Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.

Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in situ expression maps of hundreds of genes. We use direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high-throughput and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental and tissue biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to high-throughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.

Interneuron diversity in the human dorsal striatum.

Deciphering the striatal interneuron diversity is key to understanding the basal ganglia circuit and to untangling the complex neurological and psychiatric diseases affecting this brain structure. We performed snRNA-seq and spatial transcriptomics of postmortem human caudate nucleus and putamen samples to elucidate the diversity and abundance of interneuron populations and their inherent transcriptional structure in the human dorsal striatum. We propose a comprehensive taxonomy of striatal interneurons with eight main classes and fourteen subclasses, providing their full transcriptomic identity and spatial expression profile as well as additional quantitative FISH validation for specific populations. We have also delineated the correspondence of our taxonomy with previous standardized classifications and shown the main transcriptomic and class abundance differences between caudate nucleus and putamen. Notably, based on key functional genes such as ion channels and synaptic receptors, we found matching known mouse interneuron populations for the most abundant populations, the recently described PTHLH and TAC3 interneurons. Finally, we were able to integrate other published datasets with ours, supporting the generalizability of this harmonized taxonomy.

BirthSeq, a new method to isolate and analyze dated cells in different vertebrates.

Embryonic development is a complex and dynamic process that unfolds over time and involves the production and diversification of increasing numbers of cells. The impact of developmental time on the formation of the central nervous system is well documented, with evidence showing that time plays a crucial role in establishing the identity of neuronal subtypes. However, the study of how time translates into genetic instructions driving cell fate is limited by the scarcity of suitable experimental tools. We introduce BirthSeq, a new method for isolating and analyzing cells based on their birth date. This innovative technique allows for in vivo labeling of cells, isolation via fluorescence-activated cell sorting, and analysis using high-throughput techniques. We calibrated the BirthSeq method for developmental organs across three vertebrate species (mouse, chick and gecko), and utilized it for single-cell RNA sequencing and novel spatially resolved transcriptomic approaches in mouse and chick, respectively. Overall, BirthSeq provides a versatile tool for studying virtually any tissue in different vertebrate organisms, aiding developmental biology research by targeting cells and their temporal cues.

Nanostructured Copper Selenide Coatings for Antifouling Applications.

The accumulation of microorganisms, plants, algae, or small animals on wet surfaces that have a mechanical function causes biofouling, which can result in structural or other functional deficiencies. The maritime shipping industry must constantly manage biofouling to optimize operational performance, which is a common and long-lasting problem. It can occur on any metal structure in contact with or submerged in ocean water, which represents additional costs in terms of repairs and maintenance. This study is focused on the production of antifouling coatings, made with nanoparticles of copper selenide (CuSe NPs) modified with gum arabic, within a water-base acrylic polymeric matrix. During the curing of the acrylic resin, the CuSe NPs remain embedded in the resin, but this does not prevent the release of ions. The coatings released copper and selenium ions for up to 80 days, and selenium was the element that was released the most. The adhesion of film coatings to metallic substrates showed good adhesion, scale 5B (ASTM D3359 standard). Antimicrobial activity tests show that the coatings have an inhibitory effect on Escherichia coli and Candida albicans. The effect is more noticeable when the coating is detached from the substrate and placed on a growing medium, compared to the coating on a substrate. Scanning electron microscopy (SEM) observations show that nanostructured CuSe coatings are made up of rod-shaped and spherical particles with an average particle size of 101.6 nm and 50 nm, respectively. The energy dispersive X-ray spectroscopy (EDS) studies showed that the ratio of selenium nanoparticles is greater than that of copper and that their distribution is homogeneous.

ThyroidPrint®: clinical utility for indeterminate thyroid cytology.

