Stephen Matheson🌵🌲 · @sfmatheson
714 followers · 726 posts · Server fediscience.org

Last talk of the conference:
Karin Pelka, Gladstone/UCSF
gladstone.org/people/karin-pel

Spatially organized hubs in

pubmed.ncbi.nlm.nih.gov/344500

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

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)
pubmed.ncbi.nlm.nih.gov/367029

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#tumors #scrnaseq #coloncancer #cancer #colon #immune #cssinglecells23

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
714 followers · 721 posts · Server fediscience.org

Now Siddharth Dey, UCSB
deylab.com/

Photo-sensitive barcodes combined with topologically imposed light gradients enable spatially-resolved and

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
biorxiv.org/content/10.1101/20

#cssinglecells23 #epigenomics #Transcriptomics #SingleCell

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
714 followers · 720 posts · Server fediscience.org

Next is Melanie Samuel from BCM
thesamuellab.org/

Molecular regulation of cell and function in the

"Our brain is the ultimate time machine" 🙂

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

Possibility that could be harnessed

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

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#cssinglecells23 #phagocytosis #Microglia #synapses #brain #plasticity #immune

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
714 followers · 717 posts · Server fediscience.org

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

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

Looks at with spatial
now

Developed CoGAPS matrix factorization, can identify cell state transitions

Using PhysiCell to build models
physicell.org/



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#cssinglecells23 #SingleCell #cancer #scrnaseq #Proteomics #pancreaticcancer

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
714 followers · 717 posts · Server fediscience.org

Final session of the great conference is

Cell identity in situ

#cssinglecells23

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
713 followers · 713 posts · Server fediscience.org

Judith Zaugg from EMBL
embl.org/groups/zaugg/

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

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

tools for inference & evaluation of enhancer-mediated gene regulatory networks called GRaNIE and GRaNPA 😃
embopress.org/doi/full/10.1525

example of problem: embopress.org/doi/full/10.1525

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#cssinglecells23 #variation #epigenetics

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
713 followers · 710 posts · Server fediscience.org

Second half of the "variation and information" session
led off by Sam Morris of WashU
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
biorxiv.org/content/10.1101/20




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#cellfate #cellidentity #stemcells #reprogramming #adipocytes #cssinglecells23

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
713 followers · 707 posts · Server fediscience.org

Yogesh Goyal at Northwestern Feinberg
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*


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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#cssinglecells23 #SingleCell #cellfate

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
713 followers · 705 posts · Server fediscience.org

Now Katie Pollard from UCSF
docpollard.org/

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

lab builds models and tools

did microdissection then single-cell ATAC-seq
developed CellWalker to solve challenges in resolving regulatory elements
genomebiology.biomedcentral.co




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#cssinglecells23 #SingleCell #genomics #geneexpression #neuroscience #computationalbiology #statistical

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 701 posts · Server fediscience.org

Last speaker of the day is the keynote:
Xiaowei Zhuang
Harvard University
zhuang.harvard.edu/pi.html

Spatially resolved genomics and cell atlas of the

Explaining MERFISH, now I get it 🤓

Now have adapted to : pubmed.ncbi.nlm.nih.gov/362724

and to thick tissue:
biorxiv.org/content/10.1101/20

Now discussing this epic MERFISH atlas of the whole mouse brain
biorxiv.org/content/10.1101/20

use imputation to infer cell-cell interactions (several hundred cell types), cool

#cssinglecells23 #epigenome #brain #SingleCell

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 699 posts · Server fediscience.org

Now Neda Bagheri at U of Washington
bagherilab.com/

Emulating emergent spatio-temporal cell population dynamics with algorithms remains challenging

Population dynamics arise from autonomous decisions
e.g. in context of progression

Created tool called ARCADE = Agent-based Representation of Cells And Dynamic Environments
bagherilab.com/resources.php

But model is computationally expensive...
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#cssinglecells23 #systemsbiology #computationalbiology #cancer #SingleCell #machinelearning

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 697 posts · Server fediscience.org

