title: Genetic diversity of Collaborative Cross mice reveals FFAR3 as a target for ILC2 anti-inflammatory reprogramming

city: Nashville

first: Mark

last: Rusznak

state: Tennessee

address: 1161 21st Ave S

department: Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine

institute: Vanderbilt University Medical Center

summary: Pulmonary group 2 innate lymphoid cells (ILC2s) are key drivers of Type 2 inflammation in diseases like asthma, yet the molecular mechanisms regulating their function are incompletely understood. Using the genetically diverse Collaborative Cross (CC) mouse panel, we mapped a quantitative trait locus (QTL) that governs ILC2 prevalence in the lung after aeroallergen exposure. This QTL creates a large population of ILC2s in the lung that are resistant to activation and have diminished Type 2 effector function. We identified free-fatty acid receptor 3 (FFAR3) as a gene responsible for this effect and demonstrated that FFAR3 signaling reprograms ILC2s to an anti-inflammatory state by promoting their survival, reducing Type 2 cytokine production, and enhancing IL-10 expression. This reprogramming is mediated by epidermal growth factor receptor (EGFR) upregulation. We showed that FFAR3's anti-inflammatory effect is conserved in human ILC2s, making it a potential therapeutic target for Type 2 inflammation.

overall_design: Naive group 2 innate lymphoid cells (ILC2s) were isolated from the unchallenged lungs of mice by flow cytometry. We obtained ILC2s from both female C57BL/6J mice and female CC030/GeniUnc (Collaborative Cross) mice. Experiment 1: ILC2s were sorted from unchallenged C57BL/6J and CC030/GeniUnc lungs directly into buffer for analysis, allowing for comparison of C57BL/6J and CC030/GeniUnc ILC2s in the naive state. Cells were sorted separately from 3 mice of each strain. Experiment 2: ILC2s were flow sorted from CC030/GeniUnc, and all ILC2s were cultured with IL-33, TSLP, and IL-2. ILC2s received either DMSO vehicle or AR420626 treatment (FFAR3 agonist, 10uM). ILC2s were isolated from 5 CC030/GeniUnc, and cells from each biological replicate were split between vehicle and treatment condition to allow for paired samples. Cells were harvested at Day 2 and Day 6 of culture for analysis.

first: Shinji

last: Toki

first: Yajing

last: Hao

first: Marc

middle: J

last: Todd

first: Liddy

last: Malone

first: Julia

last: Goodhead

first: Catherine

last: DuPuy

first: Dominique

last: Babin

first: Christian

middle: M

last: Warren

first: Masako

last: Abney

first: Matthew

last: Stier

last: Thomas

first: Jing

last: Li

last: Jacobse

last: Petrovic

first: Jacqueline-Yvonne

last: Cephus

first: Shelby

middle: N

last: Kuehnle

first: Allison

last: Norlander

first: Fang

first: Jeremy

last: Goettel

first: Darla

middle: R

last: Miller

last: Lynch

first: Daniel

middle: P

last: Cook

first: Dawn

middle: C

last: Newcomb

first: Fei

last: Zou

first: R Stokes

last: Peebles Jr


title: Human naïve-like T follicular regulatory cells are primed for differentiation into mature Tfr and disrupted during severe infections. (treatment with TPC or IL2)

status: Public on Nov 14 2025

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

type: Expression profiling by high throughput sequencing

summary: Regulatory T cells (Tregs) play a pivotal role in maintaining immune self-tolerance and homeostasis. T Follicular regulatory cells (Tfr) are a specific Treg population expressing the chemokine receptor CXCR5 and is known to regulate antibody production and prevent autoantibody induction. However, the stages of Tfr formation have still not been clarified. Here we found that 30-50% of Tfr in human blood have a naïve-like phenotype (nTfr, CD45RA+CD45RO−Foxp3+CXCR5+). nTfr are expandable in vitro while retaining suppressive capacity. nTfr are transcriptionally similar to nTreg ex-vivo but after stimulation, they gain increased expression of Tfr-related suppressive molecules such as IL1RA, suggesting they are primed for full differentiation into mature Tfr. We also found that nTfr has enhanced wound healing capacity, indicating a non-canonical function of this Treg subset. Further, we demonstrate that nTfr but not nTreg are significantly reduced in the blood of COVID-19 and sepsis patients and that this loss is correlated with increased anti-Interferon-γ antibodies. Together, these data suggest that Tfr are disrupted at the earliest stage of their formation during severe disease and may be an important therapeutic target in future vaccine developments.

overall_design: nTreg and nTfr cells were isolated from human PBMCs using fluorescence-activated cell sorting (FACS). nTreg cells were sorted as CD4+CD25+CD127−CD45RA+CD45RO− CXCR5− cells, while nTfr cells were sorted as CD4+CD25+CD127−CD45RA+CD45RO−CXCR5+cells. eTreg cells were sorted as CD4+CD25+CD127−CD45RA−CD45RO+ CXCR5− and eTfr cells were CD4+CD25+CD127−CD45RA−CD45RO+CXCR5+.

first: Janyerkye

last: Tulyeu

first: James

last: B. Wing

first: Jonas

last: N. Søndergaard


title: Human naïve-like T follicular regulatory cells are primed for differentiation into mature Tfr and disrupted during severe infections.


title: Transcription Factor Yin-Yang 1 governs cardiac metabolic reprogramming in response to exercise or pathological stress

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

country: USA

institute: University of Pittsburgh

summary: The pleiotropic transcription factor Yin Yang 1 (YY1) regulates cellular metabolism in a stage- and tissue-dependent manner. However, its role in cardiac energetic regulation remains unclear. We found that cardiac-specific YY1 knockout (cYY1 KO) mice exhibited cardiac dysfunction after two weeks of swimming exercise, suggesting an impaired adaptive cardiac response. Further analysis revealed that exercise-induced upregulation of transcription factor networks controlling cardiac metabolism, including peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α), was blunted in cYY1 KO mice. Consistently, citrate synthase activity, an indicator of mitochondrial content, was reduced in these mice. In response to transaortic constriction (TAC), cYY1 KO mice developed significantly exacerbated heart failure. RNA sequencing showed downregulation of metabolic genes and pathways, including PGC-1α, in TAC cYY1 KO mice hearts. Additionally, mitochondrial complex protein levels and complex I activity were reduced, consistent with suppressed metabolic gene transcription. Previously, we observed increased YY1 expression in hearts subjected to both exercise and TAC. However, while cardiac metabolism was enhanced with exercise, it was impaired with TAC. We found that p300 binding to YY1 increased during exercise, whereas histone deacetylase 3 (HDAC3) binding to YY1 increased in TAC hearts. These findings suggest that YY1-mediated transcriptional regulation of metabolic genes is modulated by the epigenetic regulators p300 and HDAC3.

overall_design: All these samples are C57BL/6 male mice. All samples were obtained from heart tissues of MerCreMer control mice or cardiac-specific Yin-Yang 1 knockout mice, one week after transverse aortic constriction surgery.

first: Manling

last: Zhang

first: Zishan

last: Peng

first: Haiqing

last: Ping

first: Zoe

last: Li

first: Jia-Jun

first: Silvia

first: Ning

last: Feng


title: Human Immuno-Lung Organoid Model to Study Macrophage-Mediated Lung Cell Senescence Upon SARS-CoV-2 Infection [snMultiomics]

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we utilized spatial transcriptional assays (NanoString CosMx) to analyze both explant and autopsy samples from non-COVID and COVID-19 lungs, identifying activation of proinflammatory macrophages. We then created macrophage-alveolar and macrophage-airway organoid models, integrating hPSC-derived macrophages with alveolar or airway organoids, and discovered that proinflammatory macrophages induce lung cell senescence through via the THBS1-(ITGA3+ITGB1) pathway. This study not only establishes immune-lung organoid models for studying macrophage-mediated host damage but also highlights the previously unrecognized role of the THBS1-(ITGA3+ITGB1) pathway in lung cell senescence during infectious diseases.

overall_design: scRNA-seq analysis identified increased senescence in lung cells, including AT2 cells, within immune-alveolar organoids upon SARS-CoV-2 infection. The increase of senescence in lung cells was further confirmed in alveolar organoids co-cultured with proinflammatory macrophages. CosMx analysis and immunostaining validated the upregulation of senescence in lung cells within lung explant samples.

first: Jianwen

last: Que

first: Yuling

last: Han

first: Liuliu

last: Yang

first: Dongliang

last: Leng

first: Tuo

first: Jian

last: Ge

first: Yinshan

last: Fang


title: Human Immuno-Lung Organoid Model to Study Macrophage-Mediated Lung Cell Senescence Upon SARS-CoV-2 Infection

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

overall_design: Refer to individual Series


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

summary: The central nervous system represents a uniquely immune-privileged environment, with inflammatory responses involving several resident CNS-specific cell types. While stereotyped cellular and transcriptional responses recur across varied diseases, relevant signaling pathways and regulatory networks are not fully understood. Here, we describe a screening platform based on high-throughput RNA-seq analysis and glial cell state gene set scores that enables multimodal investigation of inflammatory networks at scale. As proof-of-concept, we investigate genetically heterogeneous mice from a large-scale chemical mutagenesis screen to identify novel functionally relevant variants in six genes previously linked to human CNS disorders: Nrros, Ctsd, Smpd1, Idua, Nlrp1a, and Inpp5d . We leverage the rich and readily-interpretable data from our study to demarcate distinct inflammatory states arising from each mutation. In all, our work provides a methodology for discovering novel regulators of CNS neuroimmune homeostasis and provides a validated analysis framework for identifying discrete neuroinflammatory modules that are engaged divergently across disease contexts.

overall_design:
RNA-seq was performed on brain RNA from a large cohort of ENU-mutagenized mice. Brain RNA was converted into a 3' cDNA library using  SMART-Seq® v4 3’ DE Kits and sequenced as 1152-plex libraries on Illumina instruments. RNA-seq data was mined to identify abnormal inflammation states, and exome sequencing of genomic DNA was utilized to identify candidate causal variants.

