SCOG Virtual Lecture Series
‘Recent Advances in Single Cell Omics’:
35. Bart Deplancke (EPFL Lausanne)

We are excited to announce the next speaker in our SCOG Virtual Lecture Series ‘Recent Advances in Single Cell Omics’: Bart Deplancke (EPFL Lausanne)

Abstract:

‘Engineering next-generation single cell phenomics technologies’
Single cell transcriptomics (scRNA-seq) is transforming biomedical research by providing unique insights into a cell’s identity and characteristics. However, several key single cell-related technological challenges remain, including the need for methods that i) are tailored toward low-input cell samples to process small, individual tissues; ii) enable linking the transcriptome of a cell to a high-resolution image of that same cell; and 3) allow retrieving the transcriptome of a cell without lysing it to support downstream phenotyping or direct trajectory inference. In this technology-centric talk, I will present my lab’s efforts to address each of these challenges. Specifically, I will introduce DisCo, a deterministic, mRNA-capture bead and cell co-encapsulation dropleting system. DisCo enables precise particle and cell positioning and droplet sorting control through combined machine-vision and multilayer microfluidics, enabling continuous processing of low-input single cell suspensions at high capture efficiency. I thereby will discuss how further integration of high-resolution imaging into DisCo is paving the way for an interconnecting robotic image and scRNA-seq (IRIS) platform uniquely enabling the selection, sorting, and molecular as well as phenotypic characterization of individual cells. Finally, I will introduce Live-seq, a novel cell lysis-devoid, single cell transcriptomics approach that can act as a transcriptomic recorder to predict cell response heterogeneity and that can can be used to perform sequential transcriptome profiling on cells to directly map cell trajectories.

Biography:

Bart Deplancke graduated as a Biochemical Engineer at Ghent University (Belgium, 1998) after which he pursued doctoral studies in Immunobiology at the University of Illinois (USA) and postdoctoral work in regulatory genomics at the Harvard and UMass Medical Schools. In 2007, he established his lab at the EPFL School of Life Sciences where he is now Full Professor, Vice-Dean of Innovation, and Swiss Institute of Bioinformatics member and is developing new experimental and computational approaches to study the biology of the genome. The Deplancke Lab has by now built a sizeable toolkit, involving microfluidics, high-throughput sequencing, and single cell genomics. This toolkit is being used to address questions pertaining to cellular development, with a primary focus on adipose biology, as well as to how genomic variation affects molecular and organismal diversity. In 2017, he was elected to the National Research Council of the Swiss National Science Foundation, and in 2021, he received the 2021 Cloëtta Prize for outstanding contributions to biomedical research. He is also the co-founder of two Biotech companies (Genohm, Acquired by Agilent in 2018; and Alithea Genomics).

Further information on participation, the program and the application for a lecture can be found below.