Rong Fan at Yale
fan-lab.org/

Spatial Multi-Omics Sequencing at Cellular Level via Deterministic Barcoding in Tissue

first slide called "2006--the ice age of single-cell biology," referring to review article by Johanna Joyce

Recent great technical advance: spatial CITE-seq
nature.com/articles/s41587-023

and spatial ATAC-seq



#cssinglecells23 #epigenetics #Transcriptomics

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 696 posts · Server fediscience.org

Aviv Regev (Genentech)
gene.com/scientists/our-scient

From cell to perturbation atlases

Deciphering causal intra- and intercellular circuits

Using Perturb-seq
biorxiv.org/content/10.1101/20



Now want to do multiple perturbations in one cell... do effects combine? Can do this with orig Perturb-seq, then categorize interactions

But the space of interactions is far bigger than the number of cells (in universe)

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#geneexpression #cssinglecells23 #systemsbiology

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 696 posts · Server fediscience.org

first speaker of this session:
Leeat Keren, Weizmann Institute of Science
Escalating high-dimensional imaging using combinatorial multiplexing and

Why can't combinatorial staining approaches (used with ) work with proteins?
overlapping signals cause big math problems

And... about 10,000X more abundant than RNA

idea: use structure of biological images to constrain math solutions after combinatorial staining of proteins

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#deeplearning #cssinglecells23 #proteins #rna

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 692 posts · Server fediscience.org

Third major session at Conceptual Power of Single-Cell Biology
is "Cells in context"
chaired by Melanie Samuel (BCM) and Karin Pelka (Gladstone/UCSF)

Very cool topics incoming

#cssinglecells23

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 690 posts · Server fediscience.org

Sophie Dumont at UCSF
dumontlab.ucsf.edu/

size alters attachment stability and alignment order in mammalian

Lab interested in and emergent mechanics across scales.... "biological structures build themselves" using only local cues they get global information. mitotic spindle a great example

kinetochores attach, sense tension, can make mistakes which are corrected. how does this work when chromosomes vary in size?

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#cssinglecells23 #selforganization #mitosis #kinetochore #Chromosome

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 689 posts · Server fediscience.org

Polly Fordyce at Stanford
fordycelab.com/

Question: How do factors activate transcription?
Outside the DNA binding domain of a TF, there are numerous disordered domains, including activation domains that interact with co-activators--
very little known about that

activation domains are disordered, poorly conserved, and binding to co-activators is very low affinity

developed a platform to measure, tech called STAMMP

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#cssinglecells23 #microfluidic #transcription

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 689 posts · Server fediscience.org

Second half of morning session on Emerging concepts in gene regulation** **kicks off with

Songpeng Zu, UCSD
beyondpie.github.io/

Comprehensive single-cell analysis of chromatin accessibility in the adult mouse

117 dissections (!) across whole mouse brain, using SnapATAC2

Putting data on CATlas (catlas.org)

biorxiv.org/content/10.1101/20





#cssinglecells23 #neuroscience #epigenomics #chromatin #SingleCell #brain

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 685 posts · Server fediscience.org

Loic Binan of the Broad:
All-optical genetic screens of intracellular and intercellular circuits with Perturb-FISH

Various CRISPR-based methods to look (multiplexed) at outcomes after knockdown to explore gene expression circuits, those are great, but want richer data (morphology etc)

one guide per cell (knock down one gene per cell) see via MERFISH, then identify the perturbed gene via in situ T7 transcription (same chemistry as MERFISH)

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#cssinglecells23 #transcriptome #transcriptional

Last updated 1 year ago

Stephen Matheson🌵🌲 · @sfmatheson
709 followers · 685 posts · Server fediscience.org

Now Aki Minoda, Radboud University, The Netherlands
ru.nl/en/departments/radboud-i
talking about
the Mukin Mouse Ageing Atlas
(mukin means -free in Japanese)

from tissues sampled at 2 and 19 months in mice, then including

Looking at influence of on changes in e.g. expansion of cell types, aka

#cssinglecells23 #inflammaging #immune #aging #microbiota #lipidomics #omics #SingleCell #germ

Last updated 1 year ago