Presentation Order:
Alyssa
Hannah
Shah
Keaton
Time: biweekly, Wednesday 9:30-11:50
Writing 9:30-10:30---5-10 min/person
Research Presentation: 30 minutes talk+discussion
Hannah
Transcriptome-wide splicing network reveals specialized regulatory functions of the core spliceosome
Alternative RNA splicing is central to gene regulation and disease, yet the roles of individual spliceosome components remain poorly defined. Rogalska et al. systematically knocked down 305 genes encoding spliceosome subunits and regulatory proteins in human cancer cells, chosen for their known or predicted roles in RNA processing. Using siRNA-mediated knockdowns coupled with deep RNA sequencing, they profiled transcriptome-wide consequences of each perturbation. This large-scale screen revealed component-specific effects, with distinct factors driving exon skipping, intron retention, or alternative splice site selection. These findings highlight the intrinsic regulatory complexity of the spliceosome and provide a comprehensive resource to interrogate functional similarities, compensatory mechanisms, and cross-regulation among splicing factors. Although knockdown approaches may not fully capture complete loss-of-function or account for adaptive cellular responses, the dataset nonetheless offers a framework for dissecting splicing networks in physiology and disease and suggests new avenues for therapeutic targets.
Shah
Imidazole propionate is a driver and therapeutic target in atherosclerosis
Traditional risk factors (cholesterol, blood pressure) fail to fully explain or predict early atherosclerosis, and the role of gut microbiota ,and their derived metabolites, remain poorly understood. Inorder to fill the gap, the authors identified imidazole propionate (ImP) through untargeted metabolomics in Apoe⁻/⁻ mice, where ImP levels were elevated in high-cholesterol diet mice and correlated with aortic plaque burden, which was confirmed in two independent human cohorts (PESA, IGT) by using targeted metabolomics and vascular imaging, showing that plasma ImP is associated with subclinically active atherosclerosis. Then the authors tried to see the sole effect of ImP by administering ImP to chow-fed Apoe⁻/⁻ and Ldlr⁻/⁻ mice which induced plaques without altering cholesterol. Oil Red O staining, flow cytometry, and scRNA-seq of the aorta showed ImP drives inflammation throgh mTOR activation in myeloid cells. Further, genetic deletion of I1R (Imidazole-1-receptor) in myeloid cells or pharmacological blockade with the I1R antagonist AGN192403 abolished ImP and high cholesterol-induced atherosclerosis. The findings of the Imp is very interesting, but what is the microbial source of Imp and what enzymes produce it remain unknown which can provide a broader context in targeting components involved in the development of early atherosclerosis.
Alyssa
Despite the importance of pseudouridine (Ψ) and N1-methylpseudouridine (m1Ψ) RNA-modification in immune evasion for endogenous mRNA and mRNA technologies, the biochemical mechanism that prevents TLR7/8 activation has not been researched. Herein, the authors use cell-free systems with synthetic RNA to first demonstrate that Ψ prevents the endonuclease activity of RNAse T2, the lysosomal endonuclease critical for ssRNA recognition by TLR7/TLR8, by blocking the preferred cleavage site, guanosine – uracil (GU). Ψ has an additional electron that prevents the transferase activity of RNAse T2 from cleaving ssRNA. Ultimately, Ψ prevents RNAse T2 from generating TLR7 ligand, 2,3-cGMP. Interestingly, when U, Ψ, and m1Ψ are artificially introduced alone, they are able to bind TLR8, but only U and m1Ψ can activate it. This has implications for mRNA technologies, including the COVID-19 mRNA vaccine, which relies on m1Ψ mRNA. Overall, deeper understanding of this technology revealed a potential weakness and makes way for improvements.
Sean
Resistin-like molecule γ attacks cardiomyocyte membranes and promotes ventricular tachycardia
Ischemic heart disease is one the leading cause of death worldwide, as one of the major of the major risk factors being arrhythmias, like ventricular tachycardia (VTAC) and ventricular fibrillation (VFIB), post myocardial infarction (MI). Scientist have studied how Resistin-like molecule gamma (RELMgamma) causes membrane defects in distressed cardiomyocytes. Using cell culture and immunofluorescence, they demonstrated that these RELMgamma molecules target the externalized phosphatidylserine and cause pore to open ultimately lead to non-apoptotic cell death. In mouse models, resistin knockout following MI induction resulted in a twelve-fold reduction in VTAC compared to controls. The understanding of these mechanism open pathways to help prevent post MI arrythmias and lead way for possible clinical interventions involving therapeutist agents to alleviate arrhythmias in neutrophil-rich inflammation.
Hannah
Kupffer cell programming by maternal obesity triggers fatty liver disease
Early-life exposure to maternal obesity is known to increase chronic disease risk, but the cellular drivers remain undefined. This study presents the concept of liver-resident macrophages, known as Kupffer cells (KCs), as "intergenerational messengers" which undergo irreversible developmental programming through maternal obesity as they regulate the development of fatty liver disease (FLD) in offspring. By employing multi-omics approaches, including single-nucleus RNA and ATAC sequencing, lipidomics, and proteomics, combined with in vivo mouse models of maternal high-fat diet exposure, KC depletion, and genetic manipulation of HIF1-alpha signaling, researchers uncover how maternal obesity during pregnancy leads to FLD development in offspring. Results demonstrate that maternal obesity activates HIF1alpha in fetal KCs, leading to metabolic reprogramming and increased expression of lipid-promoting factors like apolipoproteins, which predispose offspring to FLD. The stability of the epigenetic cellular programming findings requires extensive research to be translatable into clinical therapies, however, the potential of therapeutic interventions targeting HIF1a pathways and cellular reprogramming to prevent FLD development as an early intervention strategy is appealing.
Shah
Mitochondria protect against an intracellular pathogen by restricting access to folate
Although mitochondrial metabolite production and high demands of consumption for these processes are well-known, whether host cells exploit mitochondrial metabolism to limit intracellular pathogens was unclear. Using human cancer cell lines, fibroblasts, and mouse models, the authors combined CRISPR knockouts, isotope tracing, proteomics and metabolomics to examine Toxoplasma gondii infection. They identified Activation Transcription Factor 4 (ATF4) as key regulator which increased mitochondrial DNA (mtDNA) copy number. Further They identified stress induced by infection resulted in activation of ATF4 through OMA1-HR1 pathway which then activated one-carbon metabolism enzymes MTHFD2 and SHMT2, which consume folate. Further using flow cytometry to track ATF4 KO cells, they found the pathogen proliferation was dependent on folate availability indicating a folate competition between the pathogen and mitochondria. Although the work highlights a novel mitochondrial defense mechanism based on folate competition, the exact parasite effectors that trigger the response remain unidentified and their use of cancer cell lines indicate untrustworthiness as these cell lines have modified mt-DNA copy numbers.
Sean
Platelets sequester extracellular DNA, capturing tumor-derived and free fetal DNA
Platelets have shown to play a fundamental role in immunity by their ability to sense pathogen-derived nucleic acids and internalizing DNA and RNA viruses, triggering inflammatory responses. However, whether platelets contain any DNA and if so, its origin have not been investigated. Using a panel of clinical participants and immunofluorescence techniques researchers found that platelet DNA (pDNA) can mirror cell-free DNA (cfDNA) allowing for platelets to be early biosensors for pregnancy testing or detecting cancer associated mutations. Importantly, this DNA is protected from degradation and can be released upon activation which speaks to the dynamic role’s platelets can have as DNA reservoirs. Platelets are abundant, easy to isolate and provided a protected DNA reservoir which can allow for clinical benefits down the line.
