Subcellular Resolution Research Articles

Probe set selection for targeted spatial transcriptomics

AbstractTargeted spatial transcriptomic methods capture the topology of cell types and states in tissues at single-cell and subcellular resolution by measuring the expression of a predefined set of genes. The selection of an optimal set of probed genes is crucial for capturing the spatial signals present in a tissue. This requires selecting the most informative, yet minimal, set of genes to profile (gene set selection) for which it is possible to build probes (probe design). However, current selections often rely on marker genes, precluding them from detecting continuous spatial signals or new states. We present Spapros, an end-to-end probe set selection pipeline that optimizes both gene set specificity for cell type identification and within-cell type expression variation to resolve spatially distinct populations while considering prior knowledge as well as probe design and expression constraints. We evaluated Spapros and show that it outperforms other selection approaches in both cell type recovery and recovering expression variation beyond cell types. Furthermore, we used Spapros to design a single-cell resolution in situ hybridization on tissues (SCRINSHOT) experiment of adult lung tissue to demonstrate how probes selected with Spapros identify cell types of interest and detect spatial variation even within cell types.

Spatially Controlled MicroRNA Imaging in Mitochondria via Enzymatic Activation of Hybridization Chain Reaction.

Live-cell imaging of RNA in specific subcellular compartments is essential for elucidating the rich repertoire of cellular functions, but it has been limited by a lack of simple, precisely controlled methods. Here such an approach is presented via the combination of hybridization chain reaction and spatially restricted enzymatic activation with organelle-targeted delivery. The system can localize engineered DNA hairpins in the mitochondria, where target RNA-initiated chain reaction of hybridization events is selectively activated by a specific enzyme, enabling amplified RNA imaging with high precision. It is demonstrated that the approach is compatible with live cell visualization and enables the regulatable imaging of microRNA in mitochondria. Since in situ activation of the signal amplification with enzyme eliminates the need for genetically encoded protein overexpression, it is envisioned that this simple platform will be broadly applicable for precise RNA imaging with subcellular resolution in a variety of biological processes.

An automated high-content screening and assay platform for the analysis of spheroids at subcellular resolution.

The endomembrane system is essential for healthy cell function, with the various compartments carrying out a large number of specific biochemical reactions. To date, almost all of our understanding of the endomembrane system has come from the study of cultured cells growing as monolayers. However, monolayer-grown cells only poorly represent the environment encountered by cells in the human body. As a first step to address this disparity, we have developed a platform that allows us to investigate and quantify changes to the endomembrane system in three-dimensional (3D) cell models, in an automated and highly systematic manner. HeLa Kyoto cells were grown on custom-designed micropatterned 96-well plates to facilitate spheroid assembly in the form of highly uniform arrays. Fully automated high-content confocal imaging and analysis were then carried out, allowing us to measure various spheroid-, cellular- and subcellular-level parameters relating to size and morphology. Using two drugs known to perturb endomembrane function, we demonstrate that cell-based assays can be carried out in these spheroids, and that changes to the Golgi apparatus and endosomes can be quantified from individual cells within the spheroids. We also show that image texture measurements are useful tools to discriminate cellular phenotypes. The automated platform that we show here has the potential to be scaled up, thereby allowing large-scale robust screening to be carried out in 3D cell models.

Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data.

Spatially resolved transcriptomics (SRT) has become the method of choice for characterising the complexity of biomedical tissue samples. Until recently, scientists were restricted to SRT methods that can profile a limited set of target genes at high spatial resolution or transcriptome-wide but at a low spatial resolution. Through recent developments, there are now methods that offer both subcellular spatial resolution and full transcriptome coverage. However, utilising these new methods' high spatial resolution and gene resolution remains elusive due to several factors, including low detection efficiency and high computational costs. Here, we present Sainsc (Segmentation-free analysis of in situ capture data), which combines a cell-segmentation-free approach with efficient data processing of transcriptome-wide nanometre-resolution spatial data. Sainsc can generate cell-type maps with accurate cell-type assignment at the nanometre scale, together with corresponding maps of the assignment scores that facilitate interpretation of the local confidence of cell-type assignment. We demonstrate its utility and accuracy for different tissues and technologies. Compared to other methods, Sainsc requires lower computational resources and has scalable performance, enabling interactive data exploration. Sainsc is compatible with common data analysis frameworks and is available as open-source software in multiple programming languages.

