title: Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [RNA-seq]

status: Public on Aug 06 2025

first: Sebastien

last: Talbot

summary: Peri-neural invasion (PNI) is a well-established poor prognostic factor in multiple cancer types. However, the mechanisms driving the PNI's detrimental clinical effect remain elusive. Here, we provide clinical and mechanistic insights into PNI and cancer-induced injury of tumor-associated nerves (TANs) and their role in resistance to anti-PD-1 therapy. Our work demonstrates that poor response to anti-PD-1 therapy in cutaneous squamous cell carcinoma (cSCC), melanoma, and gastric cancer is associated with PNI and TANs injury. Ultrastructural electron microscopy analysis reveals that direct contact between cancer cells and nerve fibers leads to cancer-induced nerve injury (CINI) via myelin degradation. Injured neurons respond by autonomously initiating an interleukin (IL)-6 and interferon (IFN) type I inflammatory response. This inflammatory response alters the immune activity in the peri-neural niche in melanoma, cSCC, and pancreatic adenocarcinoma, leading to an immuno-suppressive activity aimed at nerve healing and regeneration. As the tumor grows, the CINI burden increases, the inflammatory signal within the niche becomes chronic, and eventually skews the general immune tone within the tumor microenvironment to a suppressive and exhaustive state. The CINI-driven anti-PD-1 resistance can be reversed by targeting multiple steps in the CINI signaling process: denervating the tumor, conditional knockout of the transcription factor mediating the injury signal within neurons (cKO-Atf3), knockout of the IFN-a receptor signaling (Ifnar1-/-), or by combining anti-PD-1 and anti-IL-6-receptor blockade. Our findings demonstrate the direct immuno-regulatory roles of TANs and their therapeutic potential.

overall_design: Bulk RNA sequencing of lung metastasis–innervating neurons was performed following intravenous injection of 5 × 105 B16F10-eGFP melanoma cells or vehicle into nociceptor neuron reporter mice (Trpv1Cre::Td-tomatofl/wt). Two weeks later, the mice were euthanized, and lung metastases were visually confirmed in the B16F10-eGFP-inoculated group. Jugular nodose ganglia (JNC) were dissected into ice-cold HEPES-buffered DMEM (Thermofisher, #12430062). For each biological replicate, JNC from Three mice were pooled and transferred into HEPES-buffered DMEM containing 1 mg/mL collagenase IV (Sigma, #C5138) and 2.4 U/mL dispase II (Sigma, #04942078001), then incubated at 37 °C for 70 minutes. After washing with DMEM, ganglia were gently triturated using glass Pasteur pipettes of decreasing diameter. Cells were centrifuged at 200 g over a 15% BSA gradient in PBS to remove debris, stained with SYTO 40 (10 μM, Thermofisher, #S11351) for 5 minutes at room temperature to distinguish cells from axonal debris, washed with PBS, and resuspended in sterile flow cytometry buffer (PBS with 2% FBS and 1 mM EDTA). The cell suspension was filtered through a 70 µm mesh (VWR, #10204-924), and nociceptor neurons (td-tomato+) were FACS-enriched on a BD FACSAria cell sorter24 , collected directly into 500 µL TRIzol reagent (Invitrogen, #15596026), and stored at −80 °C until RNA extraction, following established protocols33. Library preparation was conducted at the Institut de Recherche en Cancérologie et en Immunologie (IRIC), Université de Montréal. RNA quality was confirmed on an Agilent Bioanalyzer, with all samples achieving an RNA Integrity Number (RIN) ≥ 7.5. Libraries were prepared using a poly(A)-enrichment, single-stranded RNA-seq method (KapaBiosystems, KAPA RNA Hyperprep Kit, #KR1352) and sequenced on an Illumina NextSeq500 platform with 75-cycle single-end reads. Basecalling was performed using Illumina RTA 2.4.11, and demultiplexing was done with bcl2fastq 2.20 (allowing one mismatch in the index). Trimmomatic was used to remove adapter sequences and low-quality bases from the 3′ end of each read, and the resulting high-quality reads were aligned to the GRCm38 mouse genome using STAR v2.5.11, which also generated gene-level read counts. Differential expression analysis was performed in DESeq2 using normalized read counts, and genes were considered differentially expressed if they had an adjusted p-value (false discovery rate, FDR) < 0.05. Log2 fold changes and −log10 p-values were calculated from the normalized data, and additional data analysis and visualization were carried out in RStudio.

first: Balood

last: Mohammad

first: Nikpoor

last: Amin Reza


title: RNA Polymerase II pausing enhances estrogen receptor-alpha binding on promoters in RNA-dependent manner

status: Public on Aug 07 2025

city: Bengaluru

first: Rajat

last: Mann

state: Karnataka

address: Rajiv Gandhi Nagar, Kodigehalli

country: India

institute: National Center for Biological Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Regulated pausing of RNA polymerase II (Pol II) is essential for enabling rapid and coordinated transcriptional responses to signalling cues. Pausing also contributes to the formation of nucleosome-free regions with the help of chromatin remodellers. However, if these nucleosome free regions engage with transcription factors to stimulate the transcription potential of paused promoters is not known. In this study, we demonstrate that ligand-induced estrogen receptor-alpha (ERα) binding is stabilized at Pol II-paused sites. This stabilization results from an increased dwell time of ERα on chromatin as revealed by single-particle tracking experiments. Notably, short chromatin-associated RNAs, generated by the stalled Pol II, contribute to enhancing ERα binding at paused promoters. We also observe that pausing increases histone H3K27 acetylation (H3K27ac) levels, which primes paused promoters for robust transcriptional activation upon release. Collectively, these findings suggest that paused Pol II plays a central role in enhancing transcription factor binding through an RNA-dependent mechanism. This, in turn, results in a more vigorous transcriptional response following pausing release, thus contributing to the fine-tuning of ERα-mediated gene regulation.

overall_design: Chromatin Immunoprecipitation (ChIP-seq) for the ERα/FLAG/H3K27ac/Pol II was performed upon 72 hours of hormone deprivation and 1 hour of E2 signalling (10nM). In H3K27ac and PolII ChIP the IP was spiked in with drosophila chromatin. In DRB treatment experiments cells were first treated with 1hour of DMSO/DRB/TRP and then the E2 ligand was added in the same media.

first: Dimple

last: Notani


title: A unified mechanism for mitochondrial damage sensing in PINK1-Parkin-mediated mitophagy

city: Bethesda

first: Derek

last: Narendra

state: MD

address: 35 CONVENT DR RM 2A-215

department: National Institute of Neurological Disorders and Stroke

country: USA

institute: National Institutes of Health

summary: Damaged mitochondria can be cleared from the cell by mitophagy, using a pathway formed by the recessive Parkinson’s disease genes PINK1 and Parkin. Whether the pathway senses diverse forms of mitochondrial damage by a common mechanism, however, remains uncertain. Here, using a novel Parkin reporter in genome-wide screens, we identified that diverse forms of mitochondrial damage converge on loss of mitochondrial membrane potential (MMP) to activate PINK1. Loss of MMP, but not the PAM import motor, blocked progression of PINK1 import through the translocase of the inner membrane (TIM23), causing it to remain bound to the translocase of the outer membrane (TOM). Ablation of TIM23 was sufficient to arrest PINK1 in TOM, irrespective of MMP. Meanwhile, TOM (including subunit TOMM5) was required for PINK1 retention on the mitochondrial surface. The energy-state outside of the mitochondria further modulated the pathway by controlling the rate of new PINK1 synthesis. Together, our findings point to a convergent mechanism of PINK1-Parkin activation by mitochondrial damage: loss of MMP stalls PINK1 import during its transfer from TOM to TIM23.

overall_design: Genome-wide CRISPRi screen utilizing a dual sgRNA library in HeLa dCas9 BFP KRAB MFN2 Halo mCherry Parkin, HeLa dCas9 BFP KRAB MFN2 Halo, or HEK293 dCas9 BFP ZIM3 cells. Cells were sorted on d7 post transduction via FACS into low (bottom 30% MFN2 Halo expressing cells) and high bins (top 30% MFN2 Halo expressing cells). Each screen was done in duplicate. HeLa cells were treated with antimycin/oligomycin and HEK293 cells were treated with CCCP.

first: Julia

middle: A

last: Thayer

first: Jennifer

middle: D

last: Petersen

first: Xiaoping

last: Huang

first: Luiza

middle: M

last: Gruel Budet

first: James

last: Hawrot

first: Daniel

last: Ramos

first: Shiori

last: Sekine

first: Yan

last: Li

first: Michael

middle: E

last: Ward

middle: P


title: Progression of uterine aging in mice

city: Calgary

first: Myriam

last: Hemberger

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

type: Expression profiling by high throughput sequencing

summary: Reproductive decline with advanced maternal age is majorly driven by functional changes to the uterus in mice. Here, we conducted an aging time course series in female mice and assessed changes to the uterine transcriptomes between young females and those aged between 24 weeks and 52 weeks and over. We also assessed the impact of key candidates of aging driver genes in the human endometrial Ishikawa cell line. Our results show an increase in transcriptional heterogeneity in the uterus as a function of maternal age. However, these changes are largely distinct from organismal aging and highlight that aging of reproductive tissues, notably the endometrium, is driven by a unique set of aging driver genes.

overall_design: RNA-seq profiling of 1) E3.5 dpc whole tissue intact uteri was obtained from young and aged virgin wild-type C57BL/6 mice that were mated with vasectomized wild-type males; and 2) endometrial epithelial organoids obtained from young and aged non-mated virgin wild-type C57BL/6 mice. All collected samples were processed for RNA-sequencing analysis.

