Marty Yang

Human organoid tumor transplantation identifies functional glioblastoma-microenvironment communication mediated by PTPRZ1 Ge and Kan et al. develop and benchmark a human organoid tumor transplantation (HOTT) system to uncover how microenvironmental cues influence glioblastoma states. They identify a non-catalytic role for microenvironmental PTPRZ1 in driving mesenchymal programs and extending tumor microtubes in patient tumor cells.

Human organoid tumor transplantation identifies functional glioblastoma-microenvironment communication mediated by PTPRZ1

A human tumor-immune organoid model of glioblastoma Baisiwala et al. introduce iHOTT, an autologous organoid co-culture system that preserves human tumor-immune interactions and T cell clonal responses. iHOTT mirrors clinical responses to PD-1 blockade and provides a platform for evaluating personalized immunotherapy strategies in glioblastoma.

A human tumor-immune organoid model of glioblastoma

CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis CRISPR screens in iPSC-derived neurons reveal that the E3 ubiquitin ligase CRL5SOCS4 ubiquitinates tau, that CUL5 expression is correlated with resilience in human Alzheimer’s disease, and that electr...

After a long review process, I'm excited that our paper is finally in print: www.cell.com/cell/fulltex...

TL;DR: We use CRISPR screens in iPSC-derived neurons to find a new tau E3 ligase and a relationship between oxidative stress, the proteasome, and tau proteolytic fragments.

More below 👇

Dissecting gene regulatory networks governing human cortical cell fate - Nature Systematic screening of transcription factors reveals conserved mechanisms governing cortical radial glia lineage progression across primates and provides a framework for functional dissecti...

1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification
www.nature.com/articles/s41...

Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀

Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function

now revised and journal accepted at www.science.org/doi/10.1126/...

🧵👇

Conservation and alteration of mammalian striatal interneurons - Nature An analysis of cell-type diversity in brain samples from a variety of mammalian species, both during development and in adult animals, reveals that the TAC3 initial class of striatal interneurons is c...

Our new manuscript, led by Emily Corrigan, examines inhibitory neuron diversity across approximately 160 million years of evolutionary divergence, as part of BRAIN Initiative Cell Atlas Network (BICAN) developing brain atlas package: www.nature.com/articles/s41...

ZMYND11 Restrains KMT2A to Enable a Neuronal Developmental Program Mutations in the chromatin reader and tumor suppressor ZMYND11 are the cause of ZMYND11-related syndromic intellectual disability (ZRSID), a disorder characterized by symptoms such as language and mot...

Very pleased to share this work from my time as a graduate student with the Greenberg lab. We investigate the molecular function of ZMYND11, a tumor suppressor and chromatin reader which is also a cause of syndromic intellectual disability. Preprint available now: www.biorxiv.org/content/10.1...

🧠🌟🐭 Excited to share some of my postdoc work on the evolution of dexterity!

We compared deer mice evolved in forest vs prairie habitats. We found that forest mice have:
(1) more corticospinal neurons (CSNs)
(2) better hand dexterity
(3) more dexterous climbing, which is linked to CSN number🧵

The first (of hopefully many) reports to come from our collaboration with @hjp.bsky.social

We present a new type of cell fitness assay that allows you to both quantify and explain differences across human donors in cell proliferation and sensitivity to environmental toxicants.

ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...

Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization.
www.science.org/doi/10.1126/...

Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we:

1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs

bsky.app/profile/bior...

Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate https://www.biorxiv.org/content/10.1101/2025.09.23.678137v1

The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...

Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)

I'm really happy to announce that my two main postdoctoral works have been published in the same issue of Developmental Cell! First, the final form of the mouse cortical organoid protocol (tinyurl.com/bddfmx8n), which I recently presented at Development presents (tinyurl.com/36udcpme) and…

A mouse organoid platform for modeling cerebral cortex development and cis-regulatory evolution in vitro: Developmental Cell www.cell.com/developmenta...

This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

The Anne West lab at Duke is hiring a postdoc to work on nuclear cell biology in neurogenesis. Please help me spread the word! Applications to west@neuro.duke.edu.

