Biology subjects

Han, Y.

Publications and source records attributed to Han, Y..

At least 199 records · Page 11Linked to original sources

bioRxiv2023

Transposon elements shape population divergence of rice blast fungus Magnaporthe oryzae

Dynamic transposition of transposable elements (TEs) in fungal pathogens have significant impact on genome stability, gene expression, and virulence to the host. In Magnaporthe oryzae, genome plasticity resulting from TE insertion is a major driving force leading to the rapid evolution and diversification of this fungus. Despite their importance in M. oryzae population evolution and divergence, our understanding of TEs in this context remains limited. Here we conducted a genome-wide analysis of TE transposition dynamics in the 11 most abundant TE families in M. oryzae populations. Our results show that these TEs have specifically expanded in recently isolated M. oryzae rice populations, with the presence/absence polymorphism of TE insertions highly concordant with population divergence on Geng/Japonica and Xian/Indica rice cultivars. Notably, the genes targeted by clade-specific TEs showed clade-specific expression patterns and are involved in the pathogenic process, suggesting a transcriptional regulation of TEs on targeted genes. Our study provides a comprehensive analysis of TEs in M. oryzae populations and demonstrates a crucial role of recent TE bursts in adaptive evolution and diversification of the M. oryzae rice-infecting lineage. IMPORTANCEM. oryzae is the causal agent of the destructive blast disease, which caused massive loss of yield annually worldwide. The fungus diverged into distinct clades during adaptation toward two rice subspecies, Xian/indica and Geng/japonica. Although the role of TEs in the adaptive evolution was well established, mechanisms underlying how TEs promote the population divergence of M. oryzae remains largely unknown. In this study, we reported that TEs shape the population divergence of M. oryzae by differentially regulating gene expression between Xian/Indica-infecting and Geng/Japonica-infecting populations. Our results revealed a TE insertion mediated gene expression adaption that led to the divergence of M. oryzae population infecting different rice subspecies.

genomics↗

bioRxiv2023

SeMOE allows for quantitative glycan perception and exhibits anti-cancer potentiality

Metabolic oligosaccharide engineering (MOE) is a classical chemical approach to perturb, profile and perceive glycans in physiological systems, but probes upon bioorthogonal reaction require accessibility and background signal readout makes it challenging to achieve absolute glycan quantification. Here we develop SeMOE, a selenosugar-based metabolic oligosaccharide engineering strategy that combines elemental analysis and MOE to enable the absolute quantification and mass spectrometric imaging of glycome in a concise procedure. We demonstrate that SeMOE probes allow for perception, absolute quantification and visualization of glycans in diverse biological contexts. We demonstrate that chemical reporters on conventional MOE can be integrated into a bifunctional SeMOE probe to provide multimodality signal readouts. We further show the anti-cancer potentiality of SeMOE probes. SeMOE thus provides a convenient and simplified method to "see more" of the glyco-world.

bioengineering↗

bioRxiv2023

High-content microscopy reveals a morphological signature of bortezomib resistance

Drug resistance is a challenge in anticancer therapy, particularly with targeted therapeutics and cytotoxic compounds. In many cases, cancers can be resistant to the drug prior to exposure, i.e., possess intrinsic drug resistance. However, we lack target-independent methods to anticipate resistance in cancer cell lines or characterize intrinsic drug resistance without a priori knowledge of its cause. We hypothesized that cell morphology could provide an unbiased readout of drug sensitivity prior to treatment. We therefore isolated clonal cell lines that were either sensitive or resistant to bortezomib, a well-characterized proteasome inhibitor and anticancer drug to which many cancer cells possess intrinsic resistance. We then measured high-dimensional single-cell morphology profiles using Cell Painting, a high-content microscopy assay. Our imaging- and computation-based profiling pipeline identified morphological features typically different between resistant and sensitive clones. These features were compiled to generate a morphological signature of bortezomib resistance, which correctly predicted the bortezomib treatment response in seven of ten cell lines not included in the training dataset. This signature of resistance was specific to bortezomib over other drugs targeting the ubiquitin-proteasome system. Our results provide evidence that intrinsic morphological features of drug resistance exist and establish a framework for their identification.

cancer biology↗

bioRxiv2023

The Pseudokinase Ulk4 promotes Shh signaling by regulating Stk36 ciliary localization and Gli2 phosphorylation