Alyssa
WSTF nuclear autophagy regulates chronic but not acute inflammation
Despite shared pathways/programs, chronic and acute inflammation are inherently different from inception, but the underlying mechanisms enforcing responses are unclear. Herein, the authors investigate nuclear autophagy (a process enriched in chronic inflammation), revealing the chromatin remodeling protein WSTF is depleted via autophagy-mediator ATG8 to chronic but not acute stimuli, permitting inflammatory phenotypes. WSTF in the nucleus binds NF-κB, facilitating target chromatin closure, leading to elevated cytokine secretion, as assessed by ATAC-Seq of replicative/oncogene-induced senescence. The authors experimentally blocked WSTF nuclear loss via overexpression or WSTF-peptides to specifically prevent ATG8 binding in models of metabolic-dysfunction-associated steatohepatitis (MASH), Osteoarthritis, and oncogene-induction. While enforced nuclear WSTF led to reduced immune infiltration and fibrosis in MASH and OA, long-term it led to widespread tumor foci in the otherwise controlled oncogene-induction model. Overall, WSTF nuclear localization determines NF-κB-mediated inflammation to chronic stimuli, making it a powerful and specific target of chronic disease for future therapeutic development.
Keaton
Glycosaminoglycan-driven lipoprotein uptake protects tumours from ferroptosis
Growing tumors take up exogenous lipids and face oxidative stress, which can trigger ferroptosis. The authors of this study sought to understand how cancer cells take up exogenous lipids and what advantages this may confer. To address these questions, the authors performed several CRISPR screens of metabolic genes in various cancer cell lines treated with human lipoproteins, and they evaluated cell proliferation, LDL uptake, and lipoprotein-dependent genes. Through these screens, they identified glutathione peroxidase 4 (GPX4) as essential for preventing ferroptosis in the absence of lipoproteins, and they also identified multiple genes in the glucuronic acid synthesis pathway as essential for mediating lipoprotein uptake. In vitro and in vivo functional studies revealed that lipoprotein uptake, especially of HDL, prevented ferroptosis and promoted tumor growth. Although the logic of this study felt scattered at times, it identified a novel set of pathways essential for growth and proliferation of various types of cancer.
Keaton
A single theory for the evolution of sex chromosomes and the two rules of speciation
Evolutionary biologists have struggled to unite two well-validated theories on the evolution of sex chromosomes: Haldane's Rule (hybrid inviability or sterility is more frequent in the XY sex), and the large X effect (X chromosomes have a disproportionate impact on hybrid fitness). The authors of this study recently proposed a unifying theory, involving 3 steps: 1) gene regulators on the Y chromosome evolve to become degenerate and are silenced, while X-linked regulators develop dosage compensation (DC), 2) X-linked regulators controlling DC genes continue to evolve and diverge between species, 3) when hybrids are formed, the XY sex loses more fitness because it inherits cis-regulators from one parent, but trans-regulators from both, resulting in mismatched gene regulation. To validate their theory, the authors simulated the independent evolution of 20 diploid species, simulating individual-based mutations, recombination, and gene expression regulation. Although the bulk of the data and methods are relegated to the depths of a lengthy supplement, this work appears to reconcile several long-standing questions in their field.
Sean
STAT5 and STAT3 balance shapes dendritic cell function and tumour immunity
Immune checkpoint blockade (ICB) is an effective cancer treatment, but its efficacy depends on dendritic cell-mediated tumor antigen presentation. In this study, researchers demonstrate the significant, opposing tumor-suppressing and tumor-promoting properties of STAT5 and STAT3. Using RNA-seq data from tumors before ICB treatment and correlating them with treatment outcomes, it was shown that patients with greater type 1 dendritic cell (DC1) maturation and a higher STAT5-to-STAT3 ratio had a better response to treatment and longer overall survival. They investigated whether STAT3 degradation could enhance DC1 maturation and allow for effective immune response. Using STAT3 knock-in and knock-out mice, they showed that STAT3 deficiency enhances T cell function, causing slower tumor progression in vivo. Based on these findings, they used a highly selective and effective PROTAC degrader of STAT3, SD-36, and observed reduced tumor volume across different tumors and an increase in immune activation markers. This evidence supports the potential for clinical trials that can test whether this treatment is effective in human patients.
Alyssa
A distinct priming phase regulates CD8 T cell immunity by orchestrating paracrine IL-2 signals
High affinity CD8 T cell clonal expansion and effector differentiation are crucial to an effective immune response; however, fundamental questions into early T cell interactions with antigen presenting cells (APCs) that determine T cell trajectories have not been answered. Herein, the authors carefully visualized CD8 T cell migration in lymph nodes up to 8 days post infection (d.p.i) using intravital microscopy (IVM), a high-resolution imaging of live tissues. Importantly, the authors discovered that antigen-specific (e.g. OT-1) T cells, that clonally expanded on 1 d.p.i., re-engaged with APCs on 3 d.p.i. through T cell receptor (TCR) binding. Interestingly, while TCR affinity did not determine initial clonal expansion on 1 d.p.i, only high affinity CD8 T cells re-engaged, which was associated with greater proportions of effector T cells on 8 d.p.i. Overall, the authors provided high-resolution support towards critical hypotheses in adaptive immunity and discovered a novel secondary engagement time for CD8 T cells that selects high affinity TCRs; understanding fundamental principles of immune cell dynamics is vital to improving vaccination and cancer immunotherapy.
Hannah
Clonal tracing with somatic epimutations reveals dynamics of blood ageing
Aging alters hematopoiesis by expanding certain stem cell clones, but current methods lack the ability to track both clonal identity and cell state in native human tissues without genetic manipulation. This study introduces EPI-Clone, a transgene-free, single-cell method based on single-cell targeted methylome analysis (scTAM-seq) that simultaneously profiles DNA methylation and surface proteins. It distinguishes stable CpGs for clone identification from dynamic CpGs reflecting differentiation states. Clonal assignments validated against LARRY lentiviral barcodes showed high accuracy in tracing stem and progenitor lineages. Applied to young and aged mice and humans across bone marrow, blood, and endothelium, EPI-Clone revealed that aging promotes expansion of dominant, myeloid-biased clones with reduced regenerative potential, while rare clones retain multipotency. In humans, both mutated and non-mutated clones show similar lineage biases, suggesting clonal expansion occurs via mutation-dependent and -independent mechanisms. Although the need for custom tissue-specific CpG panels limits generalizability, EPI-Clone enables scalable, high-resolution lineage and state mapping in aging hematopoiesis without genetic modification.
