Biology subjects

Cepko, C. L.

Publications and source records attributed to Cepko, C. L..

At least 19 recordsLinked to original sources

bioRxiv2026

Creation of a High-Resolution, Continually Evolvable Lineage Tracer

Cellular diversity is required for the proper function of many tissues, including the retina, with its ~130 cell types.1-3 Previous lineage studies suggested that retinal progenitor cells (RPCs) generate cell diversity through biased cell divisions.4-9 However, the extent to which each progenitor cell contributes to diversity, and the overarching rules governing the lineages of the collection of progenitor cells, are unknown. While classic lineage tracing approaches including retroviral labeling4,6,10, dye injection11,12, and time-lapse microscopy13,14 were used to make the foundational insights regarding retinal lineages, they cannot be used to interrogate multigenerational lineages at scale. Here we describe the creation of an evolvable lineage tracing tool, "SCRIBBLE" for Sequential Combinatorial Recorder for Iterative Barcode-Based Lineage Evolution. SCRIBBLE uses prime editor to iteratively edit a barcode sequence while preserving the order of genesis of clonally related progeny. Through a series of rationally designed high-throughput screens and design optimizations, we identified novel sequences that support a high level of barcode editing and information content. Evaluation of SCRIBBLE in embryonic mouse retina recapitulated known lineages in retinal development, demonstrating that SCRIBBLE is capable of high-resolution lineage tracing in a complex tissue.

developmental biology↗

bioRxiv2026

Combined Disruption of Multiple Cytokine Signaling Pathways Enables One-Step Anterograde Tracing with Vesicular Stomatitis Virus

Defining the direct postsynaptic targets of selected neuronal populations remains a major challenge for neural circuit mapping. Vesicular stomatitis virus (VSV) spreads efficiently in the anterograde direction, but replication-competent VSV undergoes multistep spread and therefore cannot distinguish direct from indirect downstream targets. Here, we developed a glycoprotein-deleted VSV (VSVdG)-based strategy for one-step anterograde tracing using AAV-mediated trans-complementation with several adaptations. In this system, VSVdG was engineered to encode Cre, allowing a Cre-dependent AAV to express VSV-G only after VSVdG infected the same cells, thereby limiting VSV-G expression to a short time window. To reduce VSV-M-mediated cytotoxicity, we introduced the M33A/M51R double-mutant VSV-Md variant. Using the basal ganglia circuit as a model, these adaptations enabled VSVdG spread from the striatum to expected downstream targets in mice of both sexes. Efficient VSVdG-based one-step spread required loss of type I interferon signaling in IFNAR1-knockout mice and additional suppression of cytokine-mediated antiviral responses that were independent of type I and type II interferon signaling. This was achieved either by AAV-mediated delivery of rabies virus phosphoprotein from the CVS-N2c strain or by a cytokine-blocking antibody cocktail. Although cells labeled by VSV transmission were confined to expected brain regions, the downstream labeled cells included both neurons and glia, revealing an important limitation for interpreting this approach as strictly neuron-to-neuron monosynaptic anterograde spread. Overall, this study provides a proof-of-concept VSVdG strategy for one-step anterograde circuit tracing and defines viral toxicity, innate immunity, and cell-type specificity constraints that must be addressed to develop a monosynaptic anterograde viral tracer.

neuroscience↗

bioRxiv2026

AAV-NRF2 protects retinal and choroidal vasculature in a GDF15-dependent manner in an oxidative damage model of AMD

Oxidative stress is proposed to be a driver of age-related diseases. Age-related macular degeneration is one such disease, where the retinal pigment epithelium (RPE) is affected early in the disease. Vasculature damage also occurs, sometimes preceding RPE damage. To model some aspects of dry AMD, we used the NaIO3 mouse model of oxidative damage. Disruption of the deep retinal vascular plexus, disorganization and death of capillaries within the choriocapillaris, and marked electroretinographic decline were observed. AAV overexpressing the transcription factor, NRF2, which induces anti-oxidation enzymes and represses inflammation, was tested for protection of damage. The BEST1 promoter limited expression to the RPE. The RPE, photoreceptors, and vascular architecture in both retinal and choroidal compartments were protected. Conditioned medium from RPE-choroid explants, infected by AAV8/BEST1-NRF2, was sufficient to transfer partial protection in vivo, indicating that NRF2 induces a protective secreted factor(s). Analysis of RNA-seq data identified growth differentiation factor 15 (GDF15) as a candidate downstream mediator. Injection of recombinant GDF15 reproduced key protective phenotypes in vivo, whereas Gdf15-deficiency attenuated NRF2-mediated rescue. Pharmacologic inhibition of TGF-{beta} receptor signaling diminished NRF2 associated protection, supporting involvement of this signaling pathway. In a laser-induced choroidal neovascularization model, intravitreal GDF15 injection reduced fluorescein leakage and lesion size. These findings support a model in which NRF2 activation in the RPE induces expression of GDF15, which is capable of protecting the RPE, photoreceptors, and the retinal and choroidal vasculature. NRF2 and GDF15 have therapeutic potential for ocular diseases, as well as for other diseases with vascular pathology.