The Hedgehog (Hh) family of secreted proteins governs embryonic development and adult tissue homeostasis through the Gli family of transcription factors. Gli is thought to be activated at the tip of primary cilium, but the underlying mechanism has remained poorly understood. Here, we show that Unc-51-like kinase 4 (Ulk4), a pseudokinase and a member of the Ulk kinase family, acts in conjunction with another Ulk family member Stk36 to promote Gli2 phosphorylation and Hh pathway activation. Ulk4 interacts with Stk36 through its N-terminal region containing the pseudokinase domain and Gli2 via its regulatory domain to bridge the kinase and substrate. Although dispensable for Hh-induced Stk36 kinase activation, Ulk4 is essential for Stk36 ciliary tip localization, Gli2 phosphorylation and activation. In response to Hh, both Ulk4 and Stk36 colocalize with Gli2 at ciliary tip, and Ulk4 and Stk36 depend on each other for their ciliary tip accumulation. We further show that ciliary localization of Ulk4 depends on Stk36 kinase activity and phosphorylation of Ulk4 on Thr1023, and that ciliary tip accumulation of Ulk4 is essential for its function in the Hh pathway. Taken together, our results suggest that Ulk4 regulates Hh signaling by promoting Stk36-mediated Gli2 phosphorylation and activation at ciliary tip.

developmental biology↗

bioRxiv2023

nELISA: A high-throughput, high-plex platform enables quantitative profiling of the secretome

We present the nELISA, a high-throughput, high-fidelity, and high-plex protein profiling platform. DNA oligonucleotides are used to pre-assemble antibody pairs on spectrally encoded microparticles and perform displacement-mediated detection. Spatial separation between non-cognate antibodies prevents the rise of reagent-driven cross-reactivity, while read-out is performed cost-efficiently and at high-throughput using flow cytometry. nELISA can measure both protein concentration and their post-translational modifications. We assembled an inflammatory panel of 191 targets that were multiplexed without cross-reactivity nor impact on performance vs 1-plex signals, with sensitivities as low as 0.1 pg/mL and measurements spanning 7 orders of magnitude. We then performed a large-scale inflammatory-secretome perturbation screen of peripheral blood mononuclear cells (PBMCs), with cytokines as both perturbagens and read-outs, measuring 7,392 samples and generating [~]1.4M protein data points in under a week; a significant advance in throughput compared to other highly multiplexed immunoassays. We uncovered 447 significant cytokine responses, including multiple putatively novel ones, that were conserved across donors and stimulation conditions. We validate nELISA for phenotypic screening, where its capacity to faithfully report hundreds of proteins make it a powerful tool across multiple stages of drug discovery.

bioengineering↗

bioRxiv2023

A comprehensive catalog with 100 million genes and 3,000 metagenome-assembled genomes from global cold seep sediments

Cold seeps harbor abundant and diverse microbes that represent a tremendous potential for biological applications and also have a significant influence on biogeochemical cycles. Though recent metagenomic studies have expanded our understanding of the microbial community and function of seep microorganisms, the knowledge of diversity and genetic repertoire of global seep microbes is lacking. Here, we collected a compilation of 165 metagenomic data from 16 cold seep sites across the globe to construct comprehensive gene and genome catalogs. The non-redundant gene catalog was comprised of 147 million genes (clustered at 95% amino acid identity), and 35.72% of them could not be assigned to a function with the currently available databases. A total of 3,164 species-level representative metagenome-assembled genomes (MAGs) are obtained, most of which (94.31%) belong to novel species. Of them, 81 ANME species are identified covering all subclades except ANME-2d, and 23 syntrophic SRB species spanning Seep-SRB1a Seep-SRB1g, and Seep-SRB2 clades. The non-redundant gene and MAGs catalogs are a valuable resource that enables expanded knowledge of the structure and functions of cold seep microbiomes.

microbiology↗

bioRxiv2023

On the use of quartets for reconstructing cell lineage trees under an unbiased error and missingness model