first: Aleksandra

middle: O

last: Tsolova

first: Anshul

last: Jadli

first: Anastasios

last: Mastrokolias

first: Alexa

last: Krala

first: Gavin

last: Kelsey

first: Hilary

last: Critchley

first: Wendy

last: Dean


title: Therapeutically targeting perivascular macrophage effector function improves CD8+ T-cell infiltration and response to chemotherapeutic drugs in cancer [CD206+LYVE-1+]

city: London

middle: N

last: Arnold

address: New Hunt’s House, Great Maze Pond

department: Cancer and Pharmaceutical Sciences

country: United Kingdom

institute: King's College London

summary: The tumor microenvironment (TME) plays a crucial role in cancer progression and represents an appealing target for cancer treatment. Tumor-associated macrophages (TAMs) are an abundant stromal cell type in the TME and, due to their plasticity, TAMs can be exploited to promote a pro-tumoral response. TAMs have been implicated in facilitating a variety of pro-tumoral pathways including resistance to anti-cancer therapeutics, immune suppression, angiogenesis, and metastasis. However, pan-TAM depleting approaches have not delivered robust clinical outcomes as single agents. This might be explained due to their non-selective targeting of both pro- and anti-tumoral macrophage subsets. As such, therapeutically targeting key pro-tumoral TAM subsets may be a more desirable and efficacious strategy. Our group has recently characterised a subpopulation of pro-angiogenic and immune-suppressive TAMs which can be identified by their expression of the lymphatic vessel endothelial hyaluronan receptor-1 (LYVE-1). LYVE-1+ TAMs reside spatially proximal to blood vasculature and adopt a collaborative multi-cellular ‘nest’ arrangement which supports their biological activity. LYVE-1+ TAMs selectively express high levels of the immunomodulatory enzyme heme oxygenase-1 (HO-1), an enzyme which catabolizes heme to generate the biologically active catabolites carbon monoxide (CO), biliverdin and ferrous iron. Genetic inactivation of HO-1 in LYVE-1+ TAMs improve anti-tumor CD8+ T-cell infiltration into the TME and enhances the immune-stimulating effects of chemotherapy, resulting in sustain control of tumor growth in a spontaneous MMTV-PyMT murine model of breast cancer. This highlights that HO-1 represents a key effector pathway of these cells that prevents immune-elimination of tumors. Considering translation of these observations, unfortunately, current HO-1 inhibitors are not orally bioavailable, which limits their utility for chronic diseases, such as cancer, where daily administration would be required. In response to this hurdle, we developed a next generation HO-1 inhibitor called KCL-HO-1i. We demonstrate in pharmacokinetic studies that KCL-HO-1i is orally bioavailable in murine models with a serum half-life of around 3hours. Furthermore, oral delivery of KCL-HO-1i alongside standard of care chemotherapy delivers durable tumor control in MMTV-PyMT mice. We have characterised the response of the TME to KCL-HO-1i using flow cytometry, immunofluorescence and RNA sequencing approaches and demonstrate that KCL-HO-1i targeting perivascular LYVE-1+ TAM function supports a broader switch from an immunological ‘cold’ to ‘hot’ TME which provides a more favourable immune landscape for improving the response to chemotherapeutic drugs. Taken together, our data support the use of KCL-HO-1i as novel immunotherapeutic for targeting the function of perivascular TAMs in cancer.

overall_design: 6 MMTV-PyMT mice were divided in 2 treatment groups with 3 mice each group and were treated either with the Vehicle or KCL-HO-1i inhibitor. Tumours have been harvested and digested into single-cell supensions. Then, the cells have been sorted in order to get 5000 cells  CD206+LYVE-1+ for each condition.

first: Meriem

last: Bahri

first: Jit

last: Sarkar


title: HNRNPC and m6A RNA methylation control oncogenic transcription and metabolism in T-cell leukemia- ONT DRS study

city: Gent

first: Igor

last: Fijalkowski

address: Sint-Pietersnieuwstraat 33

country: Belgium

institute: Ugent

summary: RNA homeostasis is dysregulated in cancer and impacts disease progression and therapy resistance. N6-methyladenosine (m6A), the most abundant epitranscriptomic modification in eukaryotic mRNA, plays a pivotal role in RNA biology, affecting transcript stability, translation, and splicing. Our study uncovers the extensive m6A changes in T-cell acute lymphoblastic leukemia (T-ALL) patient samples for the first time. It reveals m6A’s regulatory role in the oncogenic MYC and cholesterol biosynthesis pathways. In addition, we discovered that T-ALL is highly dependent on the m6A reader heterogeneous nuclear ribonucleoprotein C (HNRNPC). HNRNPC is transcriptionally controlled by MYC and is an essential regulator of m6A-modified transcripts. Consequently, transcriptional silencing of HNRNPC profoundly impairs oncogenic pathways and critically diminishes leukemia cell growth. Additionally, the levels of the m6A demethylase fat mass and obesity-associated (FTO) are significantly elevated in T-ALL cells compared to normal cells, and to other types of leukemia. Targeting FTO shows therapeutic potential in preclinical disease models and synergizes with clinically relevant therapeutics. Our findings underscore the integral role of RNA methylation in orchestrating cancer cell oncogene expression and metabolism, and highlight promising novel therapeutic avenues for the treatment of T-cell leukemia.

overall_design: To investigate the persistence of m6A methylome through xenografting we studied the m6A landscape of Primary diagnosis T-ALL patients, matching xenografted material and healthy thymocytes.

first: Jonas

last: De Kesel

first: Tim

last: Pieters

first: Cristina

last: Borin

first: Manou

last: Wittouck

first: Jolien

last: Van Laere

first: Lindy

last: Reunes

first: Marino

last: Caruso

first: Bijal

last: Thakkar

first: Bruno

last: Palhais

first: Wouter

last: Sleeckx

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: Deforce

first: Kim

last: De Keersmaecker

first: Steven

last: Goossens

first: Tom

last: Taghon

first: Valentina

last: Serafin

first: Eva

last: Maria Novoa

first: Eric

last: Wang

first: Panagiotis

last: Ntziachristos


title: Fate mapping of peripherally derived macrophages reveals a long-lasting engrafted population that maintains a distinct transcriptomic profile for up to 8 months after Traumatic Brain Injury IV

city: San Francisco

first: Susanna

last: Rosi

state: CA

address: 2200 Island Dr

institute: Altos labs

summary: Traumatic Brain Injury (TBI) is one of the most established environmental risk factors for the development of dementia and long term neurological deficits representing a critical health problem for our society. It is well-established that TBI-induced neuroinflammation contributes to the long-lasting cognitive deficits and engages brain-resident macrophages (microglia) as well as monocytes-derived macrophages (MDMs) recruited from the periphery. While numerous studies have characterized microglia response to TBI, and the critical role of early infiltrated MDMs in the development of cognitive dysfunctions, the fate of MDMs in TBI remains unknown. Microglia and MDMs have distinct embryological origins and it is unclear if MDMs can fully transition to microglia after infiltrating the brain. This gap in knowledge is due to the fact that after brain engraftment, MDMs stop expressing their signature markers, thus making discrimination from resident microglia cells elusive. Here, for the first time, we longitudinally trace the fate of MDMs by taking advantage of two complementary yet distinct fate mapping mouse lines, CCR2-creERT2 and Ms4a3-cre, where inflammatory monocytes are permanently labeled even after in situ reprogramming. We demonstrated that early infiltrated MDMs persist in the brain for up to 8 months after TBI in adult female and male mice. Notably, MDMs retain their phagocytic activity while remaining transcriptomically distinct from microglia, and show a signature associated with aging and disease. Our data significantly advance the understanding of long-lasting MDMs and provide critical knowledge for developing more targeted therapeutic interventions for myeloid cells.

overall_design: Single-nucleus RNA-seq of brain samples from human patients with and without TBI.

first: Maria Serena

last: Paladini

first: Benjamin

last: Yang

first: Xi

last: Feng

first: Elma

middle: S

last: Frias

first: Karen

last: Krukowski

first: Rene

last: Sit

first: Maurizio

last: Morri

first: Wendy

last: Lam

last: Pedoia

first: Stefka

last: Tyanova

first: Marco

last: Colonna

first: Amber

middle: L

last: Nolan


title: Fate mapping of peripherally derived macrophages reveals a long-lasting engrafted population that maintains a distinct transcriptomic profile for up to 8 months after Traumatic Brain Injury I

overall_design: RNA-seq profiling of microglia and monocyte-derived macrophages (MDMs) collected from whole brains of Ccr2-creERT2::Ai14D mice at 8 months with and without traumatic brain injury (TBI).


title: Fate mapping of peripherally derived macrophages reveals a long-lasting engrafted population that maintains a distinct transcriptomic profile for up to 8 months after Traumatic Brain Injury III

overall_design: RNA-seq profiling of peripheral monocytes, and microglia and monocyte-derived macrophages (MDMs) collected from whole brains of Ms4a3-cre::Ai14D mice at 7 and 30 days with and without traumatic brain injury (TBI).


title: Therapeutically targeting perivascular macrophage effector function improves CD8+ T-cell infiltration and response to chemotherapeutic drugs in cancer

first: James

last: Arnold

overall_design: 30 MMTV-PyMT mice were divided in 6 treatment groups with 5 mice each group and were treated with different combinations of chemotherapy and immunotherapy

first: Meriem

last: Bahri

first: Jit

last: Sarkar


title: HNRNPC and m6A RNA methylation control oncogenic transcription and metabolism in T-cell leukemia

first: Igor

last: Fijalkowski

summary: RNA homeostasis is critical for cancer progression and therapy resistance. N6-methyladenosine (m6A), the most abundant epitranscriptomic modification in eukaryotic mRNA, has recently been found to be critical for various aspects of RNA biology, such as transcript stability, translation, and splicing. Our study showcases extensive m6A changes in T-cell acute lymphoblastic leukemia, affecting oncogenic MYC targets and cholesterol biosynthesis. We also demonstrate that leukemia cells strongly depend on the m6A reader HNRNPC, which we found to be a key regulator of these MYC targets and cholesterol biosynthesis. Consequently, HNRNPC silencing profoundly impaired these m6A-regulated pathways, resulting in significantly reduced leukemia growth. Corroborating results were collected by inhibiting the m6A demethylase FTO, which was demonstrated to be therapeutically relevant in preclinical disease models, while also synergizing with chemotherapeutics. Collectively, we reveal a novel role of m6A in coordinating the crosstalk between oncogenic expression and metabolism and provide therapeutic avenues against T-cell leukemia.

overall_design: We investigated the effects of genetic and pharmacological modulation of the m6A pathway in T-cell acute lymphoblastic leukemia. RNAseq and m6A-eCLIP experiments were performed upon inhibition of pathway writers (METTL3) and erasers (FTO). In addition eCLIP experiments were performed for a relevant pathway reader (HNRNPC). Gene expression was evaluated in all experimental conditions.

first: Jonas

last: De Kesel

first: Tim

last: Pieters

first: Cristina

last: Borin

first: Manou

last: Wittouck

first: Jolien

last: Van Laere

first: Lindy

last: Reunes

first: Marino

last: Caruso

first: Bijal

last: Thakkar

first: Bruno

last: Palhais

first: Wouter

last: Sleeckx

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: Deforce

first: Kim

last: De Keersmaecker

first: Steven

last: Goossens

first: Tom

last: Taghon

first: Valentina

last: Serafin

first: Eva

last: Novoa

first: Eric

last: Wang

last: Ntziachristos


title: Deletion of centrally conserved domain intergenic to H19 and Igf2 perturbs adult skeletal muscle specific Igf2 expression

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Intergenic to H19 and Igf2, there is a previously identified centrally conserved domain (ccd ) that includes two sequences with high conservation between human and mouse. At one of these sequence elements there is DNAse1 Hypersentitivity sequence (HSS), CTCF binding and chromatic interaction/looping to sequence upstream of Igf2 on both parental alleles. In earlier studies, removal of ccd sequence from the maternal allele resulted in activation of the normally repressed maternal Igf2 in neonatal limb. We have generated an independent ccd (floxed) deletion allele. Deletion of ccd from both the maternal and paternal allele also results in elevated levels of Igf2 expression from the respective alleles in adult skeletal muscle.  Capture C analysis of adult skeletal muscle nuclei uncovers new chromatin interactions in ccd deletion alleles.

overall_design: Capture-C on F1 hybrid neonatal limb and adult skeletal muscle derived from reciprocal crosses between C57BL/6 (B6) mice heterozygous for described deletion and mice homozygous for the Mus Castaneous on Chromosome 7 strain (C7).