Molecular testing contributes to improving the diagnosis of indeterminate thyroid nodules (ITNs). ThyroidPrint® is a ten-gene classifier aimed to rule out malignancy in ITN. Post-validation studies are necessary to determine the real-world clinical benefit of ThyroidPrint® in patients with ITN. A single-center, prospective, noninterventional clinical utility study was performed, analyzing the impact of ThyroidPrint® in the physicians' clinical decisions for ITN. Demographics, nodule characteristics, benign call rates (BCRs), and surgical outcomes were measured. Histopathological data were collected from surgical biopsies of resected nodules. Of 1272 fine-needle aspirations, 109 (8.6%) were Bethesda III and 135 (10.6%) were Bethesda IV. Molecular testing was performed in 155 of 244 ITN (63.5%), of which 104 were classified as benign (BCR of 67.1%). After a median follow-up of 15 months, 103 of 104 (99.0%) patients with a benign ThyroidPrint® remained under surveillance and one patient underwent surgery which was a follicular adenoma. Surgery was performed in all 51 patients with a suspicious for malignancy as per ThyroidPrint® result and in 56 patients who did not undergo testing, with a rate of malignancy of 70.6% and 32.1%, respectively. A higher BCR was observed in follicular lesion of undetermined significance (87%) compared to atypia of undetermined significance (58%) (P < 0.05). False-positive cases included four benign follicular nodules and six follicular and four oncocytic adenomas. Our results show that, physicians chose active surveillance instead of diagnostic surgery in all patients with a benign ThyroidPrint® result, reducing the need for diagnostic surgery in 67% of patients with preoperative diagnosis of ITN.

Identifying the neurodevelopmental and psychiatric signatures of genomic disorders associated with intellectual disability: a machine learning approach.

BACKGROUND: Genomic conditions can be associated with developmental delay, intellectual disability, autism spectrum disorder, and physical and mental health symptoms. They are individually rare and highly variable in presentation, which limits the use of standard clinical guidelines for diagnosis and treatment. A simple screening tool to identify young people with genomic conditions associated with neurodevelopmental disorders (ND-GCs) who could benefit from further support would be of considerable value. We used machine learning approaches to address this question. METHOD: A total of 493 individuals were included: 389 with a ND-GC, mean age = 9.01, 66% male) and 104 siblings without known genomic conditions (controls, mean age = 10.23, 53% male). Primary carers completed assessments of behavioural, neurodevelopmental and psychiatric symptoms and physical health and development. Machine learning techniques (penalised logistic regression, random forests, support vector machines and artificial neural networks) were used to develop classifiers of ND-GC status and identified limited sets of variables that gave the best classification performance. Exploratory graph analysis was used to understand associations within the final variable set. RESULTS: All machine learning methods identified variable sets giving high classification accuracy (AUROC between 0.883 and 0.915). We identified a subset of 30 variables best discriminating between individuals with ND-GCs and controls which formed 5 dimensions: conduct, separation anxiety, situational anxiety, communication and motor development. LIMITATIONS: This study used cross-sectional data from a cohort study which was imbalanced with respect to ND-GC status. Our model requires validation in independent datasets and with longitudinal follow-up data for validation before clinical application. CONCLUSIONS: In this study, we developed models that identified a compact set of psychiatric and physical health measures that differentiate individuals with a ND-GC from controls and highlight higher-order structure within these measures. This work is a step towards developing a screening instrument to identify young people with ND-GCs who might benefit from further specialist assessment.

Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications.

Elucidating spatiotemporal changes in gene expression has been an essential goal in studies of health, development, and disease. In the emerging field of spatially resolved transcriptomics, gene expression profiles are acquired with the tissue architecture maintained, sometimes at cellular resolution. This has allowed for the development of spatial cell atlases, studies of cell-cell interactions, and in situ cell typing. In this review, we focus on padlock probe-based in situ sequencing, which is a targeted spatially resolved transcriptomic method. We summarize recent methodological and computational tool developments and discuss key applications. We also discuss compatibility with other methods and integration with multiomic platforms for future applications.

A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.

The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.

