Daphne Superville
@dasuperville.bsky.social
📤 102
📥 211
📝 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
9 months ago
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reposted by
Daphne Superville
Cell Reports Medicine
2 days ago
Online now: Mutational landscape of normal breast tissues adjacent to invasive breast cancer
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Mutational landscape of normal breast tissues adjacent to invasive breast cancer
Suwalska et al. show that cancer-adjacent normal breast tissues share genomic alterations with cancer, and many changes in cancer-relevant genes arise from specific combinations of germline polymorphisms. This supports gradual mutation-driven malignant transformation of normal cells and suggests context-dependent co-oncogenic function for common and rare germline polymorphisms.
http://dlvr.it/TQFxrz
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reposted by
Daphne Superville
Barbara Marte
4 days ago
new out in Nature
www.nature.com/articles/s41...
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Nutrient requirements of organ-specific metastasis in breast cancer - Nature
How the complex interplay between multiple nutrients within the microenvironment dictates potential sites of metastatic cancer growth is explored.
https://www.nature.com/articles/s41586-025-09898-9
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Daphne Superville
Arjun Raj
13 days ago
Blog post: Just quit Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com/pub/arjunraj...
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Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.
https://open.substack.com/pub/arjunrajlab/p/just-quit?r=37ev25&utm_medium=ios
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Daphne Superville
Ivan Zanoni
15 days ago
#WeekendRead
!
#NeutrophilPower
!
@drusqui.bsky.social
Aroca &co show
@jem.org
that neutrophil intrinsic circadian clock can be exploited by targeting CXCR4 to decrease vascular & myocardial damage by relocating neutrophils within the wound core, thus sparing injury to healthy neighboring cells!
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A circadian checkpoint relocates neutrophils to minimize injury
Aroca-Crevillén et al. identify a circadian checkpoint in neutrophils, mediated by the CXCL12–CXCR4 axis, that limits tissue injury by inhibiting their int
https://doi.org/10.1084/jem.20250240
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Daphne Superville
Cell Reports
25 days ago
eIF3d and eIF3e mediate selective translational control of hypoxia that can be inhibited by small molecules
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eIF3d and eIF3e mediate selective translational control of hypoxia that can be inhibited by small molecules
Purdy et al. report that eIF3e/eIF3d are required for hypoxia-induced selective mRNA translation and induction of pro-metastatic phenotypes. eIF3e and eIF3d RNA signatures correlate with worsened overall survival in patients with breast cancer, and the acute translational hypoxic response mediated by eIF3e/eIF3d can be inhibited by novel small molecules.
http://dlvr.it/TPtlvx
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Daphne Superville
Cancer Cell
27 days ago
Online Now: IL-36γ armored CAR T cells reprogram neutrophils to induce endogenous antitumor immunity
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IL-36γ armored CAR T cells reprogram neutrophils to induce endogenous antitumor immunity
Zuo et al. demonstrate IL-36γ armored CAR T cells reprogram neutrophils with antigen-presenting and tumoricidal functions, inducing durable antitumor efficacy in the absence of lymphodepletion through activating endogenous immune effectors, which represents a broadly applicable strategy to overcome key barriers to adoptive cell therapies for solid tumors.
http://dlvr.it/TPrkHK
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Daphne Superville
Fabian Theis
27 days ago
🚀 New preprint! The Human Cytokine Dictionary - 9.7M cells, 12 donors, 90 cytokines - our largest human single-cell perturbation atlas yet. Users can map cytokine activity in their own data. Huge thanks to Lukas, Sören, Larsen, Parse Bio & Seelig lab! 🔗
www.biorxiv.org/content/10.6...
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Daphne Superville
Fabian Theis
about 1 month ago
Nature Methods names AI agents a “Method to Watch”! We've started building active-learning loops with perturbation models, where AI proposes experiments & data closes loop. Supplying such models to agents could transform exp design into theory search.
www.nature.com/articles/s41...