This study consists of the following series:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294402
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294446
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294465
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294528
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294535
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294643
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294665
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294686
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294826
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294832
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294836
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294845
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294849
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294911
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294926
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294936
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294958
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294968
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294978
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294983
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294988
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294992
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294994
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294996

first: Christopher

last: Bohlen

first: Lisa

middle: A

last: Miosge

first: Brad

last: Friedman


title: SF3A3 Drives Tumorigenesis in Endometrial Cancer by Enhancing c-FOS Expression and Represents a Potential Therapeutic Target

city: Hangzhou

first: Wei

last: Yu

state: Zhejiang

address: 268 Kaixuan Road

department: Institute of Translational Medicine

country: China

institute: Zhejiang University

summary: Aberrant expression of splicing factors is increasingly recognized as a critical driver of cancer progression. Herein, we unravel SF3A3, a core component of the spliceosome, being highly expressed in endometrial cancer (EC) and playing an oncogenic role by driving splicing alterations, and consequently promoting tumor progression and therapeutic resistance. Mechanistically, We found through RIP seq data that SF3A3 could specifically bind to a series of genes, including c-FOS. Subsequent experiments have confirmed that SF3A3 coud regulate the alternative splicing of c-FOS, an anti-apoptotic gene implicated in resistance to cisplatin, a first-line chemotherapeutic agent for EC. SF3A3 facilitates the inclusion of exons 2 and 3 in c-FOS, resulting in the production of full-length c-FOS, which promotes tumor progression and cisplatin resistance.

overall_design:
We overexpressed GFP-SF3A3 in KLE cells and extracted RNA bound to SF3A3 protein through IP experiments, which were then sent for RNA seq sequencing

Antibodies used in this study:
anti-SF3A3 (Cell Signaling Technology, catalog number ab157194)
anti-GFP (Proteintech, catalog number 66002-1-Ig) [Used for wb]
GFP beads(AlpalifeBio, catalog number ktsm1301) [Used for RIP-seq]

first: Yi

last: Gu

first: Wunan

last: Huang

first: Lexin

last: Liu

first: Liangjian

last: Ma

first: Weihua

last: Wang

first: Zhongkai

last: Cao

first: Xiaolei

last: Liang

first: Xiangjun

first: Lidan

last: Hu


title: Comparative gene expression profiling of high-grade serous ovarian cancer cells exposed to cisplatin or CX-5461

city: Melbourne

first: Paul

last: Neeson

state: Victoria

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: We use RNA-seq to characterise the transcriptional programs of proliferating OVCAR3, OVCAR4, OVCAR8, AOCS14 and AOCS30 cells versus those undergoing cisplatin- or CX-5461-induced senescence.

overall_design: OVCAR3, OVCAR4, OVCAR8, AOCS14 and AOCS30 cells were exposed to cisplatin, CX-5461, or vehicle controls for 48 hours. The drug was washed out and replaced with fresh media. At 6 days post-washout, total RNA was extracted for RNA-seq.

first: Chan

last: Keefe T.

first: Cerra

last: Carmelo

first: Tancock

last: Madeleine R.C.

first: Thio

last: Niko


title: Epicutaneous Staphylococcus aureus exposure triggers lung inflammation via epithelia-intrinsic IL-36R signaling in a murine model of the atopic march

city: Baltimore

first: Sabrina

last: Kline

state: Maryland

address: 1550 N Orleans St Suite 216

department: Dermatology

institute: Johns Hopkins Medicine

summary: Investigation of the pathways involved in neutrophilic lung inflammation associated with epicutaneous S. aureus exposure

overall_design: Dorsal fur of mice was shaved and depilated, followed by epicutaneous S. aureus (1e8 CFU) and cockroach antigen exposure using  for 7 days. On day 10, 11 and 12, cockroach antigen was applied intratracheally. On day 13, the lungs were perfused and excised. RNA was extracted and sent for RNA  sequencing.

first: Yoshine

last: Saito

first: Laine

middle: E

last: Feller


title: Human Immuno-Lung Organoid Model to Study Macrophage-Mediated Lung Cell Senescence Upon SARS-CoV-2 Infection [scRNA-seq]

first: Shuibing

last: Chen

summary: In this study, we utilized spatial transcriptional assays (NanoString CosMx) to analyze both explant and autopsy samples from COVID and non-COVID-19 lungs, identifying activation of proinflammatory macrophages. We then created macrophage-alveolar and macrophage-airway organoid models, integrating hPSC-derived macrophages with alveolar or airway organoids, and discovered that proinflammatory macrophages induce lung cell senescence through via the THBS1-(ITGA3+ITGB1) pathway. This study not only establishes immune-lung organoid models for studying macrophage-mediated host damage but also highlights the previously unrecognized role of the THBS1-(ITGA3+ITGB1) pathway in lung cell senescence during infectious diseases.

first: Jianwen

last: Que

first: Yuling

last: Han

first: Liuliu

last: Yang

first: Dongliang

last: Leng

first: Tuo

last: Zhang

first: Jian

last: Ge

first: Yinshan

last: Fang


title: Sox6 enhances vascular smooth muscle cell phenotypic switching and elevates blood pressure by activating autophagy

city: Beijing

first: Xilan

last: Dong

state: Beijing

address: 北京市门头沟区永定镇石龙西路阜外医院西山科研基地

institute: Fuwai hospital

summary: Background: Sox6 has been shown to play a crucial role in the development of the cardiovascular system. However, its potential role in hypertension and vascular function remains unclear. Methods:  In vascular smooth muscle cells (VSMCs), we employed gain- and loss-of-function approaches combined with RNA sequencing, autophagy flux assessment, and phenotype characterization. Additionally, we established a mouse model with Sox6 overexpression via adeno-associated virus 2 (AAV2) to validate the findings in vivo. Conclusions: Our findings revealed that Sox6 regulates VSMC plasticity and elevates blood pressure by activating autophagy. Therefore, Sox6 inhibition potentially represents a novel strategy for treating hypertension and vascular remodeling.

overall_design: RNA-seq profiling of control and Sox6 knockdown mouse vascular smooth muscle cells (VSMCs).

first: Qianhui

last: Ling

first: Linjing

last: Cong

first: Haizeng

first: Jun

last: Cai

first: Zhenzhen


title: Pathogenetic mechanism of muscle-specific ribosome in heart failure

first: Xuebing

last: Wu

address: 630 West 168th Street, P&S 10-401

institute: Columbia University

summary: The heart employs a specialized ribosome in its muscle cells to translate genetic information into proteins, a fundamental adaptation with an elusive physiological role. Its significance is underscored by the discovery of neonatal patients suffering from often fatal heart failure caused by rare biallelic variants in RPL3L, a muscle-specific ribosomal protein that replaces the ubiquitous RPL3 in cardiac ribosomes. RPL3L-linked heart failure represents the only known human disease arising from mutations in tissue-specific ribosomes, yet the underlying pathogenetic mechanisms remain poorly understood despite an increasing number of reported cases. While the autosomal recessive inheritance pattern suggests a loss-of-function mechanism, Rpl3l-knockout mice display only mild phenotypes, attributed to up-regulation of the ubiquitous Rpl3. Interestingly, living human knockouts of RPL3L have been identified. Here, we report two new cases of RPL3L-linked severe neonatal heart failure and uncover an unusual pathogenetic mechanism through integrated analyses of population genetic data, patient cardiac tissue, and isogenic cells expressing RPL3L variants. Our findings demonstrate that patient hearts lack sufficient RPL3 compensation. Moreover, contrary to a simple loss-of-function mechanism often associated with autosomal recessive diseases, RPL3L-linked disease is driven by a combination of gain-of-toxicity and loss-of-function. Most patients harbor a recurrent toxic missense variant alongside a non-recurrent variant. The non-recurrent variant is often loss-of-function and enables partial compensation through RPL3, similar to Rpl3l-knockout mice. However, the recurrent missense variant exhibits increased affinity for the RPL3/RPL3L chaperone GRWD1 and 60S biogenesis factors, retains 28S rRNA in the nucleus, disrupts ribosome biogenesis, and induces severe cellular toxicity that extends beyond the loss of ribosomes. These findings elucidate the pathogenetic mechanisms underlying muscle-specific ribosome dysfunction in neonatal heart failure, providing critical insights for genetic screening and therapeutic development. Our findings also suggest that gain-of-toxicity mechanisms may be more widespread in autosomal recessive diseases, especially for those involving genes with paralogs.

overall_design: RNA-seq from ventricular tissue of explanted human heart

first: Michael

last: Murphy

first: Mythily

last: Ganapathi

first: Teresa

last: Lee

first: Wendy

last: Chung


title: Single cell sequencing of VZV gE antigen-specific T cells with vaccination and age

city: Rochester

first: Abhinav

last: Jain

address: 200 1st ST SW

institute: Mayo Clinic

summary: Generation and maintenance of a protective, durable T cell memory is incompletely understood. Here, we use single cell sequencing of VZV gE antigen-specific T cells (CD4+ or CD8+) after vaccination of younger or older adults to assess T cell heterogeneity and functional signatures.

overall_design: VZV-reactive, human peripheral blood CD4 and CD8+ T cells extracted from vaccine recipent young and older individuals underwent single cell CITESeq (RNA and Protein) and TCR sequencing.

first: Ines

last: Sturmlechner

first: Jorg

last: Goronzy


title: Single nuclear RNA sequencing reveals unique hepatocyte population in small bowel resection induced liver injury

city: St. Louis

first: Daniel

middle: Mimbs

last: Alligood

state: Missouri

address: 425 Euclid Ave - BJCIH 7118

department: Pediatric Surgery

institute: Washington University in St. Louis

summary: We employed a single nuclear RNA sequencing approach to study intestinal failure associated liver disease (IFALD) in a preclinical murine model of short gut syndrome. To understand pathogenesis of IFALD, we performed single nuclear sequencing of murine liver tissue from an preclinical murine model of short gut syndrome.

overall_design: 8 week old male mice were subjcted to 75% proximal small bowel resection and compared to sham operated mice (transection and re-anastomosis). Mice were feed a liquid diet ad lib (Test Diet LD101). Mice were harvested at the 2 week time point. Liver samples were taken from the left anterior lobe and stored in RNALater at -80C. 6 samples (3 sham and 3 SBR) were selected for single nuclear sequencing.

first: Alex

last: Park

last: Guo

first: David

last: Alvarado

first: Deborah

last: Rubin

first: Nicholas

middle: O

last: Davidson

first: Brad

middle: W

last: Warner


title: Parenchymal, airway, and vessel spatial transcriptomics signature in COPD

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Space Profiling for WTA RNA transcriptomics in lung parenchymal, airway, and vessel of COPD and control patients.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We assessed paraffin-embedded and OCT-embedded lung sections from 48 patients, which were classified as Never Smoker Controls (NSC, n6), Smoker Controls (SC, n10), and COPD GOLD1-4 patients (n34 patients).

first: Joselyn

last: Rojas-Quintero

first: Francesca

last: Polverino


title: RNA-seq in keratinocytes knocking down SIRT7 under ionizing radiation conditions

city: Guangzhou City

first: Jin

last: Yi

address: Shatai South Road

department: department of toxicology

institute: Southern Medical University

summary: To dissect the mechanism of SIRT7's radioprotective function in keratinocytes HaCaT cells, we knocked down SIRT7 using siRNA and performed RNA-seq analysis.

overall_design: HaCaT cells were treated with siControl or siSIRT7 and then exposed to ionizing radiation. RNA of the treated cells was extracted and prepared for RNA-seq.

first: Yi

last: Jin

first: Yanjie

last: Kuang

first: Jieyu

last: Liu

first: Liang

last: Zhou


title: KMT2D controls cerebellar granule cell differentiation by temporally activating neuronal transcriptional factor genes

