Nick Leigh

🗓️ 23-26 June 2026 🇸🇪
#PALS #summerschool in #OMICS is back!
Soon registration and info about speakers for the 3rd edition!

Organized by @claudiocantu81.bsky.social and me, @remeseiro-lab.bsky.social, with the support from @scilifelab.se and @kawresearch.bsky.social

Molecular basis for de novo thymus regeneration in a vertebrate, the axolotl The molecular, cellular, and functional restoration of the axolotl thymus after de novo regeneration is described.

Can't believe my postdoc paper is finally out. Christmas came early this year, holy moly 🎄

Molecular basis for de novo thymus regeneration in a vertebrate, the axolotl | Science Immunology www.science.org/doi/10.1126/...

Wooo!! Congrats!!

Yesterday @jacoates.bsky.social and I gave talks on pre-prints hosted by the @lunduniversity-med.bsky.social . Jonny gave a great primer on the history of pre-prints and debunked myths about them. I spoke on our experiences with preprints and was encouraged to see this feedback after the talks👇

One of your future coworkers in the Currie Lab, an adorable axolotl.

💥OUR LAB IS HIRING!!💥

We are hiring a research assistant/lab manager to assist with managing our axolotl colony and enabling some kick-ass science! Looking for high levels of organization, collaboration, problem solving and curiosity.

Application link: tinyurl.com/3tpvphpm
#SciJob #JobAlert

Decoding sex differences in human immunity through systems immunology Abstract. Immune function varies widely across humans. Biological sex is a key factor underlying human immune variability, with men presenting with more se

I'm thrilled to share that my first co-authored review, "Decoding sex differences in human immunity through systems immunology," on Oxford Open Immunology! I'm so grateful for the opportunity to have worked with Tianze Cao and @consigliocr.bsky.social on this. doi.org/10.1093/oxfi...

Decoding sex differences in human immunity through systems immunology Abstract. Immune function varies widely across humans. Biological sex is a key factor underlying human immune variability, with men presenting with more se

‼️Our first review is out‼️

Decoding sex differences in human immunity through systems immunology shorturl.at/EsAkE

We discuss how #SystemsImmunology decodes #SexDifferences in #HumanImmunity, paving the way for tailored, sex-informed treatments.

Excellent work by @resabut.bsky.social & Tianze Cao!

CellTalk HHD | Human Heart Development Research CellTalk-Human Heart Development is a BBSRC funded consortium established to find out more about how cells come together to build the heart as it grows inside the womb.

🫀Job alert 🧬 come and be our colleague! Join a BBSRC-funded consortium aiming to understand how the human heart develops - you will be contributing multimodal single cell & spatial transcriptomics data using zebrafish and human cardiac organoids as models. Learn more: www.heartdevelopment.org (1/4)

Immune-mediated cardiac development and regeneration The complex interplay between the immune and cardiovascular systems during development, homeostasis and regeneration represents a rapidly evolving fie…

Just published! Our Review on how immune cells masterfully orchestrate heart development and regeneration. Beyond fighting pathogens, they're actually building & repairing your heart! Learn how cutting-edge technologies are driving therapeutic opportunities here www.sciencedirect.com/science/arti...

Come and work with us OOH @oxforddpag.bsky.social: ❤️ organoids to study 1) failing hearts and 2) metabolite signalling, with @novonordisk.bsky.social and wonderful colleagues 1) Andrew Lewis & Chris Toepfer @rdmoxford.bsky.social; 2) Yimon Aye @oxfordchemistry.bsky.social. Reach out if interested!

UniStem Day 2025: A Decade of Inspiring Future Scientists in Lund Lund University.

🔬👩‍🔬What sparked your interest in science?👨‍🔬🧫

For 10 years, #UniStemDay at Lund Stem Cell Center has invited students to step into the lab, meet scientists & explore science. This year, 200 joined us for hands-on experiments & career inspiration!

📖 Read more:
www.stemcellcenter.lu.se/article/unis...

Great write-up from Alexis! UniStem is an amazing initiative and given the current attacks on science it’s critical we work to educate and motivate the future generation to be pro-science.