Cancer progression and treatment can be informed by reconstructing its evolutionary history from tumor cells. However, traditional methods assume the input data are error-free and the output tree is fully resolved. These assumptions are challenged in tumor phylogenetics because single-cell sequencing produces sparse, error-ridden data and because tumors evolve clonally. Here, we find that methods based on quartets (four-leaf, unrooted trees) withstand these barriers. We consider a popular tumor phylogenetics model, in which mutations arise on a (highly unresolved) tree and then (unbiased) errors and missing values are introduced. Quartets are implied by mutations present in two cells and absent from two cells. Our main result is that the most probable quartet identifies the unrooted model tree on four cells. This motivates seeking a tree such that the number of quartets shared between it and the input mutations is maximized. We prove an optimal solution is a consistent estimator of the unrooted cell lineage tree; this guarantee includes the case where the model tree is highly unresolved, with error defined as the number of false negative branches. Lastly, we outline how quartet-based methods might be employed when there are copy number aberrations and other challenges specific to tumor phylogenetics.

evolutionary biology↗

bioRxiv2023

JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations

Image-based profiling has emerged as a powerful technology for various steps in basic biological and pharmaceutical discovery, but the community has lacked a large, public reference set of data from chemical and genetic perturbations. Here we present data generated by the Joint Undertaking for Morphological Profiling (JUMP)-Cell Painting Consortium, a collaboration between 10 pharmaceutical companies, six supporting technology companies, and two non-profit partners. When completed, the dataset will contain images and profiles from the Cell Painting assay for over 116,750 unique compounds, over-expression of 12,602 genes, and knockout of 7,975 genes using CRISPR-Cas9, all in human osteosarcoma cells (U2OS). The dataset is estimated to be 115 TB in size and capturing 1.6 billion cells and their single-cell profiles. File quality control and upload is underway and will be completed over the coming months at the Cell Painting Gallery: https://registry.opendata.aws/cellpainting-gallery. A portal to visualize a subset of the data is available at https://phenaid.ardigen.com/jumpcpexplorer/.

bioinformatics↗

bioRxiv2023

Social Behavior Atlas: A computational framework for tracking and mapping 3D close interactions of free-moving animals

The study of social behaviors in animals is essential for understanding their survival and reproductive strategies. However, accurately tracking and analyzing the social interactions of free-moving animals has remained a challenge. Existing multi-animal pose estimation techniques suffer from drawbacks such as the need for extensive manual annotation and difficulty in discriminating between similar-looking animals in close social interactions. In this paper, we present the Social Behavior Atlas (SBeA), a novel computational framework that solves these challenges by employing a deep learning-based video instance segmentation model, 3D pose reconstruction, and unsupervised dynamic behavioral clustering. SBeA framework also involves a multi-camera setup to prevent occlusion, and a novel approach to identify individual animals in close social interactions. We demonstrate the effectiveness of SBeA in tracking and mapping the 3D close interactions of free-moving animals using the example of genetic mutant mice, birds, and dogs. Our results show that SBeA is capable of identifying subtle social interaction abnormalities, and the models and frameworks developed can be applied to a wide range of animal species. SBeA is a powerful tool for researchers in the fields of neuroscience and ecology to study animal social behaviors with a high degree of accuracy and reliability.

neuroscience↗

bioRxiv2023

Differential expression of RET and GDNF family receptor, GFR-α1, between striatum and substantia nigra following nigrostriatal lesion: a case for diminished GDNF-signaling