cell biology↗

bioRxiv2026

Neuronal overexpression of Nrf2 reduces dystrophic neurites in 5XFAD Alzheimer's disease model mice

BackgroundThe hallmark lesions of the Alzheimers disease (AD) brain are amyloid plaques consisting of the {beta}-amyloid protein and neurofibrillary tangles comprised of hyperphosphorylated, aggregated tau protein, which both cause neuronal dysfunction and loss. One goal of neuroprotective therapies is to maintain normal neuronal function and survival in the presence of toxic pathologies such as plaques and tangles. A potential neuroprotective target is nuclear factor erythroid 2-related factor 2 (Nrf2) transcription factor, which regulates the expression of many antioxidant and detoxification genes. Nrf2 mRNA is decreased in AD brains, and deletion of the Nrf2 gene causes increased BACE1 and A{beta} production and worsened cognitive deficits in amyloid pathology mouse models. Overexpression of Nrf2 in astrocytes has been shown to be protective against neurodegeneration, but the role of Nrf2 is neurons is unclear. MethodsWe overexpressed Nrf2 from birth in neurons of 5XFAD amyloid pathology model mice using AAV8, hypothesizing that neuronal Nrf2 overexpression decreases cortical neuron loss and reduces plaque load by decreasing BACE1 levels. We quantified protein levels by immunoblot and neuropathology by immunofluorescent staining, using two-way ANOVA to measure differences between genotypes and AAV treatments. To assess genetic changes, we performed bulk mRNA seq. ResultsWhile neuronal overexpression of Nrf2 in 5XFAD mice did not prevent neuronal loss as measured by NeuN labeling, decrease neuroinflammation by Iba1 or GFAP labeling, or reduce amyloid load by A{beta} antibody or methoxy-XO4 staining, we show that increased Nrf2 expression reduces BACE1 protein levels, especially in swollen axonal dystrophic neurites around amyloid plaques. Other proteins that accumulate in dystrophic neurites were also reduced, indicating decreased dystrophic neurites overall. Immunoblot analysis suggested increased autophagy was unlikely to play a role, while bulk mRNA sequencing indicated changes in lipid metabolism and microtubule stability may have contributed to reduced dystrophic neurite formation. ConclusionsDystrophic neurites impair action potential conductance and contribute to tau seeding and spreading. Their reduction by neuronal Nrf2 overexpression may protect neurons against these pathologic changes. Further study of the mechanisms by which Nrf2 reduces dystrophic neurites may lead to therapeutic strategies that can limit neuritic damage caused by cerebral amyloid accumulation.

neuroscience↗

bioRxiv2026

Host Endoplasmic Reticulum Stress and Interferon Responses Contribute to AAV-Induced Ocular Toxicity

Adeno-associated viruses (AAVs) are popular gene therapy vectors, but AAVs can cause toxicity. This is particularly evident following expression of some transgenes, e.g. GFP, in the retinal pigment epithelium (RPE), which leads to loss of RPE cells and photoreceptors. Here, we sought to unravel the toxicity mechanism(s). Several transgenes, self and non-self, were tested for toxicity. Some transgenes were toxic while others were not, with no clear correlation for toxicity with regards to self vs non-self transgenes. RPE RNA-sequencing revealed upregulation of translational processes, cell stress, cytokine release, antiviral responses, and leukocyte infiltration pathways. Toxicity-inducing pathways were explored for causality by injecting toxic AAVs into mice deficient for intrinsic, innate, or adaptive immune pathways. The CHOP KO partially alleviated toxicity for RPE but not photoreceptors, whereas the type I interferon receptor KO partially alleviated toxicity for photoreceptors but not RPE. In situ hybridization of interferon pathway transcripts (IFNB1, IFNAR1) revealed that the RPE and retina can produce and potentially respond to interferon. These data suggest that transgene-induced cell stress responses in the RPE lead to RPE cell death, while interferon signaling contributes to the death of photoreceptors.