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Artificial intelligence agents for biology - Nature Methods
Artificial intelligence agents may have a transformative effect on how biological research is performed.
https://www.nature.com/articles/s41592-025-02958-y
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Daphne Superville
Nature Metabolism
about 1 month ago
RESEARCH | L Shen, W Zhu, L Qin, M Lu et al (Fudan U, CAS; CN) 🧪 Acetate accumulation and metastasis of hepatocarcinoma cells is driven by a metabolic interaction involving HCC-derived lactate and acetate secretion from tumour-associated macrophages
www.nature.com/articles/s42...
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Tumour-associated macrophages serve as an acetate reservoir to drive hepatocellular carcinoma metastasis - Nature Metabolism
Acetate accumulation and metastasis of hepatocarcinoma cells is driven by a metabolic interaction involving HCC-derived lactate and acetate secretion from tumour-associated macrophages.
https://www.nature.com/articles/s42255-025-01393-9
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Daphne Superville
Cancer Cell
about 1 month ago
Distinct T cell functions enable efficient immunoediting and prevent tumor emergence of developing sarcomas
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Distinct T cell functions enable efficient immunoediting and prevent tumor emergence of developing sarcomas
Cheung et al. describe efficient T cell control of nascent neoantigen+ and nearby neoantigen-negative sarcoma cells, underlying a ∼50% reduction in tumor penetrance. This otherwise imperceptible immunoediting process is revealed by time-resolved profiling of autochthonously arising, muscle-derived sarcoma cells expressing fluorescent reporter-embedded model T cell antigens within the native tissue environment.
http://dlvr.it/TPmDyT
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Daphne Superville
Waggoner Lab
about 1 month ago
Somatic evolution following cancer treatment in normal tissue
@nature.com
@nickymcgranahan.bsky.social
@ucl.ac.uk
@crick.ac.uk
@charlesswanton.bsky.social
www.nature.com/articles/s41...
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Daphne Superville
Waggoner Lab
about 1 month ago
Review: Neutrophil extracellular traps in cancer: immune modulation, therapy resistance, and the dilemma of targeting
www.nature.com/articles/s41...
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Daphne Superville
Cancer Cell
about 1 month ago
Online Now: When blood mutations turn beneficial
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When blood mutations turn beneficial
Clonal hematopoiesis (CH), an expansion of hematopoietic clones harboring somatic mutations, is common in patients with solid tumors and associates with poor outcomes. In this issue of Cancer Cell, a study shows that, in response to immunotherapy, TET2-mutant CH enhances macrophage antigen presentation and CD8⁺ T cell activation, thereby improving therapeutic efficacy.
http://dlvr.it/TPhrmN
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reposted by
Daphne Superville
Chris McGinnis
about 1 month ago
Excited to present our newest pre-print, “Bispecific T cell engagers control solid tumors through clonal replacement and IL2-driven effector differentiation of CD8 T cells.”
www.biorxiv.org/content/10.6...
Fantastic collaboration b/n the Satpathy, Sage, and Garcia labs at Stanford
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reposted by
Daphne Superville
Barbara Marte
about 1 month ago
and the Research Briefing to go with it
www.nature.com/articles/d41...
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Order in which cancer-driving mutations occur affects the chance of tumour development
Randomly acquired mutations face strong negative selection, except on certain cancer-promoting backgrounds.
https://www.nature.com/articles/d41586-025-03748-4
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reposted by
Daphne Superville
Cell - a Cell Press journal
about 1 month ago
Now online! The effect of shingles vaccination at different stages of the dementia disease course
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The effect of shingles vaccination at different stages of the dementia disease course
A natural experiment found that herpes zoster vaccination reduced the occurrence of mild cognitive impairment and deaths due to dementia, indicating that the vaccine may slow the progression of dementia throughout its clinical disease course.
http://dlvr.it/TPcFJ6
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reposted by
Daphne Superville
Giorgio Gilestro
about 1 month ago
@nature.com
asked me to write an op-ed on the perspective of the AI reviewing process, prompted by the recent partnership between
@biorxivpreprint.bsky.social
and
@qedscience.bsky.social
Hope my perspective adds value to the conversation.
www.nature.com/articles/d41...