Anti-hyperglycemic activity of aqueous extracts of cells produced in Ibervillea sonorae (S. Watson) Green cell culture on murine model / Actividad anti-hiperglucémica del extracto acuoso de células producidas en cultivo celular de Ibervillea sonorae (S. Watson) Green en un modelo murino

Ibervillea sonorae (S. Watson) Greene, is a plant native to Mexico, where its roots have been used traditionally for treating Diabetes Mellitus. The aim of this work was to establishment of cell cultures of stem explants of I. sonorae and evaluation of the anti-hyperglycemic activity of cell aqueous extract on a murine model of streptozotocin-induced diabetic rats. Cell extracts had 2.29 mg palmitic acid/g extracted, and other compounds with pharmacological activities like palmitoyl ethanolamide and palmitoyl tryptamine were also identified. Diabetic rats treated with aqueous cell extract decreased glucose levels from 350 mg/dL to 145 mg/dL, AST and ALT from 164 U/L to 49 U/L and 99 U/L to 53 U/L, respectively. Additionally, there were no changes in the cellular morphology of the pancreas, liver, kidneys, and spleen. These results revealed that the cell aqueous extract from stem explants has anti-hyperglycemic activity.

Ibervillea sonorae (S. Watson) Greene, es una planta originaria de México, donde sus raíces se han utilizado tradicionalmente para el tratamiento de la Diabetes Mellitus. El objetivo de este trabajo fue el establecimiento de cultivos celulares de explantes de tallo de I. sonorae y la evaluación de la actividad anti-hiperglucémica del extracto acuoso celular en un modelo de ratas diabéticas inducidas con estreptozotocina. El extracto celular contiene 2.29 mg de ácido palmítico/g extracto y se identificaron otros compuestos como palmitoil etanolamida y palmitoil triptamina. Las ratas diabéticas tratadas con extracto celular disminuyeron los niveles de glucosa de 350 mg/dL a 145 mg/dL, AST y ALT de 164 U/L a 49 U/L y 99 U/L a 53 U/L, respectivamente. Además, no hubo cambios en la morfología celular del páncreas, hígado, riñones y bazo. Estos resultados indican que el extracto de células de explantes de tallo de I. sonorae tiene actividad anti-hiperglucémica.

The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.

Histone 3 lysine27-to-methionine (H3-K27M) mutations most frequently occur in diffuse midline gliomas (DMGs) of the childhood pons but are also increasingly recognized in adults. Their potential heterogeneity at different ages and midline locations is vastly understudied. Here, through dissecting the single-cell transcriptomic, epigenomic and spatial architectures of a comprehensive cohort of patient H3-K27M DMGs, we delineate how age and anatomical location shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We show that stem-like oligodendroglial precursor-like cells, present across all clinico-anatomical groups, display varying levels of maturation dependent on location. We reveal a previously underappreciated relationship between mesenchymal cancer cell states and age, linked to age-dependent differences in the immune microenvironment. Further, we resolve the spatial organization of H3-K27M DMG cell populations and identify a mitotic oligodendroglial-lineage niche. Collectively, our study provides a powerful framework for rational modeling and therapeutic interventions.

Epidemiological characteristics of Omicron and Delta SARS-CoV-2 variant infection in Santiago, Chile.

The variant of concern (VOC) SARS-CoV-2 Omicron (B.1.1529) has been described as a highly contagious variant but less virulent than the current variant being monitored (VBM) Delta (B.1.617.2), causing fewer cases of hospitalizations, symptomatology, and deaths associated with COVID-19 disease. Although the epidemiological comparison of both variants has been previously reported in other countries, no report indicates their behavior and severity of infection in Chile. In this work, we report for the first time the effect of the Omicron and Delta variants in a cohort of 588 patients from the Hospital de Urgencia Asistencia pública (HUAP), a high-complexity health center in Santiago, Chile. This report is framed at the beginning of Chile's third wave of the COVID-19 pandemic, with a marked increase in the Omicron variant and a decrease in the circulating Delta variant. Our results indicated a similar proportion of patients with a complete vaccination schedule for both variants. However, the Delta variant was associated with a higher prevalence of hospitalization and more significant symptomatology associated with respiratory distress. On the other hand, our data suggest that vaccination is less effective in preventing infection by the Omicron variant. This antecedent, with a low severity but high contagiousness, suggests that the Omicron variant could even collapse the primary health care service due to the high demand for health care.

Impact of secondary salts, temperature, and pH on the colloidal stability of graphene oxide in water.