Lensless On-Chip Chemiluminescence Imaging for High-Throughput Single-Cell Heterogeneity Analysis.

High-throughput single-cell heterogeneity imaging and analysis is essential for understanding complex biological systems and for advancing personalized precision disease diagnosis and treatment. Here, we present a miniaturized lensless chemiluminescence chip for high-throughput single-cell functional imaging with subcellular resolution. With the sensitive chemiluminescence sensing and wide field of view of contact lensless imaging, we demonstrated the chemiluminescent imaging of over 1000 single cells, and their membrane glycoprotein and the high-throughput single-cell heterogeneity of membrane protein imaging were examined for precision analysis. Furthermore, the functional adhesion and heterogeneity of single live cells were imaged and explored. This miniaturized lensless on-chip CL-CMOS imaging platform enables high-throughput single-cell imaging and analysis with high sensitivity and subcellular resolution, providing new techniques for the cellular study of biological heterogeneity and has potential application in precision disease diagnosis and treatment at the point-of-care settings.

Mesoscopic axially swept oblique plane microscope for the imaging of freely moving organisms with near-isotropic resolution

Rapid three-dimensional imaging over extended fields of view (FOVs) is crucial to the study of organism-wide systems and biological processes in vivo. Selective-plane illumination microscopy (SPIM) is a powerful method for high spatio-temporal resolution in toto imaging of such biological specimens. However, typical SPIM implementations preclude conventional sample mounting and have anisotropic imaging performance, in particular when designed for large FOVs over 1 mm diameter. Here, we introduce axial sweeping of the illumination into a non-orthogonal dual-objective oblique plane microscope (OPM) design, thereby enabling the observation of freely moving animals over millimeter-sized FOVs, at close to isotropic, sub-cellular resolution. We apply our mesoscopic axially swept OPM (MASOPM) to image the behavioral dynamics of the sea anemone Nematostella vectensis over 1 × 0.7 × 0.4 mm at 1.7 × 2.6 × 3.7 µm resolution and 0.5 Hz volume rate.

Exploring the Intracellular Distribution of Se Compounds Delivered by Biodegradable Polyelectrolyte Capsules Using X‐Ray Fluorescence Imaging

AbstractSelenium (Se) compounds hold promise as potential therapeutics for cancer due to their diverse biological functions and redox‐regulating properties. In this study, the encapsulation of a hydrophobic selenium compound inside 5 µm sized biodegradable polyelectrolyte capsules consisting of poly‐L‐arginine and dextran is investigated. While the encapsulated form of the compound showed comparable cellular uptake and cytotoxicity as the free drug, e.g. no improved anti‐cancer efficacy is achieved, the investigation yielded crucial insights. Utilizing subcellular resolution synchrotron X‐ray fluorescence imaging (XFI), the intracellular location of the Se compound is successfully visualized by demonstrating the degradation of the capsules and the following redistribution of the compound, without exogenous labeling. By applying a quantitative fitting approach, the intracellular Se mass is determined to be 0.09 ± 0.01 pg after degradation of the carrier. This highlights the potential of XFI as a powerful tool for tracking intracellular dynamics of metal‐based drugs, which may facilitate drug development in the clinic.

Challenges and Opportunities in the Clinical Translation of High-Resolution Spatial Transcriptomics.

Pathology has always been fueled by technological advances. Histology powered the study of tissue architecture at single-cell resolution and remains a cornerstone of clinical pathology today. In the last decade, next-generation sequencing has become informative for the targeted treatment of many diseases, demonstrating the importance of genome-scale molecular information for personalized medicine. Today, revolutionary developments in spatial transcriptomics technologies digitalize gene expression at subcellular resolution in intact tissue sections, enabling the computational analysis of cell types, cellular phenotypes, and cell-cell communication in routinely collected and archival clinical samples. Here we review how such molecular microscopes work, highlight their potential to identify disease mechanisms and guide personalized therapies, and provide guidance for clinical study design. Finally, we discuss remaining challenges to the swift translation of high-resolution spatial transcriptomics technologies and how integration of multimodal readouts and deep learning approaches is bringing us closer to a holistic understanding of tissue biology and pathology.