first: Joanne

last: Thorvaldsen

first: Aimee

last: Juan

first: Yee-Hoon

last: Foong

first: Christopher

last: Krapp

first: Marisa

last: Bartolomei


title: The role of the cardiac lymphatics and LYVE-1-dependent macrophages during neonatal mouse heart regeneration and transition to fibrotic repair

status: Public on Aug 05 2025

city: Oxford

first: Paul

middle: Richard

last: Riley

address: IMS-Tetsuya Nakamura Building, Old Road Campus

institute: University of Oxford

summary: In adult mice, “heart attack” or myocardial infarction (MI) activates the cardiac lymphatics, which undergo sprouting angiogenesis (lymphangiogenesis) and function to drain interstitial fluid and traffic macrophages to mediastinal lymph nodes (MLNs). This prevents oedema and reduces inflammatory/fibrotic immune cell content to improve cardiac function. Given the importance of the adult cardiac lymphatics in macrophage clearance after injury, we investigated their role across the neonatal “regenerative window”. At post-natal day 1 (P1) neonatal mice fully regenerate their heart following MI, in a pro-regenerative macrophage-dependent manner, whereas equivalent injury at post-natal day 7 (P7) leads to scarring driven by pro-fibrotic macrophages. We hypothesised that lymphatics respond and function differently during this “window” to clear macrophage-specific subtypes, depending upon their requirement for regeneration versus fibrotic repair. Normal lymphatic growth and sprouting was evident in intact neonatal hearts until P16, with strain-dependent developmental differences. The response to injury revealed limited lymphangiogenesis (lymphatic vessel growth and sprouting) and minimal clearance of macrophages from P1 compared to P7 infarcted hearts, as determined by adoptive transfer, and monitoring of cleared macrophages to MLNs. This is coincident with maturation of lymphatic endothelial cell junctions across the neonatal period via transition from “zipper” (impermeable) to “button” (permeable) -type junctions and altered signalling between lymphatic endothelial cells and macrophages, including differential expression of the lymphangiocrine factor Reelin (RELN). Finally, in mice lacking the lymphatic endothelial receptor-1 (LYVE-1), that exhibit impaired transmigration of interstitial macrophages to lymphatic vessels, magnetic resonance imaging (MRI) revealed a surprising impaired functional outcome in P1 mice 28 days post-MI. Given our observations that pro-regenerative macrophages at P1 are not trafficked, this suggested a distinct role for LYVE-1 in tissue-resident macrophages, consistent with its expression pattern in developing and post-natal hearts. Macrophage-specific deletion of Lyve1 during neonatal heart injury revealed impaired heart regeneration, characterised by persistent fibrosis, a reduced neovascular response and reduced function. ScRNA-seq of Lyve1 deficient CD45+ cells revealed a loss of tissue-resident macrophages and an increase in recruited monocytes which is predicted to increase inflammation and fibrosis, worsening the outcome post-MI. Collectively, this study reveals that cardiac lymphatics are developmentally compromised for clearance in early neonates, which enables retention of pro-regenerative tissue-resident macrophages, and that LYVE-1 plays an essential role in maintaining this population to promote heart regeneration and prevent inflammation and fibrotic repair.

overall_design: To interrogate the molecular role of LYVE-1 in macrophages, scRNA-seq analysis of pooled CD45+ enriched cells from neonatal Lyve1-KO versus wildtype (WT) hearts (n = 5 per group) was conducted at 7 days after surgical induction of myocardial infarction at P2, thus capturing all immune cells including macrophages at a timepoint consistent with the observed impaired neovascularisation in hCD68-CreERT2;Lyve1flox/flox animals

first: Benjamin

middle: G

last: Chapman

first: Konstantinos

last: Klaourakis

first: Carla

last: de Villiers

first: Mala

last: Gunadasa-Rohling

first: Maria-Alexa

last: Cosma

first: Susanna

last: Cooper

first: Kshitij

last: Mohan

first: Michael

last: Weinberger

first: Carolyn

last: Carr

first: David

middle: R

last: Greaves

last: Jackson

first: Daniela

last: Pezzolla

first: Robin

last: Choudhury

first: Joaquim

last: Vieira


title: Stromal SRD5A2 promotes prostate growth through WNT5A-LEF1-IGF1 signaling in benign prostatic hyperplasia

city: Boston

first: Christina

last: Sharkey

address: 99 Brookline Ave

institute: Beth Israel Deaconess Medical Center

summary: Steroid 5 alpha-reductase type 2 (SRD5A2) is a key enzyme in androgen metabolism and a pharmacologic target in benign prostatic hyperplasia (BPH). While SRD5A2 is known to mediate stromal-epithelial interactions that influence prostate growth, the relationship between baseline SRD5A2 expression and prostate volume remains unclear. In this study, we analyzed SRD5A2 expression in human prostate tissues from the Medical Therapy of Prostatic Symptoms (MTOPS) trial and institutional biorepository cohorts. Quantitative assessments were performed and correlations were evaluated between expression level of SRD5A2, WNT5A, prostate volume, and tissue signaling profiles. SRD5A2 expression was significantly associated with total prostate and transition zone volume. Stromal-specific WNT5A expression showed a strong positive correlation with SRD5A2, while neither serum nor tissue dihydrotestosterone levels correlated with SRD5A2 expression. In Srd5a2-null mice, Wnt5a expression in the prostate stroma was dependent on Srd5a2 and showed region-specific regulation. Mechanistically, SRD5A2 overexpression in human prostate stromal cells upregulated WNT5A and Lymphoid Enhancer-Binding Factor 1 (LEF1), activated insulin-like growth factor 1 (IGF1) signaling, increased proliferation, and reduced apoptosis. Conditioned media from these cells enhanced epithelial proliferation through paracrine IGF1 activity. This study provides the first evidence that SRD5A2 promotes prostate growth through a stromal WNT5A-LEF1-IGF1 paracrine signaling axis independent of androgen levels, suggesting a novel therapeutic mechanism relevant for BPH patients with resistance to conventional 5 alpha-reductase inhibitor therapy.

overall_design: Generation of Srd5a2-null (Srd5a2-/-) and heterozygous (Srd5a2+/–) mice model was previously described (Sharkey et al. 2024). Male Srd5a2+/- (Het) were crossed with wild-type (WT) C57BL6 female mice. The offspring of these heterozygous mice were bred further to obtain one-quarter of Srd5a2-null (KO) male offspring from the third generation. Prostate was harvest from WT, HET and KO mice. Total RNA was extracted from prostate tissue and sent for bulk RNA sequencing.

first: Boqing

last: Gu

first: Xingbo

last: Long

first: Yao

last: Tang

first: Nicolas

last: Patsatzis

first: Steven

last: Li

first: Aria

last: Olumi

first: Zongwei

last: Wang


title: Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in synovial sarcoma [BR_ChIP-seq]

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: Synovial Sarcoma (SS) is driven by the SS18::SSX translocation event and is often diagnosed in patients under 30. In general, SS is refractory to chemotherapy and other therapeutic approaches. SS18::SSX does not directly bind to DNA. Instead, SS18::SSX alters ATP-dependent chromatin remodeling complex BAF (mammalian SWI/SNF complex) complexes away from a wild-type SS18-containing canonical (cBAF) complex towards a SS18::SSX-containing non-canonical (nc)BAF complex to drive a SS-specific transcription program with subsequent tumor formation. Small molecule targeted therapies are expanding beyond the kinome, providing additional tools to treat cancers that are not yet amenable to targeted therapies. Here, we demonstrate that SS18::SSX activates the SUMOylation program and SS are sensitive to the small molecule SAE1/2 inhibitor, TAK-981 (subasumstat). Mechanistically, we demonstrate TAK-981 de-SUMOylates the cBAF and Polybromo-associated BAF complex (PBAF) complex member, SMARCE1. The result of which is stabilization and restoration of cBAF complexes on chromatin, shifting away from the dominant SS18::SSX-ncBAF-complex driven transcriptome. This phenotypic shift is associated with DNA damage and cell death, resulting in tumor inhibition across both human and mouse SS tumor models. As such, TAK-981 combined with standard-of-care chemotherapy enhances induced synergistic activity through increased DNA damage, leading to tumor regressions. Targeting the SUMOylation pathway in SS restores cBAF complexes and blocks the SS18::SSX-ncBAF transcriptome, identifying a therapeutic vulnerability in SS, and positioning the in-clinic TAK-981 as a novel candidate to treat this refractory cancer.

overall_design: Chromatin Immunoprecipitation DNA sequencing (ChIP seq) for SS18::SSX, SMARCA4, KDM2B and H3K27ac in SYO.1 and HS-SY-II synovial sarcoma cell lines

first: Konstantinos

middle: V

last: Floros

first: Carter

middle: K

last: Fairchild Jr

first: Jinxiu

first: Kun

last: Zhang

first: Jane

last: Roberts

first: Richard

last: Kurupi

first: Bin

last: Hu

first: Vita

last: Kraskauskiene

first: Nayyerehsadat

last: Hosseini

first: Shanwei

last: Shen

first: Melissa

last: Inge

first: Kylie

last: Smith-Fry

first: Li

first: Afroditi

last: Sotiriou

first: Krista

last: Dalton

first: Asha

last: Jose

first: Elsamani

middle: I

last: Abdelfadiel

first: Yanli

last: Xing

first: Ronald

last: Hill

first: Jamie

last: Slaughter

first: Mayuri

last: Shende

first: Madelyn

last: Lorenz

first: Mandy

last: Hinojosa

first: Benjamin

last: Belvin

first: Zhao

last: Lai

first: Sosipatros

last: Boikos

first: Angeliki

last: Stamatouli

first: Janina

last: Lewis

first: Masoud

middle: H

last: Manjili

first: Kristoffer

last: Valerie

first: Renfeng

first: Ana

last: Banito

first: Andrew

last: Poklepovic

first: Jennifer

last: Koblinski

first: Trevor

last: Siggers

first: Kevin

middle: B


title: HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs [ATAC, Cut & Tag]

city: Dallas

first: Nikhil

last: Munshi

address: 5323 Harry Hines Blvd

department: Cardiology

institute: UT Southwestern

summary: Sub-nuclear localization of heterochromatin enables stable lineage-specific gene repression.  The mechanisms by which pioneer transcription factors (TFs) access these loci to selectively activate lineage-specific genes remain poorly understood.  Here, using a model of TF-induced cardiac reprogramming, we show that Hand2’s ability to reprogram cells requires its selective compartmentalization within perinucleolar heterochromatin wherein many key target genes reside. We identify the nucleolar targeting region of Hand2, which is mechanistically separable from DNA-binding. Using a series of separation of function mutants, we find that compartmentalization creates high local concentrations of Hand2 homodimers required for binding of suboptimal DNA motifs within lineage-specific gene enhancers.  Altogether, our results establish a causal relationship between TF sub-nuclear localization and selective activation of lineage-specific gene programs. Thus, our data support the notion that lineage-specific programs are functionally compartmentalized within the nucleus, and we provide a mechanistic model by which TF sub-nuclear localization orchestrates selective activation of lineage specific genes.