genetics↗

bioRxiv2025

Humanized Extracellular Vesicles for Efficient RNA Delivery

Engineered extracellular vesicles (EVs) are a class of non-viral delivery vectors for RNA-based vaccines and gene therapies. A specialized form of engineered EVs, known as enveloped protein nanocages (EPNs), has been developed to enhance cargo loading and delivery. When EPNs are equipped with a viral fusogen, such as vesicular stomatitis virus glycoprotein (VSV-G), they have been shown to deliver proteins or RNA efficiently into recipient cells. Comparisons across different EPN types and optimization of their different features have been difficult, as assays for their activity have not been reported for single, active units. As we were interested in optimizing EVs, we first developed a biological titration assay inspired by the methods used for infectious viral particles. With this assay, we optimized EVs using a modular platform, creating EVs composed predominantly of human-derived protein components. This system achieved efficient RNA delivery, with functional titers comparable to those of lentiviral vectors. The optimized chimeric proteins comprising the EV particles integrate domains from human epsin 1, human citramalyl-CoA lyase beta-like protein (CLYBL), and human CEP55. The constructs also include a short 21-amino-acid peptide from a non-human source for RNA packaging, resulting in an EV-based RNA delivery system with reduced immunogenicity compared with EPNs and retroviral virus-like particles (VLPs). Significance StatementWe developed engineered extracellular vesicles (EVs) as RNA delivery vehicles to address limitations of virus-like particles (VLPs) and lipid nanoparticles (LNPs) in gene therapies and vaccines. We first developed an assay for individual active particles, using methods typically employed for viral titrations. This approach allowed iterative optimization of a modular EV platform. Our optimized particles comprise primarily human proteins and reach titers that comparable to those of lentiviral vectors.

bioengineering↗

bioRxiv2025

A Congenic C57BL/6 rd1 Mouse Model for Retinal Degeneration Research

Retinitis pigmentosa is an inherited retinal disease caused by thousands of mutations in approximately 100 different genes. The most widely used mouse model for retinitis pigmentosa has the retinal degeneration 1 (rd1) mutation in the Pde6b gene, which elicits rapid retinal degeneration and vision loss. A major limitation of these models is that these rd1 strains are not congenic, which prevents the use of appropriate controls. Furthermore, many strains have mutations in other genes which introduces genetic variability and may confound results. To address this issue, we backcrossed the rd1 allele from FVB mice onto a C57BL/6J genetic background over many generations, producing a C57BL/6J.Pde6brd1 strain that was confirmed to be congenic to C57BL/6J mice. We show that this strain recapitulates the electroretinogram and optomotor results expected for mouse strains containing the rd1 mutation. Examination of retinal structure in cross sections of eyes isolated from C57BL/6J.Pde6brd1 mice show a degree of thinning of the outer nuclear layer expected for a rd1 mutation, resulting in nearly complete loss of the outer nuclear layer by postnatal day 35. We anticipate that this C57BL/6J.Pde6brd1 strain could become an asset for the field of retinitis pigmentosa research.

genetics↗

bioRxiv2025

Massively parallel reporter assay for mapping gene-specific regulatory regions at single nucleotide resolution

Precise gene regulation is essential for the development and function of complex tissues, yet comprehensive mapping of cis-regulatory modules (CRMs) remains challenging due to limitations in throughput, resolution, and the ability to assay within specific cell types. Here, we introduce two complementary approaches--a locus-specific massively parallel reporter assay (LS-MPRA) and a degenerate MPRA (d-MPRA)--specifically designed to address some of these shortcomings. LS-MPRA leverages bacterial artificial chromosomes (BACs) to generate high-complexity libraries spanning large genomic regions, enabling unbiased interrogation of millions of DNA fragments potentially relevant for the regulation of a specific gene or set of genes. The d-MPRA employs systematic mutagenesis to resolve the functional architecture of CRMs at nucleotide resolution, thereby nominating critical nucleotides as potential TF binding sites, or for other regulatory roles. We applied these methods to retinal genes that are stably expressed in differentiated cells of the retina, in rod photoreceptors and in subsets of bipolar interneurons, using both in vivo and ex vivo preparations of mouse tissue. LS-MPRA recapitulated some of the known CRMs for these genes--such as the proximal promoter region of Rho--and identified potentially novel CRMs, including those located within neighboring genes. The method was then applied to a gene that is dynamically expressed in subsets of retinal progenitor cells, Olig2, where it identified three distinct CRM regions (Olig2-NR1, NR2, and NR3). D-MPRA and subsequent motif analyses nominated critical TF binding sites within these regions. CUT&RUN experiments confirmed direct binding of these candidates. Moreover, extending LS-MPRA to chick retina and spinal cord demonstrated the applicability of these methods across species and tissues. Together, the integrated LS-MPRA and d-MPRA strategies provide a robust, high-resolution platform for discovery of the cis-regulatory code underlying tissue-specific gene expression. It does not require prior knowledge of potential CRMs, and is quite rapid and straightforward to deploy, using typical molecular biology methods. The fragment size can be scaled to create short CRMs, e.g. for cell type-specific expression within viral vectors. It should enable CRM discovery at a scale and affordability for laboratories wishing to focus on a particular locus or set of loci.