Shah
ROS transfer at peroxisome-mitochondria contact regulates mitochondrial redox
Although the relation between peroxisome dysfunction and mitochondrial oxidative stress has been well studied, the underlying mechanisms are unknown. Utilizing different human derived cancer cell lines, the authors used time lapse confocal microscopy, proximity labeling, gene knockouts and induced oxidative stress via rotenone and galactose, identified ACBD5 (peroxisome membrane protein) and PTPIP51 (outer mitochondrial membrane protein), providing physical contact between the two organelles. The results further showed the contact was triggered by mitochondrial oxidative stress which resulted in transfer of reactive oxygen species to peroxisome indicated by increased oxidation status and catalase localization in peroxisome. This transfer was shown to depend on direct interaction between the coiled-coil domains of ACBD5 and PTPIP51, as ACBD5 deletion mutants failed to form contacts, rescue mitochondrial oxidative stress, and impaired peroxisomal redox response under stress, while restoring contact rescued these phenotypes. Although the results seem important, the authors don't mention the exact triggering molecular mechanism; while the physiology of cancer cells varies from normal cells, the study needs to be further explored for more authentic results and applications.
Ash
Human neuron subtype programming via single-cell transcriptome-coupled patterning screens
Rohan
The expansion of human T-bethighCD21low B cells is T cell dependent
It was unclear which signals drive the abnormal development of T‑bet^high CD21^low B cells in human autoimmune diseases. This paper investigates that gap by combining gene expression (RNAseq), chromatin accessibility (ATACseq), cell culture experiments, and analysis of patients with single-gene immune defects. The authors show that T cell–derived signals—CD40L, IL‑21, and IFNγ—together with B cell receptor activation, are essential for these B cells to expand. In vitro cultures lacking any of these signals fail to produce the full T‑bet^high CD21^low phenotype, and patients with defects in those pathways have reduced numbers of these cells. Studying rare immunodeficiency patients confirmed that disrupting each signal blocks abnormal B cell expansion. These findings suggest that targeting CD40L, IL‑21, or IFNγ pathways could treat related autoimmune disorders, but further studies and clinical trials are needed to confirm effectiveness and safety.
Aarika:
IgG memory B cells expressing IL4R and FCER2 are associated with atopic diseases
While it was previously known that some IgG memory B cells are precursors of pathogenic IgE plasma cells, specific features of these memory cells were unknown. Using single-cell RNA sequencing of B cells from both healthy and atopic individuals, scientists identified a novel population of IgG memory B cells with type- 2 markers. The scientists found that these special type 2 IgG cells were more common in atopic patients than healthy ones. Furthermore, naive B cells in atopic patients had more CD23 (a type-2 marker) and were more sensitive to IL-4 and IL-13 signaling, indicating increased readiness to class switch to IgE plasma cells. When stimulated, the atopic type 2 cells produced more IgE antibodies as well.These findings help explain why atopic individuals produce excessive IgE in response to harmless environmental antigens. Scientists also hypothesized that there might be long lived allergen specific clones of the IgG cells which can cause persistence of allergic symptoms though a patient's lifetime.
Aria:
Rohan/Rahul
Aarika: Experimental rhinovirus infection induces an antiviral response in circulating B cells which is dysregulated in patients with asthma
https://pmc.ncbi.nlm.nih.gov/articles/PMC10138744/
While upper respiratory tract infections are normally harmless and asymptomatic, these viruses can trigger episodes in asthmatic patients. This study explored the cellular side of inflammatory responses in patients with asthma, and focused on additional functions of B cells beyond the more thoroughly studied antibody production. B cells purified from healthy and asthmatic patients were stimulated with RV and interferon-alpha (IFN-α). On day three of the infection the healthy B cells had upregulated antibody and antiviral genes, and increased production of the MX1 protein which produces antiviral responses. By day seven, expression of the protein IFI44L peaked, while levels of pro-inflammatory cytokines increased, indicating a shift from an antiviral to a more inflammatory response. However, some of the asthmatic patients’ B cells had a dysregulated response to IFN stimulation, including exaggerated expression of antiviral genes. The scientists hypothesized that this upregulation can end up decreasing the effectiveness of the response to the RV virus. The B cells were also found to contain RV RNA, suggesting that B cells are involved and even directly stimulated by the virus, and take a more active role in inflammation.
Aria: Critical roles of chronic BCR signaling in thedifferentiation of anergic B cells into age-associated Bcells in aging and autoimmunity
https://www.science.org/doi/epdf/10.1126/sciadv.adt8199
Age-associated B cells (ABCs) have been implicated in the pathogenesis of autoimmunity, prompting researchers to investigate whether ABCs originate from anergic B cells and identify the mechanism that drives this differentiation. They directed mouse models using HEL-specific MD4 x ML5 transgenic mice, which expressed a defined self-antigen and allowed for the tracking of anergic B cells. The researchers evaluated BCR signaling activity to determine if the self-antigen exposure was contributing to the ABC formation and also tested the inhibition of the signaling using Btk (Bruton’s tyrosine kinase) to observe if it could prevent the transition. This study suggests that consistent BCR involvement will differentiate anergic B cells into ABCs, concluding that targeting this signaling pathway may result in better treatment.
Keaton
BRAF oncogenic mutants evade autoinhibition through a common mechanism
The B-Raf (BRAF) proto-oncogenic kinase is one of the most commonly mutated genes in cancer and a major therapeutic target; however, the structural basis of BRAF activation in oncogenic mutants is unknown. The authors of this study used cryo-electron microscopy (cryoEM) to resolve the structure of wild-type BRAF as well as 3 distinct classes of oncogenic mutants, unexpectedly revealing that all 3 classes of mutants displayed similar conformational changes in the cysteine-rich domain (CRD) and kinase domain (KD). This conformation mimicked a pre-activated state where the CRD was released from an autoinhibitory pocket, freeing the KD to engage its substrate. The authors then used bioluminescence resonance energy transfer (BRET) to demonstrate that a drug targeting KD conformation restored interactions between the KD and the autoinhibitory pocket, highlighting the shared mechanism across the mutants. This study characterized a number of oncogenic BRAF mutants and identified a shared pathogenic feature which can be targeted for further therapeutic interventions.
Hannah
Obesity, a major risk factor for metabolic diseases such as type 2 diabetes and liver disease, demands deeper insight into the cellular stress responses and mitochondrial mechanisms that preserve energy homeostasis. This study identifies the cytosolic chaperone PPID as a key mediator of mitochondrial outer membrane (OMM) protein biogenesis, acting downstream of the ER stress sensor PERK. Using adipose-specific PERK knockout mice under high-fat diet stress, the authors observe impaired mitochondrial respiration and reduced levels of TOM70, an OMM import receptor, along with modest downregulation of PPID protein levels. They propose that PERK stabilizes PPID by preventing its lysine ubiquitination and that PPID promotes TOM70 insertion into the OMM. However, the functional evidence remains correlative and the mechanistic connection between PERK and PPID, as well as PPID's direct role in TOM70 insertion, is not fully established. While the proposed PERK–PPID–TOM70 axis is a conceptually intriguing model for ER-mitochondria communication, future studies are needed to clarify causality, assess physiological impact, and strengthen mechanistic insight.