Recent Development of Chemigenetic Hybrid Voltage Indicators Enabled by Bioconjugation Chemistry.

Fluorescent voltage indicators enable the optical recording of electrophysiology across large cell populations with subcellular resolution; however, their application is often constrained by a limited photon budget. To address this limitation, advanced bioconjugation methods have been employed to site-specifically attach bright and photostable organic dyes to cell-specific protein scaffolds in live cells. The resulting chemigenetic hybrid voltage indicators enable sustained monitoring of voltage fluctuations with an exceptional signal-to-noise ratio, both in vitro and in vivo. This Viewpoint discusses recent advancements in the development of these indicators through bioconjugation chemistry.

Quality control for single-cell analysis of high-plex tissue profiles using CyLinter.

Tumors are complex assemblies of cellular and acellular structures patterned on spatial scales from microns to centimeters. Study of these assemblies has advanced dramatically with the introduction of high-plex spatial profiling. Image-based profiling methods reveal the intensities and spatial distributions of 20-100 proteins at subcellular resolution in 103-107 cells per specimen. Despite extensive work on methods for extracting single-cell data from these images, all tissue images contain artifacts such as folds, debris, antibody aggregates, optical aberrations and image processing errors that arise from imperfections in specimen preparation, data acquisition, image assembly and feature extraction. Here we show that these artifacts dramatically impact single-cell data analysis, obscuring meaningful biological interpretation. We describe an interactive quality control software tool, CyLinter, that identifies and removes data associated with imaging artifacts. CyLinter greatly improves single-cell analysis, especially for archival specimens sectioned many years before data collection, such as those from clinical trials.

Real-time simultaneous visualization of lactate and proton dynamics using a 6-μm-pitch CMOS multichemical image sensor

Multi-analyte detection and imaging of extracellular chemical signaling molecules are crucial for understanding brain function and molecular pathology. In this work, we present a 6-μm-pitch, CMOS-based multichemical image sensor that enables the simultaneous visualization and spatiotemporal multimodal analysis of the lactate and proton (H+) dynamics without any labeling. Using semiconductor lithography, gold electrode patterns functioning as lactate-sensing regions were formed on a potentiometric sensor array. Lactate is detected potentiometrically because of redox reactions using lactate oxidase and horseradish peroxidase. The resulting multichemical image sensor exhibited a pH sensitivity of 65 mV and a superior detection limit of 1 μM for lactate with a reasonable selectivity. Furthermore, diffusion images of lactate and H+ distributions were obtained concurrently, allowing for simultaneous real-time imaging of the two chemicals with subcellular resolution. We believe that our novel imaging device can be successfully applied to extracellular microenvironments in tissue or cell samples as an effective bioimaging tool.

Orthogonal dispersion modeling of double-stage VIPA spectrometer in SBS system

Brillouin microscopy enables the assessment of the mechanical properties of biological tissues by mapping the Brillouin shift in three-dimensional (3D), all-optical, label-free, non-contact, and subcellular resolution. The virtually imaged phased array (VIPA) etalon is widely utilized for measuring Brillouin spectra owing to its superior light throughput, large angular dispersion, and rapid signal acquisition capabilities. The VIPA-based spectrometer plays a significant role in Brillouin microscopy, but it is highly sensitive to factors such as the tilt angle, beam radius, lens focal length, and so on. Here, we propose an orthogonal dispersion model based on paraxial wave theory. This model is employed to explore the output intensity distribution and dispersion characteristics of a double-stage VIPA spectrometer. To validate the proposed model, we develop a stimulated Brillouin scattering (SBS) system by leveraging the optimal spectrometer parameters to measure the Brillouin frequency shift in pure water. We demonstrate the capabilities of this model in mitigating spectral dispersion and enhancing spectral measurement accuracy by optimizing the spectrometer's system parameters. This work is pivotal for the future deployment of the double-stage VIPA spectrometer in SBS-based microscopy applications.

Two-Photon Microscopy to Measure Calcium Signaling in the Living Brain.

