Hower Lee

I work with spatial omic technologies and stuff. PhD student at Mats Nilsson Lab @matsnilssonlab

[Luciano Martelotto 🛠🧬💻🇦🇺 @LGMartelotto]

We GoT a Filling…uuuuhoooo

𝗧𝗮𝗿𝗴𝗲𝘁𝗲𝗱 𝘀𝗲𝗾𝘂𝗲𝗻𝗰𝗶𝗻𝗴 𝗼𝗳 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝘀 𝘃𝗶𝗮 𝗥𝗡𝗔-𝘁𝗲𝗺𝗽𝗹𝗮𝘁𝗲𝗱 𝗴𝗮𝗽 𝗳𝗶𝗹𝗹𝗶𝗻𝗴 𝗼𝗳 𝗼𝗹𝗶𝗴𝗼𝗻𝘂𝗰𝗹𝗲𝗼𝘁𝗶𝗱𝗲𝘀 𝗳𝗼𝗿 𝘀𝗶𝗻𝗴𝗹𝗲-𝗰𝗲𝗹𝗹 𝗥𝗡𝗔-𝘀𝗲𝗾

Download here: https://t.co/CRAFwIFNqY…

1/ 🧬 New preprint! We developed GoT-Multi-Gap — a method to detect expressed mutations in single cells without needing to know the variant sequence in advance.
Built on RNA-templated gap filling.

Thread 🧵👇

2/ The problem: detecting mutations in scRNA-seq is hard. Coverage is sparse, and capture methods lose sensitivity the farther a mutation sits from the transcript end. Ligation-based approaches (like our earlier GoT-Multi) require allele-specific probes — limiting scalability.
3/ Our solution: exploit the dual enzymatic activity of Bst FL polymerase. It reverse-transcribes across a gap between flanking probes on mRNA, then uses nick translation to activate the downstream probe for ligation. No allele-specific design needed.
4/ The trick: the downstream probe starts with a 5’-OH (ligation-incompetent). After Bst fills the gap and nicks the terminus, a 5’-phosphate is exposed → SplintR ligase seals the nick. The mutation sequence gets written into the product automatically.
5/ We validated the chemistry in situ with padlock probes + rolling circle amplification on 18S rRNA. Key insight: exonuclease-resistant backbone mods on the downstream probe fine-tune polymerase vs. nick-translation competition, boosting efficiency.
6/ We then built this into 10x Flex (GoT-Multi-Gap). Three cell lines (MCF-7, SK-BR-3, LnCAP), 61 SNVs targeted across a range of gap sizes. Critically — the gap-filling step didn’t perturb Flex performance. UMI counts, gene counts, correlations all preserved.
7/ Results: among targets with ≥10 genotyped cells, mutant calls showed 80-100% specificity to the expected cell line. The main driver of detection sensitivity? Target transcript abundance (Pearson R=0.37, P<0.01).
8/ What didn’t matter much: gap length (4-12 bp), mutation position within the gap, and probe GC content (within the 44-72% window). The assay captures variants across the full gap with comparable sensitivity.
9/ Bottom line: GoT-Multi-Gap enables simultaneous whole-transcriptome + multiplexed mutation profiling from the same single cell, without prior knowledge of variant identity. Scalable, compatible with existing workflows, and ready for complex mutational landscapes.
10/ Huge thanks to all authors and absolute special shout out to @MircaSaurty, @lee_hower and @Kellieiswise and the incredible team @WeillCornell and @scilifelab.

[Development @Dev_journal]

Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology

Read this Techniques &amp; Resources Article by Hower Lee @lee_hower, Marco Grillo, Mats Nilsson @MatsNilssonLab @scilifelab &amp; colleagues:
https://t.co/FqlsybMhWl

[MatsNilssonLab @MatsNilssonLab]

🎉 Exciting news! Our latest work is now published in @Dev_journal!

The open-source solution for RNA-targeted in situ sequencing provides an accessible and efficient method for spatially resolved gene expression analysis and spatial multi-omics.