Shah
Sex biased pathophysiology of the carotid stenosis has not been examined by prior studies at sub-cellular levels using single-cell RNA sequencing. Using smart-seq2 and FACS sorting of the human carotid plaque tissues from 15 patients with integration of 135 tissue-specific gene regulatory networks (GRNs) from STARNET study, they identified sex-biased subclusters with distinct phenotypes regardless of the similar major cell types. The results showed female subclusters exhibited osteogenic SMCs, inflammatory TREM1⁺/TREM2⁻ macrophages, and endothelial cells undergoing endothelial-to-mesenchymal transition, while males showed contractile and chondrogenic SMCs, angiogenic ECs, and remodeling macrophages. Integration with GRNs revealed GRN33, GRN122, and GRN174 as female-enriched inflammatory and immune-regulatory networks, while GRN195 and GRN177 were male-specific and linked to angiogenesis and SMC contractility. Further, functional assay of GRN195 in human aortic endothelial cells via overexpression of PLVAP and FAM110D showed altered cell proliferation, adhesion, and chromatin structure. The authors validated these GRNs in six independent human and mouse datasets revealing sex-specific molecular mechanisms in atherosclerosis, suggesting an appropriate therapeutic approach considering sex biases.
Gabo
Lysosome repair fails in ageing and Alzheimer’s disease
Researchers struggled to study the link between lysosomal failure and Alzheimer's disease due to a lack of realistic in-vitro models. Traditional models rely on differentiating induced pluripotent stem cells, but these lack epigenetic markers of age: crucial to studying Alzheimer’s disease. Transdifferentiation, a recent alternative, uses microRNA-induced conversion of patient-derived fibroblasts to neurons. However, this method still leads to partial resetting of the epigenome, as microRNA conversion induces a permissive chromatin environment. Chou et al. improved upon transdifferentiation by creating a technique that retains epigenetic information, utilizing neuronal-specific transcription factors rather than microRNA for conversion. Rigorous comparisons with animal models confirmed that neurons from aged and genetically predisposed Alzheimer’s patients retained key features needed to study lysosomal dysfunction, leading to a deeper understanding of lysosomal failure in Alzheimer’s disease.
Alyssa
Macrophages recycle phagocytosed bacteria to fuel immunometabolic responses
Multigenerational cell tracking of DNA replication and heritable DNA damage
Cellular heterogeneity stochastically arises within lineages and can drive cancer transformation, however, its study has been limited to retrospective analyses which cannot resolve the inciting factors nor when sister cell asymmetry emerges in subsequent generations. Herein, the authors detail a method for individual live cell tracking for a 70 hour timescale (encompassing up to 4 generations) to trace differences in cell cycling entry and DNA damage markers between sister cells following oncogene activation. The authors directly observe that the phase of the cell cycle that damage occurs determines sister cell asymmetry and the type of mutation incurred. While this study explores a powerful new method for multi-generational cell tracking of DNA damage markers, it cannot control for nor capture heterogeneity due to asymmetric protein distribution during mitosis. Further, this study is limited to a short timescale which may not encompass a realistic amount of time for DNA repair for all cell types. Overall, this method has potential to aid in future exploration into tumor heterogeneity to improve cancer eradication and treatment responses.
Shah
Diet outperforms microbial transplant to drive microbiome recovery in mice
Gut microbiome restoration after antibiotic disturbance remains an important clinical question. To investigate the question, the authors compared the efficiency of diet and fecal microbiota transplant (FMT) on microbiome recovery in mice. Using shotgun metagenomics, metabolomics, and metabolic modeling, the authors revealed that mice fed with fiber-rich regular chow (RC) diet showed rapid and robust recovery of microbial diversity, metabolic functions, and metabolite production while those on a Western-style diet (WD) showed prolonged dysbiosis, functional collapse, and impaired pathogen resistance. The results further showed that RC diet promoted microbial diversity by promoting syntrophic microbial interactions and ecological succession due to complex carbohydrates compared to WD which favored dominance by a single species with limited cooperation due to greater availability of simple sugars. The results also revealed FMT alone failed to rescue recovery under WD, highlighting the central role of dietary environment. This study challenges the concept of microbial transplantation alone can rescue microbial imbalances and reveals diet to be a primary therapeutic strategy for microbiome restoration.
Keaton
Selective inhibition of stromal mechanosensing suppresses cardiac fibrosis
During cardiac fibrosis, which is a key feature of heart failure, cardiac fibroblasts (CF) become activated by mechanical stiffening of the heart, leading them to lay down additional fibrotic extracellular matrix (ECM), further stiffening the heart in a pathogenic feedback loop. To identify drivers of this loop, the authors of this study cultured iPSC-derived CFs under a range of mechanical and TGFβ signaling activation or inhibition conditions, and both scRNAseq and immunostaining confirmed the importance of TGFβ and the YAP/TAZ mechanosensors in CF activation. Through scRNAseq meta-analysis, the authors identified the YAP/TAZ signaling mediator SRC as a disease-associated druggable target. To validate their findings, the authors employed a mouse transverse aortic constriction chronic heart failure model, finding that combination pharmacologic inhibition of TGFβ signaling and SRC improved cardiac function and returned CFs to quiescent states similar to those identified in their earlier scRNAseq analysis. Although these findings require further mechanistic investigation and in vivo validation, this study demonstrated therapeutic potential in disrupting the CF feedback loop.
Hannah
PRDM16-dependent antigen-presenting cells induce tolerance to gut antigens
This study addresses the unresolved question of which immune cell types mediate tolerance to food antigens, a critical process for preventing allergic and autoimmune responses. While previous work suggested a role for antigen-presenting cells (APCs) expressing the transcription factor RORγt in driving peripheral regulatory T cell (pTreg) development in response to gut microbes, their role in oral (food) tolerance was unclear. Using a combination of mouse genetics, single-cell transcriptomics, chromatin accessibility profiling, and immune assays, the authors identify a rare, myeloid-derived subset of tolerogenic dendritic cells (tolDCs) marked by PRDM16 and RORγt expression that are essential for inducing pTregs in response to dietary antigens. Mice lacking these tolDCs fail to develop oral tolerance and instead mount inflammatory Th2 responses, leading to enhanced allergic susceptibility. Parallel analyses of human gut and lymphoid tissues reveal a conserved population of PRDM16⁺RORC⁺ tolDCs, supporting their relevance across species. Future work must clarify the developmental origin and stability of these cells in humans, though their rarity and complexity pose key translational challenges.
Aish
Activation of lysosomal iron triggers ferroptosis in cancer
Alyssa
Transcriptional repression facilitates RNA:DNA hybrid accumulation at DNA double-strand breaks
RNA:DNA hybrids at DNA double-strand breaks (DSB) are an ill-defined phenomenon that’s impact on repair has been intensely debated. Herein, the authors track transcription and RNA polymerases recruitment at DSBs via nascent transcript sequencing, RNA-DNA hybrid sequencing, and ChIP-Seq of targeted DSB induction cell systems. In this way, the authors support that RNA:DNA hybrids are byproducts of translational repression, rather than enforced mediators of repair. Importantly, they espouse transcribing RNA binds to the template ssDNA during 5’ end resection and must be removed to maintain genomic integrity. Overall, the authors present the first high-resolution data of this phenomenon, supporting a fundamental theory of DNA repair effectiveness that is crucial to our basic understanding of the repair mechanism.