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio


title: KMT2D controls cerebellar granule cell differentiation by temporally activating neuronal transcriptional factor genes [CUT&RUN]

summary: Spatiotemporal gene expression is the fundamental feature for cellular differentiation, including neurogenesis. The epigenetic mechanism underlying spatiotemporal gene regulation during in vivo cellular differentiation remains largely unknown. The cerebellum contains ~80% of the total number of neurons in the human brain. Granule cells (GCs) constitute the vast majority of cerebellar neurons, and GC genesis is spatiotemporally regulated. Here, we show that Atoh1-Cre-mediated knockout (ACKO) of the Kmt2d gene encoding the lysine methyltransferase KMT2D (MLL4 and a COMPASS-like enzyme) in the cerebellar GC lineage in mice inhibits cerebellar GC differentiation while increasing cerebellar cell proliferation. Kmt2d ACKO impaired cerebellum-associated behaviors and caused facial peculiarity, microcephaly, and smaller body size (Kabuki syndrome-like characteristics) in mice. KMT2D temporally activates neuronal differentiation programs in cerebellar GC lineage. KMT2D-mediated activation of the key neuronal transcription factor genes En2, Pax6, and Myt1l is critical for GC differentiation. KMT2D positively programs super-enhancers/enhancers associated with these genes. Single cell RNA-seq analysis showed that Kmt2d ACKO inhibited the transition of GC progenitor to GCs while having a cell-non-autonomous impact on other cerebellar cells. These findings provide a unique epigenetic mechanism in which KMT2D temporally orchestrates gene expression required for cerebellar GC differentiation by programming neuronal enhancers.

overall_design: CUT&RUN assays were performed using CUTANA ChIC/ CUT&RUN Kit. Analysis was performed with Pluto (https://pluto.bio) software.

first: Shilpa

middle: S

last: Dhar

first: Lee

last: MinGyu


title: RNA-seq was used to determine the miRNAs expression profiles of Ctrl-EVs and M. bovis NX2-EVs.

city: Yinchuan

first: Yiming

last: Wu

state: Ningxia

address: 539, Helanshan West Road

institute: Ningxia university

summary: In this work, we detect the effect of EVs derived from M. bovis-infected BMEC cells (M. bovis NX2-EVs) on regulating the inflammatory response of BoMac. The results indicate M. bovis-infected BMEC cells promote the inflammatory response in BoMac cells by releasing EVs. We furtherly identify the miRNAs in EVs involved in promoting inflammatory response. Understanding their cargo content will provide new insights into the molecular mechanisms of these respective EVs.

overall_design: We extracted total RNA from Ctrl-EVs and M. bovis NX2-EVs，performed gene expression profiling analysis


title: Effect of miRNA26b knockout on vascular calcification [scRNA-seq]

city: Edinburgh

first: Andrea

last: Caporali

state: Scotland

address: 47, Little France Crescent Edinburgh

country: United Kingdom

institute: University of Edinburgh

summary: Vascular calcification is the abnormal deposition of calcium phosphates within the blood vessels. Although it significantly contributes to the development of cardiovascular disease, much remains unknown about the mechanisms driving this process. Recent advances have shown that microRNAs (miRNAs) could be critical in regulating the biological processes driving vascular calcification. Here, we investigated whether miRNA-26b (miR-26b) could regulate vascular calcification. By performing scRNA-seq of the aorta of miR-26b knockout (miR-26bKO) mice, we identified cell-specific targets and demonstrated that components of the BMP signalling pathway are dysregulated in the aortic cell types.

overall_design: To investigate the contribution of miRNA26b to the development of vascualr calcification in mice we generated miRNA26b knockout model (miRNA26bKO) . We performed scRNA-seq using the whole aorta from deliniate regualated pathways in individual cell types. The whole mouse aorta was harvested from 6-month-old wild-type and miR-26bKO mice  (wildtype n = 3 and miR26bKO n = 3) to determine the transcriptomes. The aorta was dissected from surrounding tissue, and the perivascular fat was removed. Upon digestion of tissue using protocol as reported below, cells were isolated and sorted using a FACS Aria II instrument and BD FACSDiva software (BD Biosciences).

first: Diana

last: Buitrago Luna

first: Hywel

last: Dunn-Davies

first: Tijana

last: Mitic


title: Effect of miRNA26b knockout on vascular calcification [RNA-seq]

summary: Vascular calcification is the abnormal deposition of calcium phosphates within the blood vessels. Although it significantly contributes to the development of cardiovascular disease, much remains unknown about the mechanisms driving this process. Recent advances have shown that microRNAs (miRNAs) could be critical in regulating the biological processes driving vascular calcification. Here, we investigated whether miR-26b could regulate vascular calcification. By performing bulk RNA-seq of the aorta of miR-26bKO mice, we identified cell-specific targets and demonstrated that BMP signalling is dysregulated in aortic cells.

overall_design: To inivestigat the contribution of miRNA26b to the development of vascualr calcification in mice we generated miRNA26b knockout model (miRNA26bKO) . We performed RNA-seq using the whole aorta from deliniate regualated pathways.The whole mouse aorta was harvested from 6-month-old wild-type and miR-26bKO mice. The aorta was dissected from surrounding tissue, and the perivascular fat was removed. Total RNA was isolated  using Qiazol reagent and miRNeasy mini Kit (217004, QIAGEN, Germany).Bulk RNA-seq to determine the transcriptomes of the aorta of 6-month old age mice (wildtype n = 3 and miR26bKO n = 3) .


title: Function of PLAGL1 during osteogenesis of condyle

city: Shanghai

first: Jiahui

last: Du

address: Zhizaoju Road 639

institute: Shanghai Jiao Tong University

summary: We show that PLALG1 promotes osteogenesis during condyle development.

overall_design: We detected the function of PLAGL1 in mouse condyle cell during osteoblastic differentiation followed osteoblastic induction with b-glycerophosphate (b-GP) (5 mM), ascorbic acid (50 ug/ml), and dexamethasone (100 nM) in a-MEM.


title: Self-organizing human heart organoids with an autologous tissue-resident macrophage immune niche

city: East Lansing

first: Aitor

last: Aguirre

state: MI

address: 775 Woodlot Dr

department: Biomedical Engineering

institute: Michigan State University

summary: Congenital heart defects (CHDs) are the most common birth defect in humans, accounting for 1% of all births per year in the United States. The exact pathogenesis of CHDs remains largely unknown due to several reasons: complex interaction of genetic and environmental factors, lack of appropriate animal models, and the inability to directly study human heart development. Our group recently developed an advanced, three-dimensional (3D) human heart organoid (hHO) system derived from human pluripotent stem cells (hPSCs) (Lewis-Israeli et al., Nat Comm, 2021) to address this gap. The hHOs recapitulated human heart development to a significant extent and could be used for disease modeling maternal diabetes-induced CHDs. Although our current hHO system mimics many aspects of the developing human heart, it still lacks some key features, such as embryonic tissue-resident macrophages (MPs). In mice, MPs contribute to electrical conductance, lymphatic channel development, and endothelial network patterning, however their role in human heart development remains poorly understood.  We hypothesize that MPs are important contributors to heart development in humans, as they are present in embryonic human hearts, and we investigated their role in a novel in vitro hHO with integrated MPs (hHMOs). We created a stepwise protocol to generate hHOs with integrated MPs from human pluripotent stem cells. We used immunofluorescence confocal microscopy (IF) to visualize MPs within the hHOs and flow cytometry to confirm their presence in the hHOs over 60 days. We also utilized single cell RNA sequencing (scRNAseq) data of hHMOs to identify cell population and gene expression changes over time.  scRNAseq demonstrated expansion of cardiomyocyte populations and notable decreases in other cell populations in the hHMOs, such as conductance cells, stromal cells, and epicardial cells. The hHMOs recapitulate early aspects of immune cell integration in the developing heart and can be used to identify developmental changes induced by resident MPs.

overall_design: Human heart organoids (hHOs) derived from H9-hESCs. hHOs were sampled based on inclusion (hHMOs) or exclusion of macrophages (hHOs) and the day of development: Day 15 hHO, Day 15 hHMO, Day 26 hHO, and Day 26 hHMO. Cells from these samples were dissociated using a previously described protol using cardiomyocyte dissociation medium and analyzed with scRNAseq.

first: Colin

last: O'Hern

first: Artem

last: Kiselev

first: Sangbum

last: Park


title: PTEN, a master driver of nonhealing phenotype in venous leg ulcers, suppresses immune response, angiogenesis and lymphangiogenesis

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: RNA-Seq was performed on healing and non-healing  venous leg ulcers, and transcriptomes were compared to those of human acute wounds (AW). A robust suppression of inflammatory response, lymphangiogenesis and angiogenesis was hallmark of non-healing, in contrast to healing VLUs that showed similarity to physiological healing. Diminished inflammatory response in non-healing VLUs was due to impaired leukocyte transmigration and egression, with suppression of kinases’ activity, including AKT, ERK, JNK1/2, SRC, and PDGFR, underlining the non-healing signature. Bioinformatic analyses pinpointed PTEN as a master negative regulator of the processes and signaling pathways suppressed in non-healing VLU. Indeed, increased PTEN was confirmed in non-healing compared to healing VLUs on scRNA-Seq and protein level. Functional in vivo murine studies confirmed that pharmacological PTEN inhibition enhances immune response, and proinflammatory signals, leading to accelerated wound closure. We identify PTEN as a master regulator of non-healing VLU phenotype that orchestrates multiple key processes responsible for impaired healing. Targeting PTEN as a therapeutic approach may shift non-healing VLUs into healing trajectory allowing for progression of wound closure.

overall_design: Transcriptome profiles from patients with healing and non-healing venous leg ulcers generated by deep sequencing using Illumina Novaseq 6000

first: Jelena

last: Marjanovic

first: Irena

last: Pastar

first: Marjana

last: Tomic-Canic


title: KMT2D controls cerebellar granule cell differentiation by temporally activating neuronal transcriptional factor genes [RNA-seq]

first: Pluto

last: Bio


title: Cholesterol 25-hydroxylase enhances immunosuppressive function of MDSCs in colorectal cancer

city: Wenzhou

first: Dongqin

last: Zhou

address: Chashan Street

institute: Wenzhou Medical University

summary: Myeloid-derived suppressor cells (MDSCs) represent a substantial population of immunosuppressive cells within the tumor microenvironment (TME) of colorectal cancer. Previous studies have established a strong association between the immunosuppressive activity of MDSCs and the reprogramming of cholesterol metabolism; however, the underlying mechanisms remain to be fully elucidated. In this study, we identified that cholesterol 25-hydroxylase (CH25H) and its metabolite, 25-hydroxycholesterol (25HC), are significantly elevated in MDSCs associated with colorectal cancer. The knockdown of CH25H led to a decrease in the immunosuppressive capabilities of MDSCs, which was linked to the inhibition of Arginase-1 (ARG1) expression; conversely, the administration of 25HC counteracted this effect. Mechanistically, 25HC was shown to downregulate the Cyclic GMP–AMP synthase (cGAS)–stimulator of interferon genes (STING) (cGAS-STING) pathway and its downstream signaling component, TANK binding kinase 1(TBK1). Upon phosphorylation and activation, TBK1 inhibited ARG1 production. In summary, our findings indicate that CH25H-mediated accumulation of 25HC enhances the immunosuppressive function of MDSCs and promotes immune evasion in colorectal cancer by suppressing the STING-TBK1- receptor-interacting protein kinase 3(RIPK3) signaling axis. This study uncovers a novel signaling pathway involving CH25H and STING in tumor immunomodulation and suggests that targeting cholesterol metabolism may provide a promising therapeutic strategy for colorectal cancer immunotherapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for