overall_design: To investigate the impact of sub-nuclear localization of Hand2 on gene expression we profiled reprogramming experiments expressing different separation of function mutants via ChIP-seq and RNA-seq

first: Munshi

last: Nikhil

first: Kulkarni

last: Kartik


title: Axial Nephron Fate Switching Demonstrates a Plastic System Tunable on Demand

city: Los Angeles

first: Nils

last: Lindstrom

state: California

address: 1425 San Pablo St, BCC 413

institute: University of Southern California

summary: The human nephron is a highly patterned tubular structure. Approximately 1 million nephrons form in each kidney during embryonic and fetal development and develop specialized cells that regulate bodily fluid homeostasis, blood pressure, and urine secretion throughout life. This raises the question of how these cells originally develop. Here we interrogate early human nephron patterning using an iPSC-based kidney organoid system that generates hundreds of developmentally synchronized nephron structures. We show that human nephron patterning is controlled by integrated WNT/BMP/FGF signaling. Imposing a WNThigh/BMPlow state established a distal identity that matures into thick ascending loop of Henle cell identities by activating FGF. Simultaneous suppression of FGF signaling reverts cells to a proximal cell-state, thereby indicating the dependence on FGF signaling for distal cell formation in the human nephron. Our system highlights plasticity in nephron identities and mechanisms controlling normal patterning.

overall_design: Single-nuclei RNA-sequencing data from control and distal-enriched (treated with 10 uM Ly29 for 48 hours between differentiation days 10-12, and 1uM CHIR and 1.5 uM LDN between differentiation days 11-12) kidney organoids. Single-nuclei data are from differentiation day 28 and include both DMSO control and treated organoids. Raw data were aligned to hg38, and these processed snRNA-seq data used in Figure S6 (all organoid cells) are provided as an .rds file.

first: Mary Anne

last: Achieng


title: Vasculogenic Precedes Neurogenic Differentiation in DPSC Transplanted into Root Canals

city: Ann Arbor

first: Ririko

last: Tsuboi

state: MI

address: 1011 N.University, Rm 2420

department: Cariology, Restorative Sciences, Endodontics

institute: University of Michigan

summary: Dental pulp stem cells (DPSC) constitute a neural crest-derived stem cell population endowed with multipotency and self-renewal. While the process of DPSC differentiation has been studied extensively in vitro, very little is known about mechanisms underpinning the differentiation of human DPSC in vivo. Here, we induced vasculogenic, odontoblastic, or neurogenic differentiation of human DPSC for 7 days in vitro and performed single cell sequencing. Then, human DPSC tagged with GFP (DPSC-GFP) seeded in human tooth slice/scaffolds were transplanted into immunodeficient mice. Single cell sequencing of DPSC-GFP sorted by flow cytometry was performed 7 and 21 days after transplantation. We observed major shifts in patterns of gene expression when DPSC were induced to undergo vasculogenic, odontoblastic, or neurogenic differentiation in vitro. Although some DPSC retained mesenchymal stem cell (MSC) markers (indicating asymmetric cell division and self-renewal), each differentiation protocol resulted in a unique gene expression signature in vitro. In vivo, stem cell markers that were highly expressed in DPSC pre-transplantation gradually decreased in expression after 7 and 21 days. In contrast, vascular endothelial cell markers were highly expressed 7 days after transplantation, while neuronal markers were highly expressed 21 days after transplantation. In conclusion, DPSC cells are heterogeneous with clearly distinct cell clusters, all of which contain cells with unique differentiation potential. Notably, the microenvironment created when human DPSC are transplanted inside a human root canal in vivo induces vasculogenic differentiation first, which is then followed by neurogenic differentiation.

overall_design: RNS-seq profiles of dental pulp stem cells before and after differentiation into three different cell types (angiogenic, neurogenic, and odontogenic), and RNA-seq profiles of DPSCs extracted 7 and 21 days after subcutaneous transplantation into mice.


title: Microglia lineage relaxation towards a lymphoid-like state protects against Alzheimer’s disease.

city: New York

first: Pinar

last: Ayata

state: New York

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mt Sinai

summary: Amyloid plaques, a hallmark of Alzheimer's disease (AD), combine chemical and physical properties foreign to normal brain tissue. These "non-self" plaque patterns trigger local tissue responses in the brain, including microglia activation. Microglial response to the plaques can be both protective, aiming at amyloid clearance and neuroprotection, and harmful, associated with microglia-driven inflammation and neurotoxicity. Here, we provide evidence that the microglial neuroprotective response to amyloid plaques involves a relaxation of the microglia lineage specification toward a lymphoid-like state. We found that a subpopulation of plaque-associated microglia downregulates the microglia lineage-specifying transcription factor PU.1 and de-represses several lymphoid-expressed genes, including those that play a key role in receptor-mediated signaling in B and T lymphocytes. The shift toward the lymphoid lineage is associated with an increased signaling capacity of PU.1low microglia that supports microglia maintenance at the plaque. Functionally, we show that PU.1low microglia protect neurons and reduce plaque-associated damage in a mouse model of amyloid deposition. Engineered genetic downregulation of PU.1 in microglia in the healthy brain emulates phenotypic features of plaque-associated microglia, promotes microglia-plaque association in disease, and protects against the loss of functional neuronal connections and associated behaviors, including cognition and memory in mice. We propose that the plaque-induced microglia lineage relaxation represents a novel mechanism of the microglial responses in the presence of AD pathology that is adaptive in nature and protective by function.

overall_design: Microglial RNAs were isolated based on the eGFP-L10a expression of ribosomes.

first: Jessica

last: Crowley

first: Matthew

middle: F

last: Challman

first: Maud

last: Gratuze

first: Sebastian

last: Werneburg

first: Vinaya

last: Sahasrabuddhe

middle: T

last: Chan

first: Hayley

middle: J

last: Strasburger

first: Violeta

last: Durán-Laforet

first: Travis

last: Faust

first: Robert

last: Murphy

first: Taoyu

last: Mei

first: Anna

middle: A

last: Pimenova

first: Diogo

last: Ribeiro

first: Emma

middle: C

last: Hays

first: Carmen

last: Romero-Molina

first: Francesca

last: Garretti

first: Tulsi

last: Patel

first: Jason

last: Ulrich

first: Edoardo

last: Marcora

first: John

middle: W

last: Murray

first: Andreas

last: Beyer

first: Dorothy

last: Schafer

first: David

last: Holtzman

first: Alison

last: Goate

first: Alexander

last: Tarakhovsky

first: Anne

last: Schaefer


title: Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in synovial sarcoma

first: Mikhail

last: Dozmorov

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Antithrombin-binding heparan sulfate is ubiquitously expressed in epithelial cells and suppresses pancreatic tumorigenesis

city: Athens

first: Ryan

middle: Joseph

last: Weiss

state: GA

address: 315 Riverbend Road

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: 3-O-sulfation of heparan sulfate is the key determinant for the binding and activation of the serine protease inhibitor antithrombin. This interaction is the basis of the anti-thrombotic treatment using heparin, a fractionated form of heparan sulfate derived from porcine entrails and bovine lung. Antithrombin-binding heparan sulfate (HSAT) is also expressed in human tissues, although it is generally thought to be rare and restricted to endothelial cells, mast cells, or follicular fluid. Here we show that HSAT is ubiquitously expressed in the basement membranes of epithelial cells in multiple tissues, indicating that HSAT is more abundant than previously realized. HSAT is expressed by healthy pancreatic ductal cells and its expression is increased in neoplastic progression of premalignant pancreatic intraepithelial neoplasia lesions (PanINs) but reduced in mature metastatic pancreatic ductal adenocarcinoma (PDAC). Genetic inactivation of HS3ST1, a key enzyme in HSAT synthesis, in murine PDAC cells eliminated HSAT expression, induced an inflammatory phenotype, suppressed markers of apoptosis, and increased metastasis in an experimental mouse model. HSAT-positive PDAC tumors bind AT, which inhibits the generation of active thrombin by tissue factor (TF) and Factor VIIa. These findings suggest that expression of HSAT acts as a tumor suppressor through recruitment of AT and that the loss of HSAT in progression to PDAC increases inflammation and metastatic potential. Furthermore, plasma from PDAC patients showed an accumulation of HSAT suggesting its possible utility as a marker of tumor formation. Fully understanding the function of HSAT in healthy tissues and how it contributes to pancreatic tumorigenesis could pave the way for the development of novel strategies for early diagnosis and potential therapy.

overall_design: To investigate the role of 3-O-sulfation of heparan sulfate in pancreatic ductal adenocarcinoma (PDAC) development, we orthotopically transplanted murine HS3ST1-/- or WT PDAC cells  into syngeneic mice. We isolated RNA and performed RNA-seq on tumors after two weeks of growth. We then performed analyses of gene ontology and gene set enrichment.

first: Thomas

last: Mandel Clausen

first: Joanna

last: Coker


title: Fate mapping of peripherally derived macrophages reveals a long-lasting engrafted population that maintains a distinct transcriptomic profile for up to 8 months after Traumatic Brain Injury II

first: Susanna

last: Rosi

overall_design: RNA-seq profiling of monocyte-derived macrophages (MDMs) collected from whole brains of Ccr2-creERT2::Ai14D mice at 7 and 30 days after traumatic brain injury (TBI).

first: Maria Serena

last: Paladini

first: Benjamin

last: Yang

first: Xi

last: Feng

first: Elma

middle: S

last: Frias

first: Karen

last: Krukowski

first: Rene

last: Sit

first: Maurizio

last: Morri

first: Wendy

last: Lam

first: Valentina

last: Pedoia

first: Stefka

last: Tyanova


title: LAM cell mTOR dysregulation induces IL6 and paracrine AT2 cell senescence impeding lung repair in lymphangioleiomyomatosis.

city: Nottingham

first: Roya

last: Babaei Jadidi

state: Nottinghamshire

address: Biodiscovery institute

institute: University of Nottingham

summary: LAM is a rare disease which causes lung cysts and respiratory failure. TSC2 deficient ‘LAM cells’ with dysregulated mTOR signalling form nodules with fibroblasts causing lung injury. We examined if mTOR dysregulation could induce senescence and impair responses to lung injury. Senescence markers p21 and p16 were increased in LAM lungs and co-localised with alveolar type 2 cells. The SenMayo senescence gene panel was upregulated in LAM alveolar type 2 cells with senescence supressed by mTOR inhibition in patients. LAM cell / fibroblast spheroid cultures induced senescence markers in alveolar type 2 cell organoids, altered their growth and delayed epithelial scratch wound repair. Upstream regulator analysis predicted alveolar type 2 cell IL6 receptor activation. IL6 was produced by LAM cells, was overexpressed in LAM serum and related to lung function, induced p16 and p21 in alveolar type 2 cells and inhibited epithelial wound resolution. Wound repair in the presence of TSC2 null but not TSC2 addback LAM cell / fibroblast spheroids was enhanced by the IL6 receptor antagonist Tocilizumab. Our findings show TSC2 loss induces senescence and IL6 production which are associated with impaired lung repair. Targeting IL6 signalling in parallel with mTOR inhibition, may reduce lung damage in LAM.

overall_design: To understand the processes driving senescence we used laser capture micro-dissection to isolate LAM nodules from lung tissue from 19 women with LAM and 3 controls. Lung tissue used for laser capture microdissection was obtained from patients at the UK LAM. RNA was extracted from laser capture and rest of lungs and analysed gene expression by RNA sequencing.