Multigenerational cell tracking of DNA replication and heritable DNA damage
Keaton
Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3
Regulatory T cells (Tregs) are essential modulators of immune function; however, ex vivo-induced Tregs lose their phenotype over time, limiting their utility in adoptive cell transfer studies. To identify determinants of Treg phenotypic commitment, the authors of this study performed a genome-wide CRISPR screen on human CD4 T cells, then measured FOXP3 expression via flow cytometry. In order to identify the transcriptomic networks controlled by the top candidate genes, the authors developed icCITE-seq, icChIP-seq, and icATAC-seq, allowing them to simultaneously measure protein expression of intracellular proteins with either mRNA or chromatin accessibility. They identified RBPJ as a regulator of Treg phenotypic commitment, which was confirmed by comparing RBPJ-KO Tregs to "natural" Tregs via RNA-seq and in a mouse model of graft-versus-host-disease. This study identified a novel regulator for Treg development, and the authors developed technical improvements that can enhance CRISPR screens in many additional contexts.
Hannah
Cell cycle duration determines oncogenic transformation capacity
A majority of cells with oncogenic mutations do not form tumors, yet the mechanisms underlying this resistance remain unclear. Researchers used single-cell RNA sequencing and cancer prone Rb- and p107-deficient mouse models to trace how oncogene-expressing cells in the retina, pituitary, and lung either transform or remain benign. By disrupting a key regulatory pathway of cell cycle progression, the SKP7-p27-CDK1/CDK2 pathway, the rate of cell division decreased, specifically lengthening the G1 phase, without triggering cancer hallmarks such as cell death or immune responses. This delay in the cell cycle prevented transformation, as cell failed to adopt the self-renewing, proliferative behaviors typical of tumors, despite carrying oncogenic mutations. Thus, temporal constraints in the cell cycle act as a critical tumor-suppressive mechanism by limiting the window in which oncogenic signals can take hold. Future work should investigate how these proliferative dynamics define transformation thresholds and whether similar mechanisms operate in other tissues or human cancers.
Aish
DNA-guided transcription factor interactions extend human gene regulatory code
While individual transcription factor binding has much evidence behind it, how pairs of transcription factors cooperate on DNA to control gene expression is undefined. To investigate this, the authors used a high-throughput CAP-SELEX assay to biochemically screen around 58,000 human TF-TF pairs for cooperative binding which revealed over 2,000 cooperative TF pairs and more than 1,100 new binding sites found in key cell-type-specific regulatory and developmental regions. Their findings show that DNA can mediate TF pair interactions, influencing cell fate even though the study does not take into account the effects of chromatin. Future tests in living cells can look into if TF pairs interact the same way in cells that contain chromatin.
Alyssa
Transcriptional repression facilitates RNA:DNA hybrid accumulation at DNA double-strand breaks
Shah
Proteostasis and lysosomal repair deficits in transdifferentiated neurons of Alzheimer’s disease
How lysosomal dysfunction contributes to Alzheimer’s disease (AD) in aged human neurons, remains a potential challenge till today. Going beyond traditional iPSC-derived neuron models, the authors generated transdifferentiated neurons (tNeurons) directly from aged and AD patient (both sporadic and familial) fibroblasts to preserve age-related vulnerabilities. Using proteomics, live-cell assays, and lysosomal markers, the authors revealed constitutive lysosomal damage and impaired ESCRT-mediated repair in AD neurons. The authors further showed that small molecules restoring lysosomal integrity reduced protein (amyloid β and tau) accumulation and cytokine secretion, suggesting novel therapeutic targets for AD. Although the significance of the mechanisms in the brain environment with complex tissue organization remains to be validated, this work establishes lysosomal repair failure as a promising avenue for intervention in Alzheimer’s disease.
Shah
Matrix-producing neutrophils populate and shield the skin
Neutrophils are not only immune defenders but also active producers of extracellular matrix (ECM) proteins such as collagen, elastin, fibronectin, and enzymes required for ECM maturation. The authors used multistep strategy combining omics, immunofluorescence and genetic modeling to examine the matrix producing neutrophils primarily localized in subepidermal region of the skin. The results revealed that ECM gene expression in neutrophils followed a circadian rhythm and was driven by TGFβ signaling via activation of SMAD3. Knockout of the TGFβ receptor or deletion of collagen in neutrophils resulted in the failure of neutrophils to produce ECM leading to weaker, more permeable skin and impaired collagen ring formation around wounds which facilitated bacterial invasion. Although the authors identified TGFβ signaling responsible for ECM production by neutrophils in the skin, the source of this signaling remains unclear which needs further exploration, particularly in the context of various diseases.
Hannah
This study addresses a major unresolved question in developmental cell biology: how early mammalian embryos, which lack centrosomes and efficient spindle assembly, maintain mitotic fidelity. Challenging the long-standing microtubule-centric model, the authors reveal that actin filaments independently organize chromosomes and regulate spindle size during early divisions. Using live imaging in mouse embryos, they uncover a contractile nuclear actin network that gathers chromosomes to the center via filament disassembly, and a branched perispindle actin cage that restricts spindle elongation—both critical for accurate mitosis. They also show that myosin-10 tethers chromosomes to actin cables in prophase, establishing spatial order before spindle formation. Although similar actin structures were observed in human embryos, the functional relevance in humans remains to be directly tested. These discoveries redefine the cytoskeletal logic of mitosis by positioning actin as a primary architect of chromosome segregation, opening new avenues for understanding aneuploidy, infertility, and early developmental failure in humans.
Alyssa
CTC1-STN1-TEN1 controls DNA break repair pathway choice via DNA end resection blockade
Homologous recombination (HR) and Nonhomologous DNA end joining (NHEJ) are antagonistic pathways of DNA repair; however, the exclusion mechanism is unknown. Herein, the authors used targeted point mutations and protein-protein interface prediction tools to provide high resolution interaction networks of major proteins and domains in HR and NHEJ. They resolve CTC1-BLM interactions as the major determinant of HR vs. NHEJ and that loss of this interaction by point mutation can increase HR in BRCA1-deficient cancer cells. Overall, this work can be expanded to better understand BRCA1-deficient cancer cell drug resistance.
Aish
Spatially clustered type I interferon responses at injury borderzones
Myocardial infarction triggers harmful inflammation that contributes to heart damage, but how this inflammation is initiated and organized apart from immune cell involvement remains unclear. Using spatial transcriptomics in mice and humans found that cardiomyocytes initiate a Type I interferon response at the injured borderzone which formed clusters of interferon-induced cells (IFNICs). These clusters are caused by stress, DNA leakage, and Irf3 activation. Notably, Irf3 activation in cardiomyocytes disrupts the normal function of fibroblasts which is essential for effective cardiac muscle regeneration. By knocking out Irf3 in specific cell types, it showed that Irf3 cardiomyocytes cause sterile inflammation. Targeting Irf3 activity in cardiomyocytes could help stop harmful inflammation without suppressing the whole immune system. The authors suggest that future work should explore cardiomyocyte-specific delivery of Irf3 inhibitors in larger animal models or human trials.
