Daphne Superville
@dasuperville.bsky.social
📤 101
📥 205
📝 4
UCSF PhD candidate @gogalab | MIT ‘17 🦫 | 🇦🇷 🇺🇸|
#metastasis
#tumormicroenvironment
pinned post!
Running NMF on your scRNAseq data? Check out my updates to Lyndsay Murrow's DECIPHER-seq package, now compatible with Seurat v5 objects and rliger v2!
github.com/dasuperville...
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GitHub - dasuperville/DECIPHER-seq-v2: Data and code to reproduce results from DECIPHER-seq paper. Updated for use with Seurat v5 objects and rLiger v2.
Data and code to reproduce results from DECIPHER-seq paper. Updated for use with Seurat v5 objects and rLiger v2. - dasuperville/DECIPHER-seq-v2
https://github.com/dasuperville/DECIPHER-seq-v2
6 months ago
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Daphne Superville
Eric Topol
4 days ago
Comprehensive biologic characterization of a 117-year old supercentenarian, the world's oldest living person
www.cell.com/cell-reports...
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Daphne Superville
Cell Reports
6 days ago
Evolution of a melanoma that escapes allogeneic rejection
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Evolution of a melanoma that escapes allogeneic rejection
Rokan et al. evolved mouse melanoma to bypass immune barriers, making it transplantable. Transplantable tumors activated antiviral signals and blocked immune attack. Similar traits appear in some human melanomas, helping us understand how cancer evades immune detection and the histocompatibility barrier.
http://dlvr.it/TNF9PJ
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Daphne Superville
Samarth Hegde
7 days ago
🔬Our paper from the
@miriammerad.bsky.social
lab is now online! This is a story shaped over years of cross-disciplinary endeavor at
@sinaiimmuno.bsky.social
and labs across the world. 🧵:
www.nature.com/articles/s41...
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Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumours - Nature
An understanding of the molecular mechanisms promoting the generation of immunoregulatory and tumour-promoting monocytes and macrophages is key to breaking the cycle of tumour myelopoiesis and develop...
https://www.nature.com/articles/s41586-025-09493-y
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reposted by
Daphne Superville
bioRxiv Cancer Bio
8 days ago
Type I interferon signaling instills divergent metastatic phenotypes and immunotherapy responses
https://www.biorxiv.org/content/10.1101/2025.09.18.677123v1
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Daphne Superville
Ming Tommy Tang
8 days ago
🧵 1/ In high-dimensional bio data—transcriptomics, proteomics, metabolomics—you're almost guaranteed to find something “significant.” Even when there’s nothing there.
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Daphne Superville
Nikolai Slavov
8 days ago
What limits scientific creativity and originality ? This article thoughtfully discusses many intertwined challenges, including: Cultural Shift Daily Grind Less Is More Their arguments generally resonate, except for one: 🧵
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Daphne Superville
bioRxiv Cancer Bio
8 days ago
Loss of the tumor suppressor PTEN activates cell-intrinsic interferon signaling to drive immune resistance
https://www.biorxiv.org/content/10.1101/2025.09.17.676669v1
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Daphne Superville
bioRxiv Cancer Bio
10 days ago
LRH-1 is a novel regulator of neutrophil-driven immune responses within the tumor microenvironment.
https://www.biorxiv.org/content/10.1101/2025.09.16.676030v1
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Daphne Superville
bioRxiv Cancer Bio
10 days ago
Modulating Glutamine Metabolism Reprograms Pro-Inflammatory Differentiation in Macrophages
https://www.biorxiv.org/content/10.1101/2025.09.16.675216v1
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Daphne Superville
bioRxiv Immunology
11 days ago
Mitochondrial instability contributes to IFN-driven heart disease.
https://www.biorxiv.org/content/10.1101/2025.09.15.674036v1
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Daphne Superville
Cell Stem Cell
11 days ago
Online Now! Targeting lysozyme 2 in endocardium promotes rapid recovery by modulating remote injury signals
#stemcells
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Targeting lysozyme 2 in endocardium promotes rapid recovery by modulating remote injury signals
Fan et al. discovered that local cardiac injury triggers aberrant lysozyme 2 (Lyz2) expression in remote zones. Lyz2 acts as a remote-injury-triggered regulator of lysosomal degradation in endocardial cells, driving pathogenic extracellular matrix breakdown. Inhibiting the LYZ2-mediated injury response—via knockout or pharmacological lysosomal inhibition—confers rapid functional recovery of non-regenerative hearts.
http://dlvr.it/TN7pX5
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Daphne Superville
Waggoner Lab
11 days ago
Transcriptional states of lung cancer microenvironment reveal macrophage subtype dynamics linked to disease progression
@jimmunol.bsky.social
academic.oup.com/jimmunol/adv...
