Daniel Dan Liu

Beyond polyA: scalable single-cell total RNA-seq unifies coding and non-coding transcriptomics Non-coding RNAs represent a widespread and diverse layer of post-transcriptional regulation across cell types and states, yet much of their diversity remains uncharted at single-cell resolution. This ...

The full preprint has so much more data, from benchmarking to applications in blood and dengue virus infection (a non-polyadenylated flavivirus). Go check it out! 10/
www.biorxiv.org/content/10.1...

The thing is, Cajal-Retzius cells mostly disappear by birth. This may be why the role of MIR137 has been so elusive: it's expressed transiently and specifically during development to help set up the layers of the cerebral cortex, but perhaps has less of a role after birth. 9/

Cajal-Retzius cells are a super interesting class of neurons. They are among the earliest-born in the cortex, and occupy the outermost layer I. They guide subsequent neuron migration from the ventricular zone up into the cortical plate by secreting Reelin. 8/

And that schizophrenia risk gene, MIR137? We found it to be very specifically expressed in a special type of neurons called Cajal-Retzius cells. And it seems functional too—cells expressing MIR137 also had lower expression of MIR137 target genes. 7/

Many non-polyadenylated RNAs showed dynamic expression changes across excitatory and inhibitory neuron maturation, suggesting they may play a role in development. 6/

...and got excellent recovery of all RNA classes, including non-polyadenylated ones, many of which showed cell-type specificity. 5/

We applied this technology to the human brain across developmental timepoints and anatomical regions... 4/

Alina developed a new sequencing pipeline, called TotalX, which polyadenylates all transcripts prior to reverse transcription, allowing capture of all RNA classes. This pipeline is fully compatible with standard droplet-based
@10xgenomics.bsky.social 3' chemistry. 3/

There are now several whole-brain atlases out there, but since most of them use polyA-based RNA capture, many classes of non-polyadenylated RNA get left out (miRNA, snRNA, snoRNA, tRNA, histone RNA, many viral RNAs, to name a few). 2/

Schizophrenia is highly heritable, and one of its strongest GWAS hits is actually a microRNA called MIR137. But where and when MIR137 is expressed has been a bit of a mystery, until now. A thread on a new preprint led by Alina Isakova and @stephenquake.bsky.social 1/

Primary human NSPCs thus make a great system for modeling gliomas, allowing for modular introduction of genetic manipulations into isogenic cell types at defined developmental stages. Being human cell lines, they also recapitulate human-specific cell types not found in mice. 10/

To see if our results match up with real patient data, we reanalyzed some published GBM scRNA-seq datasets. Higher EGFR expression in the tumor indeed correlated with more GPC-like tumor cells. This suggests EGFR is not just a marker, but also a driver of the GPC-like state. 9/

The mutation-of-origin had some even more dramatic effects, with CDK4 overexpression resulting in largely neuron-like tumor cells, and EGFR interestingly expanding the GPC-like tumor cells. 8/

The cell-of-origin had some interesting effects on the resulting tumor. NSC-derived tumors had the greatest cellular heterogeneity, while OPC-derived tumors harbored more differentiated oligodendrocyte-like cells. 7/

Our lines engrafted robustly, growing and migrating aggressively. We only transplanted the cells on one side of the brain, but here you can see them invading cross-hemisphere. 6/

So we asked: can we use these primary human NSPCs to model how cell-of-origin and mutation-of-origin drive different glioma subtypes?

Using isogenic NSC, GPC, and OPC neurosphere lines, we created glioma-like lines by introducing defined combinations of oncogenic driver genes. 5/

We previously described how to purify 10 distinct neural stem and progenitor cell types from the developing brain, including tripotent radial glia (NSCs), bipotent glial progenitor cells (GPCs), and unipotent oligodendrocyte progenitor cells (OPCs). 4/
bsky.app/profile/dani...

Even more interesting is that different glioma subtypes seem to embody different stem cell hierarchies: low-grade oligodendrogliomas have a lot of mature oligodendrocyte-like cells, while diffuse midline gliomas mostly contain OPC-like cells(Figure from Suvà& Tirosh, 2020). 3/

Brain tumors known as gliomas are notoriously hard to treat, in part due to how heterogeneous the cancer cells are. In fact, glioma cells seem to mirror a corrupted neural stem cell hierarchy found in normal development. (Figure credit Neftel et al., 2019). 2/

Modeling glioma intratumoral heterogeneity with primary human neural stem and progenitor cells Gliomas are characterized by extensive intratumoral heterogeneity, recapitulating a hierarchy reminiscent of normal neurodevelopment. This facet is difficult to recapitulate in disease models. Here, W...

Our new study, “Modeling glioma intratumoral heterogeneity with primary human neural stem and progenitor cells,” is online now at @stemcellreports.bsky.social ! Spearheaded by our talented undergrad @danielgao970.bsky.social. A thread on the study: 1/

Cortical Development 2022 was the first conference I ever attended, and so it was particularly special to return to Sicily for @corticodevelopment.bsky.social 2025 as a speaker. Featuring a sneak peak on some exciting new findings on neural stem cells in the postnatal human brain (stay tuned!)

Looking forward to meeting this amazing group of neuroscientists at the @utah.edu Rising Stars Symposium!

Weissman Lab representing at the @isscr.org Athens International Symposium on Neural Stem Cells! Glad to share our work on purifying neural stem/progenitor cells from the human brain, and a preview of our work using those cells to model glioma heterogeneity.

Hi Oliver, would love to join this! MD-PhD student working on neural stem cells and human neurodevelopment here.

Our 2024 CSHL conference on human brain development and stem cell models is in full swing, with over 300 participants!

This year’s event features exciting new discoveries and dynamic discussions, driven largely by the energy & insights of trainees

#Assembloids #Organoids #Brain
#CSHL2024Brain

A huge thanks to everyone who made this study possible: my mentor Irv Weissman, the lab's brain team (Rahul, Nobuko, Joy, Anna et al.), as well as @czbiohub.bsky.social and Stanford MSTP for their support! 16/

Cell Press: STAR Protocols STAR Protocols is an open access, peer-reviewed journal from Cell Press. We offer structured, transparent, accessible, and repeatable step-by-step experimental and computational protocols from all are...

We have since published a methods paper detailing the dissociation, staining, and cell sorting protocols needed to replicate this work, which can be easily expanded to incorporate new surface markers. 15/

Purification scheme for neural stem and progenitor cells from the human brain.

And here’s our final purification scheme! My hope is that this study provides a framework for studying the cellular basis of human brain development, including cell-autonomous functions and interactions between cell types. 14/

Contrasting Rodent and Human Neocortical Development (Lui, Hansen, Kriegstein, Cell 2011)

These GPCs mostly lived in the outer subventricular zone, a layer of the cortex that is greatly expanded in primates. These cells may thus play an evolutionary role in the dramatic white matter expansion characteristic of human brains. 13/

Because we had the index sort data, we could immediately figure out how to purify these cells. Through clonal differentiation and transplant assays, we found these cells made oligodendrocytes and astrocytes, but NOT neurons. We thus named it the glial progenitor cell (GPC). 12/