The stability of graphene oxide (GO) in water is extremely relevant because of its application as an adsorbent material, as well as for its fate and behavior in the environment. Zeta potential was used to study the effect of secondary salts (carbonate, sulfate, and phosphate), temperature (20 to 60 °C), and pH (5 to 9) on the stability of six different GOs produced from natural, synthetic, and amorphous graphite-with and without the use of attrition milling. Generally, GOs produced with attrition-milled graphites had lower ζ-potentials than their unmilled counterparts because of their smaller particle sizes and higher concentration of oxygen-containing functional groups. It was observed that GO produced from graphite and synthetic graphite had ζ-potential values lower than -30 mV, even at 30 °C. However, it was observed that all the GOs studied were unstable in the presence of carbonate and sulfate salts at concentrations between 170 and 1695 mg L-1, as they reached a ζ-potential of -4.1 mV. Density-functional theory electronic structure calculations suggested that the instability of GO in the presence of carbonate and sulfate was caused by the abstraction of a proton resulting in interaction energies E int of 28.3 and 168.9 kJ mol-1, respectively. Our results suggest that temperatures above 30 °C, as well as carbonate and sulfate salts at concentrations relevant to arid and semi-arid regions, could promote the formation of agglomerates of GO, thus limiting its use and mobility in water.

De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.

With the emergence of high throughput single cell techniques, the understanding of the molecular and cellular diversity of mammalian organs have rapidly increased. In order to understand the spatial organization of this diversity, single cell data is often integrated with spatial data to create probabilistic cell maps. However, targeted cell typing approaches relying on existing single cell data achieve incomplete and biased maps that could mask the true diversity present in a tissue slide. Here we applied a de novo technique to spatially resolve and characterize cellular diversity of in situ sequencing data during human heart development. We obtained and made accessible well defined spatial cell-type maps of fetal hearts from 4.5 to 9 post conception weeks, not biased by probabilistic cell typing approaches. With our analysis, we could characterize previously unreported molecular diversity within cardiomyocytes and epicardial cells and identified their characteristic expression signatures, comparing them with specific subpopulations found in single cell RNA sequencing datasets. We further characterized the differentiation trajectories of epicardial cells, identifying a clear spatial component on it. All in all, our study provides a novel technique for conducting de novo spatial-temporal analyses in developmental tissue samples and a useful resource for online exploration of cell-type differentiation during heart development at sub-cellular image resolution.

Spatial Resolution of Mycobacterium tuberculosis Bacteria and Their Surrounding Immune Environments Based on Selected Key Transcripts in Mouse Lungs.

Mycobacterium tuberculosis (Mtb) bacilli are the causative agent of tuberculosis (TB), a major killer of mankind. Although it is widely accepted that local interactions between Mtb and the immune system in the tuberculous granuloma determine whether the outcome of infection is controlled or disseminated, these have been poorly studied due to methodological constraints. We have recently used a spatial transcriptomic technique, in situ sequencing (ISS), to define the spatial distribution of immune transcripts in TB mouse lungs. To further contribute to the understanding of the immune microenvironments of Mtb and their local diversity, we here present two complementary automated bacteria-guided analysis pipelines. These position 33 ISS-identified immune transcripts in relation to single bacteria and bacteria clusters. The analysis was applied on new ISS data from lung sections of Mtb-infected C57BL/6 and C3HeB/FeJ mice. In lungs from C57BL/6 mice early and late post infection, transcripts that define inflammatory macrophages were enriched at subcellular distances to bacteria, indicating the activation of infected macrophages. In contrast, expression patterns associated to antigen presentation were enriched in non-infected cells at 12 weeks post infection. T-cell transcripts were evenly distributed in the tissue. In Mtb-infected C3HeB/FeJ mice, transcripts characterizing activated macrophages localized in apposition to small bacteria clusters, but not in organized granulomas. Despite differences in the susceptibility to Mtb, the transcript patterns found around small bacteria clusters of C3HeB/FeJ and C57BL/6 mice were similar. Altogether, the presented tools allow us to characterize in depth the immune cell populations and their activation that interact with Mtb in the infected lung.

Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue.