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Daphne Superville
bioRxiv Immunology
11 days ago
Neutrophil and NET-driven pulmonary microvascular injury following myocardial injury: attenuation by S100A8/A9 inhibition
https://www.biorxiv.org/content/10.1101/2025.09.12.675647v1
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Daphne Superville
Cell Reports
14 days ago
Leukocytes use endothelial membrane tunnels to extravasate the vasculature
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Leukocytes use endothelial membrane tunnels to extravasate the vasculature
During paracellular transmigration, neutrophils exit the vasculature not through simple endothelial retraction but via dynamic membrane tunnels formed by overlapping endothelial cells. Using high-resolution live imaging, the authors et al. reveal that neutrophils actively remodel endothelial membranes to create 3D exit tunnels.
http://dlvr.it/TN4RBK
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Daphne Superville
Ivan Zanoni
15 days ago
#WeekendRead
#InterferonPower
! Hegde,
@miriammerad.bsky.social
&co show
@nature.com
that
#tumor-derived
factors drive NRF2 activation in bone marrow myeloid progenitors, dampening IFN-I/-III responses & favoring emergence of immunosuppressive monocyte-derived macrophages!
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Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumours - Nature
An understanding of the molecular mechanisms promoting the generation of immunoregulatory and tumour-promoting monocytes and macrophages is key to breaking the cycle of tumour myelopoiesis and develop...
https://www.nature.com/articles/s41586-025-09493-y
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Daphne Superville
Trends in Immunology
16 days ago
‘Smelling’ lipid cues: chemosensory receptors tune tumor-associated macrophage behavior
#immunology
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‘Smelling’ lipid cues: chemosensory receptors tune tumor-associated macrophage behavior
Tumor-associated macrophages (TAMs) are key regulators of the tumor microenvironment (TME), but their heterogeneity, driven by tumor-derived cues, poses challenges for therapeutic targeting and underscores the need for precise macrophage reprogramming strategies. Through a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screen, Marelli et al. identified chemosensors as lipid-sensing regulators of macrophage activity, revealing new therapeutic avenues.
http://dlvr.it/TN2gbv
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Daphne Superville
Cancer Cell
17 days ago
Dendritic cells function beyond antigen presentation
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Dendritic cells function beyond antigen presentation
In this issue of Cancer Cell, Chen et al. identify DNASE1L3-expressing dendritic cells (DCs) as enhancers of anti-tumor immunity. By degrading neutrophil extracellular traps, these DCs promote CD8⁺ T cell infiltration into tumors and enhance checkpoint blockade efficacy, extending DNASE1L3’s known immune regulatory role to physical remodeling of the tumor microenvironment.
http://dlvr.it/TN2KM2
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Daphne Superville
Cancer Cell
16 days ago
From gene lists to context drift
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From gene lists to context drift
Treatment resistance limits long-term effectiveness in cancer therapy. Conventional biomarkers typically rely on static gene expression levels. In this issue of Cancer Cell, Jassim et al. report a new approach, RECODR, which captures how gene relationships shift over time, uncovering hidden drivers of resistance and suggesting effective combination treatments.
http://dlvr.it/TN2TZ4
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Daphne Superville
Ivan Zanoni
18 days ago
💥
#ImmunometabolismPower
! Excited to have this officially out
@cp-immunity.bsky.social
💥 We show that pathogens induce the host to produce oxidized lipids which rewire the
#metabolism
of
#macrophages
, causing
#epigenetic
modifications which dampen anti-inflammatory IL-10, exacerbating
#inflammation
!