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AI reviewers are here — we are not ready
Artificial intelligence promises rapid and polite feedback on papers — but we must first review the reviewer.
https://www.nature.com/articles/d41586-025-03909-5
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Daphne Superville
Waggoner Lab
about 2 months ago
Immunological surveillance against cancer across mammals (MHC-I)
@natcomms.nature.com
@evozoodeb.bsky.social
www.nature.com/articles/s41...
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reposted by
Daphne Superville
Waggoner Lab
about 2 months ago
Unanticipated role for PCSK9 in innate immune regulation leads to novel cancer immunotherapy approach of silencing PCSK9 to reshape spatiotemporal activation of STING
@natcomms.nature.com
www.nature.com/articles/s41...
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reposted by
Daphne Superville
RyanLab_TCD
about 2 months ago
📢Last 2 weeks of
#immunometabolism
discoveries
@biomednews.bsky.social
⬇️⬇️
biomed.news/bims-imicid/...
biomed.news/bims-imicid/...
Exciting to have a paper in the collection! An inherited mitochondrial DNA mutation remodels inflammatory cytokine responses in macrophages and in vivo in mice
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Daphne Superville
Cell - a Cell Press journal
about 2 months ago
Now online! Macrophage-targeted immunocytokine leverages myeloid, T, and NK cell synergy for cancer immunotherapy
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Macrophage-targeted immunocytokine leverages myeloid, T, and NK cell synergy for cancer immunotherapy
MiTEs are myeloid-targeted immunocytokine prodrugs that block TREM2+ tumor-associated macrophages while activating cytotoxic lymphocytes via TME-specific IL-2 activity, eliciting strong anti-tumor efficacy in preclinical models with minimal systemic toxicity.
http://dlvr.it/TPMNJl
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Daphne Superville
Waggoner Lab
about 2 months ago
IFN-I signaling boosts salivary gland regeneration after irradiation
@davidecinat.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
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reposted by
Daphne Superville
Immunity
about 2 months ago
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Tame the Hydra’s head: Targeting bone marrow maladaptive myelopoiesis to reverse macrophage-mediated immunosuppression in cancer
Immunosuppressive monocyte-derived macrophages are key targets in cancer therapy; however, the mechanisms of their replenishment and functional plasticity remain elusive. In a recent issue of Nature, Hedge et al. challenge the conventional view that immunosuppressive macrophages are acquired exclusively through tumor microenvironment reprogramming; instead, their study demonstrates that the developmental fate of these macrophages is predisposed in the bone marrow.
http://dlvr.it/TPHWhq
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reposted by
Daphne Superville
Arjun Raj
about 2 months ago
Also, here’s an accessible video intro:
add a skeleton here at some point
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reposted by
Daphne Superville
Ivan Zanoni
about 2 months ago
#WeekendRead
!
#EveryCellIsAnImmuneCell
! Riedel, Mattavelli, Helal &co show
@cp-immunity.bsky.social
that fibroblasts in breast cancer metastatic lymph nodes sense tumor-derived TLR4 agonists to attract monocytes & form an immunosuppressive niche, favoring lung metastasis!
dlvr.it/TPCYjz
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A TLR4-dependent fibroblast-monocyte axis in tumor-draining lymph nodes contributes to metastasis in triple-negative breast cancer
Triple-negative breast cancer (TNBC) is characterized by high risks of relapse or metastatic disease. Mattavelli et al. identify a chemokine axis that recruits immunosuppressive monocytes to tumor-dra...
http://dlvr.it/TPCYjz
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Daphne Superville
Immunity
about 2 months ago
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Myeloid cells mediate interferon-driven resistance to immunotherapy in advanced renal cell carcinoma
Bi et al. describe cell-type-specific transcriptional signatures of interferon (IFN) signaling in renal cell carcinoma (RCC) tumors and examine effects on immunotherapy outcomes. They find that myeloid IFNγ signaling, but not tumor IFNγ signaling, predicts poor outcomes in clinical trial cohorts, pointing to myeloid cells as mediators of IFN-driven immunotherapy resistance in RCC.