developmental biology↗

bioRxiv2024

RPE-specific MCT2 expression promotes cone survival in models of retinitis pigmentosa

Retinitis pigmentosa (RP) is the most common cause of inherited retinal degeneration worldwide. It is characterized by the sequential death of rod and cone photoreceptors, the cells responsible for night and daylight vision, respectively. Although mutations in RP are mostly rod-specific, there is a secondary degeneration of cones. One possible mechanism behind cone death is metabolic dysregulation. Photoreceptors are highly metabolically active, consuming large quantities of glucose and producing substantial amounts of lactate. The retinal pigment epithelium (RPE) mediates the transport of glucose from the blood to photoreceptors and, in turn, removes lactate, which it can use as its own source of fuel. The model for metabolic dysregulation in RP suggests that, following the death of rods, lactate levels are substantially diminished causing the RPE to withhold glucose, resulting in nutrient deprivation for cones. Here, we present adeno-associated viral vector-mediated delivery of monocarboxylate transporter 2 (MCT2) into RPE cells with the aim of promoting lactate uptake from the blood and encouraging the passage of glucose to cones. We demonstrate prolonged survival and function of cones in rat and mouse RP models, revealing a possible gene agnostic therapy for preserving vision in RP. We also present the use of fluorescence lifetime imaging-based biosensors for lactate and glucose within the eye. Using this technology, we show changes to lactate and glucose levels within MCT2-expressing RPE, suggesting cone survival is impacted by RPE metabolism.

neuroscience↗

bioRxiv2023

Txnip deletions and missense alleles prolong the survival of cones in a retinitis pigmentosa mouse model

Retinitis pigmentosa (RP) is a prevalent inherited retinal degenerative disease worldwide, affecting 1 in 4,000 people. The disease is characterized by an initial loss of night vision followed by a loss of daylight and color vision. Many of the RP disease genes are expressed in the rod photoreceptors, the cell type that initiates dim light vision. Following loss of rods, the cone photoreceptors, which initiate daylight vision, also are affected and can die leading to total loss of vision. The reasons for loss of cone vision are not entirely clear, but appear to be due to loss of the rods. Previously we showed that overexpressing Txnip, an -arrestin protein, in mouse models of RP using AAV gene therapy prolonged the survival of RP cones (Xue et al., 2021). At least part of the mechanism for cone survival was a switch in the fuel source, from glucose to lactate. In addition, the mitochondria of cones were both morphologically and functionally improved by delivery of Txnip. We have gone on to test several alleles of Txnip for the ability to prolong cone survival in rd1, a mouse model of RP. In addition, proteins that bind to Txnip and/or have homology to Txnip were tested. Five different deletion alleles of Txnip were expressed in cones or the retinal pigmented epithelium (RPE). Here we show that the C-terminal half of Txnip (149-397aa) is sufficient to remove GLUT1 from the RPE cell surface, and improved rd1 cone survival when expressed specifically in the RPE. Overexpressing Arrdc4, an -arrestin that shares 60% similar protein sequence to Txnip, reduced rd1 cone survival. Reduction of the expression of HSP90AB1, a protein that interacts with Txnip and regulates metabolism, improved the survival of rd1 cones alone and was additive for cone survival when combined with Txnip. However, full length Txnip with a single amino acid change, C247S, as we tested in our original study, remains the most highly efficacious form of the gene for cone rescue. The above observations suggest that only a subset of the hypothesized and known activities of Txnip play a role in promoting RP cone survival, and that the activities of Txnip in the RPE differ from those in cone photoreceptors.

physiology↗

bioRxiv2021

Augmentation of CD47-SIRPα signaling protects cones in genetic models of retinal degeneration