Keaton
irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein assemblies on RNA
Current technologies for identifying RNA-binding protein (RBP) interactions with RNA are based on cross-link immunoprecipitation followed by RNA sequencing (CLIP-seq), which can identify RNA motifs bound to individual proteins, but cannot capture protein complexes. The authors of this study developed two novel techniques to study protein complexes bound to RNA. The first technique, called irCLIP, employs crosslinking followed by ligation to infrared dye adapters and mass spectrometry to identify RNA-bound RBP complexes. The second technique, Re-CLIP, uses two rounds of irCLIP precipitation followed by RNA-seq to identify RNA molecules that are bound to multiple RBPs. As a proof-of-concept, the authors applied these techniques to investigate EGFR signaling in an epithelial cell line, revealing dynamic shifts in RBP complex composition and identifying a novel interaction between UPF1 and HNRNPC RBPs to surveil EGFR-regulated mRNAs. IrCLIP and Re-CLIP are powerful new tools that will enable exciting discoveries of RNA-protein complex interactions.
Hannah
Regulated somatic hypermutation enhances antibody affinity maturation
High-affinity antibodies are critical for vaccine efficacy, but how B cells regulate mutation rates during affinity maturation remains unclear. This study tested the hypothesis that B cells dynamically regulate somatic hypermutation (SHM) based on B cell receptor (BCR) affinity to optimize antibody evolution. A computational model predicted that high-affinity B cells should reduce SHM to preserve beneficial mutations, a prediction the authors tested in mice immunized with SARS-CoV-2 spike and NP-OVA. They found that high-affinity B cells received more T follicular helper cell support, leading to increased c-Myc expression and faster cell cycle progression—specifically shortening G0/G1, the phase in which SHM occurs. As a result, these cells divided more rapidly but acquired fewer mutations per division, supporting an affinity-dependent regulation of SHM. While this regulated mutation strategy allows B cells to balance diversification and conservation, it may also reduce the generation of broad antibody diversity, potentially limiting responses to novel pathogens or increasing the risk of autoreactivity.
Shah
Transient silencing of hypermutation preserves B cell affinity during clonal bursting
During clonal expansion in germinal centers (GCs), B cells risk acquiring deleterious mutations that can compromise antibody affinity. This study investigates how B cells preserve affinity during rapid clonal bursts by transient silencing of Somatic Hypermutation Mutation(SHM). Using AID-Brainbow mice, immunoglobulin gene sequencing, building phylogenetic trees, and computational simulations, the authors found large groups of genetically identical B cell populations with minimal SHM in microdissected GCs following post-immunization. Further, using AID-GFP reporter mice and single-cell analysis, the authors found no signs of downregulation of SHM machinery. By employing a CDK2 (cyclin-dependent kinase 2) activity reporter, they demonstrated that SHM is confined to a short-lived G0-like phase which is bypassed during rapid cycling. Finally, image-based sorting confirmed that SHM predominantly occurs in B cells with low CDK2 activity. To conclude, the authors used mouse models with the stabilized mutatant form of cyclin D3 which resulted in continuous B cell cycling with decreased SHM rates per cell division indicated a possible role for cyclin D3 in bypassing G0-like phase during clonal bursting.
Keaton
Cytoplasmic flow is a cell size sensor that scales anaphase
During rapid cell division states such as early embryogenesis, daughter cells each are only half the size of the parent; however, the factors controlling the corresponding decrease in nuclear size during anaphase nuclear envelope reformation (NER) are unknown. To answer this question, the authors of this study performed systematic live imaging and particle imaging velocimetry (PIV) analysis of rapidly dividing early zebrafish embryos, revealing that NER timing did not scale with cell size during anaphase, but chromosome velocity and positioning did. The authors hypothesized that cytoplasmic flows could be controlling this scaling, and further PIV studies of dynein-inhibited cells found that the flows were created by dynein dragging bulk cargo. Finally, fluid mechanics modeling that suggested that boundary effects could determine cytoplasmic flow scaling, which the authors confirmed by performing PIV on confined and reduced-size embryos. This study revealed a simple mechanism controlling nuclear envelope reformation during mitosis, and further research could investigate the role of cytoplasmic flow in determining size scaling in other aspects of development.
Alyssa
Growth factor-triggered de-sialylation controls glycolipid-lectin-driven endocytosis
Glycolipid-lectin (GL-Lect) endocytosis is crucial for internalization of various integrin cargoes but whose dynamics remain poorly defined. Herein, the authors identify Galectin 3 (Gal3) GL-Lect-driven endocytosis is sensitive to epidermal growth factor (EGF) signaling via pH-regulated Neuraminidase 1 (Neu1) de-sialylation. The authors utilize chemical and genetic inhibition to reveal EGF-driven Na+/H+ transporter NHE1 activation is necessary for Neu1 to remove sialic acid on β1 integrin to allow Gal3 binding and endocytosis. They further implicate this circuitry in osteoclast bone reabsorption and invasive cell migration. Overall, this work outlines an important role of Neu1 that supports therapeutic application of neuraminidase inhibitors in cancer metastasis and bone integrity.
Hannah
Hepatic stellate cells control liver zonation, size and functions via R-spondin 3
Chronic liver disease causes over 2 million deaths globally each year, yet most treatments target fibrosis without preserving liver function. During chronic liver disease, hepatic stellate cells (HSCs) are classically known for their pathogenic role in fibrosis through activation and collagen deposition, however, their physiological functions in the healthy liver remain less understood. This study investigated the fibrosis-independent role of HSCs using genetic depletion and conditional knockout models targeting RSPO3, a WNT signaling amplifier secreted by HSCs, to assess the impact of HSC loss and the specific role of RSPO3 in liver homeostasis. The results revealed that while HSC depletion disrupted liver function entirely, conditional knockout of RSPO3 impaired liver zonation, hepatocyte gene expression, metabolic activity, and regenerative capacity without altering HSC numbers, demonstrating that quiescent HSCs, via RSPO3 signaling, are crucial for maintaining normal liver function. In disease settings, RSPO3 expression in HSCs is significantly reduced, linking HSC activation to hepatocyte decline. These findings reveal the dual role of HSCs in liver biology: supportive in homeostasis and harmful when activated, suggesting that restoring RSPO3 signaling could preserve hepatocyte function in chronic liver disease.
Alyssa
TGFβ links EBV to multisystem inflammatory syndrome in children
SARS-CoV-2 can induce multisystem inflammatory syndrome in children (MIS-C), a severe hyperinflammatory reaction that leads to multi-organ failure if unchecked. Herein, the authors interrogated peripheral blood samples from a multi-center cohort of 145 MIS-C and 221 age-matched control participants. Surprisingly, TCR-sequencing revealed SARS-CoV-2-expanded T cells in MIS-C participants were enriched in Epstein Barr Virus (EBV) clones. In line, EBV seropositivity was increased across MIS-C compared to control severe SARS-CoV-2 infections, which correlated with elevated plasma TGFβ which aids EBV reactivation and immune evasion. Although their claims require a larger sample size to evaluate the causative nature of EBV reactivation in MIS-C, targeting TGFβ is a promising therapy to limit MIS-C during dual active SARS-CoV-2 and EBV infections.