Highly multiplexed spatial mapping of transcripts within tissues allows for investigation of the transcriptomic and cellular diversity of mammalian organs previously unseen. Here we explore a direct RNA (dRNA) detection approach incorporating the use of padlock probes and rolling circle amplification in combination with hybridization-based in situ sequencing chemistry. We benchmark a High Sensitivity Library Preparation Kit from CARTANA that circumvents the reverse transcription needed for cDNA-based in situ sequencing (ISS) via direct RNA detection. We found a fivefold increase in transcript detection efficiency when compared to cDNA-based ISS and also validated its multiplexing capability by targeting a curated panel of 50 genes from previous publications on mouse brain sections, leading to additional data interpretation such as de novo cell clustering. With this increased efficiency, we also found to maintain specificity, multiplexing capabilities and ease of implementation. Overall, the dRNA chemistry shows significant improvements in target detection efficiency, closing the gap to other fluorescent in situ hybridization-based technologies and opens up possibilities to explore new biological questions previously not possible with cDNA-based ISS.

[Effectiveness of treatment with Pygeum africanum in patients with lower urinary tract symptoms and benign prostatic hyperplasia: a cross-sectional study in the real-world clinical practice in Spain (The PROFIT Study)]. / Efectividad del tratamiento con Pygeum africanum en pacientes con síntomas del tracto urinario inferior e hiperplasia benigna de próstata: estudio transversal en la práctica clínica real en España (Estudio PROFIT).

OBJECTIVES: To assess the effectivenessand tolerability of treatment with P africanum(P. africanum) in patients with lower urinary tractsymptoms (LUTS) associated with benign prostatichyperplasia (BPH) in routine clinical practice. MATERIAL AND METHODS: Cross-sectional observationalstudy in which 115 patients with LUTS/BPHtreated for 6 months with P. africanum (Tebetane® compuesto)in real-world clinical practice conditions wereincluded. The primary objective was to assess thequality of life (QoL) according to changes in the scoresof item 8 of the International Prostate Symptom Score(IPSS) questionnaire (a score ≥ 4 indicates a significantimpairment of QoL). Secondary objectives includedimprovement of urinary symptoms, urinary flow, satisfactionand compliance with treatment as well astolerability. Data were collected in a single scheduledvisit at 6 months of treatment with P. africanum andwere compared with data registered in the medicalrecords at the beginning of treatment. RESULTS: After 6 months of treatment withP. africanum, the percentage of patient with significantimpairment of QoL was 22.6% as compared with45.2% at the initiation of treatment (P 0,-001). Theoverall IPSS score showed a mean decreas of -4,-5points (median -4,0, interquartile range [IQR] -7,-0 to-2,0) and 69 patients (60%) showed a clinically significantimprovement (reduction of ≥ 4 points). Therewere significant decreases in IPSS subscales of storage(mean -1,-8; median -2,-0, IQR -3,-0 to 0 (P 0,-001)and voiding (mean -1,-9; median -2,-0, IQR -3,-0 to 0)(P 0,-001) symptoms. The degree of satisfaction and compliance with treatment was high with mean scores(median) of 6,9 (7,0) and 9,2 (10), respectively in the1-10 visual analogue scale. Treatment-related adverseeffects did not occur. CONCLUSIONS: Treatment with P. africanum during6 months improved significantly QoL and LUTS inpatients with BPH, with a high level of satisfaction andcompliance with treatment, without adverse events.