Inherited retinal diseases such as retinitis pigmentosa (RP) can be caused by thousands of different mutations, a small number of which have been successfully treated with gene replacement. However, this approach has yet to scale and may be infeasible in many cases, highlighting the need for interventions that could benefit more patients. Here, we found that microglial phagocytosis is upregulated during cone degeneration in RP, suggesting that expression of "dont eat me" signals such as CD47 might confer protection to cones. To test this, we delivered an adeno-associated viral (AAV) vector expressing CD47 on cones, which promoted cone survival in three mouse models of RP and preserved visual function. Cone rescue with CD47 required signal regulatory protein alpha (SIRP) but not microglia or thrombospondin-1 (TSP1), suggesting that CD47 interacts with SIRP on non-microglial cells to alleviate degeneration. These findings establish augmentation of CD47-SIRP signaling as a potential treatment strategy for RP and possibly other forms of neurodegeneration.

neuroscience↗

bioRxiv2021

A general approach for stabilizing nanobodies for intracellular expression

Conventional antibodies and their derived fragments are difficult to deploy against intracellular targets in live cells, due to their bulk and structural complexity. Nanobodies provide an alternative modality, with well documented examples of intracellular expression. Despite their promise as intracellular reagents, there has not been a systematic study of nanobody intracellular expression. Here, we examined intracellular expression of 75 nanobodies from the Protein Data Bank. Surprisingly, a majority of nanobodies were unstable in cells, illustrated by aggregation and clearance. Using comparative analysis and framework mutagenesis, we developed a general approach that stabilized a great majority of originally intracellularly unstable nanobodies, without compromising target-binding function. Additionally, we identified distinct sequence features impacting nanobody intracellular stability, and demonstrated mutationally stabilized nanobody expression in vivo, in the murine retina and in E. coli. This work will allow for standardized nanobody engineering for intracellular applications, potentiating a growing field of intracellular interrogation and intervention.

bioengineering↗

bioRxiv2021

AAV-Txnip prolongs cone survival and vision in mouse models of retinitis pigmentosa

Retinitis pigmentosa (RP) is an inherited retinal disease, affecting >20 million people worldwide. Loss of daylight vision typically occurs due to the dysfunction/loss of cone photoreceptors, the cell type that initiates our color and high acuity vision. Currently, there is no effective treatment for RP, other than gene therapy for a limited number of specific disease genes. To develop a gene-agnostic therapy, we screened {approx}20 genes for their ability to prolong cone photoreceptor survival in vivo. Here, we report an adeno-associated virus (AAV) vector expressing Txnip, which prolongs the survival of cone photoreceptors and improves visual acuity in RP mouse models. A Txnip allele, C247S, which blocks the association of Txnip with thioredoxin, provides an even greater benefit. Additionally, the rescue effect of Txnip depends on lactate dehydrogenase b (Ldhb), and correlates with the presence of healthier mitochondria, suggesting that Txnip saves RP cones by enhancing their lactate catabolism.

physiology↗

bioRxiv2019

Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation

Recent transcriptional profiling technologies are uncovering previously-undefined cell populations and molecular markers at an unprecedented pace. While single cell RNA (scRNA) sequencing is an attractive approach for unbiased transcriptional profiling of all cell types, a complementary method to isolate and sequence specific cell populations from heterogeneous tissue remains challenging. Here, we developed Probe-Seq, which allows deep transcriptional profiling of specific cell types isolated using RNA as the defining feature. Dissociated cells are labelled using fluorescent in situ hybridization (FISH) for RNA, and then isolated by fluorescent activated cell sorting (FACS). We used Probe-Seq to purify and profile specific cell types from mouse, human, and chick retinas, as well as the Drosophila midgut. Probe-Seq is compatible with frozen nuclei, making cell types within archival tissue immediately accessible. As it can be multiplexed, combinations of markers can be used to create specificity. Multiplexing also allows for the isolation of multiple cell types from one cell preparation. Probe-Seq should enable RNA profiling of specific cell types from any organism.

molecular biology↗

bioRxiv2019

FIN-Seq: Transcriptional profiling of specific cell types in frozen archived tissue from the human central nervous system