http://dlvr.it/TPFqml
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reposted by
Daphne Superville
Cell Reports Medicine
2 months ago
Online now: The tumor microenvironment of 14,837 breast cancers is associated with clinical outcome independently of genomic subtypes
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The tumor microenvironment of 14,837 breast cancers is associated with clinical outcome independently of genomic subtypes
Tu et al. present a systematic analysis of the tumor microenvironment across 14,837 breast cancers, identifying distinct cellular patterns that predict disease-specific survival independently of genomic and intrinsic subtypes. Characterizing microenvironment composition may provide critical prognostic markers that can complement current molecular classification for treatment selection and preventing recurrence.
http://dlvr.it/TPCXS1
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reposted by
Daphne Superville
Immunity
2 months ago
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A TLR4-dependent fibroblast-monocyte axis in tumor-draining lymph nodes contributes to metastasis in triple-negative breast cancer
Triple-negative breast cancer (TNBC) is characterized by high risks of relapse or metastatic disease. Mattavelli et al. identify a chemokine axis that recruits immunosuppressive monocytes to tumor-draining lymph nodes. By co-targeting this recruitment, the TNBC response to immune checkpoint blockade is augmented and metastasis to the lung is reduced.
http://dlvr.it/TPCYjz
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reposted by
Daphne Superville
David Usharauli
2 months ago
Interleukin-1β (IL-1β) is secreted primarily by dying monocytes rather than by live bystander monocytes, challenging established models.
#cryopyrin
#pyrin
#immunology
#science
buff.ly/2cBb3sk
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Single-cell analysis reveals cell death as driver of NLRP3-mediated secretion of IL-1β in human monocytes - Nature Immunology
Lamkanfi, Shirasaki, Izawa and colleagues show that IL-1β release in human monocytes stimulated with lipopolysaccharide or carrying NLRP3 activatory mutations is mostly restricted to cells undergoing…
https://buff.ly/2cBb3sk
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reposted by
Daphne Superville
UChicago Cancer
2 months ago
📕New in
Journal of Experimental Medicine
: Chen et al., show that radiotherapy may promote metastasis by upregulating YTHDF2 in dendritic cells, impairing MHC-1 cross presentation and CD8+ T cell activation.
Ludwig Cancer Research
https://ow.ly/BAeq50Xown3
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Daphne Superville
Journal of Experimental Medicine
2 months ago
Arja Ray,
@maxkrummel.bsky.social
et al. show that targeting CD206⁺
#macrophages
disrupts the establishment of a key antitumor immune axis.
rupress.org/jem/article/...
📘 In
#cancer
#immunotherapy
collection:
rupress.org/jem/collecti...
#SITC25
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reposted by
Daphne Superville
Cell - a Cell Press journal
2 months ago
Now online! StealTHY: An immunogen-free CRISPR platform to expose concealed metastasis regulators in immunocompetent models
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StealTHY: An immunogen-free CRISPR platform to expose concealed metastasis regulators in immunocompetent models
By sidestepping Cas9 immunogenicity, the StealTHY CRISPR platform enables immune-compatible in vivo genetic screens, directly translatable to humanized cancer models. Using this immune-stealth strategy allows for the discovery of metastatic drivers and reveals the AMH-AMHR2 axis as a clinically actionable pathway for dampening carcinoma metastasis.
http://dlvr.it/TP7fS8
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Daphne Superville
Nature Reviews Immunology
2 months ago
Highlight of
@natimmunol.nature.com
paper by
@mas-g.bsky.social
@walmsley-lab.bsky.social
showing epigenetic reprogramming of neutrophils in response to hypoxia to reduce lung tissue damage
#immunosky
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Hypoxia-induced epigenetic reprogramming of neutrophil progenitors - Nature Reviews Immunology
Sanchez-Garcia et al. report that systemic hypoxia-induced epigenetic reprogramming of neutrophil progenitors in the bone marrow reduces their effector function to limit lung tissue damage.
https://www.nature.com/articles/s41577-025-01244-4?utm_source=bluesky&utm_medium=social&utm_campaign=nri
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Daphne Superville
David Grimm
2 months ago
Known as a “lip out” or the “golfer’s curse,” the sometimes strange behavior of golf balls has bedeviled players for centuries. Now, physicists have figured out how they happen. Just don't expect the discovery to improve your game... Fun story by
@annademming.bsky.social
for
@science.org
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Have physicists finally solved the ‘golfer’s curse’?
