Patrick Murphy

Efficient and multiplexed somatic genome editing with Cas12a mice - Nature Biomedical Engineering Multiplexed editing using Cas12a transgenic mice facilitates the study of disease models with complex genotypes.

Happy to share an exciting paper from my former lab mate, Jess Hebert, showing Cas12 efficacy and use in somatic screening. Take a look if you are considering the approach! www.nature.com/articles/s41...

We look forward to the next phase of this work with help from @americanheart.bsky.social @alzassociation.bsky.social @alzheimerssoc.bsky.social @alsassociation.bsky.social @cshlnews.bsky.social @navbo.bsky.social #endftd

Congratulations to Ashok, an exceptionally talented scientist who would be a tremendous junior faculty hire. Thank you to collaborators Riqiang Yan, Cat Lutz and Aamir at JAX, members of the Murphy lab, thoughtful input from reviewers and at CSH and Gordons Brain Barriers Meetings, and the NIH.

Future questions:
- Does endothelial TDP-43 dysfunction initiate motor neuron impairment in ALS?
- Why is endothelial TDP-43 lost in AD and ALS-FTD without TDP-43 mutation (and vice versa how do some with familial mutation avoid disease)?
- How does loss of TDP-43 lead to barrier defects?

Moreover, Ashok observed changes in pathways that resembled those we had observed in capillary endothelial cells in ALS-FTD and AD of human donors. Together, this work suggests that brain endothelial TDP-43 dysfunction contributes to cognitive dysfunction.

To more carefully examine brain endothelial function, Ashok used Slco1a1-CreERT2, and found acute BBB leak, and chronic fibrin deposition, basement membrane changes, gliosis, and pTau accumulation in neurons that ultimately lead to behaviors (social and memory) resembling a mouse model of FTD.

Despite similar levels of the Tardbp mRNA, nuclear TDP-43 protein was reduced. Endothelial function was tested in Cdh5-CreERT2; Tardbp floxed mice, but systemic endothelial dysfunction limited understanding of organ specific functions.

What Ashok was able to show, by isolating and culturing brain endothelial cells, is that a single allele ALS-FTD mutation in TDP-43 disrupts formation of VE-cadherin junctions, cytoskeletal organization and barrier integrity.

Endothelial TDP-43 depletion disrupts core blood–brain barrier pathways in neurodegeneration - Nature Neuroscience Targeting the endothelium across ages and neurodegenerative diseases in 92 donors with single-cell inCITE-seq reveals similar alterations in ~40% of capillaries in AD, ALS and FTD. Endothelial TDP-43 ...

Our recent work had revealed a reduction in nuclear TDP-43 in ~40% of cerebrovascular capillaries in AD, ALS-FTD but not healthy aging www.nature.com/articles/s41... This correlated with changes in pathways critical for BBB function, but causation was unclear.

Amyotrophic lateral sclerosis and frontotemporal dementia mutation reduces endothelial TDP-43 and causes blood-brain barrier defects ALS-FTD–associated TDP-43 point mutation in endothelial cells leads to BBB loss and is replicated by gene deletion.

Despite strong headwinds, we are continuing to do our work. Congratulations to lead author Ashok Cheemala. Here, Ashok shows that even a single point mutation in TDP-43 leads to large defects in cell-cell junction and barrier www.science.org/doi/10.1126/...

Congratulations @vijayrathinam.bsky.social

It is important to recognize the many years of hard work, and continued support new insight requires. This work began many years ago (15 to be exact), with basic questions about the regulation of endothelial functions by RNA-binding proteins in Richard Hynes lab, and with the help of Chris Burge.

Many thanks to collaborator Dr. Riqiang Yan, members of the Murphy lab, our flow and sequencing facilities, our funding at NIH NINDS and earlier awards from AHA and NHLBI for contributing to this work. Most importantly, thank you to the donors who contributed to this through the NIH NeuroBioBank.

In addition to well-known roles in transcriptional regulation of inflammatory responses, NF-kB(p65) is critical for epithelial and endothelial junctions and barrier maintenance. Understanding how TDP-43 bifurcates these NF-kB(p65) responses will be key to understanding brain barrier dysfunction.

Although it is not yet clear why loss of TDP-43 affects the endothelium, an intriguing observation from our analysis of nuclear protein is that NF-kB(p65) and TDP-43 are tightly correlated in healthy endothelium - and that loss of TDP-43 in disease de-represses NF-kB mediated transcription.

