MEMP PhD Thesis Defense (1:00pm): Anubhav Sinha

Spatially precise in situ transcriptomics in intact tissues

Biological tissues are composed of cells of diverse types and states that are spatially organized with nanoscale precision over extended length scales to perform coordinated functions. Understanding patterns of gene expression in tissues is needed to understand complex cellular behaviors in health and disease. Current methods for highly multiplexed RNA imaging are limited in their spatial resolution and lack precise subcellular landmarks, limiting the ability to localize transcripts to nanoscale and subcellular compartments. Here, I describe the development of targeted expansion sequencing (targeted ExSeq), a multiplexed RNA imaging method that enables efficient detection of a predefined set of transcripts in three-dimensional tissues with nanoscale resolution. Targeted ExSeq integrates expansion microscopy, an approach for volumetric super-resolution tissue imaging through the principle of physical magnification, with targeted in situ sequencing, an approach for imaging RNA transcripts of interest. Targeted ExSeq was used to spatially map layer-specific cell type organization in the primary visual cortex in the mouse brain, nanoscale RNA localization within dendrites and dendritic spines in the mouse hippocampus, and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. The approach for targeted RNA in situ sequencing was adapted to whole-mount RNA imaging of intact pre-implantation mouse embryos. By integrating immunofluorescence and in situ sequencing with live-embryo mechanical measurements, a spatially-resolved multimodal map of pre-implantation embryogenesis was generated to study self-organization in development.

Thesis Co-Supervisor:
Edward S. Boyden, PhD
Y. Eva Tan Professor in Neurotechnology, MIT, HHMI

Thesis Co-Supervisor and Committee Chair:
Aviv Regev, PhD
Executive Vice President and Head, Genentech Research and Early Development

Thesis Readers:
George Church, PhD
Professor of Genetics, Harvard Medical School

Mario Suvà, MD, PhD
Associate Professor of Pathology, Massachusetts General Hospital and Harvard Medical School

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Zoom invitation – 

Anubhav Sinha is inviting you to a scheduled Zoom meeting.

Topic: Anubhav Sinha Thesis Defense
Time: August 4, 2023, 01:00 PM Eastern Time (US and Canada)

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