title: Prior High Fiber Intake Impinges on the Cellular Responses of Mesenteric Adipose and Intestinal Tissues to Subsequent High Fat Feeding [16s rRNA-seq]

first: Zhi

last: Peng

summary: Obesity, characterized by its chronic, recurrent and progressive nature, has become one of the most serious public health problems. As living standards improve, plant-based diet composed of whole grain and vegetable is gradually replaced by high-fat food of animal origin in daily life. The resulting increase in caloric intake is one of the major causes of obesity. In white adipose tissue, excessive calorie intake promotes adipocyte hypertrophy and hyperplasia, increases immune cell infiltration around dysfunctional adipocytes and causes rearrangement of adipocyte subpopulations. In intestinal tissue, obesity development is associated with activation of the gut microbiota to process indigestible dietary polysaccharides into short-chain fatty acid (SCFA) for intestinal absorption. At the cellular level, a high-fat/high-sugar diet induces excessive proliferation and differentiation of intestinal stem cells, leading to onset of intestinal maladaptation and obesity development. In addition, several studies have shown that a high-fat diet (HFD) can affect the enteric nervous system in multiple aspects, including neuronal density, expression of glial cell marker proteins, and ganglion size. A recent study shows that enteric glial cells play a key role in maintaining the homeostasis of the intestinal stem cell niche.

overall_design: We collected fecal samples from the two diet groups at the three time points for 16S sequencing to compare the temporal dynamics of the gut microbiome.

first: Meng

last: Xie


title: COPG1 Is a Selectively Essential Regulator  of Cancer Progression and Chemoresistance: A Comprehensive Pan-Cancer Study

status: Public on Nov 27 2025

city: 양산시

first: Susmita

last: Sen

address: 경남 양산시 물금읍 범어리 2762-1

department: Department of Anatomy

country: South Korea

institute: Pusan National University

type: Expression profiling by high throughput sequencing

summary: The coatomer complex, a key regulator of intracellular vesicular transport, has recently been implicated in cancer progression, yet a comprehensive pan-cancer analysis of its subunits has been lacking. Here, we systematically profiled genetic alterations, expression patterns, prognostic relevance, and functional dependencies of all COPI and COPII coatomer subunits across 33 cancer types using more than 10,000 tumor samples from The Cancer Genome Atlas (TCGA), complemented by functional perturbation data from CRISPR (n = 1,178) and RNAi (n = 707) screens in DepMap. Gene amplification—most notably of COPB2—was the most frequent alteration and was associated with poor survival in bladder and esophageal cancers. Mutations in COPA and SEC31A also demonstrated prognostic significance in endometrial carcinoma. Expression analyses revealed broad upregulation of coatomer genes across cancer types, with COPG1 and COPB1 emerging as strong risk-associated genes (HR > 2). Integrative functional dependency analyses further identified COPG1 and COPE as selectively essential in multiple cancer contexts, with COPG1 loss notably linked to increased drug sensitivity. Functional validation in hepatocellular carcinoma (HCC) showed that COPG1 knockdown impaired malignant phenotypes and reduced tumorigenicity in vivo. Mechanistically, COPG1 depletion induced Golgi disruption and ER stress, increased ROS production, and suppressed PI3K–AKT signaling. Moreover, COPG1 knockdown sensitized HCC cells to sorafenib and doxorubicin, whereas COPG1 overexpression conferred resistance. Collectively, our pan-cancer analysis reveals context-dependent roles of coatomer subunits and identifies COPG1 as a novel oncogenic driver and potential therapeutic target in HCC, mediating chemoresistance through redox modulation and PI3K–AKT pathway inhibition.

overall_design: Total RNA was extracted using the RNeasy Mini Kit (Qiagen). RNA quality was assessed by running 1 μl of RNA on a Bioanalyzer system (Agilent, CA, USA) to ensure the RIN and rRNA ratio. We used 100 ng of total RNA to prepare the sequencing libraries using the MGIEasy RNA Directional Library prep kit (MGI). They were quantified using the Agilent 2100 BioAnalyzer (Agilent) according to the manufacturer’s library quantification protocol. Following the cluster amplification of the denatured templates, sequencing was performed as paired-end (2 × 150 bp) using the MGI DNBSEQ-T7 platform. Data processing was performed as previously reported(15). Briefly, raw sequencing reads were processed by FastQC (RRID:SCR_014583) and aligned by STAR (RRID:SCR_004463) to the human reference genome hg38 with Ensembl annotation. Transcript abundance was quantified using RSEM5 in the units of TPM. Differential gene expression analysis was performed using DEseq2 (RRID:SCR_015687).

first: Van-Thanh

last: Duong

first: Youngin

last: Hwang

first: Seungmi

last: Kim

first: Euijin

last: Lee

first: Myoung-Eun

last: Han

first: Dongjun

first: Yun Hak

first: Sik

last: Yoon

first: Sae-Ock

last: Oh


title: Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree [RNA-seq]

status: Public on Nov 28 2025

city: Naples

first: Dario

last: Antonini

address: Strada Vicinale Cupa Cintia, 21

department: Department of Biology

country: Italy

institute: University of Naples "Federico II"

summary: The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. While mutations in the DNA binding domain of p53 cause cancer, mutations in the p63 DNA binding domain result in developmental syndromes affecting lip/palate, skin and limbs. For p53 the effect of mutations has been studied in great detail, enabling the identification of several mechanisms by which mutations inhibit high affinity binding of p53 to DNA. In this study we provide a similar detailed investigation of all currently known mutations in the p63 DNA binding domain by measuring the transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes, to elicit changes in the transcriptional program similar to those observed by wild type p63, and to bind regulatory regions in the genome. The data demonstrate that no mutation globally destabilizes and unfolds the domain. Several mutations affect the DNA binding affinity by disturbing the interaction between the DNA binding domains, thereby disrupting p63 ability to bind DNA as a tetramer cooperatively. These mutations retain partial DNA binding capacity which correlates with a milder patient phenotype.

overall_design: p63 binding occupancy was assessed by ChIP-seq with anti-p63 antibodies in BJ-Human Fibroblast expressing KLF4 alone (empty) or ΔNp63α WT (or p63 mutants) and KLF4

first: Christian

last: Osterburg

first: Marco

last: Ferniani

first: Ann-Sophie

last: Frombach

first: Ludovica

last: D’Auria

first: Susanne

first: Rebecca

last: Lotz

first: Frank

last: Löhr

first: Sebastian

last: Kehrloesser

first: Huiqing

last: Zhou

first: Caterina

last: Missero

first: Volker

last: Dötsch


title: Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin accessibility was assessed by ATAC-seq in BJ-Human Fibroblast expressing KLF4 alone (empty) or ΔNp63α WT and KLF4


title: Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree

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

overall_design: Refer to individual Series


title: Genomic localization and functions of MBD-2 with and without NuRD in DNA methylation-free C. elegans [ChIP-Seq]

city: Hong Kong

first: Wing Yee Karen

last: Yuen

address: 4S15, Kadoorie Biological Science building, The University of Hong Kong, Pok Fu Lam Road

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: While mammalian MBD2 is a well-established 5-Methylcytosine reader and component of the essential Nucleosome Remodeling and Deacetylase (NuRD) complex, the function and binding pattern of C. elegans MBD2 (Cel-MBD-2) in its 5mC-free genome remained uncharacterized. In our study, Cel-mbd-2 null mutation resulted in a wide range of severe morphological defects and sterility. We have also confirmed that Cel-MBD-2 is a key transcriptional modulator that can regulate genes in both directions. The MBD-2 binding patterns in the gene promoter or gene body are linked with the gene regulatory directions and display distinct correlations with histone modifications within and outside the context of NuRD complex.

