Last talk of the #CSSingleCells23 conference:
Karin Pelka, Gladstone/UCSF
https://pelkalab.org/

Spatially organized #immune hubs in #colon #cancer
#ColonCancer
#scRNAseq

https://pubmed.ncbi.nlm.nih.gov/34450029/

Then: predict cellular interaction networks via correlations of gene program activities across #tumors

anti-tumor hubs in tumors, ISGs including CXCR3 ligands, differs between tumor types (MMR+ or -)

have data from clinical trial (biopsies before and after treatment)
https://pubmed.ncbi.nlm.nih.gov/36702949/

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Last session of the conference! Continuing theme of "Cell identity in situ"

Parker Côté, DFCI
in Li Lab
https://ki.mit.edu/people/clinical-investigators-research-fellows/hojun-li

The #transcriptional dynamics of human #hematopoiesis at #SingleCell resolution

do #StemCells and #ProgenitorCells in #hematopoietic system (#HSPC) change with age?

HSPCs exist on a continuum of cell types

They identified #GeneExpression programs active in uncommitted cells, looking across human development (fetal to aged)

https://www.biorxiv.org/content/10.1101/2021.08.25.457678v1

#CSSingleCells23

Now Siddharth Dey, UCSB
https://deylab.com/

Photo-sensitive barcodes combined with topologically imposed light gradients enable spatially-resolved #SingleCell #transcriptomics and #epigenomics

a new technology: scSTAMP-seq which enables use of light patterning to achieve dynamic spatial resolution

adaptation of STAMP-seq

also applying to DNA methylation
https://www.biorxiv.org/content/10.1101/2023.05.06.539708v1

#CSSingleCells23

Next is Melanie Samuel from BCM
https://thesamuellab.org/

Molecular regulation of #immune cell #plasticity and function in the #brain

"Our brain is the ultimate time machine" 🙂

How to target #synapses (for intervention) while preserving them (to avoid "turning back the clock"

Possibility that #microglia could be harnessed

partnered with IMPC (impc.org) to find microglia regulators in retina
one cool hit: SIRPα
it's NOT involved in #phagocytosis... surprise

#CSSingleCells23

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First speaker of the session (Cell identity in situ)
is Elana Fertig
of Convergence Institute at Johns Hopkins
https://fertiglab.com/

She has background in weather prediction (!) ⛈️ which has convergence with predictive medicine (such as huge data sets)

Looks at #PancreaticCancer with spatial #proteomics
now #scRNAseq

Developed CoGAPS matrix factorization, can identify cell state transitions

Using PhysiCell to build models
http://physicell.org/

#cancer
#SingleCell
#CSSingleCells23

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Final session of the great conference is

Cell identity in situ

#CSSingleCells23

Judith Zaugg from EMBL
https://www.embl.org/groups/zaugg/

How do cells integrate extrinsic signals and intrinsic state? A systems #epigenetics approach

Individual uniqueness (of people) -- molecular basis of #variation
Needed: systems epigenetics framework
signaling -- TFs -- regulatory elements -- genes

tools for inference & evaluation of enhancer-mediated gene regulatory networks called GRaNIE and GRaNPA 😃
https://www.embopress.org/doi/full/10.15252/msb.202311627

example of problem: https://www.embopress.org/doi/full/10.15252/msb.20209539

#CSSingleCells23

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Second half of the "variation and information" session #CSSingleCells23
led off by Sam Morris of WashU
http://morrislab.wustl.edu/

Multi-omic lineage tracing: insights into reprogramming cell identity

her piece in *Development*, "The evolving concept of cell identity in the single cell era"

working on "induced hepatocytes", start with fibroblasts, via "induced endoderm progenitors"

new work on #adipocytes
https://www.biorxiv.org/content/10.1101/2023.06.01.543318v1

#reprogramming
#StemCells
#CellIdentity
#CellFate

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Yogesh Goyal at Northwestern Feinberg
https://www.goyallab.org/

Topic:
Tracing rare cell plasticity and diverse fate decisions in single cancer cells

Begins with reference to (and pic of) Monod's *Chance and Necessity*
#CellFate
#SingleCell
#CSSingleCells23

Emphasizing non-genetic differences between cells, something we can only see at single-cell resolution

Refers to Luria & Delbruck 1943 about bacterial resistance (to phage), relevant to cancer resistance to therapy (selected)

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Now Katie Pollard from UCSF
https://docpollard.org/

Resolving single-cell regulatory elements across species and contexts with CellWalker2

lab builds #statistical models and #ComputationalBiology tools
#neuroscience

did microdissection then single-cell ATAC-seq
developed CellWalker to solve challenges in resolving regulatory elements
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02279-1

#GeneExpression
#genomics
#SingleCell
#CSSingleCells23

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