Concepts of brain function imply congruence and mutual causal influence between molecular events and neuronal activity. Decoding entangled information from concurrent molecular and electrophysiological network events demands innovative methodology bridging scales and modalities. The MEA-seqX platform, integrating high-density microelectrode arrays, spatial transcriptomics, optical imaging, and advanced computational strategies, enables the simultaneous recording and analysis of molecular and electrical network activities at mesoscale spatial resolution. Applied to a mouse hippocampal model of experience-dependent plasticity, MEA-seqX unveils massively enhanced nested dynamics between transcription and function. Graph-theoretic analysis reveals an increase in densely connected bimodal hubs, marking the first observation of coordinated hippocampal circuitry dynamics at molecular and functional levels. This platform also identifies different cell types based on their distinct bimodal profiles. Machine-learning algorithms accurately predict network-wide electrophysiological activity features from spatial gene expression, demonstrating a previously inaccessible convergence across modalities, time, and scales.

Heart development relies on topologically orchestrated cellular transitions and interactions, many of which remain poorly characterized in humans. Here, we combined unbiased spatial and single-cell transcriptomics with imaging-based validation across postconceptional weeks 5.5 to 14 to uncover the molecular landscape of human early cardiogenesis. We present a high-resolution transcriptomic map of the developing human heart, revealing the spatial arrangements of 31 coarse-grained and 72 fine-grained cell states organized into distinct functional niches. Our findings illuminate key insights into the formation of the cardiac pacemaker-conduction system, heart valves and atrial septum, and uncover unexpected diversity among cardiac mesenchymal cells. We also trace the emergence of autonomic innervation and provide the first spatial account of chromaffin cells in the fetal heart. Our study, supported by an open-access spatially centric interactive viewer, offers a unique resource to explore the cellular and molecular blueprint of human heart development, offering links to genetic causes of heart disease.

Tissues are dynamic and complex biological systems composed of specialized cell types that interact with each other for proper biological function. To comprehensively characterize and understand the cell circuitry underlying biological processes within tissues, it is crucial to preserve their spatial information. Here we report a simple mounting technique to maximize the area of the tissue to be analyzed, encompassing the whole length of the murine gastrointestinal (GI) tract, from mouth to rectum. Using this method, analysis of the whole murine GI tract can be performed in a single slide not only by means of histological staining, immunohistochemistry and in situ hybridization but also by multiplexed antibody staining and spatial transcriptomic approaches. We demonstrate the utility of our method in generating a comprehensive gene and protein expression profile of the whole GI tract by combining the versatile tissue-rolling technique with a cutting-edge transcriptomics method (Visium) and two cutting-edge proteomics methods (ChipCytometry and CODEX-PhenoCycler) in a systematic and easy-to-follow step-by-step procedure. The entire process, including tissue rolling, processing and sectioning, can be achieved within 2–3 d for all three methods. For Visium spatial transcriptomics, an additional 2 d are needed, whereas for spatial proteomics assays (ChipCytometry and CODEX-PhenoCycler), another 3–4 d might be considered. The whole process can be accomplished by researchers with skills in performing murine surgery, and standard histological and molecular biology methods.

Solid tumours comprise many different cell types organized in spatially structured arrangements, with substantial intratumour and intertumour heterogeneity. Advances in spatial profiling technologies over the past decade hold promise to capture the complexity of these cellular architectures to build a holistic view of the intricate molecular mechanisms that shape the tumour ecosystem. Some of these mechanisms act at the cellular scale and are controlled by cell-autonomous programmes or communication between nearby cells, whereas other mechanisms result from coordinated efforts between large networks of cells and extracellular molecules organized into tissues and organs. In this Review we provide insights into the application of single-cell and spatial profiling tools, with a focus on spatially resolved transcriptomic tools developed to understand the cellular architecture of the tumour microenvironment and identify opportunities to use them to improve clinical management of cancers.

We present a spatial omics approach that combines histology, mass spectrometry imaging and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular-weight metabolites across tissue regions. The workflow is compatible with commercially available Visium glass slides. We demonstrate the potential of our method using mouse and human brain samples in the context of dopamine and Parkinson’s disease.

Capture array-based spatial transcriptomics methods have been widely used to resolve gene expression in tissues; however, their spatial resolution is limited by the density of the array. Here we present expansion spatial transcriptomics to overcome this limitation by clearing and expanding tissue prior to capturing the entire polyadenylated transcriptome with an enhanced protocol. This approach enables us to achieve higher spatial resolution while retaining high library quality, which we demonstrate using mouse brain samples. 

Cardiomyocytes play key roles during cardiogenesis, but have poorly understood features, especially in prenatal stages. Here, we characterized human prenatal cardiomyocytes, 6.5-7 weeks post-conception, by integrating single-cell RNA sequencing, spatial transcriptomics, and ligand-receptor interaction information. Using a computational workflow developed to dissect cell type heterogeneity, localize cell types, and explore their molecular interactions, we identified eight types of developing cardiomyocyte, more than double compared to the ones identified in the Human Developmental Cell Atlas. These have high variability in cell cycle activity, mitochondrial content, and connexin gene expression, and are differentially distributed in the ventricles, including outflow tract, and atria, including sinoatrial node. Moreover, cardiomyocyte ligand-receptor crosstalk is mainly with non-cardiomyocyte cell types, encompassing cardiogenesis-related pathways. Thus, early prenatal human cardiomyocytes are highly heterogeneous and develop unique location-dependent properties, with complex ligand-receptor crosstalk. Further elucidation of their developmental dynamics may give rise to new therapies.