overall_design: ChIP-seq of Cel-MBD-2 using anti-FLAG magnetic beads targeting GFP::3xFLAG::MBD-2

first: Hok Ning

last: Tsui


title: Genomic localization and functions of MBD-2 with and without NuRD in DNA methylation-free C. elegans [RNA-Seq]

summary: While mammalian MBD2 is a well-established 5-Methylcytosine reader and component of the essential Nucleosome Remodeling and Deacetylase (NuRD) complex, the function and binding pattern of C. elegans MBD2 (Cel-MBD-2) in its 5mC-free genome remained uncharacterized. In our study, Cel-mbd-2 null mutation resulted in a wide range of severe morphological defects and sterility. Coiled-coild domain deletion of Cel-mbd-2 phenocopied the null mutant and led to similar transcriptomic changes. We have also confirmed that Cel-MBD-2 is a key transcriptional modulator that can regulate genes in both directions. The MBD-2 binding patterns in the gene promoter or gene body are linked with the gene regulatory directions and display distinct correlations with histone modifications within and outside the context of NuRD complex.

overall_design:
RNA-seq of N2 wildtype and mbd-2 null mutant synchronized young adult worms. The mutant is maintained as a heterozygous stock balanced with hT2 balancer, we performed RNA-seq for both homozygous null mutants sired by heterozygous null mutant (P0) and homozygous null mutants sired by homozygous null mutant (F1) adult worms.
RNA-seq of gfp::3xflag::mbd-2 (control) and gfp::3xflag::mbd-2?CC (coiled-coil domain deletion) mutant synchronized young adult worms. The mutant is maintained as a heterozygous stock balanced with hT2 balancer, we performed RNA-seq for both homozygous coiled-coil domain deletion mutants sired by heterozygous coiled-coil domain deletion mutant (P0) and homozygous coiled-coil domain deletion mutants sired by homozygous coiled-coil domain deletion mutant (F1) adult worms.


title: CRISPR-Cas9 Screening Identifies Resistance Mechanisms to KRAS Inhibition in Pancreatic Cancer

city: Cincinnati

first: Andrew

last: Waters

state: Ohio

address: Vontz Center for Molecular Studies, Rm 1234, 3125 Eden Ave

country: USA

institute: University of Cincinnati

summary: KRAS inhibitors (KRASi) targeting various KRAS mutations have entered clinical trials for pancreatic cancer. Despite promising preliminary clinical responses, most patients relapse due to intrinsic and acquired resistance. Thus, combination treatments are essential to extend the efficacy of KRAS-targeted therapies. To further determine genetic mechanisms of KRASi resistance, we performed KRASi-anchored CRISPR-Cas9 loss-of-function screens in KRAS G12D-, KRAS G12R-, and KRAS Q61H-mutant PDAC cell lines, using six KRASi, to identify genes, that when lost, modulate sensitivity to KRAS inhibition. We pharmacologically validated several hits from our screens, including EGFR, CK2 p110 alpha and p110 gamma, and YAP, by combining targeted inhibitors with KRASi. We determined that KRAS Q61H-mutant PDAC cell lines are intrinsically less dependent on KRAS for survival than other KRAS mutational subtypes. Further, we found that EGFR inhibitor erlotinib synergized with the RAS(ON) multi-selective inhibitor RMC-7977 in KRAS Q61H-mutant PDAC cell lines, and in cell lines with highly active EGFR, by mitigating ERK rebound activity. We also developed KRASi-resistant cell lines and observed sustained ERK MAPK dependence in the KRASi-resistant cell lines despite decreased ERK activity. Our findings enhance the understanding of KRASi intrinsic and acquired resistance and identify therapeutic vulnerabilities that can potentially be exploited for KRASi combination therapies in patients with PDAC.

overall_design: RNA-Seq of 12 PDAC cell lines with the goal of identifying differences between KRAS Q61H-mutant and non-KRAS Q61H-mutant cell lines.

middle: M


title: Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree [ChIP-seq]


title: Hsp70-Bim interaction mediated mitophagy as a potential therapeutic target for CML stem cells

city: Dalian

first: Ting

last: Song

address: No.2 LingGong Road, GanJingZi District, Dalian, Liaoning, China

country: China

institute: Faculty of Medicine, Dalian University of Technology

summary: In chronic myeloid leukemia (CML), disease persistence in patients is maintained by leukemic stem cells (LSCs), which drives tyrosine kinase inhibitor (TKI) resistance. Autophagy has been proposed as a potential therapy to eradicate CML LSCs. Here, using a small-molecule inhibitor of Hsp70 (heat shock protein 70)-Bim (Bcl-2-interacting mediator of cell death) interaction, S1-10, we demonstrate that Hsp70-Bim is a target for CML stemness maintenance. Hsp70-Bim is driven by Bcr-Abl and mediates particularly stronger mitophagy in CML LSCs than differentiated CML cells and HSCs. The more selective mitophagy regulation of Hsp70-Bim than ULK1 (unc-51-like autophagy activating kinase 1) is illustrated. Pharmacological inhibition of Hsp70-Bim blocks mitophagy, leading to differentiation of CML LSCs, loss of quiescence, and loss of LSC self-renewal potential. In the patient-derived xenograft (PDX) CML models, S1g-10 reduces the number of LSCs by more than 80% after two weeks of injection, without obvious toxicity on normal red blood cells.

overall_design: RNA-seq analysis of human primary CML CD34+ cells treated with Hsp70-Bim inhibitor S1g-10 (1 μM) versus Vehicle (DMSO) for 24 hours.

first: Yang

first: Hong

last: Zhang

first: Zhiyuan

last: Hu

first: Fangkui

last: Yin

first: Zhichao


title: Gut Microbiota Profiling of Lebanese Patients with Ulcerative Colitis and Healthy Controls: A Pilot Study

city: Beirut

first: Melhem

last: Bilen

address: Bliss street

department: Department of Experimental Pathology, Immunology and Microbiology

country: Lebanon

institute: American University of Beirut

summary: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon, associated with gut microbiota dysbiosis. While global studies have explored this link, region-specific microbial profiles remain underreported. This pilot study aimed to characterize and compare, for the first time, the gut microbiota of Lebanese UC patients and healthy controls using 16S rRNA gene sequencing (V3–V4 region). Fecal samples from 11 UC patients and 11 healthy individuals were analyzed. Alpha and beta diversity metrics were computed, and gut microbial composition was assessed across taxonomic levels. Statistical comparisons used Mann-Whitney and Fisher’s exact tests. UC patients showed significantly reduced microbial diversity based on Faith’s Phylogenetic Diversity and Shannon index (p < 0.05), though evenness was unaffected. Beta diversity also revealed significant group-level dissimilarities (p < 0.05). At the phylum level, Bacteroidota was elevated in UC, while Bacillota and Actinomycetota were reduced. Genera such as Ruminococcus, Fusicatenibacter, Mediterraneibacter, Eubacterium, and Coprococcus were depleted in UC. Faecalibacterium, commonly reduced in UC, showed no significant difference. This first analysis of gut microbiota in Lebanese UC patients reveals a distinct microbial signature that partially diverges from global trends, supporting the need for region-specific microbiome studies and personalized microbiota-targeted therapies.