first: Yu

last: Chen

first: Xianghua

last: Zeng


title: SOX2 phosphorylation during mitosis limits genomic damage [RNA-Seq]

first: Charles

middle: A C

last: Williams

state: Midlothian

address: 5 Little France Dr, Bioquarter, Scottish Ctr For Regenerative Medicine, Scottish Ctr For Regenerative Medicine

department: Institute for Regeneration and Repair

summary: Pioneer transcription factors (TFs) such as SOX2 play critical roles in control of stem cell identity and are dysregulated in many human cancers. For example, SOX2 regulates the self-renewal of neural stem cells (NSCs), and is typically highly expressed in glioblastoma stem cells, where it is known to induce an immature NSC-like state. Here, we explored the regulation of SOX2 by phosphorylation during cell division and identify an unexpected role for mitotic SOX2 as an inducer of genomic damage. We find that SOX2 adopts a distinct phosphorylated state in NSCs during mitosis, regulated by the mitotic kinase CDK1. Mapping of SOX2 genome occupancy and chromatin accessibility shows that a subset of SOX2 remains bound to the interphase targets, consistent with mitotic bookmarking, but phosphorylated SOX2 is redistributed to constitutive heterochromatin, including telomeres. Ablation of SOX2 phosphorylation leads to promiscuous chromatin binding across the genome and triggers prolonged mitotic transit times and increased susceptibility to DNA damage. These findings show that excessive levels of SOX2 protein in mitosis trigger inappropriate opening of chromatin and downstream chromosomal damage. Elevated levels of SOX2 in cancers may therefore have dual oncogenic roles: imposing stemness during interphase via their well-known transcriptional roles, but simultaneously inducing genomic damage during mitosis due to their unconstrained pioneer factor activity.

overall_design: Genome binding/occupancy profiling/transcriptional profiling by high throughput sequencing

first: Dounia

last: Djeghloul

first: Nicolas

last: Veland

first: Alhafidz

last: Hamdan

first: Maria

last: Kalantzaki

first: Erika

last: Lo

first: Robert

last: Illingworth

first: Alex

last: Von Kriegsheim

first: Amanda

middle: G

last: Fisher

first: Abdenour

last: Soufi

first: Steven

last: Pollard


title: BulkRNA sequence for human breast cancer FFPT tissue; TLS-poor and TLS-rich

city: St. Petersburg

first: JUNKO

last: SAWADA

address: 600 5th Street South

institute: Johns Hopkins All Children's Hispital

summary: The formation of tertiary lymphoid structures (TLSs) in tumors is significantly correlated with prolonged patient survival, better prognosis, and improved response to immunotherapy. To assess the tumor microenvironment associated with TLS formation, we performed bulk RNA sequencing using archived FFPE human breast cancer tissues.

overall_design: Patient samples of FFPE tissues were categorized as TLS-poor or TLS-rich based on the histology of H&E staining. RNA was isolated from sections of these tissues and used for RNA sequencing

first: Junko

last: Sawada

first: Nobuyoshi

last: Hiraoka

first: Masanobu

last: Komatsu


title: Ptgs2+ Telocytes Mediate M2 Macrophages for Anti-Inflammatory Effects Following Acupuncture in the Abdominal Midline Fascia of Dysenteric Rats

city: Nanjing

first: ZhenWei

last: Zhang

state: Jiangsu

address: No. 1 Weigang

department: veterinarian

institute: Nanjing Agricultural University

summary: This study identified a subpopulation of CPTCs capable of responding to mechanical stimulus, with significant clinical implications for elucidating the cytological effects of acupuncture. Central to the response to acupuncture stimulus are Ptgs+ TCs, which form focal adhesion with all CPTC subpopulations and activate M2 macrophage through Il6-Il6st-Stat3. Thus, we conclude that Ptgs2+TCs is the fundamental essence of meridians.

overall_design: To explore the cytological mechanisms behind the skin's reaction to acupuncture, dysentery was induced in rats using Salmonella, followed by acupuncture treatment. Single-cell sequencing was performed on the abdominal midline fascia, the acupoints, in both dysentery and acupuncture-treated rats. Fascia_CT represents dysentery rat samples, while Fascia_AC represents samples from rats after acupuncture treatment. Our analysis of single-cell sequencing at the acupuncture points in both groups revealed that Ptgs2+ telocytes, a subset of telocytes, respond to acupuncture stimulation and facilitate the anti-inflammatory effects of M2 macrophages during acupuncture therapy.

first: Zhenwei

first: Haixiang

last: Huang

first: Jianming

last: Yue

first: Qianmei

last: Zhu

first: Qiusheng

last: Chen


title: Whole transcriptome sequencing of gastric cancer stem cells and non-gastric cancer stem cells

first: Xiaowei

address: No.138 Xianlin Avenue, Qixia District

institute: Nanjing University of Chinese Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: As a subpopulation of tumor cells with stemness characteristics such as self-renewal ability and high oncogenicity, gastric cancer stem cells (GCSCs) are considered to be tumor-initiating cells and are the root cause of cancer recurrence and chemoresistance. Therefore, an in-depth study of the stemness characteristics and maintenance mechanism of GCSCs is of great significance for the treatment of gastric cancer (GC). In this study, GCSCs and non-gastric cancer stem cells (Non-GCSCs) derived from tumor tissues of GC patients were used for whole transcriptome sequencing. The goal of identifying key differentially expressed circRNAs, lncRNAs, miRNAs and mRNAs associated with GCSCs. In conclusion, we mapped the molecular feathers at RNA level closely related to GCSCs and revealed certain ncRNAs with great research potentia based on the whole transcriptome sequencing.

overall_design: Whole trascriptome analysis of total RNA data on circRNAs, lncRNAs, miRNAs and mRNAs for gastric cancer stem cells (GCSCs) and non-gastric cancer stem cells (Non-GCSCs).  A total of 6 samples were collected from tumor tissues of GC patients.

first: Qiong

last: Li

first: Yanan

last: Wang

first: Ai

first: Xiaobing

last: Shen


title: Low temperature promotes culm coloration of black bamboo (Phyllostachys nigra) through modulation of coumarin accumulation

city: Hangzhou

first: Dan

last: Hou

address: 666 Wusu street, Lin'an District, Hangzhou

institute: A&F university

summary: The transcriptome analysis was performed and the putative genes involved in coumarin biosynthesis under LT were revealed

overall_design: Gene expression profiling analysis of RNA-seq data of black bamboo under different temperature treatments


title: KMT2D is essential for cerebellar granule cell differentiation

first: Kyung Pil

last: Ko

state: Tx

address: 1515 Holcombe Blvd

institute: The University of Texas M.D. Anderson Cancer Center

summary: The cerebellum contains 62%‒73% of the total number of neurons in the mouse brain. Granule cells (GCs) constitute the vast majority of cerebellar neurons. Single cell RNA-seq analyses showed that Atoh1-Cre-mediated knockout (KO) of the Kmt2d gene encoding the lysine methyltransferase KMT2D (MLL4 and a COMPASS-like enzyme) in the cerebellar GC lineage in mice inhibited cerebellar GC differentiation and downregulated neuron differentiation expression programs. In addition, Kmt2d KO inhibited the transition of GC progenitors to GCs while having a cell-non-autonomous impact on other cerebellar cells.

overall_design: To examine the effect of Kmt2d KO on cerebellar cells at the single-cell level, cells were isolated from Kmt2d fl/fl (=  WT) and Atoh1-Cre Kmt2d fl/fl (= Kmt2d KO) P5 cerebella (female and male). Then, the scRNA-seq (~300 millions read per sample) were performed to obtain single-cell transcriptomes.

first: Shilpa

last: Dhar

first: Jinho

last: Jang

first: Min Gyu

last: Lee

first: Jae-Il

last: Park


title: Effect of M . bovis NX2-EVs on gene expression in BoMac cells

first: Yiming

last: Wu

summary: Our research shows that EVs derived from M. bovis-infected BMEC cells (EVs-M. bovis NX2) could regulate BoMac cell injury by inducing inflammation. To detect the effect of EVs-M. bovis NX2 on gene expression in BoMac cells, we incubated Ctrl-EVs and EVs-M. bovis NX2 with BoMac cells for 12h, 24h. Our data provide globaly change of mRNA profile caused by EVs-M. bovis NX2.

overall_design: We extracted total RNA from Ctrl-EVs and EVs-M. bovis NX2-treated BoMac cells after 12 and 24h，performed gene expression profiling analysis


title: The genome-wide targeting of flag (ETV4) in A549 cells

city: Shijiazhuang

first: lingxiao

last: xing

state: hebei

address: 361 zhongshan Road

institute: hebei medical university

summary: The ETS family of oncogenic TFs is emerging as crucial mediators of tumorigenesis in solid tumors. New insights into the molecular mechanisms hijacked by these factors will pave the way for novel therapeutic strategies. We have previously shown that ETV4 is the preponderant ETS factor that is associated with tumor progression and a worse prognosis in NSCLC. To determine the genome-wide chromatin binding of ETV4, we performed chromatin immunoprecipitation (ChIP)-sequencing studies in A549-shETV4 cells transfected with flag-ETV4 using flag antibody. In total, 54389 ETV4 binding peaks representing 25708 genes were identified (FC > 2), and 43.71% peaks were enriched in the promoter regions. Our ChIP-seq data showed that ETV4 is enriched in many genes that related with the wnt signaling pathway, MAPK signaling pathway, cell cycle, and autophagy, etc.

overall_design: Human NSCLC cell line A549-shETV4 cells transfected with flag-ETV4, using anti-flag antibody..

first: Lingxiao

last: Xing


title: LKB1 regulates mitochondrial metabolisma and macrophage polarization

city: Indianapolis

first: Kai

last: Yang

state: IN

address: 1044 West Walnut Street

department: Department of Pediatrics

institute: Indiana University School of Medicine

summary: To investigate the function of LKB1 signaling in macrophages, we generated BMDMs from WT and LysMCre Stk11 fl/fl mice and profiled their genome-wide transcripts.

overall_design: We isolated the bone marrow from WT and LysMCre Stk11 fl/fl mice and differentiated them into bone marrow derived macrophages (BMDMs) in the presence of M-CSF (40 ng/ml) for 7 days. BMDMs were stimulated with or without IL-4 (20 ng/ml) for 24 h. Then, we performed RNA-seq to profile mRNA transcripts from WT and KO BMDMs stimulated with or without IL-4.