first: Debbie

last: Clements

first: Yixin

last: Wu

first: Ken

last: Chen

first: Suzanne

last: Miller

first: Manuela

last: Plate

first: Kyungtae

last: Lim

first: Rachel

last: Chambers

first: Emma

last: Rawlins

first: Yan

last: Xu

first: Simon

last: Johnson


title: Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells [CITE-seq]

city: New York City

first: Boris

last: Reizis

address: 550 1st Ave

department: Pathology

institute: NYU Grossman School of Medicine

summary: Plasmacytoid dendritic cells (pDCs) mount powerful type I interferon (IFN-I) responses against viruses and virus-derived nucleic acids. Only a small fraction of pDCs produces high levels of IFN-I, yet neither the molecular basis nor the purpose of this functional heterogeneity are known. We report that naive murine pDCs comprise three transcriptionally (but not epigenetically) distinct subsets. This heterogeneity is generated by tonic IFN-I signaling elicited in part by the cGAS/STING and TLR9 pathways. A small "IFN-I-naive" subset (pDC-A) was expanded in STING deficiency or after transient IFN-I receptor blockade, but was abolished by exogenous IFN-I. pDC-A showed strong cytokine responses yet were susceptible to infection with vesicular stomatitis virus (VSV). Conversely, the majority of pDCs comprised the "IFN-I-primed" subsets (pDC-B/C) that showed lower IFN-I responses but were resistant to VSV. Thus, tonic IFN-I signaling decreases the cytokine-producing capacity of pDCs but increases their virus resistance, achieving the optimal functional balance for antiviral responses.

overall_design:
We sorted splenic pDCs (IgM- IgD- TCRb- B220+ Ly6C+) from naïve C57BL/6 (B6) wild-type (WT) mice and examined them using CITE-Seq. This experiment includes 3 samples comprising 3 biological replicates.

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raw data will be provided later
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first: Joseph

middle: N

last: Pucella

first: Alireza

last: Khodadadi-Jamayran

first: Marlon

last: Stoeckius


title: Integrative Transcriptomic and Histological Analysis in Dilated Cardiomyopathy Unveils FGFR Inhibition as a Novel Therapeutic Strategy with Anti-Cardiac Fibrosis and Cardiac Protective Effects mediated by NPR1 signaling

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

summary: Single-cell analyses were conducted to further elucidate the fibrosis-inhibitory and cardioprotective effects of AZD4547, as well as the impact of cell-cell interactions. To validate these effects in the acute phase, analyses were performed at day 7 left ventricular heart samples from control, PE/Ang II-exposed without treatment, and AZD-administered mice.

overall_design: Mouse heart dissection and single-cell preparations were performed according to the protocols provided by 10x Genomics. In brief, hearts were collected from three groups: control, AngII/PE with AZD treatment, and AngII/PE with NS treatment, seven days post pump implantation. The left ventricular (LV) chambers were anatomically dissected, and the tissues were flash-frozen in liquid nitrogen for subsequent analysis.

first: Reo

last: Hata


title: Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells [Bulk RNA-seq]

overall_design: Splenocytes were isolated from B6 WT and Ifnar1-/- mice and pre-enriched by MACS depletion. Mature pDCs were sorted as CD11c-int PDCA1+, and further subdivided by expression of Sca1 and CD69. Sca1+ CD69+ pDCs were also isolated from B6 WT mice 6hr post i.v. injection with 5ug CpG-A + DOTAP. RNA was purified and sequenced. This experiment includes 5 groups with 3 biological replicates each, comprising 15 total samples.

first: Igor

last: Dolgalev


title: Drug Screening in 3D Microtumors Reveals DDR1/2-MAPK12-GLI1 as a Vulnerability in Cancer-Associated Fibroblasts

status: Public on Aug 04 2025

city: Seattle

first: Mehlam

middle: M

last: Saifudeen

state: WA

address: 1100 Fairview Ave North

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Interactions between cancer cells and surrounding stromal cells are critical for tumor biology and treatment response. We compare drug screening results from conventional 2D cancer cell lines with 3D tumor tissues and find that, on average, three times more drugs are effective in 3D microtumors. We confirmed the effectiveness of doramapimod, a compound that reduces 3D microtumor viability and suppresses tumor growth in mouse models, has no effect on cancer cell growth in monolayers. Mechanistically, doramapimod targets DDR1/2 and MAPK12 kinases in cancer-associated fibroblasts (CAFs), decreasing extracellular matrix (ECM) production and enhancing interferon signaling. These kinases regulate ECM through GLI1 activity in CAFs, independently of canonical hedgehog signaling. Inhibiting the DDR1/2-MAPK12-GLI axis enhances the effectiveness of chemotherapy and immunotherapy in patient tumor slices and preclinical models. These findings highlight the importance of DDR1/2-MAPK12-GLI axis in CAF function and demonstrate the utility of 3D tissue models in identifying microenvironment-specific therapeutic targets.

overall_design: Table S4. KPC and E0771 tumor-bearing mice were treated with doramapimod or vehicle control. Treatment was administered according to standard protocols, and tumors were harvested at the experimental endpoint. Tumor tissues were processed for total RNA extraction and downstream transcriptomic analysis.          Table S5. Human breast cancer-associated fibroblasts (CAFs) were treated with doramapimod or vehicle control under standard culture conditions. At the end of the treatment period, cells were harvested and total RNA was extracted for downstream transcriptomic analysis.    Table S7. Human breast cancer-associated fibroblasts (CAFs) were transfected with siRNA targeting DDR1, DDR2, or MAPK12, or with a non-targeting control. Transfections were performed using standard protocols, and cells were maintained under standard culture conditions for 48–72 hours. At the endpoint, cells were harvested and total RNA was extracted for downstream analysis.     Table S8. Human breast cancer-associated fibroblasts (CAFs) were treated with GANT61 or vehicle control under standard culture conditions. Following treatment, cells were harvested and total RNA was extracted for downstream transcriptomic analysis.


title: Immunoregulation of Raw264.7 by Nitrate in vitro

city: Beijing

first: Shaorong

last: Li

address: Tian Tan Xi Li No. 4

country: China

institute: Capital Mecidal University

summary: Macrophage balance is important in several diseases. Raw 264.7 is a macrophage cell line. We previous detected that sialin (encoded by Slc17a5) play a key role in modulation of Raw264.7 which induced by LPS&IFNγ(M1 cells, proinflammatory cells) or IL4(M2 cells,anti-proinflammatory cells). Results showed nitrate could decrease the pro-inflammatory Raw264.7 cells while increase anti-inflammatory Raw26.7 cells. We transfected sialin overexpression plasmid to Raw264.7 and found that sialin could directly modulates Raw264.7 without nitrate. In this study, we want to figure out which genes could be the key factor modulated by sialin.

overall_design: The monocytes mRNA profiles of M1 and M2 , transfected by Slc17a5 overexpression plasmid or empty plasmid.

first: Guangyong

last: Sun

first: Songlin

last: Wang

first: Dong

last: Zhang


title: RNA-seq dataset of the estrogen-dependent regulation of the transcriptome in mouse mammary gland epithelial organoids

city: Québec

first: Étienne

last: Audet-Walsh

state: Québec

address: 2705 boulevard Laurier

institute: CRCHU de Québec

summary: The mammary gland development in utero and during life is strongly regulated by hormones. To study the genes regulated specifically by the estrogen signaling in the mammary epithelial population, we treated mouse mammary epithelial organoids with estradiol after 24 h of culture. 11 days later, organoids were collected, and the total RNAs were purified for sequencing. The bulk mRNA-seq data obtained were verified for raw quality, and reads were pseudo-aligned on the murine reference transcriptome (Gencode vM25). Differentially expressed genes were identified using DESeq2 to better understand the impact of estrogen signaling on the mammary epithelial cell transcriptome. These data can be reanalyzed and combined with recent single-cell RNA-seq data to study estrogen receptor transcriptome at the cellular level and better understand its role in the functions of the gland in physiological conditions, such as lactation or following endocrine-disrupting chemical exposure or pathological conditions, such as breast cancer.

overall_design: 3 mammary glands from 3 nulliparous mature adult (~24 weeks) Mus musculus C57BL/6 were used to produce organoids which were then treated with either ethanol or estradiol for a duration of 11 days. All experiments were done in triplicates. RNA has been extracted and sequenced using Illumina NovaSeq 6000 in paired ends 100bp reads.

first: Aurélie

last: Lacouture

first: Mame Sokhna

last: Sylla

first: Lucas

last: Germain


title: G-quadruplexes are a source of vulnerability in BRCA2 deficient granule cell progenitors and medulloblastoma

first: Danielle

last: Keahi

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: Biallelic pathogenic variants in the essential DNA repair gene BRCA2 causes Fanconi anemia, complementation group FA-D1. Patients in this group are highly prone to develop embryonal tumors, most commonly medulloblastoma arising from the cerebellar granule cell progenitors (GCPs). GCPs undergo high proliferation in the postnatal cerebellum under SHH activation, but the type of DNA lesions that require the function of the BRCA2 to prevent tumorigenesis remains unknown. To identify such lesions, we assessed both GCP neurodevelopment and tumor formation using a mouse model with deletion of exons three and four of Brca2 in the central nervous system, coupled with global Trp53 loss. Brca2Δex3-4;Trp53-/- animals developed SHH subgroup medulloblastomas with complete penetrance. Whole-genome sequencing of the tumors identified structural variants with breakpoints enriched in areas overlapping G-quadruplexes (G4s). Brca2-deficient GCPs exhibited decreased replication speed in the presence of the G4-stabilizer pyridostatin. Pif1 helicase, which resolves G4s during replication, was highly upregulated in tumors, and Pif1 knockout in primary MB tumor cells resulted in increased genome instability upon pyridostatin treatment. These data suggest that G4s may represent sites prone to replication stalling in highly proliferative GCPs and without BRCA2, G4s become a source of genome instability. Tumor cells upregulate G4-resolving helicases to facilitate rapid proliferation through G4s highlighting PIF1 helicase as a potential therapeutic target for treatment of BRCA2-deficient medulloblastomas.

overall_design: RNA sequencing of primary mouse medulloblastomas from mice deficient in BRCA2

middle: L

first: Mary

middle: E

last: Hatten

first: Agata

last: Smogorzewska


title: Ethanol induces neuroimmune dysregulation and soluble TREM2 generation in a human iPSC neuron, astrocyte, microglia triculture model

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Alcohol use disorders (AUDs) affect substantial populations worldwide and increase the risk of developing cognitive impairments and alcohol-associated dementia. While the precise mechanisms underlying alcohol-associated neuropathology remain enigmatic, chronic inflammatory signaling likely plays an important role in alcohol-associated neurological sequalae. We hypothesize that alcohol leads to neuroimmune dysregulation among neurons, astrocytes, and microglia; and is perpetuated by innate immune signaling pathways involving cell-cell signaling. To investigate how alcohol dysregulates neuroimmune interactions in a human context, we constructed a triculture model comprising neurons, astrocytes, and microglia derived from human induced pluripotent stem cells (hiPSCs). After exposure to ethanol, we observed significant differential gene expression relating to innate immune pathways, inflammation, and microglial activation. Microglial activation was confirmed with morphological analysis and expression of CD68, a lysosomal-associated membrane protein and marker for phagocytic microglial activation. A striking finding in our study was the elevation of TREM2 expression and, specifically, TREM2 alternative splice variants that are predicted to give rise to soluble TREM2. These results suggest that ethanol exposure in the brain may lead to increased microglial activation and production of soluble TREM2219isoform through alternate splicing. Deciphering the molecular and cellular mechanisms underpinning ethanol-related neuroimmune dysregulation within a human context promises to shed light on the etiology of AUD and AUD-associated dementia, potentially driving the development of effective therapeutic strategies.