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Epigenetic silencing of interleukin-10 by host-derived oxidized phospholipids supports a lethal inflammatory response to infections
Phagocytes initiate immunity to invading microorganisms by detecting pathogen-associated molecular patterns via pattern recognition receptors. Pathoge…
https://www.sciencedirect.com/science/article/pii/S1074761325002869
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Daphne Superville
Trends in Immunology
19 days ago
Mitochondrial dysfunction in myeloid cells: a central deficit in autoimmune diseases
#immunology
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Mitochondrial dysfunction in myeloid cells: a central deficit in autoimmune diseases
Autoimmune diseases arise from genetic and environmental factors that disrupt immune tolerance. Recent studies highlight the role of myeloid cell immunometabolism, particularly mitochondrial dysfunction, in driving autoimmunity. Mitochondria regulate energy homeostasis and cell fate; their impairment leads to defective immune cell differentiation, abnormal effector activity, and chronic inflammation. We propose that chronic metabolic stress reprograms myeloid cells, fueling a vicious cycle of cell death and immune activation. Over time, this may induce several states of maladaptation in myeloid cells. Viewing autoimmune disease through a metabolic lens offers new insight into disease mechanisms and highlights potential therapeutic opportunities targeting mitochondrial function to restore immune balance.
http://dlvr.it/TMzXGF
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Daphne Superville
Elizabeth McKenna
20 days ago
Now online in Cancer Discovery
@aacrjournals.bsky.social
: An Autochthonous Model of Lung Cancer Identifies Requirements for Cellular Transformation in the Naked Mole-Rat - by Alyssa Shepard, Daniel Lester,
@kissillab.bsky.social
, and colleagues
doi.org/10.1158/2159...
@moffittnews.bsky.social
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Daphne Superville
Katherine King MD PhD
21 days ago
Central trained immunity is still a nascent field— is there true reprogramming of hematopoietic progenitors to influence innate immunity, or is this selection for lineage biased cells? We explore the nuances in this new review.
doi.org/10.7554/eLif...
awesome collab with Eva Kaufmann and team!
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Hematopoietic stem and progenitor cells as a reservoir for trained immunity
Inflammation supports selection, differentiation bias, and epigenetic reprogramming of hematopoietic stem and progenitor cells to generate innate immune memory.
https://doi.org/10.7554/eLife.106610
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Daphne Superville
Adrian Liston
25 days ago
You can also save money by cutting-costs and preventing waste. We do a low of flow cytometry, and retitrated antibodies for overnight staining, reducing costs ~100-fold while improving signal-to-noise and reproducibility
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...
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Do more with Less: Improving High Parameter Cytometry Through Overnight Staining
Recent advances in flow cytometry have allowed high-dimensional characterization of biological phenomena, enabling breakthroughs in a multitude of fields. Despite the appreciation of the unique prope...
https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.589
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Daphne Superville
Waggoner Lab
23 days ago
@nature.com
News: Newfound immune cell in mice hints at why inflammation spikes with old age
@gvconroy.bsky.social
www.nature.com/articles/d41...
on
@nataging.nature.com
report
www.nature.com/articles/s43...
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Daphne Superville
Cell Reports
23 days ago
Single-cell transcriptomic reconstruction of the human hair cycle: Capturing the temporal dynamics of skin tissue remodeling
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Single-cell transcriptomic reconstruction of the human hair cycle: Capturing the temporal dynamics of skin tissue remodeling
Yokota et al. reconstruct a time course of the human hair cycle by temporally ordering single-cell transcriptomes of 19 skin samples, each containing a single hair follicle. This time course delineates dynamic changes in gene expression of 16 cell populations and in their interactions underlying the hair-cycle-dependent tissue remodeling.
http://dlvr.it/TMvDvv
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Daphne Superville
Aguirre-Ghiso Lab
24 days ago
Pioneering trial targeting dormant residual cancer cells by L. Chodosh, A. DeMichele et al.,
@penncancer.bsky.social
Proof-of-concept that targeting dormant RTCs in breast cancer survivors depletes MRD. NCT03032406. Congratulations for this work!
www.nature.com/articles/s41...
