causal evidence for the cerebelluar involvement in the human fear extinction network and suggest that enhancing cerebellar theta oscillations may be useful to support exposure therapy.

neuroscience↗

bioRxiv2025

A post-assembly conformational change makes the SARS-CoV-2 polymerase elongation-competent

Coronaviruses (CoV) encode sixteen non-structural proteins (nsps), most of which form the replication-transcription complex (RTC). The RTC contains a core composed of one nsp12 RNA-dependent RNA polymerase (RdRp), two nsp8s and one nsp7. The core RTC recruits other nsps to synthesize all viral RNAs within the infected cell. While essential for viral replication, the mechanism by which the core RTC assembles into a processive polymerase remains poorly understood. We show that the core RTC preferentially assembles by first having nsp12-polymerase bind to the RNA template, followed by the subsequent association of nsp7 and nsp8. Once assembled on the RNA template, the core RTC requires hundreds of seconds to undergo a conformational change that enables processive elongation. In the absence of RNA, the (apo-)RTC requires several hours to adopt its elongation-competent conformation. We propose that this obligatory activation step facilitates the recruitment of additional nsps essential for efficient viral RNA synthesis and may represent a promising target for therapeutic interventions.

biophysics↗

bioRxiv2024

Constitutive expression of IκBζ promotes tumor growth and immunotherapy resistance in melanoma

BackgroundI{kappa}B{zeta}, a rather unknown co-regulator of NF-{kappa}B, is mostly inducibly expressed and can either activate or repress a specific subset of NF-{kappa}B target genes. While its role as a transcriptional regulator of various cytokines and chemokines in immune cells has been revealed, I{kappa}B{zeta}s function in solid cancer remains unclear. MethodsWe investigated I{kappa}B{zeta} expression in melanoma, and assessed its impact on target gene expression, tumor growth, and response to immunotherapy in melanoma cell lines, mouse models, and patient samples. ResultsUnlike in other cell types, I{kappa}B{zeta} protein was found to be constitutively expressed in a subfraction of melanoma cell lines, and around 35% of melanoma cases. This atypical expression pattern of I{kappa}B{zeta} did not correlate with its mRNA levels or known driver mutations, but instead seemed to result from changes in its post-transcriptional or post-translational regulation. Deleting constitutively expressed I{kappa}B{zeta} abrogated the activity and chromatin association of STAT3 and p65, leading to reduced expression of the pro-proliferative cytokines IL-1{beta} and IL-6 in melanoma cells. Consequently, loss of tumor-derived I{kappa}B{zeta} suppressed self-sustained melanoma cell growth both in vitro and in vivo. Additionally, constitutive I{kappa}B{zeta} expression suppressed the induction of the chemokines CXCL9, CXCL10, and CCL5, which impaired the recruitment of NK and CD8+ T-cells to the tumor, causing resistance to -PD-1 immunotherapy in mice. Furthermore, the expression of tumor-derived I{kappa}B{zeta} also correlated with the absence of CD8+ T-cells in human melanoma samples and progressive disease during immunotherapy. ConclusionWe propose that tumor-derived I{kappa}B{zeta} could serve as a new therapeutic target and prognostic marker that characterizes melanoma with high tumor cell proliferation, cytotoxic T- and NK-cell exclusion, and unfavorable immunotherapy responses. Targeting I{kappa}B{zeta} expression might open up a new therapy option to re-establish the recruitment of cytotoxic cells, thereby resensitizing for immunotherapy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/613946v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@76389aorg.highwire.dtl.DTLVardef@17e3f1eorg.highwire.dtl.DTLVardef@161d491org.highwire.dtl.DTLVardef@1ca9f2d_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Single-molecule magnetic tweezers reveals that TAV2b-derived peptides underwind and stabilize double-stranded RNA

Double-stranded RNA (dsRNA) has evolved into a key tool in understanding and regulating biological processes, with promising implications in therapeutics. However, its efficacy is often limited due to instability in biological settings. Recently, the development of peptidic dsRNA binders derived from naturally occurring RNA-binding proteins has emerged as a favorable starting point to address this limitation. Nevertheless, it remains unclear how these high affinity dsRNA binders alter the structure and flexibility of dsRNA. To this end, we employed single-molecule magnetic tweezers experiments to investigate the effects of TAV2b-derived peptidic dsRNA binders on the mechanical properties of dsRNA. Torque spectroscopy assays demonstrated that these peptides underwind dsRNA, while also stabilizing the duplex. Additionally, force spectroscopy experiments demonstrate that a wild type TAV2b peptide derivative extends the contour length and lowers the bending rigidity of dsRNA, while a homodimeric version triggers the formation of higher order complexes at forces below 1 pN. Our study presents a quantitative approach to investigate how these peptides alter the structure of dsRNA, and whether peptide structural design alters the affinity to dsRNA and its stability. This approach could inform the design of more potent and effective dsRNA binders in the efforts to advance RNA therapeutics.