first: Chengxian

last: Xu

first: Yucheng

last: Zhang

first: Sheng

last: Liu


title: Mechanisms of dexamethasone-induced bone toxicity in developing bone: a single-cell perspective

city: UTRECHT

first: PHILIP

last: LIJNZAAD

state: Utrecht

address: HEIDELBERGLAAN 25

department: Single Cell Facility

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Glucocorticoids, such as dexamethasone, are essential for treating severe childhood conditions, including cancer, organ transplantation, and inflammatory disorders. However, their long-term use can impair bone development, posing risks to pediatric bone health, which is vital for lifelong skeletal integrity. A mechanistic insight on how glucocorticoids negatively impact bone could improve decision-making in patient care to improve the quality of life for pediatric cancer patients and survivors. In this study, we aimed to elucidate the molecular mechanisms underlying dexamethasone-induced bone toxicity in developing bones using single-cell transcriptomics. We treated skeletally immature mice with dexamethasone for 28 days, and assessed the bone architecture with micro-computed tomography, and characterized bone and bone marrow cells from the femurs using single-cell RNA sequencing. Our findings revealed a marked reduction in osteoblast and chondrocyte cell populations and impaired function of pre-osteoblasts. Additionally, dexamethasone adversely affected B cell subsets, significantly depleting early B cell progenitors while allowing some further developed immature B cells to persist. These cellular changes were accompanied by reduced longitudinal bone growth, compromised bone architecture, and increased bone fragility at the highest doses of dexamethasone. Interestingly, unlike observations in adults, dexamethasone did not enhance osteoclast activity in our model. Overall, our study suggests that the adverse effects of dexamethasone on bone development are primarily due to its impact on osteoblastic, chondroblastic and B cell lineages, disrupting the critical signaling crosstalk between the cells necessary for bone development and hematopoiesis.

overall_design: Single-cell mRNA profiles of pooled femur bone samples of 6-week old mice treated with different Dexamethasone dosage regimes were compared to study the degree and mechanism of dexametasone toxicity to developing bone.

first: Kelly

last: Warmink

first: Philip

last: Lijnzaad

first: Tristan

last: Vermaat

first: Lisa

last: Jansen

first: Marloes

last: van Gend

first: Bajoie

first: Aleksandra

last: Balwierz

first: Natalie

last: Proost

first: Marieke

last: van de Ven

first: Johannes

last: Merks

first: Thanasis

last: Margaritis

first: Claudia

middle: Y

last: Janda


title: STING agonism overcomes STAT3-mediated immunosuppression and adaptive resistance to PARP inhibition in ovarian cancer

city: Boston

first: Jean

last: Zhao

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Background: PARP inhibition (PARPi) has demonstrated potent therapeutic efficacy in patients with BRCA-mutant ovarian cancer. However, acquired resistance to PARPi remains a major challenge in the clinic.   Methods: PARPi-resistant ovarian cancer mouse models were generated by long-term treatment of olaparib in syngeneic Brca1-deficient ovarian tumors. STAT3-mediated immunosuppression was investigated in vitro by co-culture experiments and in vivo by analysis of immune cells in the TME of human and mouse PARPi-resistant tumors. Whole genome transcriptome analysis was performed to assess the anti-tumor immunomodulatory effect of STING (stimulator of interferon genes) agonists on myeloid cells in the TME of PARPi-resistant ovarian tumors. A STING agonist was used to overcome STAT3-mediated immunosuppression and acquired PARPi resistance in syngeneic and PDX models of ovarian cancer.  Results: In this study, we uncover an adaptive resistance mechanism to PARP inhibition mediated by tumor associated macrophages (TAMs) in the tumor microenvironment (TME). Markedly increased populations of pro-tumor macrophages are found in BRCA-deficient ovarian tumors that rendered resistance to PARPi in both murine models and patients. Mechanistically, PARP inhibition elevates the STAT3 signaling pathway in tumor cells, which in turn promotes pro-tumor polarization of TAMs. STAT3 ablation in tumor cells mitigates polarization of pro-tumor macrophages and increases tumor-infiltrating T-cells upon PARP inhibition. These findings are corroborated in patient-derived, PARPi-resistant BRCA1-mutant ovarian tumors. Importantly, STING agonists reshape the immunosuppressive TME by reprogramming myeloid cells and overcome the TME-dependent adaptive resistance to PARPi in ovarian cancer. This effect is further enhanced by addition of PD-1 blockade.  Conclusions: We elucidate an adaptive immunosuppression mechanism rendering resistance to PARPi in BRCA1-mutant ovarian tumors. This is mediated by enrichment of pro-tumor TAMs propelled by PARPi-induced STAT3 activation in tumor cells. We also provide a new strategy to reshape the immunosuppressive TME with STING agonist and overcome PARPi resistance in ovarian cancer.

overall_design: PBM and PBM-R tumors: transcriptome analysis were performed on bulk tumors from PBM and PBM-R tumor-bearing mice. PBM tumors were generated by orthotopic injection of PBM tumor cells into FVB/NJ mice. PBM-R are refactory tumors generated in PBM tumor-bearing mice after long-term treatment with olaparib (50 mg/kg/day).   Myeloid cells: about 1 x10^6 PBM-R tumor cells were intraperitoneally injected to FVB/NJ mice. About 2-3 weeks after injection, mice were grouped and treated with control, olaparib, MSA-2 and MSA-2 in combination with MSA-2 for 24 hours. After treatment, myeloid cells (CD45+CD11b+) were isolated from the ascites of each mouse (n=3 per group) by EasySep Mouse CD11b positive Selection Kit II (STEMCELL Technology, #18970) and subjected for transcriptome analysis.

first: Liya

last: Ding

first: Qiwei

last: Wang

first: Shaozhen

last: Xie

first: Ziying

last: Lin


title: Achieving CD8+ T cell-dependent lethality by targeting cancer USP14 in HCC

city: Guangzhou

first: Binkui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

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

overall_design: Refer to individual Series


title: Sex differences define the molecular and cellular phenotypes of pain resolution in dorsal root ganglia

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

country: Germany

institute: University Hospital Würzburg

summary: Neuropathic pain, affecting 10% of the general population, poses a significant socioeconomic burden that current treatment options cannot sufficiently cover. While pain naturally resolves in some patients, the mechanisms driving this process remain elusive. we hypothesized that pain resolution modulates multicellular interactions of neurons, satellite glial cells (SGCs), and local macrophages within the dorsal root ganglia (DRGs). Therefore, we aimed to identify molecular and cellular processes that characterize ongoing pain resolution. With behavioral tests, we determined a 50% improvement of the pain phenotype to capture ongoing mechanisms of pain resolution. We expect to see dysregulated signaling mediators in the DRG, as well as channels and components influencing hypersensitivity, as well as regulation of an immune and inflammatory phenotype. Comparing the ipsilateral sides during hypersensitvity and pain resolution, we aim to elucidate pathways that characterize the resolution phase. Based on prior knowledge and imaging data, we expected to initially see a strong immune phenotype, with differences between male and female rats during pain resolution, potentially reflecting a difference in pain prevalence between sexes in the clinic. Pathway analysis of the bulk RNA data confirmed an ongoing immune phenotype in female rats as opposed to males. Top regulated factors after CCI, include many mediators such as NPY, VIP, Gal, IL24 and IL6. Biological processes associated with pain resolution included G-protein coupled receptor signaling, synaptic transmission and regulation of the membrane potential.

overall_design: We analyzed L4 rat DRG, that were harvested and snap frozen in liquid nitrogen after chronic constriction injury (CCI). Experimental groups were male and female rats at 1 week or 5 weeks after CCI, with investigation of both the injured, ipsilateral side and the contralateral side as control.

first: Felicitas

last: Schlott

first: Thorsten

last: Bischler


title: Achieving CD8+ T cell-dependent lethality by targeting cancer USP14 in HCC [CRISPR screen]

summary: Using the CRISPR genome editing system and a cancer cell/activated CD8+ T cell co-culture system, we identified the key genes in HCC cells that enhanced HCC cell tolerance to CD8+ T cells.

overall_design: We performed a pooled CRISPR genome-wide loss/gain-of-function screen using a lentiviral KO/activation library in PLC-PRF-5/Hep-G2 cells. The cell pools were co-cultured with activated CD8+ T cells for 7 days


title: SOX2 phosphorylation during mitosis limits genomic damage [ChIP-Seq]

first: Charles

last: Williams

overall_design: Genome binding/occupancy profiling and transcriptional profiling were performed using ChIP-seq, RNA-seq and ATACseq). This dataset refers to the ChIPseq analysis of SOX2 during mitosis. Mouse Neural Stem Cells (mNSCs) engineered with a PiggyBac transposon-based doxycycline-inducible SOX2 expression system (Martella et al., ACS Synthetic Biology, 2017) were used. Sample Preparation and Treatments: SOX2 Induction: mNSCs were treated with 1 μg/ml doxycycline for 72 hours to induce SOX2 expression. Mitotic Arrest: Cells were treated with 50 ng/ml Nocodazole to induce mitotic arrest, with or without concurrent SOX2 induction. Experimental groups include mNSCs with induced SOX2 expression, and cells arrested in mitosis with/without SOX2 induction.

first: Dounia

last: Djeghloul

first: Nicolas

last: Veland

first: Alhafidz

last: Hamdan

first: Maria

last: Kalantzaki

first: Erika

last: Lo

last: Illingworth

first: Alex

last: Von Kriegsheim

first: Amanda

last: Fisher

first: Abdenour

last: Soufi

first: Steven

last: Pollard


title: SOX2 phosphorylation during mitosis limits genomic damage [ATAC-Seq]


title: Distinct Ire1-driven transcriptional responses control morphogenesis in Candida albicans

status: Public on Nov 13 2025

city: London

first: Patrick

last: Lajoie

state: Ontario

address: Medical Sciences Building, Elgin Road

department: Anatomy and Cell Biology

country: Canada

institute: Western University

summary: The ability of pathogenic yeast Candida albicans to cause infections in humans depends on morphogenesis, the ability to switch from a spherical yeast to a filamentous hyphal form. Morphogenesis in C. albicans requires Ire1, a transmembrane protein responsible for binding misfolded proteins and initiating the Unfolded Protein Response (UPR). The UPR is a signaling pathway activated in response to the accumulation of misfolded secretory proteins in the endoplasmic reticulum (ER). Ire1 activation in the ER membrane leads to splicing of cytosolic HAC1 mRNA and subsequent UPR target gene upregulation by transcription factor Hac1. In C. albicans, the specific UPR target genes required for morphogenesis are unknown. We utilized RNA-Sequencing to assess the transcriptome of UPR-deficient cells in misfolded protein- and morphogenesis-inducing conditions. Surprisingly, we found little overlap between the datasets, suggesting that a specific Ire1 transcriptional signature drives filamentous growth. Moreover, Hac1 is only partially required for morphogenesis, suggesting a role of Hac1-independent Ire1 function in filamentation. We propose that the cell wall stress response and regulated Ire1-dependent decay (RIDD) are potential Hac1-independent mechanisms connecting Ire1 to morphogenesis in C. albicans.

overall_design: To characterize the UPR in C. albicans and its role in morphogenesis, we used a control strain (DAY286) and a strain with dimished expression of UPR activator Ire1 (ire1DX). Strains were grown with the proteotoxic stressor tunicamycin at 30°C for two hours and with morphogenesis-inducing fetal bovine serum at 37°C for four hours. Control samples were untreated and grown at 30°C for two hours. Each condition was performed in triplicate.