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Targeting dormant tumor cells to prevent recurrent breast cancer: a randomized phase 2 trial - Nature Medicine
A combination of mouse model data and data from a randomized phase 2 trial in patients with breast cancer in remission demonstrates feasibility, safety and a reduction in residual tumor cells followin...
https://www.nature.com/articles/s41591-025-03877-3
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Daphne Superville
Cell Reports
25 days ago
Distinct roles for NF-κB in hematopoietic stem cells and the bone marrow milieu in promoting hematopoietic aging
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Distinct roles for NF-κB in hematopoietic stem cells and the bone marrow milieu in promoting hematopoietic aging
Chia et al. find that inflammatory NF-κB signaling serves distinct functions within HSCs vs. the bone marrow milieu: HSC-intrinsic NF-κB promotes HSC quiescence and limits function, while an inflamed milieu directs HSC epigenomic reprogramming toward myeloid bias. Omics signatures of both HSC-intrinsic and milieu inflammation occur in aged mice and humans.
http://dlvr.it/TMrsDt
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Daphne Superville
Science Magazine
about 1 month ago
Dietary saturated fatty acids skew monocytes and macrophages in the lungs toward an inflammatory phenotype and exacerbate airway inflammation in mice, shows a study that decrypts the connection between diet and lung immune cell activation.
#ScienceTranslationalMedicine
https://scim.ag/3JzRozE
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Dietary saturated fatty acids promote lung myeloid cell inflammasome activation and IL-1β–mediated inflammation in mice and humans
Obesity-associated saturated long-chain fatty acids regulate lung macrophage phenotype and function at steady state and during lung inflammation.
https://scim.ag/3JzRozE
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Daphne Superville
Metastasis Research Society
about 1 month ago
🚨Excited for the 2nd MRS Early Career Research Virtual Meeting on Nov 18-19, 2025! Trainees & Junior Faculty (within 3 years of starting your lab), share your work! Abstract Deadline: Sept 12, 2025. Submit here:
bit.ly/47KLyp2
❗Free registration for MRS Members!
#MRS
#Research
#EarlyCareer
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Daphne Superville
bioRxiv Cancer Bio
about 1 month ago
Cancer cell phagocytosis induces an anti-inflammatory gene regulatory program in macrophages
https://www.biorxiv.org/content/10.1101/2025.08.18.670953v1
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Daphne Superville
Lorenz Adlung Lab
about 1 month ago
Classical macrophage activation reprograms nucleotide metabolism by suppressing de novo synthesis and enhancing salvage pathways (through nitric oxide...) @natmetabolism.nature.com
doi.org/10.1038/s422...
🧪 Great N&V's on metabolic immune control by @ryanlab.bsky.social
www.nature.com/artic...
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Classically activated macrophages undergo functionally significant nucleotide metabolism remodelling driven by nitric oxide
Nature Metabolism - John et al. show that upon classical activation, macrophages undergo nitric oxide-driven reprogramming of nucleotide metabolism, which affects immune functions and responses.
https://doi.org/10.1038/s42255-025-01337-3
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Daphne Superville
Nature Metabolism
about 1 month ago
RESEARCH | @simonsterson.bsky.social @katajistolab.bsky.social et al. Intestinal stem cells enriched for old mitochondria have enhanced ability to regenerate the epithelial niche 🧪
https://bit.ly/3HwPkb3
?utm_source=bluesky&utm_medium=social&utm_campaign=natmetab
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Old mitochondria regulate niche renewal via α-ketoglutarate metabolism in stem cells - Nature Metabolism
Andersson et al. show that intestinal stem cells enriched for old mitochondria are metabolically distinct and have enhanced ability to regenerate the epithelial niche.
https://bit.ly/3HwPkb3
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Daphne Superville
Ming Tommy Tang
about 1 month ago
scplotter provides a set of functions to visualize single-cell sequencing data in an easy and efficient way
github.com/pwwang/scpl...
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Daphne Superville
Eric Topol
about 1 month ago
What I love about interferons is their simplicity ;-) But seriously a great
@cellcellpress.bsky.social
new review of IFNs that are our 1st line of defense vs infections and have a critical role in many inflammatory an autoimmune diseases
www.cell.com/cell/fulltex...