biophysics↗

bioRxiv2024

An alternative mechanism for activation of innate immune signaling by MDA5

Long double-stranded (ds) RNA in the cytosol acts as a potent inflammatory molecule recognized by the receptor MDA5, triggering the innate immune response. Mutations affecting MDA5 ATPase activity lead to severe pathological conditions. MDA5 nucleoprotein filament assembly-disassembly dynamic is proposed to regulate dsRNA recognition, though the exact mechanism remains unclear. Here, we employed magnetic tweezers to monitor the assembly and manipulate MDA5 filaments at the single dsRNA level. Following a slow nucleation event, MDA5 assembles cooperatively and directionally into (partial) filaments and utilizes ATP hydrolysis to compact dsRNA via single-stranded (ss) RNA loop extrusion, even against a significant opposing force. This compacted state is further stabilized by oligomerization of MDA5s caspase recruitment domain (CARD) and requires high force to be disrupted. ssRNA gaps impaired compaction, suggesting a new mechanism for dsRNA recognition. We propose that MDA5 mediated dsRNA compaction captures viral dsRNA, preventing further usage for viral replication.

biophysics↗

bioRxiv2024

Drosophila larvae demonstrate associative learning and memory in response to thermal conditioning

Organisms have evolved the ability to detect, process, and respond to many different surrounding stimuli in order to successfully navigate their environments. Sensory experiences can also be stored and referenced in the form of memory. The Drosophila larva is a simple model organism that can store associative memories during classical conditioning, and is well-suited for studying learning and memory at a fundamental level. Much progress has been made in understanding larval learning behavior and the associated neural circuitry for olfactory conditioning, but other sensory systems are relatively unexplored. Here, we investigate memory formation in larvae treated with a temperature-based associative conditioning protocol, pairing normally neutral temperatures with appetitive (fructose, FRU) or aversive (salt, NaCl) stimuli. Associative memory is tested using thermal gradient geometries, and we quantify navigation strength towards or away from conditioned temperatures. We find that larvae demonstrate short-term associative learning. They navigate towards warmer or colder temperatures paired with FRU, and away from warmer temperatures paired with NaCl. These results, especially when combined with future investigations of thermal memory circuitry in larvae, should provide broader insight into how sensory stimuli are encoded and retrieved in insects and more complex systems.

animal behavior and cognition↗

bioRxiv2024

Coenzyme A biosynthesis in Bacillus subtilis: Discovery of a novel precursor metabolite for salvage and its uptake system

The Gram-positive model bacterium Bacillus subtilis is used for many biotechnological applications, including the large-scale production of vitamins. For vitamin B5, a precursor for coenzyme A synthesis, there is so far no established fermentation process available, partly due to the incomplete knowledge on the metabolic pathways that involve this vitamin. In this study, we have elucidated the complete pathways for the biosynthesis pantothenate and coenzyme A in B. subtilis. We have identified the enzymes involved in the pathway and have identified a salvage pathway for coenzyme A acquisition that acts on complex medium even in the absence of pantothenate synthesis. This pathway requires rewiring of sulfur metabolism resulting in the expression of a cysteine transporter. In the salvage pathway, the bacteria import cysteinopantetheine, a novel naturally occurring metabolite, using the cystine transport system TcyJKLMN. This work lays the foundation for the development of effective processes for vitamin B5 production.

microbiology↗

bioRxiv2024

Unraveling the Role of 12-cis-Oxo-Phytodienoic Acid in the Wound Response of Arabidopsis thaliana: Insights from Transcriptomic and Complementation Studies

12-cis-Oxo-phytodienoic acid (OPDA), the main precursor of the key plant growth and defense hormone jasmonoyl-isoleucine (JA-Ile), is believed to have distinct signaling roles in plants responses to stress. In Arabidopsis, insights into OPDA functions have been gained from studying a mutant, which is affected in the conversion of OPDA by missing OPDA REDUCTASE3 (OPR3). opr3 mutants, however, accumulate JA-Ile through a cytosolic bypass mediated by OPR2. Therefore, wound-induced transcriptome of opr2opr3 in comparison to wild-type and allene oxide synthase mutant was analyzed to unravel OPDA signaling. Results showed that OPDA lacked a distinct transcriptional signature, whereas known OPDA-response genes were wound-induced independently of OPDA. The application of OPDA to opr2opr3 resulted in a distinct transcriptional response compared to the endogenous rise of OPDA in the same mutant, with the activation of the sulfur assimilation pathway genes occurring only with the external application of the compound. These findings suggested a compartmentalization of endogenously produced OPDA, investigated further through trans-organellar complementation. OPR3 complemented opr2opr3 mutants in fertility and wound-induced JA-Ile production regardless of its localization. Since in vitro enzymatic studies revealed OPR3s activity on both OPDA and 4,5-ddh-JA, conclusions on translocation of OPDA were not unequivocal. Dissecting the conversion of either OPDA or 4,5-ddh-JA by OPR2 and OPR1 organelle variants pointed, however, to a strong OPDA compartmentalization supporting its lacking signaling function.