overall_design: Cross-sectional, observational, case-control pilot study using 16S rRNA gene sequencing.

first: Fayez

last: Yassine

first: Hassan

last: Abbas

first: Abdallah

last: Kurdi

first: Reem

last: Mansour

first: Fadi H

last: Mourad

first: Ghassan

last: Matar


title: Chromatin folding principles underlying the generation of antibody diversity

status: Public on Nov 26 2025

city: Baltimore

first: Noah

last: Ollikainen

address: 251 Bayview Blvd.

institute: National Institutes of Health

summary: Achieving a diverse repertoire of antigen receptors for effective adaptive immunity requires rearrangement of gene segments into unique combinations via V(D)J recombination.  To illuminate precise mechanisms underlying this process, we combined biophysical simulations with experimental data to model chromatin folding and dynamics of the mouse immunoglobulin heavy chain gene (Igh) locus.  Simulations that best recapitulated experimental data on locus structure and recombination of wild-type and mutated Igh alleles identified three novel chromatin folding principles.  First, we found that prominent structural features of the Igh locus, such as the 3’-anchored stripe, required cohesin loading throughout the locus rather than at the stripe anchor.  Second, the Eµ enhancer was best modeled as a bi-directional loop extrusion blocker though it does not bind the known extrusion blocker CTCF.  Third, we found that utilization of VH genes to obtain maximum diversity required both widespread cohesin loading as well as long-range associations between H3K27ac-marked regions.  Our findings provide a conceptual framework to understand chromatin folding principles that enable antibody diversity and reveal mechanisms of long-range genome communication.

overall_design: Capture Hi-C of the Igh locus in an IGCR1-deleted pro-B cell line

first: Fei

last: Ma

first: Fatima

middle: Z

last: Braikia

first: Ranjan

last: Sen


title: Disruption of Mitochondrial Dynamics and Stasis Leads to Liver Injury and Tumorigenesis

city: Kansas City

first: Wen-Xing

last: Ding

state: Kansas

address: 3901 Rainbow Blvd.

department: Department of Pharmacology, Toxicology and Therapeutics

institute: University of Kansas Medical Center

summary: In this study, we first demonstrate that the expression levels of DNM1L, a key mitochondrial fission gene, are highly heterogeneous in human HCC samples. Specifically, DNM1L expression was significantly higher in some HCC samples and lower in others, suggesting abnormal expression patterns in human HCC. To investigate the role and mechanisms of mitochondrial dynamics in liver pathophysiology and tumorigenesis, we generated several genetically engineered mice that were either deficient in fission, fusion, or both, followed by rigorous histological and biochemical analyses, as well as multiple omics approaches.

overall_design: 2M and 6M Dnm1l KO, Mfn1/2 KO, and Dnm1l/Mfn1/2 TKO mouse liver were collected and send for RNA-Seq analysis.

first: Xiaowen

first: Xiaoli

last: Wei

first: Zheyun

last: Peng

first: Wanqing

last: Liu

first: Hongmin

last: Ni


title: Direct Targeting of the Oncogene Microphthalmia-Associated Transcription Factor (MITF) by Fragment-Based Discovery

city: Cambridge

last: Ji

state: MA

address: 250 Massachusetts Ave

institute: Novartis Biomedical Research


title: Differential expression profiles of plasma exosomal microRNAs in obstructive sleep apnea patients

city: changsha

first: xing

last: lyu

address: NO.139 Renmin road

department: Laboratory Medicine

institute: The Second Xiangya Hospital, Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary: Obstructive sleep apnea (OSA) is a prevalent respiratory disorder, with an estimated global prevalence of over one billion individuals, exhibiting a wide spectrum of severity. In this study, clinical data and whole blood samples were obtained from non-OSA individuals and OSA patients.we performed high-throughput sequencing to analyze differential expression of miRNAs between non-OSA exosomes (n=4) and OSA-Exos (n=6). This analysis identified 15 miRNAs exhibited significantly different expression levels between the two groups, with 7 upregulated and 8 downregulated in OSA-Exos compared to CON-Exos.

overall_design: miRNA profiling by high throughput sequencing

first: Xing

last: Lyu

first: Jingyao

last: Cai

first: Hui

last: Gong

first: Shisheng

last: Li

first: Min

last: Hu

first: Shengyu

last: Tan

first: Xiangyu

last: Zhang


title: Identification of  pro- and anti-tumorigenic signals from the injury microenvironment following depletion of Nf1 in myelinating Schwann cells

city: Zürich

first: Salome

last: Stierli

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

summary: The loss of Nf1 in mSC is not sufficient to induce tumourigenesis, however, we found that after sciatic nerve injury, Nf1- deficient mSCs formed neurofibromas specifically at the wound site (Ribeiro et al., 2013). Remarkably, in contrast to the tumorigenic behaviour of Nf1- deficient SCs at the wound site, they behaved and repaired normally in the distal stump. This indicated that whereas the normal nerve environment suppresses neurofibroma formation, the injury site of the nerve is a tumour- promoting environment, fostering the development of neurofibromas. Using bulk RNA seq, comparing the injury site with the distal stump of Nf1 KO vs Control nerve fragments, we identified TGFB as pro-tumorigenic microenvironmental signal that is highly expressed by pro-tumorigenic macrophages at the site of injury in Nf1-Ko mice.

overall_design: RNA seq profiling of regenerating nerve fragments of Nf1 KO and control mice at 14 days follwing nerve injury. 6 nerve fragments (each fragment had a size of 0.5mm) were combined from multiple mice for each sample. 3 independent samples were sequenced for each region and genotype of interest. Genotypes: P0-CreERT2:YFPfl/fl:Nf1+/+ (CTL) and P0-CreERT2:YFPfl/fl:Nf1fl/fl (loss of Nf1 im myelinating Schwann cells, Nf1 KO)

first: Alison

middle: C

last: Lloyd

first: Alex

last: Power

first: Cristina

last: Venturini

first: Ilaria

last: Napoli


title: Variability in intrinsic promoter strength underlies the temporal hierarchy of the Caulobacter SOS response induction

city: Bengaluru

first: Anjana

last: Badrinarayanan

state: Karnataka

address: Bellary Road

country: India

institute: National Centre for Biological Sciences

summary: Bacteria encode for gene regulatory networks crucial for sensing and repairing DNA damage. Upon exposure to genotoxic stress, these transcriptional networks are induced in a temporally structured manner. A case in point is of the highly conserved SOS response that is regulated by the LexA repressor. Studies have proposed that affinity of LexA towards promoters of SOS response genes is the primary determinant of its expression dynamics. Here, we describe an additional level of regulation beyond LexA properties that modulates the SOS response gene expression pattern. Using transcriptomic analyses, we reveal a distinct temporal hierarchy in the induction of SOS-regulated genes in Caulobacter crescentus. We observe that LexA properties are insufficient in predicting the temporal hierarchy of these genes. Instead, we find that intrinsic promoter strength underlies the order of gene activation, with differential sigma factor association as a key factor in modulating gene expression timing. Our findings highlight a novel regulatory layer in SOS dynamics and underscore the importance of promoter properties in shaping bacterial stress responses.

overall_design: RNA-seq was performed on Caulobacter crescentus strains with or without exposure to mitomycin C DNA damage.