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Daphne Superville
Andrei Goga
about 1 month ago
New work from stellar scientists Jeremy Williams and Roman Camarda. Many contributors including the amazing Zena Werb and Atul Butte Work explores how breast cancer cells interact directly with adipocytes via gap junctions, leading to lipid release.
@ctbatucsf.bsky.social
@ucsfcancer.bsky.social
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Tumor cell-adipocyte gap junctions activate lipolysis and contribute to breast tumorigenesis
Nature Communications - Breast cancer cells interact with neighbouring adipocytes, but the mechanisms are not fully understood. Here, the authors show that triple-negative breast cancer (TNBC)...
https://www.nature.com/articles/s41467-025-62486-3.epdf?sharing_token=aVBA3eu2kk0pCrGd0XpUbdRgN0jAjWel9jnR3ZoTv0Ngos7QJFm3WWMuuXx3Kn3OS39L1a0Uf1GlpxfQtUxAxP-0F6WMyru5-3PyxYRqqtDyOSJcFSRha2I8Cz8lyqU1MgPRDXJ_Xr5NOlXPoqM1ULez6M-R2Sa6D4xk4GLwUSk%3D
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Daphne Superville
Cell Reports
about 1 month ago
Analysis of nanomedicine primary tumor vs. metastasis targeting using clinical-stage core-crosslinked polymeric micelles
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Analysis of nanomedicine primary tumor vs. metastasis targeting using clinical-stage core-crosslinked polymeric micelles
Rizzo et al. describe an imageable breast cancer mouse model to study nanomedicine targeting to primary tumors vs. metastases. Clinical-stage polymeric micelles preferentially accumulate in metastases over healthy tissues, albeit less efficiently than in primary tumors, due to collagen crosslinking. Docetaxel-loaded micelles show superior efficacy and reduced toxicity compared to Taxotere.
http://dlvr.it/TMbKLW
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Daphne Superville
about 1 month ago
🚨Women with ER(–) breast cancer who took aprepitant (anti-nausea drug, NK1R blocker) had a 31% lower risk of metastasis or death (p<0.001) in large Norwegian study by Botteri & Chang. More doses = better survival 📉.Clinically validates our our work by
@veenapadmanaban.bsky.social
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Daphne Superville
bioRxiv Cancer Bio
about 1 month ago
Temporal Clonal Tracing and Functional Perturbation Reveal Niche-Adaptive and Tumor-Intrinsic IFNγ Dependencies Driving Ovarian Cancer Metastasis
https://www.biorxiv.org/content/10.1101/2025.08.13.669778v1
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Daphne Superville
Eric Topol
about 2 months ago
Platelets sequester and harbor cell-free tumor DNA, which could enhance our ability to make early, microscopic diagnosis of cancer
@science.org
science.org/doi/10.1126/...
science.org/doi/10.1126/...
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Daphne Superville
Nature Cell Biology
about 2 months ago
🍹Mondal et al. report that
#autophagy
inhibition promotes p63 activation and metastasis in
#BreastCancer
. This process depends on NBR1, which forms cytoplasmic p62/SQSTM1 condensates that sequester the ITCH ubiquitin ligase and prevents p63 degradation. 👉https://rdcu.be/eADAA
bit.ly/3HxkL4Y
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Autophagy-targeted NBR1–p62/SQSTM1 complexes promote breast cancer metastasis by sequestering ITCH - Nature Cell Biology
Mondal et al. report that autophagy inhibition promotes p63 activation and metastasis in breast cancer. This process depends on NBR1, which forms cytoplasmic p62/SQSTM1 condensates that sequester the ...
https://bit.ly/3HxkL4Y
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Daphne Superville
Eric Topol
about 2 months ago
When mRNA vaccines are wrongly attacked, this is one of many examples of what you're missing. A broad spectrum prevention strategy against viruses
www.science.org/doi/10.1126/...
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Daphne Superville
Nuria Lopez-Bigas
about 2 months ago
New paper from our lab - @bbglab.bsky.social. Oncodrive3D: fast and accurate detection of structural clusters of somatic mutations under positive selection
academic.oup.com/nar/article/...