🔗 https://t.co/RrmV3Aev6P

[MatsNilssonLab @MatsNilssonLab]

🚨Job Alert🚨

Our Staff Scientist position at @sangerinstitute is now up and running. Do not hesitate.
Apply today: https://t.co/UHKjd8I3ge
LinkedIn: https://t.co/iKBnfxUc4M

[Hower Lee @lee_hower]

Lastly, this preprint was only possible with the help of my colleagues @sergiomarco96 @chrislangseth @MarcoGrillo and collaborators 😁 .. N/N

[Hower Lee @lee_hower]

This is our humble attempt to democratize in situ transcriptomics for the masses. Here in this preprint, we @MatsNilssonLab have put together an end to end solution for targeted in situ transcriptomics that is compatible with immunostaining and other labelling methods. ... 1/N

[bioRxiv @biorxivpreprint]

Open-source, high-throughput targeted in-situ transcriptomics for developmental biologists https://t.co/gz3Pt2BpMF #bioRxiv

[Hower Lee @lee_hower]

We know the current commercial offerings for in situ transcriptomics are extremely pricey. Hopefully the community will find this useful and easy to implement on their model system of choice on a shoestring. ..3/N

[MatsNilssonLab @MatsNilssonLab]

Thrilled to share our latest collab publication in @natureneuro

Congrats to Xiaofei Li, @chrislangseth @lee_hower @dgyllborg and collaborators @adameykolab @slinnarsson @joalunatkthse Erik Sundström @HDCA_Sweden @scilifelab
https://t.co/szP5FpFAXg

[MatsNilssonLab @MatsNilssonLab]

🔬 LAB MANAGER WANTED 🔬

The Nilsson Lab at @scilifelab &amp; @Stockholms_univ is seeking a talented Lab Manager to join our diverse and international team! 💻🧪

Apply now: https://t.co/GaYkmz42qR

[MatsNilssonLab @MatsNilssonLab]

Great work from both Erik and @sergiomarco96 from the lab and collaborators @FilbinMariella @IlonLiu ! A fantastic use of #InSituSequencing to profile the spatial organisation of diffuse midline #glioma. 🔥🔥🔥🔥🔥🔥

[MatsNilssonLab @MatsNilssonLab]

🔥New Publication🔥 @sergiomarco96 and collaborators @CarolinaWahlby @gapartel mapped the cellular diversity in the developing human heart with segmentation free #spage2vec on #InSituSequencing data. Fantastic job from all! #SpatialBiology

[MatsNilssonLab @MatsNilssonLab]

🔥New publication🔥from @M_Hilscher together with @GoCasteloBranco @chrislangseth @PKukanja

Here, authors revealed spatial gradients and neighboring preferences of fine oligodendrocyte lineage cells in young and adult brain and spinal cord
@BMCBiology
https://t.co/cn5gqFXcOc

[MatsNilssonLab @MatsNilssonLab]

🚨 New Publication🚨
Anastasia Magoulopoulou et al in collab with @BeritCarow used #InSituSequencing to define the spatial distribution of immune environments surrounding Mycobacterium tuberculosis bacteria and clusters in infected mouse lung.

https://t.co/mQZnH5arSC

[MatsNilssonLab @MatsNilssonLab]

New Publication from @lee_hower, @sergiomarco96 and @dgyllborg! Here, the authors benchmarked a kit from @CARTANAbio (now @10xGenomics), against traditional #cDNA based #HybISS.

Congrats to all 🎉🔥🔬!
https://t.co/rJNiSwjay3

[Hower Lee @lee_hower]

@AlydeBalzac Hey aly, You’re too kind! Hope to see u soon! 🙂

[Hower Lee @lee_hower]

A pleasure of mine to be involved as a course instructor! Made a couple of friends while at it too 🥹. Hope to be a part of #EMBOspatialgeneexpression course again when it runs again!

[MatsNilssonLab @MatsNilssonLab]

Tgt w @joalunatkthse, @EMBO and Samakovlis Lab, we successfully concluded the first “Spatial Analysis of Gene Expression in Tissues” course @ @scilifelab last week. A huge thank you to all the course instructors and participants that made this event an overwhelming success 🤩

[Hower Lee @lee_hower]

@Nagudelo715 You’re very much welcome! It was fun and hopefully see u soon 🙂🙂

[Hower Lee @lee_hower]

A pleasure to contribute some #InSituSequencing data towards the overall project success! Couldn’t have done it without @chrislangseth 🫡

[GonçaloCasteloBranco @GoCasteloBranco]

@dvd_bruggen's last piece of work in the lab, on the first waves of human oligodendrogenesis, is out @Dev_Cell!
https://t.co/lsQ6pyDdgb
w/ Erik Sundström Fabio Pohl @PKukanja @mandy_meijer @kabbe_m @MossiAlejandro @slinnarsson @MatsNilssonLab @chrislangseth @M_Hilscher @lee_hower

[GonçaloCasteloBranco @GoCasteloBranco]

@dvd_bruggen's last piece of work in the lab, on the first waves of human oligodendrogenesis, is out @Dev_Cell!
https://t.co/lsQ6pyDdgb
w/ Erik Sundström Fabio Pohl @PKukanja @mandy_meijer @kabbe_m @MossiAlejandro @slinnarsson @MatsNilssonLab @chrislangseth @M_Hilscher @lee_hower