first: Samuel

last: Stack-Couture

first: Gabriela

last: Nunes Marsiglio Librais

first: Bryan

last: Lung

first: Julie

last: Genereaux

first: Viola

last: Halder

first: Vanessa

last: Dumeaux

first: Rebecca

last: Shapiro


title: HTGTS-TCR-seq for profiling of mouse and human T-cell receptor α and β gene rearrangements and diversity [RACE]

first: Haiqiang

last: Dai

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell  Science

summary: Developing αβ T lymphocytes generate T-cell receptor (TCR) diversity through V(D)J recombination, which assembles Tcra and Tcrb genes from germline variable (V), diversity (D), and joining (J) segments. Approaches to characterize TCR rearrangements and diversity are critical for studying T-cell development and immune function. Several existing methods, such as multiplex PCR and 5′RACE, have advanced the field; however, each carries inherent technical limitations. Here, we present High-Throughput Genome-Wide Translocation Sequencing–based TCR sequencing (HTGTS-TCR-seq), a complementary and cost-effective strategy for quantitative profiling of Tcra and Tcrb gene rearrangements. HTGTS-TCR-seq employs a limited set of 3-5 J or V region primers to enrich for V(D)J recombination products, allowing detection of both productive and nonproductive rearrangements. Application to wild-type murine thymocytes at defined developmental stages, as well as young and aged T cells, reveals stage-specific V and J usage and age-associated repertoire alterations. Analysis of Wapl-knockout preselection double-positive thymocytes uncovers a cell division-independent role for the cohesin-unloading factor WAPL in Tcra rearrangement. Moreover, analysis of human peripheral T cells demonstrates conserved complementarity-determining region 3 (CDR3) features and subset-specific Vβ usage across species. Collectively, HTGTS-TCR-seq provides an efficient and accessible approach for quantifying TCR rearrangements and diversity across development, aging, and immune-related conditions.

overall_design: We employed 5'RACE to validate HTGTS-TCR-seq assay by extracting DNA and RNA from preselection DP and total thymocytes.

first: Rui

last: Luo

first: Yawei

last: Song

first: Meichen

last: Wang

first: Longhao

last: Zou

first: Fangtai

last: Jiao

first: Tiange

last: Yang

first: Guangchuan

first: Wei

last: Wu

first: Hai-Qiang


title: TRIM21 Enhances IL-17A Signaling and Drives Autoimmune Myocarditis by Promoting TRAF3 Lysosomal Degradation in Cardiac Fibroblasts

city: Suzhou

first: Li

last: Min

address: 199 Ren-ai Road

department: Institute of Biology and Medical Sciences

institute: Soochow University

summary: Myocarditis is a major health concern worldwide, often progressing to dilated cardiomyopathy (DCM) and sudden death, particularly in young individuals. However, the mechanisms driving the transition from acute myocarditis to inflammatory DCM (DCMi) remain unclear. Autoimmune responses, especially those involving interleukin (IL)-17A signaling, have been implicated, though the specific cellular targets and upstream regulators in the cardiac environment are not well understood. Here, we identify TRIM21, an E3 ubiquitin ligase, as a key regulator in this process. Using the experimental autoimmune myocarditis (EAM) model, we show that TRIM21 expression is significantly upregulated in cardiac fibroblasts (CFs) during DCMi and upon IL-17A stimulation. Surprisingly, TRIM21 deficiency attenuated EAM progression, reducing inflammatory neutrophils and Ly6Chigh monocytes/macrophages infiltration. Bone marrow chimeric and IL-17A neutralization experiments confirmed TRIM21's role in CFs, where it promotes IL-17A signaling by facilitating TRAF3 degradation via K27-linked polyubiquitination. These findings identify TRIM21 as a new target in CFs and uncover a regulatory mechanism for IL-17A signaling, suggesting that therapies targeting TRIM21 may need to be adapted to different microenvironments.

overall_design: To investigate the regulatory mechanism of E3 ubiquitin ligase TRIM21 in autoimmune myocarditis, we constructed an autoimmune myocarditis model using BALB/C and TRIM21 knockout mice. Subsequently, we performed RNA sequencing on the hearts of control mice on day 0 and BALB/C and TRIM21 knockout mice subjected to experimental autoimmune myocarditis (EAM) for 21 days. Finally, we conducted gene expression profile analysis using the RNA-seq data obtained.

first: Yahui

first: Xuege

last: Huang

first: Lin

last: Wei

first: Jing

last: Guo


title: Tumor exosomes aggravate mitochondrial damage in myocardial ischemia/reperfusion injury

city: Harbin

first: Zhongting

last: Mei

state: Heilongjiang

address: Baojian Road 157

institute: Harbin Medical University

summary: Exosomes can fuse with the cytoplasm of target cells to perform regulatory functions. Small RNAs are major regulatory components of exosomes, we therefore analyzed small RNA contents in plasma exosomes derived from cancer versus non-cancer mice. Small RNA expression array data revealed that 20 pre-miRNAs and 38 miRNAs with fold change > 1.4 and p-value < 0.05 in the exosomes derived from cancer group compared with those in the non-cancer group.

overall_design: Small RNA expression of plasma exosomes was measured in lung cancer and non-cancer mice (n=3/group).


title: Maximizing efficacy of cancer nanovaccines and immune cells landscape in responders and non-responders to immunotherapy

first: Mi

last: Liu

address: 1435 of Yunxuan Lou, Du Shu Hu Xiao Qu,, Gong Ye Yuan Qu

department: Pharmaceutics

summary: The therapeutic efficacy of cancer vaccines can be optimized from 3 aspects: adjuvants, vaccine formulation, and processing of tumor antigens. Herein, various different adjuvants, such as toll like receptors and STING agonists etc., and their combinations were compared in cancer nanovaccines loaded with whole tumor antigens were illustrated. By comparing different sized nanovaccines and micronvaccines, 200nm-400nm and 2.5μm were discovered to be optimal sizes of nanovaccines and micronvaccines. Rapid freezing, fixation, heating, salting-out, ethanol precipitate can affect the immunogenicity of tumor antigens and efficacy of cancer vaccines. The optimal cancer vaccine can cure all or most tumor-bearing body in melanoma mouse model, lung cancer mouse model, subcutaneous pancreatic cancer model, orthotopic pancreatic cancer model, melanoma lung metastasis model. In addition, the immune cell profiles were systematically investigated using single-cell sequencing, in blood, splenocytes and draining lymph nodes of healthy mice, PBS treated tumor-bearing mice, vaccine-treated non-cured mice and cured mice after different time. By comparing 21 samples, some featured clusters and markers, such as S100A4, KLRG1, SIPR5, CXCR3, IL2Ra, IKZF2, CX3CR1, S100A8, and S100A9 etc., were identified to distinguish responders and non-responders to immunotherapy. These biomarkers were verified and confirmed the feasibility of predicting therapeutic efficacy in mouse cancer model and cancer patients. In summary, this study presented a method to optimize cancer nanovacines from different aspects, systematically investigated immune cell profiles in non-responders and responders to immunotherapy, and discovered some featured biomarkers for predicting or distinguishing responders and non-responders to immunotherapy.

overall_design: Healthy mice, tumor-bearing mice treated with PBS, non-cured mice or cured mice were sacrifaced. Blood,Spleen and drainining lymph nodes were collected. PBMC, single cell suspension of splenocytes or single cell suspension of draining lymph node cells were prepared for single cell sequencing analysis. Transcriptome analysis, TCR analysis and BCR analysis were conducted.

first: Xiangxiang

last: Xu

first: Lu

last: Diao

first: Ao

last: Zhu

first: Jin

first: Yuhan

first: Xianlan

last: Chen

first: Yan

last: Zheng

first: Jun

last: Zhao


title: Hepatocyte-specific epidermal growth factor receptor (EGFR) deletion attenuates acetaminophen-induced liver injury in mice [RNA-seq AVITI]

city: Pittsburgh

first: Shuchang

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Epidermal growth factor receptor (EGFR) is mostly known for its proliferative role in liver. Our earlier investigations indicated a paradoxical cell-death promoting facet of EGFR in acetaminophen (APAP)-induced liver injury (AILI) model. The current study investigates this unexpected role of EGFR in promoting AILI using a hepatocyte-specific EGFR deletion mouse model. Hepatocyte-specific EGFR-deficient mice were generated by administering AAV8-TBG-CRE in EGFRfl/fl mice and were subsequently treated with a severely toxic dose (500 mg/kg) of APAP. Liver injury, regeneration and associated signaling pathways were assessed at different time intervals. EGFR deletion significantly attenuated the progression of liver injury (beyond 12hr post-APAP) without altering early liver injury (up to 6 hr) following APAP overdose. Consistently, the key injury initiating events such as APAP-protein adducts formation and early JNK activation remained intact in EGFR-deficient mice. However, EGFR deletion restricted prolonged JNK activation and its mitochondrial translocation, resulting in reduced propagation of mitochondrial damage and release of cell death drivers. Further, the replenishment of antioxidant glutathione (GSH), which is known to limit the progression of liver injury, was strikingly faster in EGFR-deficient mice. RNA-seq analysis and consequent validation revealed marked upregulation of autophagy and its transcriptional regulator TFEB, a key response to remove damaged mitochondria, in EGFR-deficient mice. Paradoxically, EGFR deletion also promoted compensatory liver proliferative response secondary to decreased progression of liver injury. Overall, hepatocyte-specific EGFR deletion halted the progression of AILI. Our study established an unexpected death promoting function of EGFR in AILI progression, which has wide implications in liver biology.

overall_design: Wild-type and hepatocyte-specific EGFR knockout mice were given 500 mg/kg of Acetaminophen (APAP). Liver tissues were harvested at 0, 1, 3, 6, 12, and 24hr post-APAP overdose. Bulk RNA-seq was measured using AVITI sequencer

first: Siddhi

last: Jain

first: Gillian

last: Williams

first: Ranjan

last: Mukherjee

first: Anne

last: Orr

first: Jia-Jun

first: Silvia

first: Joseph

last: Locker

first: Bharat

last: Bhushan


title: s-Adenosylmethionine (SAM) diet defines offspring epigenetic modification and intergenerational immune response.

city: Zunyi

first: yan

last: Zhang

state: Guizhou

address: Honghuagang

department: College of Basic Medicine

institute: Zunyi Medical University

summary: At the beginning of the experiment, a concentration of 50μM was used The treatment of Caenorhabditis elegans with MS adenosylmethionine has been found to promote the natural immunity of nematodes and increase their survival rate in Pseudomonas aeruginosa. We found that this elevated immunity has an epigenetic phenomenon that can be inherited to its offspring. To further explore its molecular mechanism, we aim to investigate the gene expression differences between S-adenosylmethionine treatment and untreated, as well as the similarities and differences in gene expression between S-adenosylmethionine treatment and offspring

overall_design: Using a concentration of 50 μ M-adenosylmethionine was used to treat Caenorhabditis elegans, and the nematode was placed in Pseudomonas aeruginosa to test its natural immune ability.

first: Yingwen

last: Cui


title: Single cell transcription revealing key transcription factors in embryonic kidney development

city: Guangdong

first: jing xian

last: huang

state: Guangzhou

address: 暨南大学石牌校区学生宿舍2栋302

institute: jinan university

summary: The development of the kidney is a complex process involving the differentiation of renal progenitor cells into various specialized cell types. We used single cell RNA sequencing to analyze the diversity of NPCs(renal progenitor cell) and identified key transcription factors that are crucial for the differentiation of these progenitors into renal tubular epithelial cells and podocytes.