Two-photon microscopy enables imaging of calcium signaling at cellular or subcellular resolution up to hundreds of microns deep in the living brain. Changes in the brightness of fluorescent calcium indicators provide a readout of calcium levels over time, affording information about neuronal activity and/or calcium-dependent subcellular signaling. Here, we describe a protocol for repeated two-photon imaging of calcium signals in mice expressing a genetically encoded calcium indicator that have been implanted with a chronic cranial window.

Real-Time Imaging Assessment of Stress-Induced Vascular Inflammation Using Heartbeat-Synchronized Motion Compensation.

Chronic mental stress accelerates atherosclerosis through complicated neuroimmune pathways, needing for advanced imaging techniques to delineate underlying cellular mechanisms. While histopathology, ex vivo imaging, and snapshots of in vivo images offer promising evidence, they lack the ability to capture real-time visualization of blood cell dynamics within pulsatile arteries in longitudinal studies. An electrically tunable lens was implemented in intravital optical microscopy, synchronizing the focal plane with heartbeats to follow artery movements. ApoE-/- mice underwent 2 weeks of restraint stress before baseline imaging followed by 2 weeks of stress exposure in the longitudinal imaging, while nonstressed mice remained undisturbed. The progression of vascular inflammation was assessed in the carotid arteries through intravital imaging and histological analyses. A 4-fold reduction of motion artifact, assessed by interframe SD, and an effective temporal resolution of 25.2 Hz were achieved in beating murine carotid arteries. Longitudinal intravital imaging showed chronic stress led to a 6.09-fold (P=0.017) increase in myeloid cell infiltration compared with nonstressed mice. After 3 weeks, we observed that chronic stress intensified vascular inflammation, increasing adhered myeloid cells by 2.45-fold (P=0.031), while no significant changes were noted in nonstressed mice. Microcirculation imaging revealed increased circulating, rolling, and adhered cells in stressed mice's venules. Histological analysis of the carotid arteries confirmed the in vivo findings that stress augmented plaque area, myeloid cell and macrophage accumulation, and necrotic core volume while reducing fibrous cap thickness indicating accelerated plaque formation. We visualized the 3-dimensional structure of the carotid artery and 4-dimensional dynamics of the venules in the cremaster muscle. Dynamic focusing motion compensation intravital microscopy enabled subcellular resolution in vivo imaging of blood cell dynamics in beating arteries under chronic restraint stress in real time. This novel technique emphasizes the importance of advanced in vivo imaging for understanding cardiovascular disease.

Long-term three-dimensional high-resolution imaging of live unlabeled small intestinal organoids via low-coherence holotomography

Organoids, which are miniature in vitro versions of organs, possess significant potential for studying human diseases and elucidating their underlying mechanisms. Live imaging techniques play a crucial role in organoid research and contribute to elucidating the complex structure and dynamic biological phenomena of organoids. However, live, unlabeled high-resolution imaging of native organoids is challenging, primarily owing to the complexities of sample handling and optical scattering inherent in three-dimensional (3D) structures. Additionally, conventional imaging methods fail to capture the real-time dynamic processes of growing organoids. In this study, we introduce low-coherence holotomography as an advanced, label-free, quantitative imaging modality designed to overcome several technical obstacles for long-term live imaging of 3D organoids. We demonstrate the efficacy of low-coherence holotomography by capturing high-resolution morphological details and dynamic activities within mouse small intestinal organoids at subcellular resolution. Moreover, our approach facilitates the distinction between viable and nonviable organoids, significantly enhancing its utility in organoid-based research. This advancement underscores the critical role of live imaging in organoid studies, offering a more comprehensive understanding of these complex systems.

Longitudinal intravital microscopy of the mouse kidney: inflammatory responses to abdominal imaging windows.

Intravital microscopy enables direct observation of cell biology and physiology at subcellular resolution in real time in living animals. Implanted windows extend the scope of intravital microscopy to processes extending for weeks or even months, such as disease progression or tumor development. However, a question that must be addressed in such studies is whether the imaging window, like any foreign body, triggers an inflammatory response, and if that response alters the biological process under investigation. To directly evaluate this question, we conducted large-scale intravital microscopy of the kidney of LysM-EGFP mice over time after implantation of abdominal imaging windows. These studies demonstrate that windows stimulated a variety of changes consistent with a foreign body response. Within a few days of implantation, leukocytes were recruited to the window and the region between the window and kidney where, over the next 16 days, they increased in number in an expanding volume that developed a new vascular network. These changes were accompanied by a dramatic increase in glomerular albumin permeability within 2 - 5 days of implantation. Similar results were obtained from mice implanted with windows coated with PLL-g-PEG, but not from immune-deficient mice. These studies demonstrate the importance of evaluating whether implanted windows induce an inflammatory response, and whether that response impacts the processes under evaluation in longitudinal intravital microscopy studies.