Most importantly, big thanks to everyone involved--the co-1st authors I highlighted in the thread and co-last authors @andrassimon.bsky.social and @maxyunlab.bsky.social. It was a huge effort from many and this work opens the door to approaches we could only dreamed about a few years ago!
(15/x)

We now have some leads to key components of newts regenerative ability. Now it's time to dig into the functional relevance of these findings and whether they indeed underpin the remarkable regenerative capacity of newts 🦎!
(14/x)

annotation of miRNA and ESCC-miRNA across the newt genome

Continuing evaluation of RNAs, previous work had indicated an expansion of embryonic stem cell-specific miRNAs in P. waltl. Ketan went on to confirm this expansion in this new higher contiguity assembly, perform a genome-wide annotation of miRs, and define 4 novel P. waltl miR groups.
(13/x)

volcano plot comparing circRNA expression in developing larvae verus the adult regenerating limb

Ketan noted that TEs can create circRNA. These have recently emerged as RNA molecules with roles in processes like transcription and stemness. Sleuthing the newt genome for circRNA, TEs appeared to facilitate circRNA genesis. Importantly, some circRNA were enriched during regeneration!
(12/x)

TEs ability to jump around the genome means they can have a major influence on genomic architecture. PhD student and co-first author Ketan Mishra dug into how TEs may be changing the newt genome.
(11/x)

So, it seems that salamanders are unable to control TE accumulation in their genomes, so could this accumulation be beneficial?
(10/x)

stacked bar chart of contribution to genome length from transposable elements in human, frog, axolotl, and newt.

Now back to the TEs…co-first author Svetlana Iarovenko found that unlike other giant genomes, the TE-driven expansion of the newt genome appears due to more DNA elements as compared to RNA elements that have driven expansion in other species with giant genomes (like the axolotl).
(9/x)

Fgf5 locus compared between gar, lungfish, frog, newt, and axolotl

Though the newt genome is massive, newts lose genes over evolution. We found that Fgf5 was lost in newts and lost in other species with giant genomes. This suggests that giant genomes may be susceptible to disruptions at this locus or that disruptions at this locus facilitate genome expansion.
(8/x)

ribbon plot comparing chordate linkage group locations on chromosomes between newt, axolotl, and gar

Before we dive into the TEs, annotation efforts from co-first authors Ahmed Elewa and Tom confirmed that though their genome size is massive, the # of protein-coding genes is similar to other vertebrates. We also found that the general layout of their genome matched well with related species.
(7/x)

So how did the newt genome get so big? Similar to #axolotl our findings indicate that the P. waltl has an expanded genome due to a massive accumulation of transposable elements (TEs). An amazing ¾ of the genome is repeat elements!
(6/x)

Enter long-read DNA sequencing; now we can dramatically increase the size of each puzzle piece and make each piece more unique. A manageable puzzle to solve, at least for co-first author Thomas Brown—the genome assembler behind the this newt genome!
(5/x)

Due to technical limitations imposed by short read DNA sequencing, the highly repetitive nature of salamander genomes has made them notoriously difficult to assemble. Imagine a puzzle with millions of tiny pieces that are all the same color—this would be a nearly impossible puzzle.
(4/x)

While there are different means by which genomes expand over evolutionary time, salamanders have long been noted to have highly repetitive genomes. This massive accumulation of transposable (repeat) elements drove the expansion of the #axolotl salamander genome. www.nature.com/articles/nat...
(3/x)

Creating high-quality genome assemblies has been challenging for salamanders due to their enormous genomes.

Salamander genomes are 4-43X larger than the human genome!

How did salamander genomes get so big?

(2/x)

Iberian ribbed newt crawling on a white background

The newt Pleurodeles waltl has amazing biological features, like the ability to regenerate tail and limbs!

Are the secrets to this regenerative capacity in their genome?

In this collaborative work from the Leigh, Yun, and Simon labs we explored this question.

www.cell.com/cell-genomic... (1/x)

A #Pleurodeles on the cover. Interested in this #giantgenome, #salamander #regeneration, #noncodingRNA landscape? Pls check out: www.cell.com/cell-genomic.... Many great labs involved, special thanks to co-senior authors
@maxyunlab.bsky.social, and @niche-leigh.bsky.social

Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration Understanding molecular mechanisms behind newts’ exceptional regenerative capability has been limited because of their large, repeat-element-rich genome. Brown et al. present the most complete chromos...

Newt Genome assembly is out. Congratulations @andrassimon.bsky.social @maxyunlab.bsky.social @niche-leigh.bsky.social labs.🍻 www.cell.com/cell-genomic...

Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration Understanding molecular mechanisms behind newts’ exceptional regenerative capability has been limited because of their large, repeat-element-rich genome. Brown et al. present the most complete chromos...

And the newt genome ms is finally out! www.cell.com/cell-genomic... Thanks @andrassimon.bsky.social @niche-leigh.bsky.social labs for an amazing collab, and specially Tom Brown for great assembly skills.
@dcgenomecenter.bsky.social
@crtd-tud.bsky.social
@mpicbg.bsky.social
@poldresden.bsky.social