OBJETIVO: Evaluar la efectividad y latolerabilidad del tratamiento con Pygeum africanum (P.africanum) en pacientes con síntomas del tracto urinarioinferior (STUI) asociados a hiperplasia benigna depróstata (HBP) en la práctica clínica habitual.MATERIAL Y MÉTODOS: Estudio observacionaltransversal en el que se incluyeron 115 pacientes conSTUI/HBP tratados durante 6 meses con P. africanum (Tebetane® compuesto) en condiciones de prácticaclínica real. El objetivo primario fue evaluar la calidadde vida (CdV) en función del cambio en la pregunta 8del cuestionario de Puntuación Internacional de losSíntomas Prostáticos (IPSS) (puntuación ≥ 4 indicaafectación significativa de la CdV). Los objetivos secundariosincluyeron la mejoría de síntomas urinarios,flujo urinario, satisfacción y cumplimiento con eltratamiento, así como la tolerabilidad del mismo. Losdatos se recogieron en una única visita programada alos 6 meses de tratamiento con P. africanum y se compararoncon los registrados en la historia clínica alinicio del tratamiento. RESULTADOS: Tras 6 meses de tratamiento conP. africanum, el porcentaje de pacientes con afectaciónsignificativa de la CdV fue del 22,6% en comparacióncon un 45,2% al inicio del tratamiento (P 0,001).La puntuación global del IPSS disminuyó de mediaen -4,5 puntos (mediana -4,0, rango intercuartílico [RIQ] -7,0 a -2,0) y 69 pacientes (60%) mostraron unamejoría clínicamente significativa (disminución ≥ 4puntos). Se observaron disminuciones significativasen las subescalas del IPSS de los síntomas de llenado(media -1,8; mediana -2,0, RIQ -3,0 a 0) (P 0,001) yvaciado (media -1,9; mediana -2,0, RIQ -3,0 a 0) (P 0,001). El grado de satisfacción y cumplimiento con eltratamiento fue elevado con valores medios (mediana)de 6,9 (7,0) y 9,2 (10) respectivamente, en una escalaanalógica visual 1-10 cm. No se registraron efectosadversos relacionados con el tratamiento. CONCLUSION: El tratamiento con P. africanum(P. africanum) durante 6 meses mejoró significativamentela CdV y los STUI en pacientes con HBP, con unalto grado de satisfacción y cumplimiento con el tratamiento,sin registrarse reacciones adversas.

Evidence of autochthonous transmission of urinary schistosomiasis in Almeria (southeast Spain): An outbreak analysis.

BACKGROUND: Schistosomiasis is endemic in 78 countries belonging to tropical and subtropical areas. However, autochthonous transmission of urogenital schistosomiasis was reported in Corsica (France) in 2013. We present evidence of autochthonous transmission of urogenital schistosomiasis in Almería (Spain) in 2003. METHODS: Description of the outbreak in farmers and subsequent epidemiological studies aimed at searching for Bulinus snails and their genotypic characteristics. RESULTS: The outbreak affected 4 farmers out of a group of 5 people who repeatedly bathed that summer in an irrigation pool in the area. Two of them presented macroscopic hematuria with bilharziomas, showing the presence of Schistosoma eggs in bladder biopsies. Two others were asymptomatic but the serology for schistosomiasis was positive. In 2015, the presence of the vector Bulinus truncatus was demonstrated in Almería in water collections of appropriate characteristics. DNA sequencing proving that local B. truncatus species were base-to-base identical to B. truncatus from Senegal. CONCLUSIONS: We present a new outbreak of autochthonous transmission of urogenital schistosomiasis in Europe. Although no new cases of autochthonous transmission have been reported, some other cases may have occurred at that time or later on and be unnoticed as many cases of schistosomiasis are asymptomatic or present mild and unspecific symptoms.

Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps.

BACKGROUND: A range of spatially resolved transcriptomic methods has recently emerged as a way to spatially characterize the molecular and cellular diversity of a tissue. As a consequence, an increasing number of computational techniques are developed to facilitate data analysis. There is also a need for versatile user friendly tools that can be used for a de novo exploration of datasets. RESULTS: Here we present MATLAB-based Analysis toolbox for in situ sequencing (ISS) expression maps (Matisse). We demonstrate Matisse by characterizing the 2-dimensional spatial expression of 119 genes profiled in a mouse coronal section, exploring different levels of complexity. Additionally, in a comprehensive analysis, we further analyzed expression maps from a second technology, osmFISH, targeting a similar mouse brain region. CONCLUSION: Matisse proves to be a valuable tool for initial exploration of in situ sequencing datasets. The wide set of tools integrated allows for simple analysis, using the position of individual reads, up to more complex clustering and dimensional reduction approaches, taking cellular content into account. The toolbox can be used to analyze one or several samples at a time, even from different spatial technologies, and it includes different segmentation approaches that can be useful in the analysis of spatially resolved transcriptomic datasets.