overall_design: Kidney samples were obtained from human aborted embryos and analyzed using single-cell sequencing

first: Yong

last: Dai

first: Jingxian

last: Huang


title: Achieving CD8+ T cell-dependent lethality by targeting cancer USP14 in HCC [scRNA-seq]

first: Binkui

last: Li

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of PD-1 therapy responsive and resistant patients samples.

overall_design: We generated scRNA-seq profiles for primary tumors from patients with treatment-naïve HCC. The fresh biopsies, which were collected during ultrasound-guided fine-needle aspiration, were rapidly digested into single-cell suspensions and analyzed by droplet-based single-cell transcriptome profiles (10× Genomics system)


title: HTGTS-TCR-seq for profiling of mouse and human T-cell receptor α and β gene rearrangements and diversity [HTGTS_TCR-seq]

city: Shanghai

first: Haiqiang

overall_design: We employed HTGTS-TCR-seq to asess rearrangement events and TCR repertoire changes across developmental stages and T cell subsets at DNA level. DN3 thymocytes, preselection DP thymocytes from mice and CD4+ and CD8+ T cells from human PBMCs were FACS sorted. Total thymocytes and splenic CD4+ and CD8+ T cells from young and aged mice were collected. Genome DNA were extracted, sonicated and utilized to conduct HTGTS-TCR-seq.

first: Rui

last: Luo

first: Yawei

last: Song

first: Meichen

last: Wang

first: Longhao

last: Zou

first: Fangtai

last: Jiao

first: Tiange

last: Yang

first: Guangchuan

first: Wei

last: Wu

first: Hai-Qiang


title: HTGTS-TCR-seq for profiling of mouse and human T-cell receptor α and β gene rearrangements and diversity [RNA-seq]

overall_design: We employed RNA-seq to asess the deletion efficiency of Wapl in preselection DP thymocytes and to explore whether deletion of Wapl led to dysregulation of certain development-related genes.


title: Transcriptional signatures of dermal papilla cells during cashmere growth

city: Shenyang

first: Huiling

last: Xue

address: 120 Dongling Road,110866 Shenyang,China

institute: Shenyang Agricultural University

summary: This study investigates regulatory molecules and machanisms of cashmere growth by profiling dermal papilla cells (DPCs) from secondary (SHF) and primary hair follicles (PHF) during the early and mid-anagen phases in both male and female cashmere goats. A comprehensive genome-wide transcriptomic analysis was then performed to characterize the differentially expressed molecular signatures associated with follicle types (SHF vs. PHF), developmental phases, and sex.

overall_design: RNA-seq was performed on dermal papilla cells from secondary and primary hair follicles of male and female cashmere goats during early (June) and mid-anagen (October).

first: Yanlei

last: Liu

first: Minglin

first: Xinyue

last: Liang

first: Xinghui


title: Perimenopausal State Oestradiol to Progesterone Imbalance Drives Alzheimer’s Risk via ERRα Dysregulation and Energy Dyshomeostasis [EnrichedNeuron_RNASeq]

city: Sha Tin

first: Jacquelyne

last: Sun

state: New Territories

address: Room 612A, Mong Man Wai Building,

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Sex-biased differences in Alzheimer’s disease (AD) are well documented, but the mechanisms underlying increased vulnerability in postmenopausal women remain unclear. This study aimed to model the effects of perimenopausal hormonal fluctuations on AD pathophysiology. Using a VCD-induced accelerated ovarian failure model in young female C57BL/6J and 3xTg mice, we simulated a perimenopausal state with hormonal changes characterized by elevated oestradiol levels and reduced progesterone levels. Supporting human brain transcriptomic and metabolomic data from the ROSMAP study revealed that impaired oestrogen-related receptor alpha (ERRα) function was a key driver of female sex-biased vulnerability. In female mice, progesterone-guided oestrogen receptor signalling maintained ERRα activity by regulating neuronal cholesterol homeostasis and the TCA cycle. Hormonal imbalances disrupted this mechanism, triggering an aspartate-driven “minicycle,” which increased glutamate release, neuronal excitability, ATP depletion, and energy crisis susceptibility. This study demonstrates how perimenopausal hormonal imbalances exacerbate AD risk via ERRα dysfunction, linking neuronal cholesterol and energy homeostasis to disease vulnerability.

overall_design: To investigate the overall effects of Esrra knockdown in neurons, stereotaxic injections was performed and neuronal cells from the mouse brains were enriched using Miltenyi Biotech's enrichment protocol for neurons before the enriched neuronal fraction was sent for transcriptomic profiling.

first: Kim Hei-Man

last: Chow


title: Antioxidant program of islet-resident macrophages preserves β cell physiology

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades, INSERM U1151

summary: Macrophages residing within mouse pancreatic islets display an activated phenotype at steady state, yet the molecular signatures underlying their polarization remain unclear. To investigate islet macrophage heterogeneity under physiological conditions, we isolated islet-resident immune cells from chow diet-fed adult male mice and performed single-cell RNA sequencing.

overall_design: Islets were isolated and pooled from 6–8 mice, dissociated into single cells, and CD45+ immune cells were FACS-sorted. These cells were then subjected to single-cell RNA sequencing using the 10X Genomics platform.

first: A

last: Grosjean

first: M

last: Diedisheim

first: E

last: Dalmas

first: LG

last: Baudrin

first: S

last: Baulande


title: Transcriptional profiling of Hutchinson-Gilford Progeria patients identifies primary target pathways of the disease-causing progerin protein

city: Bethesda

first: Sandra

last: Vidak

state: MD

address: 9000 Rockville Pike

institute: NIH

summary: Hutchinson Gilford Progeria Syndrome (HGPS) is an ultra-rare pediatric premature aging disorder. The disease is caused by a point mutation in the LMNA gene leading to the production of the dominant-negative progerin isoform of the nuclear envelope protein lamin A. Disease severity and progression amongst the population of ~140 known patients is variable. Numerous cellular pathways have been implicated in the disease mechanism, including mTOR signaling, stem cell differentiation and the oxidative stress response. Most of mechanistic insights into the disease have come from studies using cellular or mouse models of HGPS. To probe the clinical relevance of previously implicated cellular pathways and to address the extent of gene expression heterogeneity between patients, we have performed transcriptomic analysis of a comprehensive set of HGPS patients. We find misexpression of several of the major HGPS-associated cellular pathways across the patient population, particularly of multiple signaling pathways as well as the Unfolded Protein Response (UPR) and mesodermal cell fate specification. Variability amongst individual patients was limited with misregulation of the major pathways observed in most patients. Comparing the transcriptome of patients with an inducible HGPS cell model, we distinguished immediate-early cellular response pathways from secondary adaptive pathways and identify mTOR, the UPR, UV response, apoptosis and TNFa signaling via NFkB as primary targets of the disease-causing progerin protein.

overall_design: RNA-seq profiling of primary human HGPS fibroblasts and primary human wild type control fibroblats, as well as hTERT-immortalized GFP-progerin doxycycline inducible dermal fibroblast cell line where progerin was expressed for 0 or 6 days.

first: Sohyoung

last: Kim

first: Tom

last: Misteli


title: CHN1 as a Predictive Biomarker for Atopic Dermatitis-related Depression

city: Wuhan

first: Yifei

last: Wang

address: Baofeng street

institute: Huazhong University of Science and Technology

summary: The comorbidity of Atopic Dermatitis (AD) and depression has garnered increasing attention in recent years. Yet, the immunopathological mechanisms underlying this connection remain unclear. To bridge this gap, we collected peripheral blood mononuclear cell samples from 20 AD patients with and without depression, and performed RNA sequencing analysis. By integrating bioinformatics and machine learning techniques, we aimed to uncover the immune regulatory networks and identify key genetic markers for the depression comorbidity in AD patients. Our analysis revealed 394 differentially expressed genes in AD patients with depression as compared to those non-depression counterparts. Weighted gene co-expression network analysis pinpointed a pink module encompassing 83 genes strongly linked to depression. Functional enrichment analysis of critical module genes revealed significant enrichment scores in neurotransmitter uptake and the negative regulation of T-helper (Th) 17 cell differentiation. Furthermore, machine learning models of least absolute shrinkage and selection operator and support vector machines highlighted CHN1 as a potential pivotal gene upregulated in AD patients with depression. The expression level of CHN1 demonstrated positive correlation with Th2 and Th17 cytokine families, as well as with the Hospital Anxiety and Depression Scale-Depression score and Eczema Area and Severity Index. Validation experiments on clinical samples of an additional 20 participants confirmed the significant upregulation of CHN1 in depressed AD patients. This study is the first to unveil the intricate inflammatory and immune pathways underlying AD-associated depression, shedding light on the critical role of CHN1 connecting inflammation and neuropsychiatric symptoms.

overall_design: We collected peripheral blood mononuclear cell samples from 20 AD patients with (DAD) and without depression (NAD), and performed RNA sequencing analysis.


title: The role of EHMT2 in Uveal melanoma progression [EHMT2_Inhibitors]

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: EHMT2/G9a expression is elevated in many cancer types including uveal melanoma. Here in the present study, we have identified pharmacological inhibition of EHMT2/G9a in MP41 cells and Mel92.1 cells promote the sensitivity to NK cells in vitro. By keeping this in mind, we have performed RNA-seq of inhibition of EHMT2/G9a validated cells to identify the differentially regulated genes from various pathways that are responsible for promoting resistance to NK cell mediated cytotoxicity.

overall_design: MP-41 and Mel 92.1 cells were treated with EHMT2/G9a inhibitor UNC0642 & A366, samples were harvested and were used to prepare the total RNA, followed by RiboRNA depletion with random priming and RNASeq Illumina NextSeq 500 platform, with three biological replicates for each sample.


title: Uncovering pre-sensitizing agents to FLT3 inhibitors in acute myeloid leukemia with ReSisTrace lineage tracing

city: Helsinki

first: Li

last: Shen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: FLT3 inhibitors have significantly advanced the treatment of aggressive FLT3-mutated acute myeloid leukemia (AML), yet the development of resistance remains a major therapeutic challenge. Using the single-cell lineage-tracing method ReSisTrace, we identified transcriptional signatures distinguishing pre-resistant from pre-sensitive AML cells exposed to midostaurin or quizartinib. Targeting the pre-resistance gene GSPT1 with a CC-90009 degrader synergized with FLT3 inhibitors in AML cell lines, patient samples, and a PDX model, significantly improving survival. W further identified small molecules, including vistusertib (mTOR inhibitor), linsitinib (IGF1R/INSR inhibitor), and meisoindigo (IGF1R/Src inhibitor), capable of reversing pre-resistance transcriptional programs and shifting cells toward a FLT3 inhibitor-sensitive state. In summary, ReSisTrace unveils pre-existing transcriptional features of treatment vulnerability in hematological cancers, and elucidates novel strategies for enhancing FLT3 inhibitor treatment efficacy in FLT3-ITD-positive AML.