Over the past few decades, the advent of pioneering biotechnological methods has allowed scientists to analyze the molecular components of multicellular organisms with remarkable precision. The field of transcriptomics has witnessed a rapid development of technologies for gene expression profiling of biological samples. These gene expression profiles offer crucial insights into biological processes that underlie organism development, homeostasis, and disease-causing dysregulation. Modern transcriptomics technologies can profile samples at various degrees of precision and resolution, and when combined, they contribute to a comprehensive understanding of the complex molecular mechanisms that shape entire organisms. Some of these molecular mechanisms occur at the microscopic scale, controlled by communication between nearby cells. Other mechanisms depend on coordinated efforts between large networks of cells organized into tissues and organs. Cells, tissues and organs represent hierarchical levels of structural organization, and each level plays a vital role in the proper functioning of the organism. Gene expression profiling technologies yield comprehensive data that can be harnessed to explore and characterize biological phenomena within and across these structural levels. The central theme of this thesis revolves around the use of experimental technologies and computational methods in the field of transcriptomics to enhance our understanding of multicellular life. Particular attention is directed at a technology known as Visium, which has held an important position in the field in recent years. The research articles included in this thesis demonstrate the applications of Visium and related technologies in biological research.

In article I, we present a computational toolbox for processing, analyzing, and visualizing Visium data, assembled into an open-source package written in the R programming language. The package facilitates the characterization of gene expression profiles in tissue sections and seamlessly integrates expression data with corresponding histological images. This computational framework was used extensively for the data analyses presented in articles II, III and IV and the articles listed in the extended list of publications.

In article II, we report one of the first spatiotemporal, transcriptomics atlases of the developing human heart. The atlas encompasses three developmental time points during the first trimester, and is constructed from gene expression data from isolated cells and intact tissue sections. Joint analysis of this data enabled characterization of the transcriptomic profiles and the cellular composition of anatomical domains within the heart, illuminating biological processes that underlie cardiac morphogenesis in humans.

Article III constitutes a study of the transcriptomic landscape of the murine colon generated using spatially resolved transcriptomics. By folding the organ into a roll, we successfully obtained tissue sections covering the entire colon, enabling organ-wide transcriptomic profiling. Sections were acquired from a healthy colon and a colon recovering from damage due to treatment with a tissue-damaging substance. Data-driven analysis of the healthy colon unveiled a previously undiscovered molecular regionalization from the proximal to distal parts. In the recovering colon, we observed dramatic alterations in the distal tissues, while the proximal parts remained more similar to the healthy colon. In the injured distal colon, we mapped multiple gene expression programs associated with distinct biological responses to tissue injury.

In article IV, we introduce an experimental protocol that makes the Visium method compatible with fresh frozen tissue samples with low RNA quality. The protocol was tested on human prostate cancer, lung, colon, small intestine and pediatric brain tumor tissue samples, as well as mouse brain and cartilage tissue samples. Together, these tissue samples represented a wide selection of specimens with varying composition and RNA quality. Through comparative analyses, we demonstrated that the proposed experimental protocol surpassed the standard Visium protocol in performance for samples with low to moderate RNA integrity.

Finally, in article V, we present an updated R package for Visium data analysis. This R package builds upon the work presented in article I, but offers a more versatile and efficient computational framework. The package features web-based tools for interactive data exploration, image processing methods and methods to map cell types in tissue sections. Additionally, it includes several spatially aware analysis methods that incorporate information about distances between measurements to investigate biological phenomena that exhibit spatial patterns.

Under de senaste decennierna har tillkomsten av banbrytande bioteknologiska metoder gjort det möjligt för forskare att analysera de molekylära komponenterna i flercelliga organismer med anmärkningsvärd precision. Forskningsfältet transkriptomik har bevittnat en snabb utveckling av teknologier som har utökat möjligheterna att erhålla omfattande genuttrycksprofiler från biologiska prover. Dessa genuttrycksprofiler ger avgörande insikter i biologiska processer som ligger till grund för organismers utveckling, homeostas och sjukdomsframkallande dysreglering. Moderna teknologier kan användas för att utforska prover i olika grader av precision och upplösning, och när de kombineras bidrar de till en holistisk bild av de invecklade molekylära mekanismerna som formar flercelliga organismer. Vissa av dessa molekylära mekanismer förekommer i mikroskopisk skala och styrs genom kommunikation mellan närliggande celler. Andra mekanismer är beroende av samordnade processer inom stora nätverk av celler organiserade i vävnader och organ. Celler, vävnader och organ bildar en hierarki av strukturella nivåer, och varje nivå spelar en viktig roll för att organismen ska fungera korrekt. Experimentella teknologier inom fältet transkriptomik ger omfattande data som kan användas för att utforska och karaktärisera biologiska fenomen inom och mellan dessa strukturella nivåer. Det centrala temat för denna avhandling kretsar kring användningen av experimentella teknologier och beräkningsmetoder inom biologisk forskning. Här undersöks hur dessa verktyg kan användas för att förbättra vår förståelse av flercelligt liv. Särskild uppmärksamhet riktas mot en teknologi känd som Visium, vilken haft en viktig position inom fältet de senaste åren. Forskningsartiklarna som ingår i denna avhandling visar tillämpningarna av Visium-teknologin och relaterade teknologier inom biologisk forskning. 

