Carly Whyte

Australian immunologist fascinated by the immune processes underlying cancer and allergy | @CCB_Research | Passe & Williams Foundation Fellow

[Carly Whyte @CarlyEWhyte]

Delighted to have the work from my post doc with @LabListon out in @JExpMed today! We show how the cellular context in which IL2 is expressed leads to vastly different outcomes:

https://t.co/isnFdoNczL

[Roychoudhuri Lab @RoychoudhuriLab]

Thrilled to share new work led by @JieYang437 in the lab published today in @Nature. We find that Aspirin prevents metastasis by releasing T cells from immune suppression by platelet TXA2. @Cambridge_Uni @CRUKCamCentre https://t.co/dO2v0GWKAn

[Carly Whyte @CarlyEWhyte]

@RoychoudhuriLab @JieYang437 @Nature @Cambridge_Uni @CRUKCamCentre Such a great paper!! Congrats Rahul and @JieYang437

[Carly Whyte @CarlyEWhyte]

We are excited to recruit a PhD student for 2025 @CCB_Research in Adelaide to tackle immune dysfunction in head and neck cancer.
Please share and apply: https://t.co/yGu5GAdZgC

[Luciano Martelotto 🛠🧬💻🇦🇺 @LGMartelotto]

Following several kind requests, here is a high-level summary of our pre-print in @biorxivpreprint (doi: https://t.co/m4OHy3BP5N):

STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging

STAMP is a scalable, cost-efficient method for single-cell transcriptomics and multimodal profiling through imaging. It bypasses sequencing, significantly reducing costs while enhancing throughput.
#SingleCellRNA #SpatialOmics #STAMP

The motivation for this paper comes from the limitations of current scRNA-seq methods, which are costly, inefficient, and struggle to capture low- and high-abundance transcripts. Challenges like droplet instability, cell damage, limited cell capture, cross-contamination, inefficient indexing, and high sequencing costs affect ultra-low and ultra-high cell profiling, hindering accurate analysis of complex cell populations. #Limitations #DropletMicrofluidics

STAMP addresses these issues with a scalable, cost-effective, sequencing(costs)-free approach that works efficiently across ultra-low to ultra-high cell numbers, while preserving cellular morphology and enabling multimodal profiling. #SpatialOmics #UltraLow #UltraHigh

STAMP uses an imaging-based approach to perform high-throughput RNA and protein profiling by stamping cells onto slides compatible with CosMx and Xenium platforms, allowing multimodal profiling in a single run.
#Proteomics

STAMP supports single-modal (RNA/protein) and multimodal (RNA + protein) profiling, enhancing experimental flexibility and scalability. This versatility is essential for large-scale atlases and mixed-sample experiments.
#SingleCellAtlas #MultiSampleProfiling

STAMP scales easily: from less than 100 to millions of cells. It overcomes limitations in droplet-based systems, where throughput is often constrained by sequencing costs.
#HighThroughput

STAMP handles diverse sample types: PBMCs, dissociated tumors, nuclei, and stem cells. It also excels with fragile or archived tissues, where traditional methods often fail to yield high-quality data.
#ArchivedSamples

STAMP eliminates sequencing costs, making large-scale single-cell analysis accessible to more labs. #CostEfficiency

Here’s a cost comparison between GEM-X and STAMP-X for RNA profiling:

GEM-X RNA (20k cells): $0.0764/cell
1M cells = $76,400 (cost/cell = $0.0764)
2M cells = $152.800 (cost/cell = $0.0764)
3M cells = $229,200 (cost/cell = $0.0764)

STAMP-X RNA (1M cells): $0.0075/cell
1M cells = $7,500 (cost/cell = $0.0075)
2M cells = $7,500 (cost/cell = $0.00375)
3M cells = $7,500 (cost/cell = $0.0025)

In STAMP cells remain intact after imaging, enabling further downstream applications like histological validation or additional molecular assays, adding value to each sample.
#NonDestructiveAnalysis

We tested STAMP’s sensitivity by identifying, ultra-rare, circulating tumor cells (CTCs) spiked into PBMCs at 1:100,000. Such sensitivity is essential for clinical diagnostics, particularly in rare cell detection.
#CTCs #CancerDiagnostics

In a high-throughput immuno-phenotyping experiment, STAMP profiled 1.7M PBMCs, capturing a median of 83 transcripts and 49 genes per cell. This resulted in high-resolution immune profiling.
#Immunology #HighThroughputProfiling

31 immune cell states were mapped in PBMCs, capturing rare subpopulations (Th1/Th2/Th17 and NK subtypes). Detailed immune phenotyping is critical for understanding immune diversity in health and disease.
#ImmuneMapping

Whole cells vs. nuclei: STAMP's ability to profile both whole cells and nuclei is crucial for samples with low RNA content (e.g., archived tissues), increasing the platform’s applicability.
#NucleiProfiling #SingleCellOmics

STAMP integrates RNA and protein profiling. In cancer cell line profiling, RNA and protein data showed strong correlations, confirming the platform’s robustness in multimodal data collection.
#MultimodalProfiling

STAMP’s multimodal profiling produced high-resolution immune maps, combining RNA and protein data. This approach is essential for dissecting complex immune states and understanding functional responses.

