Integrated protein and transcriptome high-throughput spatial profiling

Abstract

Spatial transcriptomics and proteomics have independently transformed our understanding of complex biological processes; however, integration of these modalities is currently limited. To overcome this challenge, we developed Spatial PrOtein and Transcriptome Sequencing (SPOTS) for high-throughput integration of transcriptome and protein profiling within the spatial context. Applying SPOTS to spleen and breast cancer samples revealed that spatially-resolved multi-omic integration provides a comprehensive perspective on key biological processes in health and disease.

Into the multiverse: advances in single-cell multiomic profiling

“…Spatial multiomic approaches are emerging -fluorophoreand oligonucleotide-conjugated antibodies can be incorporated into both in situ and array-based methods to enable parallel mRNA and protein detection, which has been demonstrated for several of the spatial transcriptomics methods mentioned previously [87,97], using the Nanostring GeoMX DSP instrument [98] and also very recently demonstrated in SPOTS [99], which combines the 10X Genomics Visium Platform with CITE-seq antibody-based protein detection. Novel approaches, such as the recently described DBiT-seq, can perform spatial profiling of mRNA and protein with 10 μm resolution [100].…”

Spatially resolved host-bacteria-fungi interactomes via spatial metatranscriptomics

“…These methods have been applied to a wide range of tissues from humans (Asp et al, 2019;Berglund et al, 2020;Hildebrandt et al, 2021) to plants (Duncan et al, 2016;Giacomello, 2021;Giacomello et al, 2017;Xia et al, 2022). Recently, methods have been developed that are capable of detecting multiple modalities such as protein and transcriptional information (Ben-Chetrit et al, 2022;Liu et al, 2020Liu et al, , 2022Merritt et al, 2020;Wang et al, 2018) or chromatin accessibility and transcriptional information (Deng et al, 2022). SmT extends the reach of multimodal spatial measurement methods by capturing information from coexisting organisms.…”

The 3D genome landscape: Diverse chromosomal interactions and their functional implications

“…High-throughput imaging technologies have shown significant strides in bridging the gap from single cells to multicellular tissues using spatial genomics and transcriptomics ( Kempfer and Pombo, 2020 ; Jerkovic and Cavalli, 2021 ; Rao et al, 2021 ; Zhao et al, 2022 ). Spatial-based DNA and RNA approaches integrated with burgeoning multiplexed protein imaging ( Hickey et al, 2021 ; Takei et al, 2021 ; Ben-Chetrit et al, 2022 ; Liu et al, 2022 ; Vickovic et al, 2022 ) will enhance the understanding of how the dynamics of genome organization and function contribute to cellular identities.…”