Although glial cell line-derived neurotrophic factor (GDNF) showed efficacy in preclinical and early clinical studies to alleviate parkinsonian signs in Parkinsons disease (PD), later trials did not meet primary endpoints, giving pause to consider further investigation. While GDNF dose and delivery methods may have contributed to diminished efficacy, one crucial aspect of these clinical studies is that GDNF treatment across all studies began [~]8 years after PD diagnosis; a time point representing several years after near 100% depletion of nigrostriatal dopamine markers in striatum and at least 50% in substantia nigra (SN), and is later than the timing of GDNF treatment in preclinical studies. With nigrostriatal terminal loss exceeding 70% at PD diagnosis, we utilized hemi-parkinsonian rats to determine if expression of GDNF family receptor, GFR-1, and receptor tyrosine kinase, RET, differed between striatum and SN at 1 and 4 weeks following a 6-hydroxydopamine (6-OHDA) lesion. Whereas GDNF expression changed minimally, GFR-1 expression decreased progressively in striatum and in tyrosine hydroxylase positive (TH+) cells in SN, correlating with reduced TH cell number. However, in nigral astrocytes, GFR-1 expression increased. RET expression decreased maximally in striatum by 1 week, whereas in the SN, a transient bilateral increase occurred that returned to control levels by 4 weeks. Expression of brain-derived neurotrophic factor (BDNF) or its receptor, TrkB, were unchanged throughout lesion progression. Together, these results reveal that differential GFR-1 and RET expression between the striatum and SN, and cell-specific differences in GFR-1 expression in SN, occur during nigrostriatal neuron loss. Targeting loss of GDNF receptors appears critical to enhance GDNF therapeutic efficacy against nigrostriatal neuron loss. Significance StatementAlthough preclinical evidence supports that GDNF provides neuroprotection and improves locomotor function in preclinical studies, clinical data supporting its efficacy to alleviate motor impairment in Parkinsons disease patients remains uncertain. Using the established 6-OHDA hemi-parkinsonian rat model, we determined whether expression of its cognate receptors, GFR-1 and RET, were differentially affected between striatum and substantia nigra in a timeline study. In striatum, there was early and significant loss of RET, but a gradual, progressive loss of GFR-1. In contrast, RET transiently increased in lesioned substantia nigra, but GFR-1 progressively decreased only in nigrostriatal neurons and correlated with TH cell loss. Our results indicate that direct availability of GFR-1 may be a critical element that determines GDNF efficacy following striatal delivery. HighlightsGDNF expression was minimally affected by nigrostriatal lesion GDNF family receptor, GFR-1, progressively decreased in striatum and in TH neurons in SN. GFR-1 expression decreased along with TH neurons as lesion progressed GFR-1 increased bilaterally in GFAP+ cells suggesting an inherent response to offset TH neuron loss RET expression was severely reduced in striatum, whereas it increased in SN early after lesion induction

neuroscience↗

bioRxiv2023

Elucidating Molecular Mechanisms of Protoxin-2 State-specific Binding to the Human NaV1.7 Channel

Human voltage-gated sodium (hNaV) channels are responsible for initiating and propagating action potentials in excitable cells and mutations have been associated with numerous cardiac and neurological disorders. hNaV1.7 channels are expressed in peripheral neurons and are promising targets for pain therapy. The tarantula venom peptide protoxin-2 (PTx2) has high selectivity for hNaV1.7 and serves as a valuable scaffold to design novel therapeutics to treat pain. Here, we used computational modeling to study the molecular mechanisms of the state-dependent binding of PTx2 to hNaV1.7 voltage-sensing domains (VSDs). Using Rosetta structural modeling methods, we constructed atomistic models of the hNaV1.7 VSD II and IV in the activated and deactivated states with docked PTx2. We then performed microsecond-long all-atom molecular dynamics (MD) simulations of the systems in hydrated lipid bilayers. Our simulations revealed that PTx2 binds most favorably to the deactivated VSD II and activated VSD IV. These state-specific interactions are mediated primarily by PTx2s residues R22, K26, K27, K28, and W30 with VSD as well as the surrounding membrane lipids. Our work revealed important protein-protein and protein-lipid contacts that contribute to high-affinity state-dependent toxin interaction with the channel. The workflow presented will prove useful for designing novel peptides with improved selectivity and potency for more effective and safe treatment of pain. SummaryNaV1.7, a voltage-gated sodium channel, plays a crucial role in pain perception and is specifically targeted by PTx2, which serves as a template for designing pain therapeutics. In this study, Ngo et al. employed computational modeling to evaluate the state-dependent binding of PTx2 to NaV1.7.

biophysics↗

bioRxiv2023

An intact amber-free HIV-1 system for in-virus protein bioorthogonal click labeling that delineates envelope conformational dynamics