STAMP excels in low-input samples. We demonstrated its ability to accurately profile as few as 100 cells, which is critical for studying rare populations in small samples.
#LowInput #RareCell

In a BMP4-driven stem cell differentiation model, STAMP captured dynamic changes from pluripotency to mesoderm and endoderm progenitors over multiple timepoints, tracking lineage differentiation.
#StemCellDifferentiation #LineageTracing

Trajectory analysis shows that STAMP’s resolution makes it a powerful tool for developmental biology and perturbation studies.
#DevelopmentalBiology #hESC

STAMP allows multi-sample profiling on a single slide, reducing batch effects and improving comparative analysis, particularly in drug response and perturbation studies.
#MultiSampleAnalysis #PerturbationScreening

STAMP represents a significant advance in single-cell research, offering scalable, multimodal RNA/protein profiling at low cost. Its versatility will support a broad range of research, from basic to clinical.
#SingleCellTechnology

Lots more coming soon...

@DrJasPlummer @hoheyn @pascual_reguant @EmanuelePitino1 @helucro @ximbaozao @irepan_salvador @Kellieiswise @m_mohenska @jc_nietos @cnag_eu @StJudeResearch @ACEpigenetics @M_ayco_N @eliseinsing Bill Flynn, Yutian Liu, Hannah Chasteen

[Luciano Martelotto 🛠🧬💻🇦🇺 @LGMartelotto]

Here we go…repurposing spatial imaging techs to achieve ultra-low to ultra-high, multiplexing, nuclei, cells, single (RNA or Protein), multimodal (RNA and Protein), super cheap! NO SEQUENCING!

@10xGenomics @nanostringtech @AkoyaBio @bruker

[Lisa Ebert @lisamebert]

We are recruiting! Come join us in Adelaide to work on cutting-edge translational research and contribute to developing CAR-T cell therapies for brain tumours. Two post-doc positions available, closing soon, details at https://t.co/rIke1TXUds

[Carly Whyte @CarlyEWhyte]

Congrats to the team @LabListon @jldvib @olivertburton on this wonderful study 👏 #TissueTregs surprising us on every turn!

[Adrian Liston @LabListon]

Biggest paper yet from the lab out now in @ImmunityCP! It is a massive #openscience resource on #tissueTregs, and what makes #Tregs tick in the #tissues. Spoiler-alert: Tissue Tregs are really different from what we all thought. 🧵 1/21

https://t.co/k8q7LhMewB

[Carly Whyte @CarlyEWhyte]

@betacellgirl @FlindersHMRI @Flinders @iMOD_lab Congratulations Claire!!

[Danika Hill @DrDanikaHill]

So great to have this preprint out in the world. My first paper in this new field
I love, #StrepA.

Thanks to @JoshOsowicki and Andrew Steer @MCRI_for_kids for providing such a cool Strep A challenge model to study, & to all our coauthors, particularly @hrcfrost & @njmoreland

[Shalin Naik @shalinhnaik]

Very excited (& nervous) to share what we've been working on the past many years. Only took 3 first authors (Schreuder the experimentalist, @DawnSLin the analyst, and @syzmath the modeller) & co-senior Weber (computational, modeller, SynBio extraordinaire) https://t.co/Wnhi6095Rb

[Adrian Liston @LabListon]

Resource: A mega-thread of various #academic #career development projects I have worked on over the years.

First up, building career options into your PhD studies, written as part of #ImmunologyFutures for @ImmunolCellBiol with @lydiamakaroff

https://t.co/yzBKkaOrli

[Tyler Burns @tjburns08]

Flow/CyTOF users and leaders: here is an interface that allows you to see exactly where a given cell on a biaxial plot is on a corresponding UMAP. More details:

[Carly Whyte @CarlyEWhyte]

@DrSarahBoyle @CancerAustralia @CanTooRunSwim Fantastic work Sarah 👏👏 well deserved!

[Luciano Martelotto 🛠🧬💻🇦🇺 @LGMartelotto]

Seeking experienced senior molecular biologist to lead all single cell/spatial applications running in my lab.

Must be willing to learn new stuff all the time & teach students!

—>Postdoc Level A or B based on experience.

Email CV & Refs to [email protected]

[Gökhan Cildir @cildir_gokhan]

Excited to be part of this massive international effort, leveraging the power of artificial intelligence in small molecule discovery. @CCB_Research @UniversitySA @AtomwiseInc https://t.co/zG3zYMj0az

[Ashraful Haque @DrAshHaque]

Immuno-PhD/Masters/Honours students, it can be hard to decide career direction. Register for our translational immunology conference (14-17 May, Melbourne) & hear from these huge companies! It could decide the next phase of your scientific career! https://t.co/gfQkvjmOxv

[Carly Whyte @CarlyEWhyte]

@DrSarahBoyle @UniversitySA @CCB_Research @theTiser This is fantastic Sarah, congratulations!!

[Carly Whyte @CarlyEWhyte]

@DrSarahBoyle @UniofAdelaide Well done Sarah 👏 very well deserved, congratulations!

[Carly Whyte @CarlyEWhyte]

@Anita_Kral @BDBiosciences @ASImmunology 👏👏

[Carly Whyte @CarlyEWhyte]

@EmanuelaPasciu1 @CMN_VIB @VIBLifeSciences @UAntwerpen Congrats Manu! So well deserved 👏👏