first: Aditya

last: Kamat

first: Asha

last: Joseph

first: Deeksha

last: Rathour


title: Intragenic Epigenetic Deregulation by IDH2 Mutations Synergizes with SRSF2 Mutations Causing Mis-splicing of Key Transcriptional Regulators [BiSulfite-seq]

city: Miami

first: Aristeidis

middle: G

last: Telonis

state: FL

address: 1550 NW 10th Ave

institute: University of Miami

type: Methylation profiling by high throughput sequencing

summary: Genes impacting DNA methylation (DNAme), like IDH2, are frequently co-mutated with splicing factors, like SRSF2, in acute myeloid leukemia (AML). These co-occurring mutations are associated with more aggressive phenotypes but the underlying molecular mechanisms remain elusive. To address this gap, we profiled wild-type, IDH2R140Q or SRSF2P95 single-mutants and IDH2R140Q/SRSF2P95 double-mutant AMLs at a deep resolution level. We find a unique set of mis-spliced genes and differentially methylated CpGs in double-mutants. Mis-spliced exons are enriched in CCNG splicing enhancers and in the corresponding DNAme changes. Using a machine-learning model, we can accurately predict exon inclusion levels from proximal CpGs. These CpGs are more likely to overlap with footprints of RNA-binding and chromatin-modifying complexes but not transcription factors. We also report unique gene expression profiles associated with each genotype; however, the differentially expressed genes do not overlap with mis-spliced transcripts. Instead, the mis-spliced genes encode for proteins that interact with the gene regulatory complexes that control the expression of these differentially expressed genes. Thus, we propose a mechanism where synergism between aberrant DNAme and splicing leads to the mis-splicing of key components in gene regulatory complexes, thus resulting in the aberrant gene expression profiles characteristic of these AMLs.

overall_design: Clinical bone marrow or peripheral blood specimens were collected from 25 de-identified AML specimens. Mononuclear cells (MNC) were isolated through Ficoll density centrifugation at diagnosis. RNA and DNA were extracted for RNA sequencing and Whole Genome Bisulfite Sequencing, respectively.

first: Maria

middle: E

last: Figueroa


title: Bacterial chromatin remodeling associated with transcription-induced domains at pathogenicity Islands.

city: Gif-sur-Yvette

first: Virginia

last: Lioy

address: 1 Avenue de la Terrasse

department: Genome Biology

country: France

institute: Institute for Integrative Biology of the Cell (I2BC)

summary: Salmonella Pathogenicity Islands (SPIs) are horizontally acquired genetic elements integrated in the chromosome of Salmonella species, which allow them to infect and survive within their hosts. The nucleoid associated protein H-NS silences SPI gene transcription and this repression is counter-silenced at precise stages of the Salmonella infectious cycle. Bistable expression of the Type Three Secretion System 1 encoded in SPI-1 is a key step in the invasion of epithelial cells by Salmonella. In bacteria, transcriptionally active units form chromatin domains with specific dynamics and subcellular localization.  How chromatin domains are formed in physiological conditions remains poorly characterized. By applying a functional genomics approach to phenotypically similar Salmonella populations, we studied the remodeling of SPI-1 chromatin upon H-NS counter silencing. Our results show that although H-NS significantly reduces pervasive transcription, high H-NS occupancy co-exists with a low spurious transcriptional activity and low RNA polymerase occupancy at silent SPIs. When SPI-1 is expressed, we observe a remodeling of SPI-1 chromatin into domains that is dependent on the HilD transcriptional regulator. We uncovered the transcriptional signature of Salmonella cells expressing SPI-1 and determined that SPI-1 chromatin domains are associated with a variable distribution of H-NS occupancy and localized close to the nucleoid periphery. Our findings support a model in which the transcriptional activation of SPI-1 genes drives the chromatin remodeling and subcellular re-localization of this pathogenicity island.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Chromomosome conformation capture, RNA-seq and ChIP-seq of Salmonella enterica serovar Thyphimurium SL1344 WT and hilE mutant.

first: Mounia

last: Kortebi

first: Mickael

last: Bourge

first: Romain

last: Le Bars

first: Erwin

last: Van Dijk

first: Charles J

last: Dorman

first: Stéphanie

last: Bury-Moné

first: Frédéric

last: Boccard

first: Virginia S


title: MHC II-restricted neoantigen vaccine reverses immune microenvironment and overcomes resistance to immune checkpoint inhibitors in cold tumors.

city: Nanjing

first: Chun

last: Lu

address: No. 8 Xuefu Road, Pukou

institute: Nanjing University


title: Intragenic Epigenetic Deregulation by IDH2 Mutations Synergizes with SRSF2 Mutations Causing Mis-splicing of Key Transcriptional Regulators [RNA-seq]


title: Transcriptomic responses of the cyanobacterium Synechococcus sp. PCC 7002 under growth-inhibiting high CO2 concentration

city: Copenhagen

first: Christian

last: Anthon

address: Thorvaldsensvej 57

country: Denmark

institute: University of Copenhagen

summary: RNA-seq study that inverstigated the transcriptomics landscape of Synechococcus sp. PCC 7002 under air (0.04%), optimal growth (4 & 8%) and growth-inhibiting high (30% CO2) aeration.

overall_design: Grown in aqua culture with constant pH but varying CO2 levels

first: Adrian

middle: S

last: Geissler

first: Elena

last: Carrasquer-Alvarez

first: Jan

last: Gorodkin

first: Niels-Ulrik

last: Frigaard

first: Stefan

last: Seemann


title: Direct Targeting of the Oncogene Microphthalmia-Associated Transcription Factor (MITF) by Fragment-Based Discovery [Cut & Tag]

first: Fei

last: Ji

summary: Despite the improvement of therapeutic options for melanoma, patients with advanced metastatic disease are still in high need of durable and tolerated treatments. Analysis of clinical data from patients receiving targeted and/or immunotherapy, along with genetic and functional studies in preclinical melanoma models, show that lineage addiction to MITF is retained throughout disease progression, thus providing the rationale to pursue therapeutic inhibition of MITF. However, direct targeting of MITF or other basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factors is unprecedented. Here, we report on the fragment-based discovery of high-affinity ligands for MITF. Fragment screening by NMR led to the discovery of weak binders to the kink pocket of MITF, which were optimized to sub-micromolar affinity by structure-based design enabled by crystallography and biophysics. Furthermore, NMR experiments and molecular dynamics simulations revealed a dynamic conformational exchange of the two helices in the asymmetric homodimer, which is perturbed by ligand binding. This work advances our knowledge on direct targeting of bHLH-LZ domains and sets the basis to further explore pharmacological inhibition of MITF.

overall_design: RNA-seq profiling of wild-type and MITF knocked-down (KD) in naïve (parental) or resistant to the Dabrafenib and Trametinib combination MELHO cells. MITF Cut&Tag chromatin profiling in WT and MITF mutant expressed UACC-257 cells

first: Deborah

last: Castelletti

first: Fanny

last: Mermet-Meillon

first: Aurore

last: Desplat

first: Kayhan Gabriel

last: Akyel

first: Edward

middle: J

last: Oakeley

first: Ulrike

last: Naumann

first: Louise

last: Barys


title: Direct Targeting of the Oncogene Microphthalmia-Associated Transcription Factor (MITF) by Fragment-Based Discovery [RNA-seq]


title: X chromosome crossover formation and genome stability in Caenorhabditis elegans are independently regulated by xnd-1