overall_design: We applied ReSisTrace to reveal cell states that are primed to FLT3 inhibitor resistance in an FLT3-ITD-mutated MOLM-13 AML cell line. Uniquely labeled, synchronized cells were allowed to divide once, after which half of the cells were analyzed by scRNA-seq (pre-treatment samples), while the other half underwent DMSO (control), midostaurin, or quizartinib treatment. The lineage labels of cells that survived the treatment were determined by scRNA-sequencing (post-treatment sample) and were used to identify pre-resistant cells in the pre-treatment sample.

first: Johanna

last: Eriksson

first: Shuyu

last: Zheng

first: Jing

last: Tang


title: Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs [ChIP-nexus]

city: Kansas City

first: Melanie

last: Weilert

state: MO

institute: Stowers Institute for Medical Research

summary: Low-affinity transcription factor motifs are an important element of the cis-regulatory code, yet they cannot be mapped by local sequence scanning without knowledge of the sequence context in which they are functional. Here we leverage sequence-to-profile models of chromatin accessibility and binding in mouse embryonic stem cells to reliably map low-affinity motifs across the genome and deduce the mechanisms by which they become functional. We show that low-affinity motifs are used by pioneer transcription factors and that their effect is disproportionately enhanced by intra-nucleosomal cooperativity with stronger pioneer motifs. By exploring the underlying nucleosome-mediated mechanism with a kinetic model, we discover that pioneer cooperativity, and not low-affinity motifs per se, renders enhancers more responsive to changes in TF concentrations by increasing their regulatory potential. These results show that low-affinity motifs can be accurately mapped and suggest that their inherently strong cooperativity is an important property of developmental enhancers.

overall_design: Chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode and single ligation (ChIP-nexus) experiments were conducted in mouse embryonic stem cell lines (R1) across wildtype lines and one set of CRISPR/Cas9 clones at an upstream Akr1cl enhancer.

first: Kaelan

last: Brennan

first: Khyati

last: Dalal

first: Sabrina

last: Krueger

first: Haining

last: Jiang

first: Rosa

last: Martinez-Corral

first: Julia

last: Zeitlinger


title: Hepatocyte-specific epidermal growth factor receptor (EGFR) deletion attenuates acetaminophen-induced liver injury in mice [RNA-seq Illumina]

first: Shuchang

last: Liu

overall_design: Wild-type and hepatocyte-specific EGFR knockout mice were given 500 mg/kg of Acetaminophen (APAP). Liver tissues were harvested at 0, 1, 3, 6, 12, and 24hr post-APAP overdose. Bulk RNA-seq was measured using Illumina sequencer.

first: Siddhi

last: Jain

first: Gillian

last: Williams

first: Ranjan

last: Mukherjee

first: Anne

last: Orr

first: Jia-Jun

first: Silvia

first: Joseph

last: Locker

first: Bharat

last: Bhushan


title: Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs [ATAC-seq]

overall_design: Assay for transposase-accessible chromatin with sequencing (ATAC-seq) experiments were conducted in mouse embryonic stem cell lines (R1) across wildtype lines and two suites of CRISPR/Cas9 clones at an Akr1cl and Btbd11 locus.


title: FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [human_Tconv_ChIP-seq]

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St.

institute: UCSF Gladstone Institutes

summary: FOXP3 is a lineage-defining transcription factor (TF) for immune-suppressive regulatory T cells (Tregs). While mice exclusively express FOXP3 in Tregs, humans also transiently express FOXP3 in stimulated conventional CD4+ T cells (Tconvs). Mechanisms governing these distinct expression patterns remain unknown. Here, we performed CRISPR screens tiling the FOXP3 locus and targeting TFs in human Tregs and Tconvs to discover cis-regulatory elements (CREs) and trans-regulators of FOXP3. Tconv FOXP3 expression depended on a subset of Treg CREs and Tconv-selective positive (NS+) and negative (NS-) CREs. Combinatorial silencing of Tconv CREs revealed their epistatic logic. The CREs are occupied and regulated by TFs we identified as critical regulators of FOXP3. Finally, mutagenesis of murine NS- revealed that it is critical for restriction of FOXP3 expression to Tregs. We discover CRE and TF circuitry controlling FOXP3 expression and reveal cell and species-specific regulation of a gene indispensable to immune homeostasis.

overall_design: ChIP-seq in human T cells. ChIP-seq was conducted in using DSG/formaldehyde fixation.

first: Jennifer

last: Umhoefer

first: Maya

last: Arce

first: Sivakanthan

last: Kasinathan

first: Sean

last: Whalen

first: Rama

last: Dajani

first: Sanjana

last: Subramanya

first: Laine

last: Goudy

last: Belk

first: Royce

last: Zhou

first: Minh

middle: T

last: N Pham

first: Wenxi

last: Zhang

first: Rosmely

last: Hernandez

first: Carinna

last: Tran

first: Nikhita

last: Kirthivasan

first: Jacob

last: Freimer

first: Cody

last: Mowery

first: Vinh

last: Nguyen

first: Mineto

last: Ota

first: Benjamin

last: Gowen

first: Dimitre

last: Simeonov

first: Gemma

middle: L

last: Curie

first: Zhongmei

last: Li

first: Andy

last: Chen

last: Corn

first: Howard

last: Chang

first: Qizhi

first: Luke

last: Gilbert

first: Ansuman

last: Satpathy

first: Katherine

last: Pollard


title: FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [CRISPRoff_RNA-seq]

first: Alexander

last: Marson

overall_design: Total RNA-seq in CRISPRoff-edited human Tconvs from 2 donors. CRISPRoff gRNAs target NS- or the AAVS1 control region (x2).

first: Jennifer

middle: M

last: Umhoefer

first: Maya

last: Arce

first: Sivakanthan

last: Kasinathan

first: Sean

last: Whalen

first: Rama

last: Dajani

first: Sanjana

last: Subramanya

first: Laine

last: Goudy

first: Julia

last: Belk

first: Royce

last: Zhou

first: Minh

last: N Pham

first: Wenxi

last: Zhang

first: Rosmely

last: Hernandez

last: Tang


title: Phase 2 Trial (COTC-030) of adjuvant inhaled recombinant human IL-15 combined with amputation and adjuvant carboplatin chemotherapy in dogs with appendicular osteosarcoma

first: Anjali

last: Garg

state: Maryland

address: Building 10, Room 1B53

department: Comparative Oncology Program,NCI

institute: National Institute of Health

summary: We have previously shown that inhaled IL-15 is associated with anti-tumor responses in dogs with pulmonary metastatic osteosarcoma (OSA) and melanoma. Here, we evaluated inhaled IL-15 combined with amputation and chemotherapy for dogs with localized OSA eligible for treatment with curative intent. In a multicenter COTC phase II trial for dogs with limb OSA, we hypothesized that 2 weeks of inhaled rhIL-15 after amputation and prior to chemotherapy would reduce the risk of metastatic failure at the completion of chemotherapy from a historical rate of 40% to 20%. Using a 2-sided alpha of 0.05, we planned an accrual of 40 dogs to test this hypothesis with 80% power. We also performed immune correlative assays and sequencing of blood immune cells (PBMCs) and primary amputation specimens. Unexpectedly, disease-free and survival outcomes for dogs in the intent-to-treat population were statistically inferior to a well-validated historical control cohort (P=0.03, P=0.003), so the trial was halted for futility. Cytotoxicity assays of PBMCs showed significant decreases after both surgery and chemotherapy with an overall decrease from the start to the end of therapy (-18.2±16.1%, P<0.001). Some dogs demonstrated positive fold change in PBMC cytotoxicity, and this correlated significantly with improved dog survival (P=0.004, r=0.62). Although plasma concentrations of key cytokines varied markedly with no significant differences between disease-free and metastatic-failure patients, inflammatory cytokines such as IL-6 showed absolute increases post-amputation and post-chemotherapy correlating with decreases in cytotoxicity. Tumor sequencing data reproduced immune signatures as observed in both human and canine cohorts, and PBMC sequencing data from 4 dogs showed upregulation of IL-15 receptor alpha on myeloid derived suppressor cells post-surgery. Inhaled IL-15 as part of multimodality approach with amputation and chemotherapy appears to be associated with worse outcomes in dogs with appendicular OSA. Correlative assays suggest significant immunological effects of amputation and chemotherapy on immune responses. These data have important implications for the design and testing of novel immunotherapy strategies involving multimodality approaches including surgery and chemotherapy.

overall_design: RNA for mRNAseq was isolated from canine frozen tumor tissue in RNAlater

first: Robert

middle: B

last: Rebhun

first: Sylvia

last: Cruz

first: Daniel

last: York

first: Christina

middle: N

last: Mazcko

first: Aryana

last: Razmara

first: Sushant

last: Patkar

middle: J

last: Judge

first: Cyrus

last: Sholevar

first: Ravi

middle: K

last: Shah

first: Anthony

last: Zamora

first: Sami

last: Al-Nadaf

first: David

last: Vail

first: Timothy

last: Fan

first: Jenna

middle: H

last: Burton

first: Madison

last: Luker

last: Skorupski

first: Amandine

last: LeJeune

first: Kevin

last: Woolard

first: Susan

last: Stewart

first: Ellen

last: Sparger

first: Jacque

last: Young

first: Tamar

last: Davidyan

first: Erich

last: Huang

first: Jessica

last: Beck

first: William

last: Murphy

first: Michael

last: Kent

last: Culp

first: Amy

last: LeBlanc

last: Canter


title: Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia [RNA-Seq DIN]

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

summary: The ubiquitous metabolite heme has diverse enzymatic and signaling functions in most mammalian cells. Through integrated analyses of mouse models, human cell lines and primary patient samples, we identify de novo heme biosynthesis as a selective dependency in acute myeloid leukemia (AML). The dependency is underpinned by a propensity of AML cells, and especially leukemic stem cells (LSCs), to downregulate heme biosynthesis enzymes (HBEs) which promotes their self-renewal. Inhibition of HBEs causes collapse of mitochondrial Complex IV (CIV) and dysregulates the copper-chaperone system inducing cuproptosis, a form of programmed cell death brought about by the oligomerization of lipoylated proteins by copper. Moreover, we identify pathways that are synthetic lethal with heme biosynthesis, including glycolysis, which can be leveraged for combination strategies. Altogether, our work uncovers a heme rheostat that controls gene expression and drug sensitivity in AML and implicates HBE inhibition as a novel cuproptosis trigger.

overall_design: The DIN model was generated by co-transducing fetal liver cells with MSCV-TRI-DNMT3AR882H-dsRed (TRI-DNMT3AR882H), MSCV-GFP-IDH2R140Q (MIG-IDH2R140Q) and MSCV-NRASG12D-TTA (MIT- NRASG12D) into sub-lethally irradiated (5.5Gy whole body irradiation delivered by an X-RAD 320 (Precision) female Ptprca recipients. Cryopreserved cells from moribund mice were transplanted into Ptprca recipients and mice were given either normal or doxycyline chow and water for 5 or 14 days. Doxycyline de-induces the expression of DNMT3AR882H. cKit+/Cd11b- DIN progenitor cells from the bone marrow and spleens of mice were isolated by FACS and subjected to RNA sequencing.

first: Lev

last: Kats