plant biology↗

bioRxiv2023

Low exposure to lithium does not induce nephrogenic diabetes insipidus but microcystic dilations of collecting ducts in a long-term rat model

Lithium induces nephrogenic diabetes insipidus (NDI) and microcystic chronic kidney disease (CKD). As clinical studies suggested that NDI is dose-dependent and CKD time-dependent, we investigated the effects of low exposure to lithium in a long-term rat model. Sprague-Dawley rats were randomly fed during six months with normal diet (controls), addition of lithium to diet, or addition of lithium and amiloride to diet, allowing reaching low steady-state plasma lithium concentrations (0.25{+/-}0.06 and 0.43{+/-}0.16 mmol/L, respectively). Exposure to low plasma lithium concentrations did not induce NDI but microcystic dilations of kidney tubules, identified as collecting ducts (CDs) using immunofluorescent staining. Both hypertrophy, characterized by an increase in the ratio of nuclei per tubular area, and microcystic dilations were observed. Principal cell-to-intercalated cell ratio was higher in dilated than in hypertrophied tubules. There was no correlation between aquaporin-2 mRNA levels and cellular remodelling of CDs. Amiloride/lithium co-administration did not allow significant consistent morphometric and cellular composition changes compared to lithium administration. To conclude, rat low exposure to lithium did not induce overt NDI but microcystic dilations of CDs, which include a marked alteration in cell composition of hypertrophied and dilated CDs, suggesting two distinct underlying pathophysiological mechanisms.

pharmacology and toxicology↗

bioRxiv2023

PCSK9 inhibition protects mice from food allergy

The Proprotein Convertase Subtilisin Kexin of type 9 (PCSK9) has been identified in 2003 as the third gene involved in familial hypercholesterolemia. PCSK9 binds to the membrane low-density lipoprotein receptor (LDLR) and promotes its cellular internalization and lysosomal degradation. Beyond this canonical role, PCSK9 was recently described to be involved in several immune responses. However, to date, the contribution of PCSK9 in food allergy remains unknown. Here, we showed that Pcsk9 deficiency or pharmacological inhibition of circulating PCSK9 with a specific monoclonal antibody (m-Ab) protected mice against symptoms of gliadin-induced-food allergy, such as increased intestinal transit time and ear oedema. Furthermore, specific PCSK9 inhibition during the elicitation steps of allergic process was sufficient to ensure anti-allergic effects in mice. Interestingly, the protective effect of PCSK9 inhibition against food allergy symptoms was independent of the LDLR as PCSK9 inhibitors remained effective in Ldlr deficient mice. In vitro, we showed that recombinant gain of function PCSK9 (PCSK9 D374Y) increased the percentage of mature bone marrow derived dendritic cells (BMDCs), promoted naive T cell proliferation and potentiated the gliadin induced basophils degranulation. Altogether, our data demonstrate that PCSK9 inhibition is protective against gliadin induced food allergy in a LDLR-independent manner.

physiology↗

bioRxiv2023

Unveiling IRF4-steered regulation of context-dependent effector programs in Th17 and Treg cells

The transcription factor interferon regulatory factor 4 (IRF4) is crucial for the differentiation and fate determination of pro-inflammatory T helper (Th)17 and the functionally opposing group of immunomodulatory regulatory T (Treg) cells. However, molecular mechanisms of how IRF4 steers diverse transcriptional programs in Th17 and Treg cells are far from being definitive. To unveil IRF4-driven lineage determination in Th17 and Treg cells, we integrated data derived from affinity-purification and full mass spectrometry-based proteome analysis with chromatin immune precipitation sequencing (ChIP-Seq). This allowed the characterization of subtype-specific molecular programs and the identification of novel, previously unknown IRF4 interactors in the Th17/Treg context, such as ROR{gamma}t, AHR, IRF8, BACH2, SATB1, and FLI1. Moreover, our data reveal that most of these transcription factors are recruited to IRF composite elements for the regulation of cell type-specific transcriptional programs providing a valuable resource for studying IRF4-mediated gene regulatory programs in pro- and anti-inflammatory immune responses.

immunology↗

bioRxiv2023

Unified fate mapping in multiview single-cell data

Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions using expression similarity or RNA velocity to reconstruct state-change trajectories. However, trajectory inference does not incorporate valuable time point information or utilize additional modalities, while methods that address these different data views cannot be combined and do not scale. Here, we present CellRank 2, a versatile and scalable framework to study cellular fate using multiview single-cell data of up to millions of cells in a unified fashion. CellRank 2 consistently recovers terminal states and fate probabilities across data modalities in human hematopoiesis and mouse endodermal development. Our framework also allows combining transitions within and across experimental time points, a feature we use to recover genes promoting medullary thymic epithelial cell formation during pharyngeal endoderm development. Moreover, we enable estimating cell-specific transcription and degradation rates from metabolic labeling data, which we apply to an intestinal organoid system to delineate differentiation trajectories and pinpoint regulatory strategies.

bioinformatics↗