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: The germ line efficiently combats numerous genotoxic insults to ensure the high fidelity propagation of unaltered genomic information across generations. Yet, germ cells in most metazoans also intentionally create double-strand breaks (DSBs) to promote DNA exchange between parental chromosomes, a process known as crossing over. Homologous recombination is employed in the repair of both genotoxic lesions and programmed DSBs and many of the core DNA repair proteins function in both processes. In addition, DNA repair efficiency and crossover distribution are both influenced by local and global differences in chromatin structure, yet the interplay between chromatin structure, genome integrity, and meiotic fidelity is still poorly understand. We have used the xnd-1 mutant of C. elegans to explore the relationship between genome integrity and crossover (CO) formation. Known for its role in ensuring X chromosome CO formation and germline development, we show that xnd-1 also regulates genome stability. xnd-1 mutants exhibited a mortal germ line, high embryonic lethality, high incidence of males, and sensitivity to ionizing radiation. We discovered that a hypomorphic allele of mys-1 suppressed these genome instability phenotypes of xnd-1 but did not suppress the CO defects, suggesting it serves as a separation-of-function allele. mys-1 encodes the histone acetyltransferase whose homolog Tip60 acetylates H2AK5, a histone mark associated with transcriptional activation that is increased in xnd-1 mutant germlines, raising the possibility that thresholds of H2AK5ac may differentially influence distinct germ line repair events. We also show that xnd-1 regulated him-5 transcriptionally, independently of mys-1, and that ectopic expression of him-5 suppressed the CO defects of xnd-1. Our work provides xnd-1 as a model in which to study the link between chromatin factors, gene expression, and genome stability.

overall_design: Identification of genes expressed in three groups (N2, XND-HC, XND-LC), with 2 groups of three replications and 1 group of two replications.

first: Judith

last: Yanowitz

first: M

middle: W

last: Krause


title: DNA methylation analysis of 293T cells expressing wild-type RUNX1 and a chimera protein RUNX11-299-SPI11-102

status: Public on Nov 25 2025

city: Yokohama

first: Shiori

last: Maeda

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

summary: Transcription factor (TF)-dependent DNA demethylation is associated with generation of specific DNA methylation profiles in normal cellular development and disease, although only a small fraction of TFs are known to promote DNA demethylation. We examined DNA methylation profiles of 293T mock, 293T wild type RUNX1, and 293T RUNX11-299–SPI11-102 cells by reduced representation bisulfite sequencing analysis. Genome-wide DNA demethylation was observed specifically at RUNX1-binding sites in 293T cells expressing a chimeric protein consisting of RUNX11-299 and SPI11-102, similar to 293T cells expressing wild type RUNX1.

overall_design: 293T cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and penicillin/streptomycin (100 U/mL, 100 mg/mL). The cells were infected overnight with the lentivirus vectors at a multiplicity of infection of 7–15 in the presence of 8 mg/mL polybrene, followed by puromycin selection at 3 µg/mL for 10 days. Genomic DNA was extracted from the 293T cells and subjected to the reduced representation bisulfite sequencing.

first: Xian-Yang

last: Qin

first: Harukazu

last: Suzuki


title: Extensive remodelling of XIST regulatory networks during primate evolution

city: Paris

first: Claire

last: Rougeulle

address: 35 rue Hélène Brion

institute: Université Paris Cité

type: Genome variation profiling by high throughput sequencing

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

sample_organism:
Callithrix jacchus
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: Refer to individual Series


title: scMultiome-seq and single-cell spatial HD data for the developing human knee

city: Boston

first: April

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Cartilage plays a crucial role in skeletal development and function, and abnormal development contributes to genetic and age-related skeletal disease. Compromises to the integrity of joint-lining articular cartilage in particular lead to debilitating chronic degenerative diseases including osteoarthritis. To better understand how human articular cartilage develops in vivo, we jointly profiled the transcriptome and open chromatin regions in individual nuclei recovered from distal femora at 2 fetal timepoints. We used these multiomic data to predict transcription factor-based regulatory networks that are important for articular chondrocyte differentiation. We developed a human pluripotent stem cell platform for interrogating the function of predicted transcription factors during chondrocyte differentiation and identified new biological roles for CREB5. We expect new regulatory networks we uncovered using multiomic data to be important for promoting cartilage health and treating disease, and our platform to be a useful tool for studying cartilage development in vitro.

overall_design:
Single cell epigenetic and transcriptomic profiling of cells isolated from human fetal femur at E59 and E72
Fresh knee samples were dissected out (along with the soft tissues surrounding them), flash frozen in OCT, and were processed using 10X Genomics visium spatial HD transcriptomics protocol. Each 10X genomics visium run has raw fatq files and input files

first: G

last: Senevirathne

first: Andrew

last: Zhu

first: Divya

last: Venkatasubramanian

first: Terence

middle: D

last: Capellini


title: NF-𝜅B is a Central Regulator of Hypoxia-Induced Gene Expression

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

country: United Kingdom

institute: University of Liverpool

summary: RNA-seq analysis investigating NF-𝜅B dependent transcriptional response following hypoxia stimulation

overall_design: HeLa cells were grown at 21% oxygen, treated with control siRNA and exposed to 0 hrs (control) or 24 hrs (control) 1% oxygen (hypoxia). HeLa cells were also treated with RelA, RelB or cRel siRNAs and exposed to 24 hrs 1% oxygen. RNA-seq was performed to measure differential transcript expression.

first: Dilem

last: Shakir


title: Splicing factor CWC22 prevents tetraploidy formation and mitotic slippage through maintenance of the BubR1 expression and CDK1 activity

city: Kyoto

first: Ryuzaburo

last: Yuki

address: 5 Misasagi-Nakauchi-cho, Yamashina-ku

institute: Kyoto Pharmaceutical Univeristy

summary: Splicing factors play a fundamental role in the process of gene expression. Several splicing factors are highly expressed in cancers and promote the proliferation. Although targeting of splicing factors prolong the duration of G2 phase and mitosis, the involvement of splicing factors in regulation of cell ploidy remains unclear. In this study, we found that knockdown of CWC22, a splicing factor, increased not only the population of G2 phase and mitosis but also tetraploid cells. Notably, CWC22 knockdown induces mitotic slippage, which exhibits rapid mitotic exit without SAC satisfaction after prolonged prometaphase duration. CWC22 knockdown led to cyclin B1 degradation and accumulation of inactive CDK1 having the inhibitory phosphorylation at Tyr15 in mitosis. The cyclin B1 overexpression and Wee1 blockage mitigated the shortage of mitotic duration by CWC22 knockdown. RNA-seq analysis indicated that CWC22 knockdown down-regulated SAC-regulatory genes, including BubR1. The shortage of mitotic duration caused by CWC22 knockdown was also mitigated by both overexpression of BubR1 and Wee1 blockage. Furthermore, CWC22 was highly expressed in pancreatic or cervical cancers, and the higher expression negatively correlated with patients’ prognosis. CWC22 knockdown induced cancer cell death after miotic slippage and prolonged G2 phase due to DNA damage accumulation. These results suggest that CWC22 not only supports proper progression of G2/M phase but also prevents mitotic slippage and tetraploid cell formation via regulation of checkpoint signaling by contributing to the proper expression of BubR1 and the CDK1 activity. These findings reveal a novel splicing factor function in genome stability.

overall_design: 4 RNA-seq samples were analyzed. 2 controls samples, 2 samples with shRNA depletion of CWC22.