Barrier dysfunction occurs early in disease development, and we observed similar but milder alterations in aged donors with Alzheimer's risk factors of diabetes and hypertension, suggesting that endothelial TDP-43 loss is an early event in disease progression.

Loss of Endothelial TDP-43 Leads to Blood Brain Barrier Defects in Mouse Models of Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Loss of nuclear TDP-43 occurs in a wide range of neurodegenerative diseases, and specific mutations in the TARDBP gene that encodes the protein are linked to familial Frontal Temporal Lobar Dementia (...

In parallel work (Science Advances next month and bioRxiv here : www.biorxiv.org/content/10.1...) we show that targeted deletion of TDP-43 in brain endothelium compromises the blood brain barrier, and leads to dysfunction of the same pathways disrupted in human capillaries with reduced TDP-43.

Why does this matter? TDP-43 mutations drive ALS-FTD, and its nuclear depletion in neurons is a hallmark of neurodegeneration. Our findings reveal TDP-43 is also lost in the capillary endothelium, where it correlates with transcriptional hallmarks of blood-brain barrier dysfunction.

We find a distinct transcriptional program that characterizes ~40% of the capillary endothelium in neurodegenerative diseases, including ALS-FTD, and Alzheimer’s, and is marked by nuclear loss TDP-43.

In a herculean effort led by talented MD/PhD student Omar M Omar, we use a novel approach for endothelial cell enrichment to create a massive dataset of endothelial changes in healthy aging and ALS-FTD and Alzheimer's Disease (92 donors). A data portal is here : murphylabvasculardata.cam.uchc.edu

Endothelial TDP-43 depletion disrupts core blood–brain barrier pathways in neurodegeneration - Nature Neuroscience Targeting the endothelium across ages and neurodegenerative diseases in 92 donors with single-cell inCITE-seq reveals similar alterations in ~40% of capillaries in AD, ALS and FTD. Endothelial TDP-43 ...

I'm happy to announce that our paper describing the first in human tissue application of inCITE-seq, to assess nuclear levels of RNA-binding proteins, and key regulators of the blood brain barrier (b-Catenin and NF-kB) is now available online from Nature Neuroscience www.nature.com/articles/s41...

NIH is again throttling research funding in defiance of a federal court order A freeze on "new and continuation awards" will "remain in place" pending DEI review, states a new internal memo.

www.motherjones.com/politics/202...

Come together, right now The chaos, conflicting information, firings, and hurtful rhetoric of the Trump administration’s approach to science over the past month are causing anxiety, grief, and concern for the scientific commu...

www.science.org/doi/10.1126/...

A source close to the situation confirmed that study sections are continuing to be cancelled. On the chopping block this week: developmental brain disorders, mechanisms of cancer therapy, and neurotoxicology of alcohol. For some labs, this was the last chance to get funding or they’ll shut down.

Antisense oligonucleotide-mediated TRA2β poison exon inclusion induces the expression of a lncRNA with anti-tumor effects Nature Communications - The oncogenic splicing factor TRA2β is reported to be upregulated in human cancers partly by increased TRA2β poison exon (PE) skipping. Here the authors show that...

Our latest work on targeting the poison exon in #RNA #splicing factor TRA2B in #cancer reveals a role for this non coding transcript and opportunities for targeting splicing factor levels across multiple tumor types
rdcu.be/d90Ra
#RNAsky @jacksonlab.bsky.social

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Petition to Reverse the NIH Indirect Cost Cap initiated by Tom Maniatis. Please amplify
Sign the Petition: chng.it/kK2HMP5pGk
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A modular platform for bioluminescent RNA tracking - Nature Communications Studying RNA dynamics in vivo often relies on fluorogenic approaches, but these can be hampered by factors such as limited sensitivity and sample autofluorescence. Here, the authors describe an ultras...

Cool new work from Jenn Prescher and coworkers @ucirvine.bsky.social, “RNA lantern” technology for bioluminescence imaging of RNA transcripts

www.nature.com/articles/s41...

Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases - Nature Genetics This analysis of single-cell RNA sequencing data from peripheral blood mononuclear cells for 474 individuals of diverse Asian ancestries in the Asian Immune Diversity Atlas links cell-type-specific sp...

Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases

www.nature.com/articles/s41...