Abstract C117: Integrative multi-omics profiling in patients of African descent diagnosed with prostate cancer reveals distinct tumor-promoting immunosuppressive niches at a single-cell level and spatial resolution

Abstract In the United States and globally, prostate cancer (PCa) mortality rates are the highest among men of African descent. 24% of the disparities in PCa remains even when controlled for access to care and stage at presentation. Moreover, the tumor microenvironment plays an essential role in tumor progression, aggressiveness, therapeutic response, and patient outcomes. Additionally, the association of the genomic findings with patient ancestry and other characteristics, such as tumor biology and transcriptomic alterations, remains poorly understood. Here, we performed a multi-Omics approach (N=447) to unravel the complexity of tumor heterogeneity and understand disease progression & distinct tumor biology influenced by genetic ancestry. We performed Whole Exome (Normal/tumor paired) Sequencing matched with Methyl Seq and Whole transcriptomic Sequencing for three datasets of our African, African American Men (AAM), and European Men (EAM). Additionally, we ran Spatial NanoString high-plex GeoMx-DSP for a total of 118 treatment-naive PCa patients (around 500 ROIs). Simultaneously, we added matched whole transcriptome Sequencing for these patients. The cohort comprised 87 AAM, 3 unknown, and 28 EAM self-reported individuals. To verify the self-reported race, the genomic ancestry was qualified using genotype and Admixture analysis. To further validate differentially expressed genes at the protein level, we performed multi-plex histological staining of 40 markers to determine the spatial resolution and neighborhood clustering within the tumor and the microenvironment. In parallel, we performed scMultiOmics sequencing (scRNA & scATAC-Seq) at a single-cell resolution (6000 cells/sample at 25K reads per cell) from an additional 12 patients (9 AAM & 3 EAM). We reconstructed a 3D model of the distinct tumor microenvironment at subcellular resolution using serially sectioned hematoxylin and eosin- stained tissue sections (CODA technology). Our results demonstrate that patients who self-report as AAM or Nigerian are assigned to high African (> 70%) Ancestry with either Yoruba (Nigeria) and/or Bantu subpopulation in the Sub-Saharan area. Additionally, high African Ancestry patients are diagnosed at a younger age and show advanced pathology stages compared to patients with European Ancestry. AAM of Yoruba descent expresses significantly higher immune-inflammatory signatures (STAT/IFNG-signaling pathway) compared to the Nigerian-Yoruba subpopulation. Our scRNA-Seq analysis shows that AAM has suppressive myeloid cells infiltrate within the tumor cells. The infiltrations of these cells change with age, Gleason Grade, and pathology stage. Moreover, AAM-tumor cells (scATAC-Seq) have increased open Chromatin accessibility with STAT motifs enrichment (p-value;0.0001), which could be the driver regulators of the immune-suppressive signature as well as influence the upregulation of STAT/IFNG signature within African Ancestry patients. Our study provides new insight into how genetic ancestry impacts immune signatures in AAM/African and contributes to PCa racial disparities. Citation Format: Isra Elhussin, Ezra Baraban1, Ashley Kiemen, Tamara L Lotan, Cathy Handy Marshall, Emmanuel Antonarakis, Moray J Campbell, Melissa Davis, Michael Dixon, Isaac Kim, Stefan Ambs, Rick Kittles, Adam B Murphy, Clayton Yates. Integrative multi-omics profiling in patients of African descent diagnosed with prostate cancer reveals distinct tumor-promoting immunosuppressive niches at a single-cell level and spatial resolution [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C117.

Mid-infrared chemical imaging of living cells enabled by plasmonic metasurfaces.