overall_design: Cultures of combined neurons, astrocytes, and microglia prepared from human iPSC were treated with 0, 20, 40 or 75 mM ethanol for 7days, followed by analysis with RNAseq.

first: Andrew

last: Boreland

first: Yara

last: Abbo

middle: P

first: Zhiping

last: Pang


title: (p)ppGpp-dependent activation of gene expression during nutrient limitation

city: Chapel Hill

first: Adam

last: Rosenthal

state: North Carolina

address: 1521 East Franklin Street, Apartment C213

department: Microbiology and Immunology

institute: UNC

summary: As rapidly growing bacteria begin to exhaust nutrients, their growth rate slows, ultimately leading to stasis or quiescence. Adaptation to nutrient limitation requires widespread metabolic remodeling that leads to lower cellular energy consumption. Examples of such changes include attenuated transcription of genes encoding ribosome components, in part mediated by the phosphorylated nucleotides guanosine tetra- and penta-phosphate, collectively (p)ppGpp. In addition, genes such as those encoding specific proteins that facilitate survival exhibit increased expression during nutrient limitation. An example is the hpf gene, encoding a broadly conserved protein responsible for protecting the ribosome from degradation under conditions limiting for ribosome synthesis. Here we show that (p)ppGpp plays a key role in the transcriptional activation of hpf as B. subtilis cells exit rapid growth. Specifically, we demonstrate that hpf transcription during nutrient limitation requires an RNAP holoenzyme containing the alternative sigma factor σH, encoded by sigH, whose expression is normally inhibited by the AbrB repressor. However, when global protein synthesis decreases, in part dependent on (p)ppGpp, AbrB levels fall, leading to increased sigH transcription and consequently hpf activation. This mechanism couples a key physiological consequence of nutrient limitation – reduced protein synthesis – with specific gene activation, thereby linking transcriptional and translational regulation. Finally, we demonstrate that (p)ppGpp is necessary for the gene expression underlying the elaboration of developmental fates including sporulation and genetic competence. Thus, the active attenuation of protein synthesis by (p)ppGpp is not only necessary for the conservation of energetic resources but also for the proper pattern of gene activation during transition to quiescence.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: wildtype and ppGpp0 cells were fixed in 1% formaldehyde at room temperature for 30 minutes. Fixed cells were pelleted by centrifugation at 6000 RPM for 3 min at room temperature and washed with 0.02% saline sodium citrate (SSC, Invitrogen). The cell were pelleted again and resuspended in 300 µl MAAM mix (4:1 V:V dilution of methanol to glacial acetic acid) and stored at 20oC until processing. ProBac-seq sample processing was done as described previously (33). Briefly, samples were pelleted and resuspended in PBS to remove MAAM. Following PBS wash to remove MAAM the cells were incubated with lysozyme (Readylyse, Epicenter) for 30 minutes in room temperature for cell wall hydrolysis. After an additional pelleting step and PBS wash the samples were further permeabilized by a 5 min incubation in PBS-Tween (PBS with 1% final concentration of Tween-20 detergent) and a subsequent wash in PBS to remove the detergent. Permeabilized cells were resuspended in 100 μl of probe binding buffer (5 × SSC, 30% formamide, 9 mM citric acid (pH 6.0), 0.1% Tween 20, 50 μg ml−1 heparin and 10% low molecular weight dextran sulfate purchased from Molecular Instruments as Probe Binding Buffer – Cells in Suspension). A transcriptome-wide probe-set containing approximately 30,000 mRNA binding probes designed against the B. subtilis genome (33) was added to each sample before placing the samples to incubate overnight at 50oC. After overnight incubation unbound probes were removed by a series of seven washes with probe wash buffer (5 × SSC, 30% formamide, 9 mM citric acid pH 6.0, 0.1% Tween 20 and 50 μg ml-1 heparin (Molecular Instruments)) and 2 final washes in PBS. Probed and washed cells were enumerated using a flow-cytometer and ~10,000 cells per condition were processed using the ProBac-Seq protocols as described in McNulty et al. Nature Microbiology 2023

first: Sathya

last: Nagarajan

first: Jonathan

last: Dworkin


first: Nils

last: Lindstrom

overall_design: Single-cell RNA-sequencing data from control and distal-enriched (treated with 10 uM Ly29 for 48 hours between differentiation days 10-12, and 1uM CHIR and 1.5 uM LDN between differentiation days 11-12) kidney organoids. Single-cell data are from differentiation day 14 and include both DMSO control and treated organoids. Raw data were aligned to hg38, annotation Ensembl 105, using splitpipe (Parse Biosciences), and these processed scRNA-seq data used in Figure S4 (all cells, nephrogenic and insterstitial) are provided as an .rds file.

first: Achieng

last: Mary Anne

first: Lindstrom

last: Nils


title: HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs [RNA-Seq]

first: Nikhil

last: Munshi

overall_design: To investigate the impact of sub-nuclear localization of Hand2 on gene expression we profiled reprogramming experiments expressing different separation of function mutants via ChIP-seq and RNA-seq

first: Munshi

last: Nikhil

first: Kulkarni

last: Kartik


title: Transcriptomic profiling of Debaryomyces hansenii reveals detoxification and stress responses to benzo(a)pyrene exposure

city: Ciudad de México

first: Francisco

last: Padilla-Garfias

state: Ciudad de México

address: Cto. Exterior s/n, C.U., Coyoacán, 04510 Ciudad de México, CDMX

department: Genética Molecular

country: Mexico

institute: Instituito de Fisiologia Celular, UNAM

summary: The environmental accumulation of polycyclic aromatic hydrocarbons (PAHs), such as benzo(a)pyrene (BaP), poses significant threats to ecosystems and public health due to their persistent nature, mutagenic potential, and well-documented carcinogenicity. In this study, we investigated the ability of the extremophilic yeast Debaryomyces hansenii to activate specialized detoxification mechanisms for BaP degradation, even under nutrient-deprived conditions. When exposed to 100 ppm BaP, D. hansenii eliminated over 70% of the contaminant within three days while maintaining normal growth dynamics. RNA-Seq analysis revealed widespread transcriptional remodeling, with 1179 genes upregulated and 1031 downregulated under BaP-only conditions, and 1067 upregulated and 977 downregulated genes during co-metabolic exposure (2% glucose + 100 ppm BaP), from a total of 6506 annotated genes. Gene Ontology (GO) and KEGG enrichment analyses highlighted the activation of xenobiotic degradation pathways, notably involving cytochrome P450 monooxygenases (CYPs), epoxide hydrolases (EHs), and glutathione S-transferases (GSTs), alongside an enhanced antioxidant response and finely tuned glutathione homeostasis. This work provides the first comprehensive transcriptomic profile of BaP detoxification in D. hansenii, revealing an intricate and highly adaptive stress response. Collectively, these findings position D. hansenii as a promising eukaryotic platform for bioremediation in saline and contaminated environments, especially where conventional microbial candidates fall short due to environmental extremes or nutrient scarcity.

overall_design: Transcriptomes of Debaryomyces hansenii were analyzed under carbon-limited conditions with or without 100 ppm benzo[a]pyrene (BaP). Two independent experiments were performed, each with three biological replicates per condition. Samples were collected on days 0 and 3 for total RNA extraction.

first: Augusto Cesar

last: Poot-Hernández

first: Minerva

last: Araiza-Villanueva

first: Martha

last: Calahorra

first: Norma Silvia

last: Sánchez

first: Antonio

last: Peña


title: CHD4 Interacts With TBX5 to Maintain the Gene Regulatory Network of Postnatal Atrial Cardiomyocytes

first: William

middle: T.

last: Pu

state: Ma

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Atrial fibrillation (AF), the most common sustained arrhythmia, affects 59 million individuals worldwide. The transcription factor TBX5 is essential for normal atrial rhythm, and its inactivation causes loss of aCM enhancer accessibility, looping, and transcriptional identity, and causes spontaneous AF. Here we investigated mechanisms by which TBX5 regulates chromatin organization. We found that TBX5 recruits CHD4, a chromatin remodeling ATPase canonically associated with the NuRD repressor complex, to 33,170 genomic regions (TBX5-enhanced CHD4 sites). Combined snRNA-seq and snATAC-seq of CHD4 knockout (KO) and control aCMs revealed that CHD4 has both gene activator and repressor functions. CHD4-repressed genes included sarcomeric proteins from non-CM cell lineages. CHD4-activated genes were characterized by TBX5-enhanced CHD4 recruitment, which enhanced chromatin accessibility and promoted the expression of aCM identity genes. This mechanism of TBX5 recruitment of CHD4 was critical for sinus rhythm because Chd4AKO mice had increased vulnerability to AF. Our findings reveal that CHD4 is essential for maintaining aCM gene expression, aCM identity, and atrial rhythm homeostasis.

overall_design: control atria and atria from Chd4 AKO mice were used as input for TBX5 and H3K27ac CUT&RUN. Two TBX5 antibodies were used and two biological replicates were used per antibody, to create a total of 4 control and 4 chd4 ako samples. For H3K27ac, two biological replicates were used for control and KO to produce 4 samples.

first: Mason

last: Sweat


title: Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies

city: Nantes

first: Marielle

last: OLOUDE

state: Loire et Atlantique

address: 30 Bd Jean Monnet

country: France

institute: The Center for Research in Transplantation and Translational Immunology

summary: Neurodevelopmental disorders (NDDs) are conditions that affect the development of the central nervous system, often identified during early childhood. These disorders include intellectual disability, communication disorders, autism spectrum disorders, and attention-deficit hyperactivity disorder (ADHD). Approximately 40% of NDDs are monogenic diseases, with at least 8% involving genes of the ubiquitin-proteasome system (UPS). This conserved proteolytic system plays a key role in protein homeostasis by degrading ubiquitin-tagged proteins. Among monogenic pathologies linked to the UPS, genetic variations directly affecting the 26S proteasome define a new subclass of NDDs known as neurodevelopmental proteasomopathies. The submitted data originate from an exhaustive study on several unique variants identified in the PSMC5 gene, which encodes the AAA-ATPase subunit PSMC5/Rpt6 of the 26S proteasome. Functional analyses conducted in this study revealed that these alterations lead to a loss of proteasome function, triggering a complex cellular program involving an inflammatory response and innate immunity remodeling. To further investigate these observations, gene expression was analyzed using NanoString on an autoimmune gene panel, revealing a type I interferon signature in the patients. These results were confirmed by 3'seq-RNA Profiling (3'SRP), which showed strong overexpression of genes in the type I interferon pathway, accompanied by transcriptional dysregulation involving alterations in innate immunity and inflammatory processes. The provided data thus confirm the central role of PSMC5 gene alterations in the pathogenesis of neurodevelopmental proteasomopathies.