Team says it has hit on an explanation for heartbreaking “lip outs”
https://www.science.org/content/article/have-physicists-finally-solved-golfer-s-curse
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reposted by
Daphne Superville
Christian Frezza
2 months ago
www.nature.com/articles/s41...
Lymph node environment drives FSP1 targetability in metastasizing melanoma
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Lymph node environment drives FSP1 targetability in metastasizing melanoma - Nature
Targeting FSP1 in lymph nodes has considerable potential for blocking melanoma progression.
https://www.nature.com/articles/s41586-025-09709-1
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reposted by
Daphne Superville
bioRxiv Immunology
2 months ago
Chronic sensing of host-derived lipids is an all-in-one signal that primes and activates NLRP3.
https://www.biorxiv.org/content/10.1101/2025.10.29.685328v1
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reposted by
Daphne Superville
Waggoner Lab
3 months ago
Acute hypoxia drives long-term dysfunctional neutrophil immunity mediated by loss of the histone modification H3K4me3 in neutrophil progenitor populations
@natimmunol.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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Daphne Superville
Nature Reviews Immunology
3 months ago
NEW Perspective by
@alazozcan.bsky.social
, Tommaso Vicanolo, Veronique Angeli, Yuval Rinkevich &
@drusqui.bsky.social
presents a model of immune cells as architects of tissue barriers, by depositing matrix components or by interactions with structural cells and the ECM
#structuralimmunity
#immunosky
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Structural immunity: immune cells as architects of tissue barriers - Nature Reviews Immunology
This Perspective presents a framework of ‘structural immunity’ that positions immune cells as architects of tissue structure. Beyond their roles in antimicrobial defence, we posit that immune cells co...
https://www.nature.com/articles/s41577-025-01230-w?utm_source=bluesky&utm_medium=social&utm_campaign=nri
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reposted by
Daphne Superville
bioRxiv Cancer Bio
3 months ago
A simple circuit to sustain intact tumor microenvironments for complex drug interrogations
https://www.biorxiv.org/content/10.1101/2025.10.26.684624v1
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Daphne Superville
Nature Metabolism
3 months ago
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A lactate–acetate interaction between macrophages and cancer cells drives metastasis
Nature Metabolism, Published online: 20 October 2025; doi:10.1038/s42255-025-01398-4Cancer cells often increase their uptake of acetate for acetyl-coenzyme A biosynthesis, a mechanism that facilitates cancer metastasis. We found that, in hepatocellular carcinoma, cancer cells induce acetate secretion from tumour-associated macrophages, driven by a cell–cell metabolic interaction involving lactate, the lipid peroxidation–aldehyde dehydrogenase 2 pathway and acetate.
https://bit.ly/4nkXEJF
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Daphne Superville
Molecular Cell
3 months ago
Conversations at the interface of metabolism and immunity
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Conversations at the interface of metabolism and immunity
The developing field of immunometabolism showcases how molecular insights inform on cellular-level responses to both internal context and environmental stimuli. For our focus issue on innate immunity, we spoke with researchers about the new doors they see opening in this area, from molecular crosstalk to therapeutic potential.
http://dlvr.it/TNpFdw
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Daphne Superville
Molecular Cell
3 months ago
Cells must vigilantly sense and respond to invading pathogens and danger signals. This focus issue explores the interconnected pathways of innate immunity from a mechanistic perspective, delving into molecular insights into defense responses across the tree of life.
www.cell.com/molecular-ce...
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Daphne Superville
Journal of Clinical Investigation
3 months ago
Citrullination in tumor immunity and therapy This Review by Michael R. Pitter & Weiping Zou discusses how citrullination regulates immune cell function within the tumor microenvironment and its potential as a target in cancer immunotherapy:
www.jci.org/articles/vie...