first: Youhei

last: Saito

first: Yuji

last: Nakayama


title: IRF3 attenuates hypoxia signaling by retaining HIF-α in the cytoplasm

city: Wuhan

first: Hongyan

last: Deng

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: Interferon regulatory factor 3 (IRF3) functions as a key transcription factor in the innate antiviral immune response, which is depended on its nuclear localization. However, its function in the cytoplasm during non-infection states remains largely unknown. In this study, we found that resting cytoplasmic IRF3 interacts with HIF-1α and HIF-2α, two master regulators of hypoxia signaling. This interaction retains HIF-α in the cytoplasm under hypoxic conditions, preventing it from exerting their transcription factor function and attenuating hypoxia signaling. Disruption of IRF3 in both mice and zebrafish resulted in increased expression of hypoxia response genes and enhanced tolerance to hypoxia. These findings suggest that, in the absence of viral infection, cytoplasmic IRF3 modulates hypoxia signaling by retaining HIF-α in the cytoplasm under hypoxic conditions.

overall_design: THP-1 cells infected without or with VSV or HSV-1 for 8 hours. IRF3-deficient or wild-type H1299 cells under normoxia (21% O2) or hypoxia (1% O2) for 24 hours.

first: Shuke

last: Jia

first: Chunchun

first: Jiale

last: Hua

first: Zixuan

last: Wang

first: Xueyi

last: Sun

first: Wen

last: Liu

first: Liyun

last: Shi

first: Wenhua

last: Li

first: Jian-Fang

last: Gui

first: Xing

first: Wuhan

last: Xiao


title: Combining CDK12 and BAF inhibition synergistically impairs cancer cell survival in triple-negative breast cancer line

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Chromatin profiling with CUT&Tag and CUTAC reveals that while CDK12 inhibition primarily disrupts DNA accessibility at Brg1 and CDK12 co-occupied promoters, BAF inhibition leads to widespread loss of enhancer accessibility. Co-inhibition causes a compounded disruption at shared co-occupied regulatory sites, resulting in loss of chromatin accessibility and transcriptional dysregulation at key loci.

overall_design: CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library.

first: Cassidy

last: Danyko

first: Monika

last: Macakova

first: Kami

last: Ahmad

first: Steven


title: Cytokine-driven glycosphingolipid metabolism modulates endoplasmic reticulum calcium homeostasis in primary human renal mesangial cells

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary: Glycosphingolipids (GSLs), including hexosylceramides (HexCers), lactosylceramides (LacCers), and gangliosides composed of one or more sugar residues attached to ceramide, are essential components of cell membranes. Dysregulated GSL metabolism has been implicated in various inflammatory and autoimmune diseases, including lupus nephritis; however, its contribution to renal cell dysfunction remains largely unexplored. In this study, we demonstrate that in primary human renal mesangial cells (hRMCs), proinflammatory cytokines relevant to lupus elicit significant upregulation and secretion of inflammatory mediators that parallel intracellular and extracellular accumulation of HexCers and elevated cytosolic calcium (Ca2+) levels. The increase in cytosolic Ca2+ was attributed to a decrease in endoplasmic reticulum (ER) Ca2+ store capacity. Pharmacological inhibition of GSL synthesis with eliglustat significantly reduced HexCers levels and restored ER Ca2+ stores, but did not impact cytokine-induced cytokine/chemokine secretion or cell viability/proliferation. Together, these data suggest that elevated GSL synthesis modulates cytokine-induced ER Ca²⁺ dysregulation in mesangial cells and may play a role in the pathogenesis of lupus nephritis.

overall_design: hRMCs (lots 12445, 17544, and 20018) were treated in quadruplicate wells in 6-well plates with vehicle, 25 ng/ml IL-1b, or 25 ng/ml IL-1b +20 nM eliglustat for 24, 48, or 72 hrs. Media was collected for ELISAs and GSL quantification, cell viability was measured by the alamar blue assay, and cells scraped into DPBS and replicate wells combined. The cell suspension was split into two tubes, centrifuged, and DPBS removed. Half the cells were used for GSL quantification, and the other half were used for RNA isolation.

first: Mariia

last: Stefanenko

first: Tessa

last: Ortiz

first: Sandra

last: Mungaray

first: Mykhailo

last: Fedoriuk

first: Oleg

last: Palygin

first: Drew

last: Moore

first: Tamara

middle: K

last: Nowling


title: PARG regulates the proteasomal degradation of TARG1

city: Oxford

first: Callum

last: Henfrey

address: Sir William Dunn School of Pathology, South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: ADP-ribosylation is a reversible modification of macromolecules critical for the regulation of genome stability, stress responses, and proteostasis. While the roles of ADPr transferases such as PARP1/2 and TNKS1/2 are well established, the functions and regulatory mechanisms of ADPr hydrolases are still poorly understood. Here, we identify a previously uncharacterized function of the poly(ADP-ribose) glycohydrolase PARG in regulating protein degradation. Using quantitative proteomics, we show that PARG inhibition depletes protein levels of the mono-ADPr hydrolase TARG1. We demonstrate that this TARG1 depletion is both PAR- and proteasome-dependent, and identify the E3 ubiquitin ligases HUWE1 and TRIP12 as mediators of this process. Our findings establish TARG1 as a substrate of PAR-dependent protein degradation and uncover a PARG-dependent mechanism controlling its stability. This work highlights a new dimension of interplay between the two ADP-ribosyl hydrolases, with implications for the refinement of PARG-targeted therapeutic strategies.

overall_design: RNA-seq in biological triplicates of U2OS WT cells treated with either DMSO or PARGi

first: Joséphine

last: Groslambert

first: Sara

last: Buch-Larsen

first: Ivo

middle: A

last: Hendriks

first: Robert

last: Kurzbauer

first: Jonas

last: Elsborg

first: Chatrin

last: Chatrin

first: Thomas

last: Agnew

first: Michael

last: Tellier

first: Evgeniia

last: Prokhorova

first: Song

last: Huang

first: Jonathan

last: Barrosso-Gonzalez

first: Roderick

last: O'Sullivan

first: Tim

last: Clausen

last: Nielsen

first: Ivan

last: Ahel


title: The effect of the two-component system GrtK and GrtR proteins of Burkholderia glumae on the metabolic detoxification of intracellular ammonia.

city: Jinju-si

first: Yongsung

last: Kang

state: Gyeongsangnam-do

address: 1 Gyeongsangdae-ro

department: Institute of Agriculture and Life Science

institute: Gyeongsang National University

summary: This study demonstrates that the two-component system, consisting of the sensor kinase GrtK and the response regulator GrtR, plays a crucial role in detecting and neutralizing toxic environmental ammonia produced as waste by Burkholderia glumae, a rice pathogen. The growth of grtK or grtR null mutants was inhibited by ammonia produced as waste in amino acid-rich media, such as Luria-Bertani broth, but no growth inhibition was observed in amino acid-free minimal media, where ammonia production is limited. Transcriptomic analysis of grtK and grtR mutants also indicated that GrtK and GrtR are involved in the metabolic detoxification of intracellular ammonia. These results suggest that GrtK is not a member of the ammonia transporter protein family but acts as an external ammonia sensor, working in conjunction with the response regulator GrtR to respond to the dangers posed by its own metabolism.

overall_design: A comparative analysis of RNA-seq profiles was performed on Burkholderia glumae wild-type BGR1 and its grtK and grtR null mutants during 12 hours of growth in amino acid-rich media, such as Luria-Bertani broth.