overall_design: 3’seq-RNA Profiling (3'SRP) performed on two types of cells : (i) Lymphocytes T cells in technical replicates: twelve control samples from unaffected unrelated individuals and four samples from subjects with pathogens variants in PSMC5 S15 (p.Glu250Val), S23 (p.Pro320Arg), S36 (p.Arg325Trp) and S37 (p.Arg325Trp). (ii) Ectodermal cells differentiated : three derived from the iPSC clones harboring the variant p.(Arg325Trp), two derived from the control isogenic WT iPSC clones and one derived from the commercial iPSC line ASE-9211

last: Oloude

first: Martin

last: Braud

first: Julie

last: Mignon

first: Cynthia

last: Fourgeux

first: Jeremie

last: Poschmann

first: Sebastien

last: Kury


title: Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [MD901_RNAseq_Day5]

city: Nice

first: Pilar

last: Dominguez

state: Provence-Alpes-Côte d'Azur

address: 151 Route de Saint-Antoine

institute: Centre Méditerranéen de Médecine Moléculaire: C3M

summary: Diffuse large B-cell lymphoma (DLBCL) refers to an aggressive lymphoma that arises from germinal center (GC) B-cells, which differentiate into plasma cells (PC) to produce high affinity antibodies. 40% of DLBCL patients relapse or are refractory to the conventional immunochemotherapy treatment, usually with fatal consequences. DLBCL is characterized by profound alterations in the epigenome, which is correlated with poor survival. The abnormal epigenetic landscape of DLBCL tumors is associated with a blockade in GC exit and differentiation programs, which are regulated by the transcription factor BCL6. This aberrant repression of BCL6-target genes is mediated by 1) increased DNA methylation and 2) loss of acetylation of the lysine 27 of histone 3 (H3K27ac)-through recruitment of histone deacetylase 3 (HDAC3). Thus, we investigated the efficacy against DLBCL of the hypomethylating agent (HMA) 5-Azacitidine (5-Aza) and a specific HDAC3 inhibitor (HDAC3i). We found that treatment with 5-Aza plus HDAC3i had a potent synergistic anti-tumor activity in vitro and in vivo, which was superior to the effect of each single drug or 5-Aza combined with non-specific HDACi and, importantly, was not associated with toxicity in normal cells. We also demonstrated that the combined 5-Aza and HDAC3i treatment induced the epigenetic remodeling of DLBCL cells, which resulted in a more potent re-expression of PC differentiation genes, including XBP1 and ATF4, compared to each drug used as single agents. Our results highlight the importance of specifically targeting multiple layers of the epigenome to maximize the efficacy of epigenetic-based therapies.

overall_design: MD901 lymphoma cells were treated with  5-Azacitidine (or vehicle) daily for 5 days, with a HDAC3 inhibitor (or vehicle) added at day 2 and 4. Cells were analyzed at day 5 (3 replicates per group).

first: Izabela

last: Todorovski

first: Emilio Manuel

last: Serrano-Lopez

first: Matt

middle: R

last: Teater

first: Killian

last: Guiraud

last: Huertas-Lopez


title: Axial Nephron Fate Switching Demonstrates a Plastic System Tunable on Demand [RNA-seq]

first: Nils

last: Lindstrom

address: 1425 San Pablo St, BCC 413

institute: University of Southern California

summary: The human nephron is a highly patterned tubular structure. Approximately 1 million nephrons form in each kidney during embryonic and fetal development and develop specialized cells that regulate bodily fluid homeostasis, blood pressure, and urine secretion throughout life. This raises the question of how these cells originally develop. Here we interrogate early human nephron patterning using an iPSC-based kidney organoid system that generates hundreds of developmentally synchronized nephron structures. We show that human nephron patterning is controlled by integrated WNT/BMP/FGF signaling. Imposing a WNThigh/BMPlow state established a distal identity that matures into thick ascending loop of Henle cell identities by activating FGF. Simultaneous suppression of FGF signaling reverts cells to a proximal cell-state, thereby indicating the dependence on FGF signaling for distal cell formation in the human nephron. Our system highlights plasticity in nephron identities and mechanisms controlling normal patterning.

overall_design: Total mRNA-sequencing data from DMSO control and distal-enriched (treated with 10 uM Ly29 for 48 hours between differentiation days 10-12, and 1uM CHIR and 1.5 uM LDN between differentiation days 11-12) kidney organoids. Bulk data are organoids from differentiation day 14 and 20 from different conditions and include both DMSO control and treated organoids. Raw data were aligned to hg38, annotation Ensembl 105, and aligned raw feature counts are provided as .txt files.

first: Mary Anne

last: Achieng


title: CHD4 Interacts With TBX5 to Maintain the Gene Regulatory Network of Postnatal Atrial Cardiomyocytes [bulk RNA-seq]

city: Boston

last: Pu

overall_design: Mice were treated with Nppa-Cre to generate CHD4 AKO and control mice. Samples were processed for bulk RNA-seq

first: Frank

last: Conlon

first: Wei

last: Shi


title: Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells [Multiome]

first: Boris

last: Reizis

overall_design: We sorted splenic pDCs (Bst2+ CD11cint Cx3cr1- CD11b-) from naïve C57BL/6 (B6) wild-type (WT) mice and examined them using 10x Genomics Mulitome approach combining single-nucleus RNA sequencing (snRNA-Seq) and assay for transposase-accessible chromatin (snATAC-seq). This experiment includes 1 sample comprising 1 biological replicate.

first: Joseph

last: Pucella

first: Eduardo

last: Esteva


title: CHD4 Interacts With TBX5 to Maintain the Gene Regulatory Network [multiome]

first: William

overall_design: Mice were treated with Nppa-Cre to generate CHD4 AKO and control mice. Samples were processed using the 10x snRNA-seq and snATAC-seq kits to generate multiome libraries

first: Mason

last: Sweat


title: CHD4 Interacts With TBX5 to Maintain the Gene Regulatory Network of Postnatal Atrial Cardiomyocytes [ChIP-seq]

overall_design:
TBX5 flox/flox mice were treated with Nppa-Cre to generate TBX5 AKO and control mice. Samples were processed for CHD4 ChIP-seq
Please note that processed data was generated from both ChIP and input raw data and is linked to the corresponding ChIP-seq sample records.


title: Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells

overall_design: Refer to individual Series


title: Acetic acid produced by Staphylococcus epidermidis remodels chromatin architecture and suppresses gene expression in Malassezia restricta [ChIP-Seq]

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Malassezia restricta and Staphylococcus epidermidis are dominant members of the human skin microbiome that interact closely, yet the molecular basis of their interaction remains unclear. In this study, we investigated how S. epidermidis-derived acetic acid (AcOH) influences chromatin organization in M. restricta. We generated the first high-resolution three-dimensional genome architecture map of M. restricta using in situ Hi-C and identified putative centromeric regions based on inter-chromosomal contact patterns. Exposure to AcOH, either by co-culture or direct treatment, led to large-scale chromatin decompaction and enhanced centromere clustering. These findings indicate that AcOH acts as an epigenetic modulator, inducing significant reorganization of nuclear architecture in M. restricta. This dataset provides a resource for understanding interkingdom interactions and the epigenetic effects of bacterial metabolites on fungal chromatin structure.

overall_design: This study examines histone acetylation dynamics in Malassezia restricta under normal and acidic conditions. ChIP-seq libraries were generated using antibodies against H3K9ac and H3K27ac under normal and pH 5.0 adjusted by HCl. These datasets reveal how low pH conditions affect chromatin acetylation patterns in M. restricta, offering insights into epigenetic responses to acidic stress.

first: Jae Min

last: Lee

first: Hyun Oh

last: Yang

first: Hideki

last: Tanizawa

first: Ken-ichi

last: Noma

first: Tae Kwon

first: Won Hee

last: Jung

first: Kyoung-Dong

last: Kim


title: The Islet-1 Interaction Partner Rnf20 Regulates   Glucose Homeostasis and Pancreatic β-cell Identity.

city: Birmingham

first: Chad

last: Hunter

state: AL

address: 1825 University Blvd

department: Medicine

institute: University of Alabama at Birmingham

summary: Diabetes is characterized by a loss of functional β-cell mass, thereby identifying factors involved in establishing and preserving β-cell identity and function is critical for future therapies aiming to combat rising diabetes incidence. While transcription factors are crucial β-cell regulators, knowledge of the interacting co-regulators facilitating gene expression is limited. Previously, we demonstrated that the Islet-1 (Isl1) transcription factor forms complexes with histone ubiquitin ligases Rnf20 and Rnf40 to regulate β-cell gene expression and insulin secretion in vitro. Here, we investigated whether Rnf20-mediated complexes are required for β-cell function in adult islets using an adult-inducible β-cell-enriched Rnf20 knockout mouse model, termed Rnf20Δβ-cell . Tamoxifen induction of Rnf20 recombination prompted a robust loss of histone 2B monoubiquitination (H2Bub1) in β-cells and imparted severe hyperglycemia and glucose intolerance, reduced plasma insulin levels following a glucose challenge, and an overall reduction in insulin content. Expression of mRNAs and proteins involved in glucose stimulated insulin secretion (GSIS) and β-cell identity were also dysregulated in Rnf20Δβ-cell mice. Furthermore, comparative loss  of either Rnf20 or Isl1 yielded a similar differential expression of numerous β-cell factors, supporting that Isl1::Rnf20  complexes and histone H2B mono-ubiquitination are critical regulators of cellular identity and function.

overall_design: To assess the transcriptional mechanisms by which Rnf20 regulates beta cell identity in an unbiased manner, we performed RNA-seq with whole islet RNA from a Rnf20 beta cell enriched knockout mouse model

first: Pierre

middle: H

last: Tanya

first: Bethea

last: Maigen

first: Coutinho

middle: V

last: Kristen

first: Liu

last: Yanping

first: Hunter

last: Chad


title: RNAseq analysis of mouse skin cells upon application of hypobaric pressure

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

institute: INSERM

summary: The impact of physiological stretching on skin cells remains poorly understood. Here we analyzed the transcriptome of immune and non-immune skin cells 6h after application of hypobaric pressure.

overall_design: Skin cells were sorted on a FACSAria instrument into CD45+ and CD45- cells.

first: Darawan

last: Tabtim-on


title: Immunoregulation of Intrahepatic Bone Marrow Monocyte–Derived Macrophages by Dietary Nitrate Prevents Nonalcoholic Fatty Liver Disease

first: Shaorong

last: Li

summary: Although nonalcoholic fatty liver disease (NAFLD) is one of the leading causes of liver disease worldwide, no efficient treatment has been approved yet. We investigated whether oral nitrate administration prevents development of diet-induced NAFLD in two mouse models. Nitrate exerted its protective effect mainly through rebalancing of pro- and anti-inflammatory bone marrow monocyte–derived macrophages (MoMFs) in the liver. Using an NAFLD model in relatively germ-free mice and bone marrow–transplanted mice with a heritable Slc17a5 mutation, we showed that nitrate can prevent NAFLD by direct regulation of MoMFs through sialin, besides via the classical nitric oxide pathway. In vitro studies revealed that nitrate directly regulates mouse and human macrophages through the sialin-Sema4A pathway. Our work demonstrated for the first time nitrate’s ability to prevent NAFLD by directly modulating the homeostasis of hepatic pro- and anti-inflammatory macrophages, which indicates a novel strategy for potential clinical application in NAFLD.