Sean
Precursors of exhausted T cells are pre-emptively formed in acute infection
Shah
MYC ecDNA promotes intratumour heterogeneity and plasticity in PDAC
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer characterized by extreme cell-to-cell variability, which makes it difficult to treat. The authors investigated how extrachromosomal DNA (ecDNA) carrying the MYC oncogene drives both intratumor heterogeneity and plasticity in PDAC. Using whole-genome sequencing of patient-derived organoids (PDOs) and AmpliconArchitect, they found that MYC is frequently amplified on ecDNA rather than on chromosomes, causing high variability in MYC copy number between cells, which was confirmed at the single-cell level by fluorescence in situ hybridization. When PDOs were stressed by removal of WNT pathway support, only organoids with high MYC ecDNA survived by expanding their ecDNA copy number, showing rapid and reversible adaptation to environmental pressures. Barcode lineage tracing further showed that the adaptation was due to pre-existing ecDNA-high clones. Although the results seem promising, making ecDNA a potential therapeutic target, only 12 out of 41 PDOs showed ecDNA amplifications, indicating the need for further experimental analysis.
Keaton
Macrophages recycle phagocytosed bacteria to fuel immunometabolic responses
Although phagocytosis of microbes by macrophages is a fundamental component of host defense, relatively little is known about the fate of phagocytosed bacteria following phagolysosomal killing and their subsequent impact on macrophage function. To answer these questions, the authors of this study performed multi-omic analysis of bone marrow-derived macrophages (BMDM) treated with live or dead E. coli, LPS-coated beads, or beads alone, and they found a significant increase in genes and proteins related to metabolism in the E. coli-treated cells. Further experiments using radiolabeled bacteria revealed that the macrophages were taking up amino acids from the phagocytosed bacteria to fuel their own metabolism, and that the macrophages were preferentially synthesizing itaconate and glutathione from the dead bacteria. This study highlights an essential mechanism controlling host-pathogen interactions, which can direct future studies into promoting host immunity.
Shah
Limited impact of Salmonella stress and persisters on antibiotic clearance
The researchers investigated why antibiotics like enrofloxacin and ceftriaxone show poor efficacy in clearing Salmonella infections in vivo despite strong performance in lab conditions. Using mouse models, tissue-mimicking chemostats, and real-time single-cell imaging, the researchers found that nutrient starvation (which slowed Salmonella tiphimurium replication) was the primary factor reducing antibiotic effectiveness. Contrary to the common belief that persister cells drive antibiotic resistance, the results revealed that DNA damage occurred slowly and uniformly across the entire bacterial population; the results also dismissed the role of stress in antibiotic resistance. Furthermore, a significant portion of bacterial death occurred after antibiotic exposure during regrowth in nutrient-rich conditions, due to unresolved DNA damage and an overwhelmed repair system. Similar results were shown in staphylococcus aureus exposed to flucloxacillin indicating common strategies utilized by bacteria to resist antibiotic activities. The findings of the study highlighted nutrient starvation as the crucial challenge to antibiotic efficacy and call for improved treatment strategies that account for slow bacterial growth in infected tissues.
Hannah
A critical challenge in vaccinology is predicting and sustaining long-lasting immunity, as some vaccines require frequent boosting. Using a systems biology approach, researchers identified an early blood transcriptional signature, detectable 3–7 days post-vaccination, that predicts antibody durability. The multi-omics study of an AS03-adjuvanted H5N1 vaccine (a vaccine for the avian influenza virus) found platelet-driven gene signatures linked to sustained responses, validated across several vaccine platforms, including COVID-19 and malaria. A predictive model based on this signature accurately forecasted antibody longevity across six vaccines from seven trials, revealing a common mechanism for long-lasting immunity. Single-cell analyses identified megakaryocytes as regulators of antibody longevity, with thrombopoietin-induced activation promoting plasma cell survival. Although the signature did not predict all vaccines (e.g., yellow fever), these findings represent a crucial step forward in accelerating vaccine development by enabling early identification of durable immune responses and optimizing adjuvants to enhance long-term immunity.
Alyssa
A subcellular map of translational machinery composition and regulation at the single-molecule level
The switching of ribosome components and associated proteins in ribosomes has been hypothesized to control translation. However, tools that can spatially and functionally annotate ribosomes are difficult to develop due to ribosome abundance and small size. Herein, the authors develop two techniques that allow single-ribosome resolution tracking of ribosome composition and location: ribosome expansion microscopy (RiboExM) and AviTag-specific Location-restricted Illumination-enhanced Biotinylation (ALIBi). These techniques assessed ribosome-associated protein knock-down impact and stimulation-dependent changes in ribosome composition and location, demonstrating organelle-specific ribosome composition for unique mRNA transcripts. Overall, this paper demonstrated the importance of investigating ribosome heterogeneity and validated novel tools for future probing across physiological conditions where translation is altered.
Keaton
Macroevolutionary divergence of gene expression driven by selection on protein abundance
Protein and mRNA abundances are tightly regulated due to their essential impact on organismal phenotypes, but the nature of the relationship between protein and mRNA abundances during evolution are unknown. To identify the coevolutionary relationship between mRNA and protein abundances, the authors of this study developed a phylogenetic model based on paired transcriptomic and proteomic data from fibroblast skin tissue from 10 mammalian species. The authors modeled mutations impacting mRNA abundance (and downstream protein abundance) or protein abundance alone, adjusting parameters to create "mRNA-driven", "protein-driven" or "independent" models, finding that the protein-driven evolution model had the best performance and that mRNA abundances adapt more quickly than protein abundances to new mutations. The authors then validated their protein-driven model in humans using eQTL data from the GTEx database, as well by demonstrating a strong correlation between predicted optimum abundances and translation efficiency estimated from human RNAseq and ribosome profiling data. Although these findings need to be validated in additional species and tissues, it provides a novel framework for estimating mRNA and protein dynamics across evolution.
Sean
Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Technology accompanying research in brain aging has failed to provide a comprehensive overview. To identify specific cellular changes throughout the life span of brain aging, researchers have created a spatially resolved single-cell transcriptomic atlas of the mouse brain over the adult life span, utilizing machine learning tools to detect the cell proximity effect. By compiling coronal brain sections from male mice at 20 different ages across their life span, they trained machine learning models to predict mouse age based on transcriptional data. Using this model, the researchers also demonstrate how T cells enhance the viral immune response of neighboring cells through gene expression. This technology is crucial for researching cell aging, as this model can be applied beyond what the researchers tested and potentially in other tissues or species in the future.
Hannah
Multiscale footprints reveal the organization of cis-regulatory elements
Cis-regulatory elements (CREs) control gene expression, but existing methods struggle to map effector protein organization genome-wide. To address this, the authors developed PRINT, a computational method that identifies DNA--protein interaction footprints of both bulk and single-cell chromatin accessibility data across multiple protein size scales. They then created seq2PRINT, a deep learning framework that leverages these multiscale footprints to infer transcription factor and nucleosome binding, as well as interpret regulatory logic at CREs. Applying seq2PRINT to human bone marrow single-cell chromatin accessibility data, they observed the sequential CRE establishment during hematopoiesis, driven by pioneer factors. Additionally, they identified age related alterations in murine hematopoietic stem cells, including a widespread reduction in nucleosome footprints and the emergence of de novo Ets composite motifs. Seq2PRINT's accuracy relies on diverse, high-quality training data, which may limit its generalizability; future work should refine its footprint resolution and broaden its application to disease models to advance our understanding of gene regulation.
Alyssa
Prolonged persistence of mutagenic DNA lesions in somatic cells
A surprising recent study revealed mutagen-induced DNA damage is not repaired efficiently and often persists across multiple cell cycles, giving rise to diverse mutations. Herein, the authors investigate the extent of DNA lesion persistence in human stem cells by generating phylogenic trees. Shockingly, 15-25% of lesions lasted 3 years, with persistence associated with exposure to known mutagens. These phylogenetic trees reveal significant mutational burdens can arise from a single insult/exposure, changing our view of DNA repair efficiency.