Kudos to Stefano, Olivia,
@fmuinos.bsky.social
and Abel
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Oncodrive3D: fast and accurate detection of structural clusters of somatic mutations under positive selection
Abstract. Identifying the genes capable of driving tumorigenesis in different tissues is one of the central goals of cancer genomics. Computational methods
https://academic.oup.com/nar/article/53/15/gkaf776/8234003
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Daphne Superville
Waggoner Lab
about 2 months ago
Clone copy number diversity is linked to survival in lung cancer
@nature.com
@zaccasimo.bsky.social
@nickymcgranahan.bsky.social
www.nature.com/articles/s41...
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Daphne Superville
bioRxiv Cancer Bio
about 2 months ago
RIG-I-dependent tumor-intrinsic type I interferon signaling restricts growth in breast cancer 3D culture
https://www.biorxiv.org/content/10.1101/2025.08.10.669545v1
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Daphne Superville
Jose M. Adrover
about 2 months ago
Here's our take on how neutrophils can be a critical link between cancer and cardiovascular disease! "Heart of the matter: Neutrophils, cancer, and cardiovascular disease", just published
@jem.org
with Saira Ambreen, Afshan McCarthy and
@drusqui.bsky.social
rupress.org/jem/article/...
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Heart of the matter: Neutrophils, cancer, and cardiovascular disease | Journal of Experimental Medicine | Rockefeller University Press
Cancer and cardiovascular disease are the leading causes of death worldwide. Cancer patients display an abnormally elevated burden of cardiovascular diseas
https://rupress.org/jem/article/222/9/e20242402/278190/Heart-of-the-matter-Neutrophils-cancer-and
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Daphne Superville
Santiago Carmona 🧬 🖥️ 🧑🏾🔬
about 2 months ago
Foundation Model Attributions Reveal Shared Inflammatory Program Across Diseases
www.biorxiv.org/content/10.1...
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Foundation Model Attributions Reveal Shared Inflammatory Program Across Diseases
Determining a gene’s functional significance within a specific cellular context has long been a challenge. We introduce a framework for quantifying gene importance by leveraging attributions learned b...
https://www.biorxiv.org/content/10.1101/2025.06.14.659567v2
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Daphne Superville
Nathan Reticker-Flynn
about 2 months ago
Interested in studying lymph node metastasis? Check out our protocol by Cort Breuer out today in
@natprot.nature.com
bsky.app/profile/nat...
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Nature Protocols (@natprot.nature.com)
New Article! Spontaneous and experimental models of lymph node metastasis https://bit.ly/4fzWoAj
https://bsky.app/profile/natprot.nature.com/post/3lwbhu2ukuc2e
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Daphne Superville
We Are R-Ladies
about 2 months ago
I love watching short
#rstats
screencasts so have been making tips and tricks videos and sharing them on YouTube recently. Many of my videos showcase my favourite R packages. I am talking about data viz today so the package of the day today is ggeasy.
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Daphne Superville
Aguirre-Ghiso Lab
about 2 months ago
Thrilled to share our first clinical trial paper on prostate cancer cell dormancy induction using an epigenetic and differentiation strategy. This was a strong team effort between physicians and basic scientists leading to this innovative clinical trial.
www.medrxiv.org/content/10.1...
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A Pilot Study of the Combination of 5-Azacitidine and All-trans Retinoic Acid in Biochemically Recurrent Prostate Cancer.
Purpose: Biochemical recurrence (BCR) after definitive local therapy remains a major clinical challenge in prostate cancer (PCa), with heterogeneous disease trajectories and few established strategies...
https://www.medrxiv.org/content/10.1101/2025.08.11.25333316v1
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Daphne Superville
Waggoner Lab
about 2 months ago
NK cells mediate preventive efficacy of intravenous BCG against lung metastasis in mice
www.nature.com/articles/s41...
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NK cells mediate preventive efficacy of intravenous BCG against lung metastasis in mice - Cancer Gene Therapy
Cancer Gene Therapy - NK cells mediate preventive efficacy of intravenous BCG against lung metastasis in mice
https://www.nature.com/articles/s41417-025-00948-y
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