overall_design: The monocytes mRNA profiles of M1 and M2 , Slc17a5 siRNA-M1 and  Slc17a5 siRNA-M2 were stimulated with or without nitrate

first: Guangyong

last: Sun

first: Songlin

last: Wang

first: Dong

last: Zhang


title: Alteration of skin fibroblast steady state contributes to healing outcomes [scRNA-seq]

status: Public on Aug 08 2025

city: New Haven

first: Yaqing

last: Huang

state: CT

address: 10 Amistad Room 304A

institute: Yale University

summary: Fibroblasts display complex functions associated with distinct gene expression profiles that influence matrix production and cell communications and the autonomy of tissue development and repair. Thrombospondin-2 (TSP-2), produced by fibroblasts, is a potent angiogenesis inhibitor and negatively associated with tissue repair. Single-cell (sc) sequencing analysis on WT and TSP2KO skin fibroblast demonstrate distinct cell heterogeneity. Specifically, we found an enrichment of Sox10+ multipotent progenitor cells, identified as Schwann precursor cells, in TSP2KO fibroblasts, while fibrosis-related subpopulations decreased. Immunostaining of tissue and cells validated the increase of this Sox10+ population in KO fibroblasts. Furthermore, in silico analysis suggested enhanced pro-survival signaling, including WNT, TGF-β, and PDGF-β, alongside a reduced BMP4 response. Additionally, the creation of two TSP2KO NIH3T3 cell lines using the CRISPR/Cas9 technique allowed functional and signaling validation in a less complex system. Moreover, KO 3T3 cells exhibited enhanced migration and proliferation, with elevated levels of pro-regenerative molecules including TGF-β3 and Wnt4, and enrichment of nuclear β-catenin. These functional and molecular alterations likely contribute to improved healing and increased neurogenesis in TSP2-deficient wounds. Overall, our findings describe the heterogeneity of dermal fibroblasts and identify pro-regenerative features of TSP2KO fibroblasts.

overall_design: we applied single-cell (sc-) to WT and TSP2KO mouse dermal fibroblasts (n=3).

first: Nuoya

first: Hao

last: Xing

first: Jingru

last: Tian

first: Dingyao

first: Daqian

last: Gao

first: Henry

last: Hsia

first: Jun

last: Lu

first: Sam

last: Raredon

first: Themis

last: Kyriakides


title: Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas [ATAC/ChIP/RNA]

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary: The mammalian SWI/SNF (mSWI/SNF) family of chromatin remodelers govern cell type-specific chromatin accessibility and gene expression and assemble as three distinct complexes: canonical BAF (cBAF), Polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF). ARID1A and ARID1B are paralog subunits that specifically nucleate the assembly of cBAF complexes and are frequently dual deleted in highly aggressive differentiated endometrial carcinomas (DECs). Here, in cellular models and primary human tumors, we find that ARID1A/B-mediated cBAF loss results in increased ncBAF and PBAF biochemical abundance and function genome-wide to maintain the DEC oncogenic signature. Further, treatment of ARID1A/1B-mutant cell lines and PDX models in vivo with a clinical-grade SMARCA4/2 ATPase inhibitor, FHD-286, markedly attenuates cell proliferation and tumor growth, and synergizes with carboplatin-based chemotherapy. Taken together, these findings reveal the oncogenic contributions of shifted of mSWI/SNF family complex abundance and chromatin-level gene regulatory functions and suggest therapeutic utility of mSWI/SNF complex small molecule inhibitors in dedifferentiated endometrial carcinoma and other cBAF-disrupted cancer types.

overall_design: Endometrial carcinoma cell lines (DECs) were treated with either Dox-induced ARID1A, ARID1B, or ARID1A and ARID1B expression. WT cell lines were also treated with either Compound-12 (SMARCA4/SMARCA2) or dBRD9. Normal and well-differentiated cancer tissue was compared to paired dedifferentiated endometrial tissue. Patient-derived xenograft models were compared to tissue treated with Compound-14 or dBRD9.

first: Jessica

last: St. Laurent

first: Alexander

last: Ying


title: Genome-wide CRISPR/Cas9 screen in HEC1B isogenic cell lines

summary: This study was designed to conduct the genome-wide CRISPR/Cas9 screen in HEC1B cells and its ARID1B knockout derivative cells.

overall_design: We conducted the screen in each cell line with  TkoV3 genome-wide CRISPR/cas9 library at a coverage of 250x. Cells were infected with TKOv3 genome-wide library (Addgene, #90294; PMID: 28655737) at a transduction efficiency of 30% aiming 500 times representation of each sgRNA. Cells were selected with puromycin for two days and 20x10^6 cells collected as a baseline. Remaining cells were kept in culture for 18 days post-infection and collected as the endpoint. Genomic DNA was isolated using QIAamp DNA Blood Maxi Kit following manufacturer’s instructions. sgRNA library was amplified from genomic DNA using Illumina-compatible index primers and sequenced by NovaSeq platform aiming for 300-500 times read coverage. The sequencing data was analyzed statistically using the MAGeCK software to identify dependenciesCells were infected with lentiviral library, which were selected by puromycin 24 hours later. 3 days after puromycin selection, half of the cells were collected as baseline. The remaining cells were maintained for an additional two weeks  for prolonged selection before harvesting as endpoints. Genomic DNA was extracted for library preparation and sequencing using Illumina.

first: Yemin


title: Acetic acid produced by Staphylococcus epidermidis remodels chromatin architecture and suppresses gene expression in Malassezia restricta

first: Yong-Joon

last: Cho

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Malassezia restricta
Malassezia sympodialis


title: Acetic acid produced by Staphylococcus epidermidis remodels chromatin architecture and suppresses gene expression in Malassezia restricta [Hi-C]

platform_organism:
Malassezia restricta
Malassezia sympodialis

overall_design: This study investigates how bacterial interactions and environmental factors influence chromatin architecture in Malassezia species using in situ Hi-C. Hi-C libraries were generated under the following conditions: 1) M. restricta co-cultured with S. epidermidis, 2) M. restricta co-cultured with S. aureus, 3) M. restricta cultured under varying pH conditions and in the presence of lactic acid, 4) M. restricta and M. sympodialis treated with acetic acid These datasets provide insights into the three-dimensional genome organization of Malassezia under diverse interkingdom and environmental stimuli, with a focus on epigenetic regulation mediated by microbial metabolites.

first: Jae Min

last: Lee

first: Hyun Oh

last: Yang

first: Hideki

last: Tanizawa

first: Ken-ichi

last: Noma

first: Tae Kwon

first: Won Hee

last: Jung

first: Kyoung-Dong

last: Kim


title: Rescue of spinal cord pathology by peripherally administered AR-targeted ASO in symptomatic AR113Q mice

city: Ann Arbor

first: Andrew

last: Lieberman

address: 1150 W Medical Center Dr.

institute: University of Michigan

summary: Degeneration of the neuromuscular system is a characteristic feature of spinal and bulbar muscular atrophy (SBMA), a CAG/polyglutamine (polyQ) expansion disorder caused by mutation in the androgen receptor (AR). Using a gene targeted mouse model of SBMA, AR113Q mice, we demonstrate age-dependent degeneration of the neuromuscular system that initially manifests with muscle weakness and atrophy and progresses to include denervation of neuromuscular junctions and lower motor neuron soma atrophy. Using this model, we tested the hypothesis that therapeutic intervention targeting skeletal muscle during this period of disease progression arrests degeneration of the neuromuscular system. To accomplish this, AR-targeted antisense oligonucleotides were administered subcutaneously to symptomatic AR113Q mice to reduce expression of polyQ AR in peripheral tissues but not in the spinal cord. This intervention rescued muscle atrophy, neuromuscular junction innervation, lower motor neuron soma size, and survival in aged AR113Q mice. Single-nucleus RNA sequencing revealed age-dependent transcriptional changes in the AR113Q spinal cord during disease progression which were mitigated by peripheral AR gene silencing. Our findings underscore the intricate interplay between peripheral tissues and the central nervous system in SBMA and emphasize the therapeutic effectiveness of peripheral gene knockdown in symptomatic disease.

overall_design: Bulk RNA-seq data from lumbar spinal cord extracted from wild-type C57BL6/J male mice, aged to 52 weeks old, having received once weekly subcutaneous injection of AR-targeting or non-targeting (NT) ASO at 25 mg/kg in sterile PBS starting at 26 weeks of age. N = 6 mice for AR-ASO, 5 mice for NT-ASO.

first: Changwoo

first: Zhigang

last: Yu

first: Curtis

last: Kuo

first: Leon

last: Tejwani

first: Rosalie

last: Grijalva

first: Eunwoo

last: Bae

first: Hien

middle: T

last: Zhao

first: Janghoo

last: Lim


title: Retinoic acid receptor-related orphan receptor α regulates bystander activation of memory CD8+ T cells

status: Public on Aug 03 2025

city: Sapporo

first: Kensuke

last: Takada

address: N21W11 Kita-ku

institute: Hokkaido University

summary: Background: Memory CD8+ T cells sense inflammation and rapidly produce interferon-γ (IFN-γ) independent of cognate antigens. This innate-like property, called bystander activation, is involved in early host defense before the antigen-specific memory response. However, the molecular mechanisms underlying this activation remain unknown. Retinoic acid receptor-related orphan receptor α (RORα) belongs to the nuclear receptor family and regulates gene transcription in ligand-dependent manner. Although RORα is highly expressed in memory CD8+ T cells, its functional relevance has not been investigated. Methods: Primary and secondary memory T cells that are sufficient or deficient of RORα were induced by adoptive transfer of naïve OT-I T cells to recipient mice and subsequent infection with Listeria monocytogenes expressing ovalbumin (LM-OVA). RORα expression in memory T cells were examined by quantitative PCR. The target genes of RORα in memory T cells were explored by RNA-sequencing and verified by RORα overexpression in postactivated T cells. The impact of RORα-deficiency on bystander activation was assessed by stimulating memory T cells with inflammatory cytokines in vitro or injecting lipopolysaccharide (LPS) into mice bearing memory T cells. Results: RORα expression was remarkably elevated in secondary memory CD8+ T cells along with the enrichment of effector-like memory T cells. RORα primarily acted as a transcription factor in regulating the gene expression of the TL1A receptor. RORα deficiency abrogated the IFN-γ production by memory CD8+ T cells in response to IL-12 + TL1A in vitro and diminished the bystander response to LPS-induced inflammation in vivo. Conclusion: This study revealed a regulatory mechanism of bystander activation. The findings also improve our understanding of how memory T cells increase their immediate protective capacity through repeated infections and vaccinations.

overall_design: ChIP-seq data of activated CD8+ T cells retrovially overexpressing Rora fused with AM tag. Cells expressing only AM tag were used as control.

first: Zimeng

last: Cai

first: Mina

last: Kozai

first: Hironobu

last: Mita

first: Hiroto

last: Takeuchi

first: Satoru

last: Mizuno

first: Kazuhiro

last: matsuo