Shah
Mapping cells through time and space with moscot
The study introduces Moscot (Multi-Omics Single-Cell Optimal Transport), a computational tool that uses Optimal Transport (OT) to map how cells change over time and space in developmental and spatial transcriptomic studies. Using large datasets like the Mouse Oragnogenesis Spatiotemporal Transcriptomics (MOSTA) atlas (mouse embryonic development, E9.5–E16.5), Moscot accurately tracked cell fate transitions, tissue organization, and gene activity. It performed better than previous methods in aligning single-cell RNA sequencing (scRNA-seq) data with spatial transcriptomics, helping to study organ development in the liver, brain, gut, and heart. Moscot also mapped pancreatic endocrine differentiation, discovering that NEUROD2 controls epsilon cell formation, which was confirmed using iPSC-derived endocrine progenitors and NEUROD2 knockout experiments. This study highlights Moscot’s ability to predict developmental pathways, integrate multiple data types, and identify important regulatory genes, making it a valuable tool for studying single-cell and spatial transcriptomic data.
Keaton
RNA control of reverse transcription in a diversity-generating retroelement
Bacteriophage diversity-generating retroelements (DGR) are essential components of bacteriophage genomes that rely on error-prone reverse transcriptases surrounded by specific RNA segments, though the functional role of these RNAs is unknown. To identify the roles of these non-template RNA segments in bacteriophage DGRs, the authors of this study performed cryo-EM on the Bordetella bacteriophage. The authors found that these RNAs were not catalytically involved in reverse transcription, but that they precisely placed template RNAs in the RT active site, allowing for efficient reverse transcription. Further analysis revealed that these RNAs are highly conserved across species, highlighting their fundamental role. This study identified a novel mechanism directing the function of an essential molecular complex, and these findings could serve as a platform for future molecular engineering.
Sean
Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Shah
Retrograde mitochondrial signaling governs the identity and maturity of metabolic tissues
Mitochondrial dysfunction contributes to metabolic disorders like type 2 diabetes (T2D) by impairing cellular identity in key metabolic tissues, a relationship that was previously unclear. To investigate this, researchers generated mouse models with β-cell-specific deletions of mitochondrial quality control genes (Clec16a, Tfam, Mfn1/2). Single cell RNAseq, ATAC-seq and other omics data showed defects in mitochondrial dynamics, genome integrity, or mitophagy disrupted oxidative phosphorylation, activating the mitochondrial integrated stress response (ISR). This retrograde signaling triggered chromatin remodeling, suppressed mature cell markers (UCN3, GLUT2), and upregulated immaturity genes, resulting in β-cell dedifferentiation, glucose intolerance, and metabolic dysfunction. Similar results were observed in hepatocytes and brown adipocytes, highlighting a conserved mechanism. Pharmacological inhibition of the ISR with ISRIB restored β-cell identity and function in vivo. Human studies using TFAM-deficient β-cells and primary islets showed similar results, linking mitochondrial quality control defects to T2D pathology. The study proposed targeting mitochondrial retrograde signaling as a therapeutic strategy to preserve and restore metabolic tissue maturity and function. However, the precise mechanism by which retrograde signaling triggered ISR induced chromatin remodeling remains unclear and needs further investigation.
Hannah
Aspartate signalling drives lung metastasis via alternative translation
Lung metastases account for over half of all metastatic cancer instances, yet the mechanisms driving their aggressiveness remains poorly understood. This paper identifies pulmonary aspartate signaling as a key regulator, showing that aspartate binds the NMDA receptor subunit GRIN2D in cancer cells, triggering a cascade that promotes elF5A hypusination via deoxyhypusine hydroxylase (DOHH). Using mouse models of metastatic breast cancer, single-cell RNA sequencing (scRNA-seq), tumor spheroid cultures in lung-like medium (LLM), and patient-derived lung metastases analyzed through publicly available transcriptomic and metabolomic data, they consistently found that aspartate levels increase specifically in metastatic lungs. This increase drives a translational program that enhances collagen synthesis via TGF-beta signaling, a process which shapes the metastatic microenvironment by promoting tumor cell survival and invasiveness. While this study establishes aspartate as an extracranial signaling molecule in metastasis, it primarily focuses on breast cancer, leaving its role in other cancers uncertain. Future research should explore aspartate's broader impact and assess NMDA receptor and DOHH inhibitors as potential therapeutic strategies.
Keaton
Nutrient-driven histone code determines exhausted CD8+ T cell fates
In diseases such as cancer or chronic viral infections, cytotoxic CD8+ T cells can progress from effector (TEFF) to "exhausted" (TEX) states, where they lose the ability to perform essential functions. Though many transcriptomic, proteomic, and epigenetic changes have been identified during this transition, the key molecular switches determining CD8+ T cell exhaustion are unknown. In this study, the authors identified differential expression of acetyl-CoA (Ac-CoA) synthetases Acss2 and Acly in TEX, leading them to hypothesize that Ac-CoA is essential for TEFF progression to TEX. The authors found that ACSS2 and ACLY complexed with histone acetyltransferases during T cell exhaustion, regulating Ac-CoA availability for histone acetylation and thus controlling epigenetic and transcriptomic changes. The authors then discovered that ACSS2 overexpression or ACLY inhibition prevented the TEFF-TEX transition in murine adoptive transfer models. This study identified a key switch controlling TEX fate and highlights the essential role of metabolism in a multitude of essential molecular functions.
Alyssa
Bone marrow niches orchestrate stem-cell hierarchy and immune tolerance
The context, or environment niche, that stem cells persist in is immensely crucial to maintaining stemness; However, investigations of stem cell niches has been stalled due to required high resolution, structure-based studies, ultimately preventing enhanced stem cell transplantation efficacy. Herein, the authors investigated hematopoietic stem cells (HSC) niche’s immunoprotection and the associated stemness espoused by HSCs across different bone niche. The authors established spatially distinct HSC populations using 3-D two-photon confocal microscopy of long bone marrow that are distinguished by nitric oxide levels and immunomodulatory receptor CD200R. NOhiCD200R+ HSCs persisted in the endosteum and were endowed with greater transplantation efficacy, suggesting greater stemness and persistence against rejection compared to other HSC populations in the diphysis. NOhi HSCs were localized to CD200hi capillaries; Endothelial-specific knock-out studies suggested this CD200:CD200R axis is crucial to maintaining NO levels in HSCs, directly imparts immunoprotection (without the need of Tregs or other regulatory immune cells), and ultimately allows longer lived HSCs. Importantly, co-transfer of CD200+ capillary cells and HSCs led to improved allogenic engraftment and lower graft rejection. Overall, this paper demonstrated the power of stem cell contexts and revealed important mechanisms maintaining HSCs. Due to the novelty of discoveries herein, it is necessary that more work go into the CD200:CD200R capillary:HSC axis proposed, especially since the demonstrated improvement in engraftment without the need of immunosuppressive therapy is a major therapeutic goal.
Sean
Spatial transcriptomic clocks reveal cell proximity effects in brain ageing