The HIV-1 envelope (Env) glycoprotein is conformationally dynamic and mediates membrane fusion required for cell entry. Single-molecule fluorescence resonance energy transfer (smFRET) of Env using peptide tags has provided mechanistic insights into the dynamics of Env conformations. Nevertheless, using peptide tags risks potential effects on structural integrity. Here, we aim to establish minimally invasive smFRET systems of Env on the virus by combining genetic code expansion and bioorthogonal click chemistry. Amber stop-codon suppression allows site-specifically incorporating noncanonical/unnatural amino acids (ncAAs) at introduced amber sites into proteins. However, ncAA incorporation into Env (or other HIV-1 proteins) in the virus context has been challenging due to low copies of Env on virions and incomplete amber suppression in mammalian cells. Here, we developed an intact amber-free virus system that overcomes impediments from preexisting ambers in HIV-1. Using this system, we successfully incorporated dual ncAAs at amber-introduced sites into Env on intact virions. Dual-ncAA incorporated Env retained similar neutralization sensitivities to neutralizing antibodies as wildtype. smFRET of click-labeled Env on intact amber-free virions recapitulated conformational profiles of Env. The amber-free HIV-1 infectious system also permits in-virus protein bioorthogonal labeling, compatible with various advanced microscopic studies of virus entry, trafficking, and egress in living cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/530526v1_ufig1.gif" ALT="Figure 1000"> View larger version (30K): org.highwire.dtl.DTLVardef@10e7728org.highwire.dtl.DTLVardef@b1078aorg.highwire.dtl.DTLVardef@65f874org.highwire.dtl.DTLVardef@9ab0e8_HPS_FORMAT_FIGEXP M_FIG C_FIG Amber-free HIV-1 infectious systems actualized minimal invasive Env tagging for smFRET, versatile for in-virus bioorthogonal click labeling in advanced microscopic studies of virus-host interactions.

microbiology↗

bioRxiv2023

RelB represses miR-193a-5p expression to promote the phenotypic transformation of vascular smooth muscle cells in aortic aneurysm

Aortic aneurysm (AA) is a potentially fatal disease with the possibility of rupture, causing high mortality rates with no effective drugs for the treatment of AA. The mechanism of AA, as well as its therapeutic potential to inhibit aneurysm expansion, has been minimally explored. Small non-coding RNA (miRNAs and miRs) is emerging as a new fundamental regulator of gene expression. This study aimed to explore the role and mechanism of miR-193a-5p in abdominal aortic aneurysms (AAA). In AAA vascular tissue and Angiotensin II (Ang II)-treated vascular smooth muscle cells (VSMCs), the expression of miR-193a-5 was determined using real-time quantitative PCR (RT-qPCR). Western blotting was used to detect the effects of miR-193a-5p on PCNA, CCND1, CCNE1, and CXCR4. To detect the effect of miR-193a-5p on the proliferation and migration of VSMCs, CCK-8, and EdU immunostaining, flow cytometry, wound healing, and Transwell Chamber analysis were performed. In vitro results suggest that overexpression of miR-193a-5p inhibited the proliferation and migration of VSMCs, and its inhibition aggravated their proliferation and migration. In VSMCs, miR-193a-5p mediated proliferation by regulating CCNE1 and CCND1 genes and migration by regulating CXCR4. Further, in the Ang II-induced abdominal aorta of mice, the expression of miR-193a-5p was reduced and significantly downregulated in the serum of patients with aortic aneurysm (AA). In vitro studies confirmed that Ang II-induced downregulation of miR-193a-5p in VSMCs by upregulation of the expression of the transcriptional repressor RelB in the promoter region. This study may provide new intervention targets for the prevention and treatment of AA.

cell biology↗

bioRxiv2023

Specific guidelines for time and space of multisensory plasticity in the superior colliculus.

The potential to combine facts from exceptional senses, and thereby facilitate detecting and localizing events, commonly develops regularly in cat superior colliculus (SC) neurons. Multisensory integration in SC neurons depends on the spatial and temporal relationships of cross-modal cues. Here, we reveal that the parallel process of short-term plasticity during adulthood that would adapt multisensory integration to reliable changes in environmental conditions. The short-term experience altered the temporal preferences of SC neurons, this short-term plasticity was limited to changes in cross-modal timing (a factor commonly induced by events at different distances from the receiver. Nonetheless the plasticity was no evident in response to changes in cross-modal spatial configuration.

neuroscience↗

bioRxiv2023

IMPACT: a web server for exploring immunotherapeutic predictive and cancer prognostic biomarkers