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Daphne Superville
Cancer Cell
3 months ago
CHI3L3+ immature neutrophils inhibit anti-tumor immunity and impede immune checkpoint blockade therapy in bone metastases
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CHI3L3+ immature neutrophils inhibit anti-tumor immunity and impede immune checkpoint blockade therapy in bone metastases
The impact of neutrophil maturation in refractory tumors such as bone metastases remains underexplored. Shi et al. demonstrate that predominant immature neutrophils inhibit anti-tumor immunity in the bone metastasis microenvironment through DKK1-CKAP4-CHI3L3 signaling. Restoring neutrophil maturation via DKK1 blockade reduces tumor burden and enhances ICB response in bone metastases.
http://dlvr.it/TNjczZ
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reposted by
Daphne Superville
Oded Rechavi
3 months ago
Here's the link to the system, try it!
qedscience.com
@qedscience.bsky.social
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q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
https://qedscience.com
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Daphne Superville
Ada Weinstock
3 months ago
Your immune system remembers skin inflammation long after it resolves because of
#interferon
alpha! Check out our new paper describing these findings just published at
@jimmunol.bsky.social
👇👇👇 It was amazing working on this with my role model
@drshrutinaik.bsky.social
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Interferon-sensitized hematopoietic progenitors dynamically alter organismal immunity
Abstract. Inflammation has enduring impacts on organismal immunity. However, the precise mechanisms by which tissue-restricted inflammation conditions syst
https://academic.oup.com/jimmunol/advance-article/doi/10.1093/jimmun/vkaf249/8283752?utm_source=authortollfreelink&utm_campaign=jimmunol&utm_medium=email&guestAccessKey=a22141ae-f0f3-4e74-bd9d-d27bc7961356
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reposted by
Daphne Superville
Cancer Cell
3 months ago
Subclonal immune evasion in non-small cell lung cancer
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Subclonal immune evasion in non-small cell lung cancer
Dijkstra et al. investigate whether individual cancer subclones differ in their immune evasion capacity. They establish organoids representing distinct subclones from multi-region lung cancer biopsies. Co-culture with T or NK cells shows heterogeneity in immune evasion across different tumor subclones, demonstrating that immune escape is shaped by subclonal evolution.
http://dlvr.it/TNfVCG
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Daphne Superville
Cell Reports Medicine
3 months ago
Online now: Optimized arenaviruses with tumor-tropic mutations promote safe anti-tumor efficacy via sustainable immune modulatory properties
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Optimized arenaviruses with tumor-tropic mutations promote safe anti-tumor efficacy via sustainable immune modulatory properties
Lang et al. show that tumor-tropic mutations in lymphocytic choriomeningitis virus (LCMV) enhance selective replication in cancer cells. The optimized LCMV promotes strong and sustainable anti-tumor efficacy and T cell-mediated immunity in murine models and is well tolerated in non-human primates, supporting its potential as a safe cancer immunotherapy.
http://dlvr.it/TNfWS7
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reposted by
Daphne Superville
Christian Frezza
3 months ago
Acidosis orchestrates adaptations of energy metabolism in tumors | Science
www.science.org/doi/10.1126/...
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Acidosis orchestrates adaptations of energy metabolism in tumors
Malignant tumors are characterized by diverse metabolic stresses, including nutrient shortages, hypoxia, and buildup of metabolic by-products. To understand how cancer cells adapt to such challenges, ...
https://www.science.org/doi/10.1126/science.adp7603
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reposted by
Daphne Superville
Cancer Cell
3 months ago
Online Now: Hidden spark: From cold to hot in BRAF colorectal cancer
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Hidden spark: From cold to hot in BRAF colorectal cancer
Immunotherapy as single-agent PD-1 blockade does not work for patients with microsatellite stable (MSS) colorectal cancer. In this issue of Cancer Cell, Morris et al. demonstrate that targeting the mitogen-activated protein kinase (MAPK) pathway in combination with immunotherapy can reprogram BRAF-V600E mutant MSS colorectal cancers toward immune responsiveness.
http://dlvr.it/TNbRx0
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