Mid-Infrared (MIR) chemical imaging provides rich chemical information of biological samples in a label-free and non-destructive manner. Yet, its adoption to live-cell analysis is limited by the strong attenuation of MIR light in water, often necessitating cell culture geometries that are incompatible with the prolonged viability of cells and with standard high-throughput workflow. Here, we introduce a new approach to MIR microscopy, where cells are imaged through their localized near-field interaction with a plasmonic metasurface. Chemical contrast of distinct molecular groups provided sub-cellular resolution images of the proteins, lipids, and nucleic acids in the cells that were collected using an inverted MIR microscope. Time-lapse imaging of living cells demonstrated that their behaviors, including motility, viability, and substrate adhesion, can be monitored over extended periods of time using low-power MIR light. The presented approach provides a method for the non-perturbative MIR imaging of living cells, which is well-suited for integration with modern high-throughput screening technologies for the label-free, high-content chemical imaging of living cells.

Abstract B076: Morphological diversity predicts functional traits in pancreatic cancer

Abstract Cell morphologies represent a phenotypic integration of intrinsic cellular processes, changes in cell state, and interactions with neighboring cells. While analyses of large cell line collections such as the Cancer Dependency Map (DepMap) have greatly enhanced discovery of novel molecular biomarkers and therapeutic targets, morphological analysis of these models has not yet been performed. Hence, there is a rich opportunity to discover novel regulators and functional properties of cell morphologies by linking image-based profiling to -omics based assays. Here, we studied the transcriptional and functional properties of 16 human pancreatic cancer cell lines, associations with distinct cell morphologies, and treatment-induced remodeling. At baseline, we observed extensive morphological heterogeneity across and within cell lines, as well as differences in multicellular organization. We categorized cell line morphologies into epithelial, mesenchymal, and spheroid, and organizational patterns into tightly aggregated, multilayered, and dispersed. We performed differential expression analysis across morphological subtypes utilizing DepMap transcriptomics data and queried functional correlates including CRISPR dependency, drug sensitivity, and proclivity for metastasis. For example, we discovered that the mesenchymal morphology and multilayered organizational pattern [WH3] were associated with metastatic potential, while expressing reduced levels of tight junction and cell adhesion genes. We then explored treatment associated morphological changes and their potential as cost-effective biomarkers for cell-intrinsic resistance to chemotherapy (e.g., 5-FU and gemcitabine) and KRAS inhibitors (e.g., MRTX1133 and RMC- 6236). Cells were treated continuously and monitored with live cell imaging (Incucyte SX5) followed by Cell Painting at the three-day endpoint. We observed conserved morphological responses to therapy across cell lines including a shift towards spindle-like cell shapes with neurite-like projections in chemotherapy-treated conditions, and a cell bloating phenomena characterized by an increase in cell area in KRAS inhibitor treated conditions. To directly link transcriptional state to morphology, we performed 1000-plex spatial molecular imaging (Nanostring CosMx) at subcellular resolution to pools of cell lines, demonstrating that morphological diversity within cell lines corresponded to distinct transcriptional states. In conclusion, this study highlights the potential of harnessing cell morphological information in a rapid, cost-effective phenotyping assay to aid precision oncology efforts leveraging patient- derived in vitro models. Citation Format: Dennis Gong, William L Hwang. Morphological diversity predicts functional traits in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B076.

Subcellular Level Spatial Transcriptomics with PHOTON.

The subcellular localization of RNA is closely linked to its function. Many RNA species are partitioned into organelles and other subcellular compartments for storage, processing, translation, or degradation. Thus, capturing the subcellular spatial distribution of RNA would directly contribute to the understanding of RNA functions and regulation. Here, we present PHOTON (Photoselection of Transcriptome over Nanoscale), a method which combines high resolution imaging with high throughput sequencing to achieve spatial transcriptome profiling at subcellular resolution. We demonstrate PHOTON as a versatile tool to accurately capture the transcriptome of target cell types in situ at the tissue level such as granulosa cells in the ovary, as well as RNA content within subcellular compartments such as the nucleolus and the stress granule. Using PHOTON, we also reveal the functional role of m6A modification on mRNA partitioning into stress granules. These results collectively demonstrate that PHOTON is a flexible and generalizable platform for understanding subcellular molecular dynamics through the transcriptomic lens.