first: Gi-Young

last: Kwak

first: Yewon

last: Nam

first: Ingyu

last: Hwang


title: Gene expression in wild-type or miR-71 KO animals with or without sodium azide stress

city: St Lucia

first: Steven

last: Zuryn

state: QLD

address: The University of Queensland

country: Australia

institute: Queensland Brain Institute

summary: Kirmes et al. identify the microRNA miR-71, which coordinates the suppression of both cell-autonomous and cell-non-autonomous mitochondrial stress signalling, thereby promoting cellular function under conditions of chronic mitochondrial damage.

overall_design: RNA-seq of whole populations of N2 or MT12993 strains treated with or without sodium azide

first: Ina

last: Kirmes


title: Differential gene expression in C. difficile rough and smooth colony variants is partially determined by CmrRST regulation

city: Chapel Hill

first: Anchal

last: Mehra

state: North Carolina

address: 125 Mason Farm Rd, 6th Floor, CB 7290, Marsico Hall

department: Department of Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

summary: Clostridioides difficile introduces phenotypic heterogeneity into populations via phase variation. C. difficile modulates phase variation through invertible DNA sequences containing regulatory information, termed switches. Inversion of a switch controls expression of the adjacent genes in an ON/OFF manner, resulting in phenotypic switching. The C. difficile cmr switch (for ‘colony morphology regulator’) coordinates several phenotypes. When cmr is ON, C. difficile displays a rough colony morphology, surface motility, and cell chaining and elongation. When cmr is OFF, colonies are smooth, and high levels of swimming motility and biofilm formation are observed. Prior work has also linked colony morphology and cmr switch orientation to virulence in the hanster model of infection (Garrett et al., PLoS Biology, 2019). The cmr-ON orientation results in the expression of cmrRST, an operon encoding a signal transduction system. CmrS is a predicted histidine kinase, and CmrR and CmrT are response regulators. We have shown that CmrR and CmrT are responsible for the observed cmr-associated phenotypes (Garrett et al., PLoS Biology, 2019). The goal of this study is to identify the genes that are regulated by CmrR and CmrT and determine how these genes contribute to colony morphology and the other cmr-associated phenotypes. To identify genes important for C. difficile colony morphology, we conducted a multi-pronged RNA-Seq study comparing the following transcriptomes: (1) Rough vs. smooth colony variants of wild-type, (2) cmr-ON vs. cmr-OFF phase-locked strains, (3) Rough, smooth, cmr-ON, and cmr-OFF vs. a ΔcmrRΔcmrT mutant, and (4) Wild-type overexpressing either cmrR or cmrT vs. a no-overexpression condition. Transcription analyses revealed that CmrRST accounts for some, but not all, transcriptional differences between rough and smooth colony morphotypes. Fewer than 20 genes were differentially expressed by CmrR and/or CmrT (≥4-fold change, p<0.05). Most of those genes appeared in the rough vs. smooth and cmr-ON vs. -OFF datasets as well, and further phenotypic analyses of CmrRST-regulated genes revealed multiple genes that mediated rough colony development.

overall_design: RNA-Seq profiling of C. difficile strains grown on agar (wildtype rough and smooth colony variants,  cmr-ON and cmr-OFF phase-locked mutants, and a ΔcmrRΔcmrT mutant), and grown in broth (wildtype overexpressing either cmrR or cmrT or a no-expression control).

first: Elizabeth

last: Garrett

first: Rita

last: Tamayo


title: Effect of age, lysosomal degradation and mitochondrial replication on mouse hematopoietic stem cell

city: New York

first: Saghi

last: Ghaffari

state: , New York

address: 1468 Madison Ave

institute: Icahn  School of Medicine at Mount Sinai

summary: Aging impairs the function of hematopoietic stem cells (HSCs), promotes clonal hematopoiesis and myeloid malignancies, and contributes to immune decline in the elderly. The role of lysosomes – the cell’s primary degradation organelles –  beyond their passive mediation of autophagy in HSC aging remains unknown. Here, we show that lysosomes in aged HSCs are depleted, damaged, hyperacidic, and aberrantly activated compared to those in young HSCs. Using single-cell RNA sequencing (scRNA-seq) and functional analyses, we demonstrate that pharmacological inhibition of damaged hyperactivated lysosomes – by a vacuolar ATPase (v-ATPase) inhibitor  that blocks lysosomal hyperacidification – restores lysosomal integrity, as well as metabolic and epigenetic homeostasis in aged HSCs. This intervention also resolves inflammatory and interferon-related transcriptional programs by enhancing lysosomal processing of mitochondrial DNA (mtDNA) and suppressing intrinsic inflammation mediated by the cGAS–STING DNA-sensing pathway.

overall_design:
Freshly FACS-isolated hematopoietic stem cells [HSCs; lineage negative (Lin-) Sca1+ cKit+ (LSK) CD150+CD48- cells] from 8 weeks (young, Y) or 20 month-old (old, O) mice or HSCs cultured 16 hours in vitro in the presence of ConA (40 nM) or ddC (40uM) or non treated (NT). All conditions were assessed by scRNA-seq in addition to freshly isolated HSC from young or old mice.
Note: HSC from young mice cultured 16h without drug were labelled "Old-like_mHSC_Cultured".
For each samples, a barcodes.tsv, a features.tsc and a matrix.mtx are available.

first: Hossein

last: Khademian

first: Maxime

last: Batignes

first: Jiajing

last: Qiu

first: Mickaël

last: M. Ménager


title: BRD4 inhibition suppresses histone H4 UFMylation to drive ferroptosis sensitivity through TXNIP

first: Tao

last: Wu

address: 24 Tongjiaxiang

institute: China Pharmaceutical University

summary: BRD4 inhibition selectively changes gene transcription which defines cell responses to BET inhibitors. Altered genes driving cell cycle arrest in solid tumor upon BET inhibitor treatment are far from clear. Here, we find that BET inhibitor JQ1 upregulates TXNIP which mediates the anti-tumor effects of JQ1. Mechanistically, JQ1 reduces histone H3K9 trimethylation at TXNIP promoter, facilitating its transcription in the presence of glucose. Increased TXNIP inhibits Histone H4 UFMylation by interfering the interaction between H4 and UFBP1. Instead of regulating cMYC expression, H4 UFMylation promotes the chromatin binding of cMYC to facilitate the transcription of cell-cycle related genes. Additionally, TXNIP prevents proteasomal degradation of P27, a CDK inhibitor. JQ1-treated solid cancer cells thus enter dormant state which is associated with cancer relapse and drug tolerance. However, these arrested cells are sensitive to ferroptosis, suggesting enhancing the functions of ferroptosis inducers with BET inhibitors. Together, our studies reveal regulators of protein UFMylation and cMYC activity, which modulate cell responses to BET inhibitors and ferroptosis inducers in solid cancer cells.

overall_design: RNA-Seq profiling of DMSO and JQ1 treated HepG2 cells

first: Zhen

last: Yang


title: Commensal-derived short-chain fatty acids disrupt lipid membrane homeostasis in Staphylococcus aureus

city: Minneapolis

first: Ryan

last: Hunter

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

summary: We used a custom Nanostring codeset targeting 33 transcriptional regulators, virulence factors, and metabolic genes to gain insight into differential gene expression in Staphylococcus aureus JE2 when grown in LB supplemented with either propionate or butyrate relative to LB alone.