Immune checkpoint inhibitors (ICIs) are a breakthrough in oncology treatment, and studies of screening predictive biomarkers of ICIs are emerging. We developed a web server named IMPACT (http://impact.brbiotech.com/) to thoroughly explore immunotherapeutic predictive or prognostic biomarkers. IMPACT contains a large dataset of 6,276 patients treated with ICIs and integrates 11 well-designed function modules, enabling an in-depth solution for biomarkers exploration. Compared with the existing tools, IMPACT was implemented with one exclusive module for interaction analysis and several optimized conventional functions for discovering novel biomarkers. Specifically, the interaction analysis of biomarker-treatment effect is essential to determine whether a biomarker is predictive and/or prognostic for ICIs. Moreover, several optimized functions allow complicated biomarker exploration, including customized selections of variant types in more detail, automatically screening meaningful co-mutations among multiple genes, and selecting cut-off values for gene expression biomarkers. In summary, IMPACT is a comprehensive analysis resource to facilitate biomarker research of ICIs.

bioinformatics↗

bioRxiv2023

Ensemble Processing and Synthetic Image Generation For Abnormally Shaped Nuclei Segmentation

Abnormalities in biological cell nuclei morphology are correlated with cell cycle stages, disease states, and various external stimuli. There have been many deep learning approaches that have described nuclei segmentation and analysis of nuclear morphology. One problem with many deep learning methods is acquiring large amounts of annotated nuclei data, which is generally expensive to obtain. In this paper, we propose a system to segment abnormally shaped nuclei with a limited amount of training data. We first generate specific shapes of synthetic nuclei groundtruth. We randomly sample these synthetic groundtruth images into training sets to train several Mask R-CNNs. We design an ensemble strategy to combine or fuse segmentation results from the Mask R-CNNs. We also design an oval nuclei removal by StarDist to reduce the false positives and improve the overall segmentation performance. Our experiments indicate that our method outperforms other methods in segmenting abnormally shaped nuclei.

cell biology↗

bioRxiv2023

Label-Free Mammalian Cell Tracking Enhanced by Precomputed Velocity Fields

Label-free cell imaging, where the cell is not "labeled" or modified by fluorescent chemicals, is an important research area in the field of biology. It avoids altering the cells properties which typically happens in the process of chemical labeling. However, without the contrast enhancement from the label, the analysis of label-free imaging is more challenging than label-based imaging. In addition, it provides few human interpretable features, and thus needs machine learning approaches to help with the identification and tracking of specific cells. We are interested in label-free phase contrast imaging to track cells flowing in a cell sorting device where images are acquired at 500 frames/s. Existing Multiple Object Tracking (MOT) methods face four major challenges when used for tracking cells in a microfluidic sorting device: (i) most of the cells have large displacements between frames without any overlap; (ii) it is difficult to distinguish between cells as they are visually similar to each other; (iii) the velocities of cells vary with the location in the device; (iv) the appearance of cells may change as they move in and out of the focal plane of the imaging sensor that observes the isolation process. In this paper, we introduce a method for tracking cells in a predefined flow in the sorting device via phase contrast microscopy. Our proposed method is based on DeepSORT and YOLOv4 and exploits prior knowledge of a cells velocity to assist tracking. We modify the Kalman filter in DeepSORT to accommodate a non-constant velocity motion model and integrate a representative velocity field obtained from fluid dynamics into the Kalman filter. The experimental results show that our proposed method outperforms several MOT methods for tracking cells in the sorting device.

cell biology↗

bioRxiv2023

Development of Multiomics in situ Pairwise Sequencing (MiP-Seq) for Single-cell Resolution Multidimensional Spatial Omics

Delineating the spatial multiomics landscape will pave the way to understanding the molecular basis of physiology and pathology. However, current spatial omics technology development is still in its infancy. Here, we developed a high-throughput multiomics in situ pairwise sequencing (MiP-Seq) strategy to efficiently decipher multiplexed DNAs, RNAs, proteins, and small biomolecules at subcellular resolution. We delineated dynamic spatial gene profiles in the hypothalamus using MiP-Seq. Moreover, MiP-Seq was unitized to detect tumor gene mutations and allele-specific expression of parental genes and to differentiate sites with and without the m6A RNA modification at specific sites. MiP-Seq was combined with in vivo Ca2+ imaging and Raman imaging to obtain a spatial multiomics atlas correlated to neuronal activity and cellular biochemical fingerprints. Importantly, we proposed a "signal dilution strategy" to resolve the crowded signals that challenge the applicability of in situ sequencing. Together, our method improves spatial multiomics and precision diagnostics and facilitates analyses of cell function in connection with gene profiles.

molecular biology↗