I artikel I beskriver vi beräkningsverktyg för bearbetning, analys och visualisering av Visium-data, sammansatt till ett paket skrivet i programmeringsspråket R. Verktygen möjliggör karaktärisering av genuttrycksprofiler i vävnadssnitt och integrering av genuttrycksdata med histologiska bilder i en interaktiv programmeringsmiljö. Denna mjukvara användes i stor utsträckning för de dataanalyser som presenteras i artiklarna II, III och IV och analyser gjorda i artiklarna listade i den utökade publikationslistan. 

I artikel II presenterar vi ett atlas för det mänskliga hjärtat under utveckling, baserat på data framställd med transkriptomiska metoder. Atlasen omfattar tre tidpunkter under den första trimestern, konstruerad med hjälp av genuttrycksdata från celler och vävnadssnitt. Integrerad analys av dessa data möjliggjorde karakterisering av genuttrycksprofiler och den cellulära sammansättningen av anatomiska domäner i hjärtat, vilket belyser de biologiska processer som ligger till grund för hjärtats morfogenes hos människor. 

Artikel III utgör en studie av genuttryckslandskapet i tjocktarmen hos möss, genererad med spatial transkriptomik. Genom att vika organet till en rulle kunde vi erhålla vävnadssnitt som täcker hela tjocktarmen, vilket möjliggjorde transkriptomisk profilering av hela organet i ett enda experiment. Vävnadssnitt togs från en frisk tjocktarm och en tjocktarm som återhämtade sig från skada inducerad med en vävnadsskadande substans (DSS-inducerad kolit). Datadriven analys av den friska tjocktarmen avslöjade en tidigare oupptäckt molekylär regionalisering från de proximala till distala delarna. I den skadade tjocktarmen fann vi dramatiska förändringar i de distala vävnaderna, medan de proximala delarna var mer jämförbara med den friska tjocktarmen. I den skadade distala tjocktarmen kartlade vi flera genuttrycksprogram associerade med distinkta biologiska svar på vävnadsskada. 

I artikel IV introducerar vi ett experimentellt protokoll som utökar tillämpningarna av Visium-metoden för att studera vävnadsprover med låg RNA-kvalitet. Protokollet testades på vävnadsprover från prostatacancer, lunga, tjocktarm, tunntarm och pediatrisk hjärntumör från människa, samt vävnadsprover från hjärna och brosk från mus. Tillsammans representerade dessa prover ett brett urval av vävnader med varierande sammansättning och RNA-kvalitet. Genom jämförande analyser visade vi att denna experimentella metod överträffade det standardiserade Visium-protokollet för prover med låg till måttlig RNA-kvalitet. 

Slutligen, i artikel V, presenterar vi en uppdaterad mjukvara (R-paket) för analys av Visium-data. Detta R-paket bygger på det arbete som presenterades i artikel I, men erbjuder mer mångsidiga och effektiva verktyg för bearbetning, analys och visualisering av data. Paketet inkluderar bland annat webbaserade verktyg för interaktiv utforskning av data, bildbehandlingsmetoder och metoder för att kartlägga celltyper i vävnadssnitt. Vidare innehåller paketet ett antal analysmetoder som inkorporerar information om avstånd mellan mätningar, vilket möjliggör undersökning av biologiska fenomen som uppvisar spatiala mönster.

The authors created a comprehensive developmental cell atlas for spatiotemporal gene expression of the human spinal cord, revealed species-specific regulation during development and used the atlas to infer novel markers for pediatric ependymomas. The spatiotemporal regulation of cell fate specification in the human developing spinal cord remains largely unknown. In this study, by performing integrated analysis of single-cell and spatial multi-omics data, we used 16 prenatal human samples to create a comprehensive developmental cell atlas of the spinal cord during post-conceptional weeks 5-12. This revealed how the cell fate commitment of neural progenitor cells and their spatial positioning are spatiotemporally regulated by specific gene sets. We identified unique events in human spinal cord development relative to rodents, including earlier quiescence of active neural stem cells, differential regulation of cell differentiation and distinct spatiotemporal genetic regulation of cell fate choices. In addition, by integrating our atlas with pediatric ependymomas data, we identified specific molecular signatures and lineage-specific genes of cancer stem cells during progression. Thus, we delineate spatiotemporal genetic regulation of human spinal cord development and leverage these data to gain disease insight.