Thousands of frozen, archived tissues from postmortem human central nervous system (CNS) are currently available in brain banks. As single cell and single nucleus technologies are beginning to elucidate the cellular diversity present within the human CNS, it is becoming clear that transcriptional analysis of the human CNS requires cell type specificity. Single cell and single nucleus RNA profiling provide one avenue to decipher this heterogeneity. An alternative, complementary approach is to profile isolated, pre-defined cell types and use methods that can be applied to many archived human tissue samples. Here, we developed FIN-Seq (Frozen Immunolabeled Nuclei Sequencing), a method that accomplishes these goals. FIN-Seq uses immunohisto-chemical isolation of nuclei of specific cell types from frozen human tissue, followed by RNA-Sequencing. We applied this method to frozen postmortem samples of human cerebral cortex and retina and were able to identify transcripts, including low abundance transcripts, in specific cell types.

neuroscience↗

bioRxiv2019

Transduction of gluconeogenic enzymes prolongs cone photoreceptor survival and function in models of retinitis pigmentosa

The hereditary nature of many retinal degenerative disorders makes them potentially amenable to corrective gene therapies. Numerous clinical trials are ongoing with the goal to rectify the genetic defect in the afflicted cell types. However, the personalized nature of these approaches excludes many patients for whom the underlying mutation is not mapped, or the number of affected individuals is too few to develop a commercially viable therapy (vide infra). Thus, a therapy that can delay visual impairment irrespective of the underlying genetic etiology can satisfy this unmet medical need. Here, we demonstrate the utility of such an approach in retinitis pigmentosa (RP) by promoting survival of cone photoreceptors by targeting metabolic stress. These cells are not primarily affected by the inherited mutation, but their non-autonomous demise leads to a decline in daylight vision, greatly reducing the quality of life. We designed adeno-associated virus (AAV) vectors that promote gluconeogenesis- a pathway found in the liver which produces glucose in response to hypoglycemia. Retinal transduction with these vectors resulted in improved cone survival and delayed a decline in visual acuity in three different RP mouse models. Because this approach extended visual function independent of the primary mutation, therapies emanating from this approach could be used as a treatment option for a genetically heterogenous cohort of patients.

neuroscience↗

bioRxiv2019

Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

Identification of the cis-regulatory elements (CREs) that regulate gene expression in specific cell types is critical for defining the gene regulatory networks (GRNs) that control normal physiology and disease states. We previously utilized non-coding RNA (ncRNA) profiling to define CREs that comprise a GRN in the adult mouse heart1. Here, we applied ncRNA profiling to the mouse retina in the presence and absence of Nrl, a rod photoreceptor-specific transcription factor required for rod versus cone photoreceptor cell fate. Differential expression of Nrl-dependent ncRNAs positively correlated with differential expression of Nrl-dependent local genes. Two distinct Nrl-dependent regulatory networks were discerned in parallel: Nrl-activated ncRNAs were enriched for accessible chromatin in rods but not cones whereas Nrl-repressed ncRNAs were enriched for accessible chromatin in cones but not rods. Furthermore, differential Nrl-dependent ncRNA expression levels quantitatively correlated with photoreceptor cell type-specific ATAC-seq read density. Direct assessment of Nrl-dependent ncRNA-defined loci identified functional cone photoreceptor CREs. This work supports differential ncRNA profiling as a platform for identifying context-specific regulatory elements and provides insight into the networks that define photoreceptor cell types.

molecular biology↗

bioRxiv2018

SABER enables highly multiplexed and amplified detection of DNA and RNA in cells and tissues

Fluorescent in situ hybridization (FISH) reveals the abun-dance and positioning of nucleic acid sequences in fixed sam-ples and can be combined with cell segmentation to produce a powerful single cell gene expression assay. However, it re-mains difficult to label more than a few targets and to visu-alize nucleic acids in environments such as thick tissue sam-ples using conventional FISH technologies. Recently, meth-ods have been developed for multiplexed amplification of FISH signals, yet it remains challenging to achieve high lev-els of simultaneous multiplexing combined with high sam-pling efficiency and simple workflows. Here, we introduce signal amplification by exchange reaction (SABER), which endows oligo-based FISH probes with long, single-stranded DNA concatemers that serve as targets for sensitive fluores-cent detection. We establish that SABER effectively ampli-fies the signal of probes targeting nucleic acids in fixed cells and tissues, can be deployed against at least 17 targets si-multaneously, and detects mRNAs with high efficiency. As a demonstration of the utility of SABER in assays involv-ing genetic manipulations, we apply multiplexed FISH of reporters and cell type markers to the identification of en-hancers with cell type-specific activity in the mouse retina. SABER represents a simple and versatile molecular toolkit to allow rapid and cost effective multiplexed imaging.

genetics↗