Two parallel lineage-committed progenitors contribute to the developing brain https://www.biorxiv.org/content/10.1101/2025.07.02.662771v1

🧵Excited to share our new preprint introducing iHOTT - an autologous tumor-immune co-culture model that captures patient-specific responses in #Glioblastoma

💥Now on
@biorxivpreprint
: biorxiv.org/content/10.1...

Led by Dr. Shivani Baisiwala, Neurosurgery Resident in the lab

Modeling tissue-resident macrophage development from mouse pluripotent stem cells Tissue-resident macrophages (TRMs) are innate immune cells that participate in tissue development, homeostasis, and immune surveillance. Extensive efforts have been made to recapitulate TRM developmen...

Excited to share our latest manuscript, a collaboration with @justinperryphd.bsky.social led by Weill Cornell Neuroscience PhD student @annbaako.bsky.social. Ann developed a new, improved mouse PSC model for studying tissue-resident macrophage differentiation.

www.biorxiv.org/content/10.1...

It’s out! The first paper from my postdoc – and first from the @bhadurilab.bsky.social – is now live @natneuro.nature.com . 🧠✨

Using a new meta-atlas generation strategy, we identified functional gene networks that more fully explain how cell types are formed in the human cortex. (1/13)

Thalamic NRXN1-Mediated Input to Human Cortical Progenitors Drives Upper Layer Neurogenesis According to the protocortex hypothesis, extrinsic thalamic signaling is necessary for refining cortical areas and cell types, but the mechanism by which these inputs shape the development and expansi...

Preprint from @bhadurilab.bsky.social: Thalamic NRXN1-Mediated Input to Human Cortical Progenitors Drives Upper Layer Neurogenesis (www.biorxiv.org/content/10.1...)

Human-chimpanzee tetraploid system defines mechanisms of species-specific neural gene regulation A major challenge in human evolutionary biology is to pinpoint genetic differences that underlie human-specific traits, such as increased neuron number and differences in cognitive behaviors. We used ...

What contributes to human specific neural specification? Check out these two wonderful preprints from a wonderful scientist Ava carter! 1. www.biorxiv.org/content/10.1...; 2. www.biorxiv.org/content/10.1...

Stay tuned! third preprint is on its way!

Metabolic Atlas of Early Human Cortex Identifies Regulators of Cell Fate Transitions Characterization of cell type emergence during human cortical development, which enables unique human cognition, has focused primarily on anatomical and transcriptional characterizations. Metabolic pr...

Delighted to share our most recent preprint led by the incredible @MilJessenya and @Jalbsoto! In this study, we generated a metabolomic atlas of human cortical development and discovered that the pentose phosphate pathway regulates radial glia cell fate. www.biorxiv.org/content/10.1...

Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naive pluripotent stem cells Pluripotent stem cells are susceptible to acquiring detrimental epigenetic abnormalities, posing a hurdle to their safe use in biomedical applications. Using pluripotent cells with defined genetic backgrounds, Stadtfeld and colleagues show that genetic variation is a major driver of epigenome stability and identify candidate regulators. These findings will enable novel approaches to stabilize the epigenome of pluripotent cells in culture.

Our collaborative project with Matthias Stadtfeld and Jason Mezey labs has now been published. We examined how genetic variation impacts regulation of DNA methylation at the control regions of imprinted genes in naive pluripotent stem cells.

www.cell.com/stem-cell-re...

⚡Next #FragileNucleosome meeting is less than a week away! Three amazing ECR scientists, 🔬@anajaneva.bsky.social, 🧠@anastasiahains.bsky.social, & 🧬@martyyang.bsky.social will discuss their research next Wed!
🗓️Don't forget to register:
us06web.zoom.us/webinar/regi...

Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers https://www.biorxiv.org/content/10.1101/2025.01.17.633622v1

Excited to share the second story from my post-doc in pre-print form! Many thanks to @vram142.bsky.social, lab members, and collaborators for contributions! In brief, we examine heterogeneity in (sub)nucleosome structure from in vivo long-read m6dA footprinting data. See Vijay's thread for details.

CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions Using a 3D co-culture system of iPSC-derived neurons and glia, termed iAssembloids, combined with CRISPRi-based screening, Li et al. investigate the effect of glial cells on neuronal activity and surv...

Our latest paper, led by Emmy Li, is out on Neuron today:

CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions

www.cell.com/neuron/fullt...