overall_design: 4 sample types, 3 biological replicates

first: Joshua

middle: R

last: Fletcher


title: OTX2 inhibits human pluripotent stem cell reprogramming toward 8-cell-like and morula-like states

city: luzhou

last: Jiang

state: sichuan

address: 1st xianglinlu

institute: southwest medical university

summary: In human embryos, major zygotic genome activation (ZGA) initiates at the 8-cell (8C) blastomere stage, marking the initiation of the ontogenesis program. Recent advancements have demonstrated that human pluripotent stem cells (hPSCs) can revert to 8C-like cells (8CLCs) with totipotency in vitro. However, the key regulators involved this transition remain largely unexplored. In this study, we identified OTX2 as a novel regulator repressing the induction of 8C-like cells (8CLCs) from hPSCs. Our findings reveal that OTX2 depletion facilitates the generation TPRX1-EGFP+ totipotent-like stem cells (TLSCs), which closely resemble the transcriptomic profile and chromatin accessibility of 8C blastomeres. Notably, TLSCs with OTX2 depletion exhibit bidirectional embryonic and extraembryonic differentiation potential in forming chimeric embryos. OTX2 influences totipotent state transition by binding at loci of key 8CLC regulator, which function in parallel with DUX4. Collectively, our findings reveal a previously unrecognized function of OTX2 in regulating totipotency and establish a new framework for generating TLSCs from hPSCs in vitro, offering significant insights for stem cell biology and regenerative medicine.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed using the 10x Genomics platform to profile cell subpopulations in 4CL and me4CL cells under both wild-type (WT) and OTX2 knockout (KO) conditions, comprising a total of four samples.

first: Bingqing

last: Xie


title: Head-to-head comparison of targeted transcriptome methods: HTG vs TempO-Seq

city: Valencia

first: Antonio

last: Fernandez-Serra

address: Profesor Beltran Baguena, 8

country: Spain

institute: Fundacion Instituto Valenciano de Oncologia

summary: In this work this HTG Edgeseq targeted RNA-seq technology is compared with another analogous approach (TempO-Seq) in order to establish its suitability in a research molecular oncology setting. Comparison was proposed at different levels of biomarkers ranging from single mRNA to more complexes including ten to thousands of genes.

overall_design: The same samples and RNA universal human controls (C1, C2 and C3) were assayed by using both approaches HTG edgeseq Human Transcriptome Panel and TempO-Seq from Biospyder. Their performance was benchmarked with different common biomarkers used in oncology

first: Raquel

last: Lopez-Reig

first: Jose Antonio

last: Lopez-Guerrero


title: Restoring mechanophenotype reverts malignant properties of ECM-enriched vocal fold cancer

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

summary: Increased extracellular matrix (ECM) and matrix stiffness promote solid tumor progression. However, mechanotransduction in cancers arising in mechanically active tissues remains underexplored. Here, we report upregulation of multiple ECM components accompanied by tissue stiffening in vocal fold cancer (VFC). We compare non-cancerous (NC) and patient-derived VFC cells – from early (mobile, T1) to advanced-stage (immobile, T3) cancers – revealing an association between VFC progression and cell-surface receptor heterogeneity, reduced laminin-binding integrin cell-cell junction localization and a flocking mode of collective cell motility. Mimicking physiological movement of healthy vocal fold tissue (stretching /vibration), decreases oncogenic nuclear β-catenin and YAP levels in VFC. Multiplex immunohistochemistry of VFC tumors uncovered a correlation between ECM content, nuclear YAP and patient survival, concordant with VFC sensitivity to YAP-TEAD inhibitors in vitro and in vivo. Our findings present evidence that VFC is a mechanically sensitive malignancy and restoration of tumor mechanophenotype or YAP/TAZ targeting, represents a tractable anti-oncogenic therapeutic avenue for VFC.

overall_design: RNA-seq profiling of HaCat, UT-SCC-11 and UT-SCC-103 cells subjected 30 min or 6h hours of vibration or no vibration (control condition; CTRL)

first: Jasmin

last: Kaivola


overall_design: Total of 38 samples were analyzed, which included primed hPSCs, naive hPSCs and TLSCs. We conducted RNA-seq to analyzed the transcriptome difference between different samples during the transition from primed hPSCs to TLSCs.


title: Dp16 liver transcriptome

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


overall_design:
Total of 12 samples were analyzed, which included primed hPSCs, naive hPSCs and TLSCs. We conducted Cuttag  to analyzed the epigeneitc difference between different samples during the transition from primed hPSCs to TLSCs.
Total of 6 samples were analyzed, which included H3K4me3, H3K27me3 and H3K9me3 in WT and OTX2-KO me4CL cells. We conducted Cuttag  to analyzed the epigeneitc difference between WT and OTX2-KO condition in me4CL cells.Total of 6 samples were analyzed, which included H3K4me3, H3K27me3 and H3K9me3 in WT and OTX2-KO me4CL cells. We conducted Cuttag  to analyzed the epigeneitc difference between WT and OTX2-KO condition in me4CL cells.


title: Epigenetic profiling of prostate adenocarcinoma and neuroendocrine prostate cancer models to understand DNMT-EZH2 crosstalk. [RNA-Seq]

first: Varadha Balaji

last: Venkadakrishnan

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

summary: EZH2-DNMT crosstalk is diverse across prostate adenocarcinoma and neuroendocrine prostate cancer.

overall_design: Epigenetic profiling was performed in prostate cancer models upon DNMT1 silencing.

first: Himisha

last: Beltran


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from adult WT and Dp16 mouse liver tissue ± high fat diet

summary: Analysis of steady-state mRNA levels in mouse liver tissue at 13-15 weeks from wild-type C57BL/6J and Dp(16)1Yey mice fed control or high fat diet.

overall_design: Comparison of control diet to high fat diet for wild-type (n=10/14) and Dp16 (n=8/13) animals.

first: Kelly

last: Sullivan

first: Lauren

last: Dunn


title: Effect of depletion of ISG20 on gene expression in EMT6 mouse breast cancer cells with RNA-Seq.

city: Baltimore

first: YONGKANG

last: YANG

state: Maryland

address: Room 673, MRB, 725 North Broadway

department: ICE

institute: Johns Hopkins University

summary: Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with the highest rates of recurrence, metastasis and patient mortality due to lack of effective targeted therapies. In this study, we demonstrate that ISG20 expression is induced by hypoxia and directly targeted by HIF-1 for transcription in TNBC cells. ISG20 functions as RNA exonuclease to target mRNAs for degradation, resulting in breast cancer stem cell specification and lung metastasis, and also cancer cell immune evasion. Mostly importantly, ISG20 silencing could markedly increase the sensitivity of TNBC to anti-PD1 immune checkpoint blockade (ICB) in a mouse model. Our data suggested that, in combination with immunotherapy, targeting ISG20 might be an effective strategy for TNBC treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EMT6 subclone of NTC and ISG20 knockdown that were exposed in 20% or 1% oxygen condition for 48 hours.

first: Yongkang

first: Gregg

middle: L

last: Semenza


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from human iPSC-derived Hepatocyte-like cells

summary: Analysis of steady-state mRNA levels in Hepatocyte-like cells differentiated from human iPSCs originating from donors with and without Down syndrome. This dataset is part of the Human Trisome Project - Trisomy 21 Model Atlas run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Hepatocyte-like cells differentiated from a panel of iPSCs reprogrammed from urine-derived kidney epithelial cells of human donors - comparison of cells with trisomy 21 (T21, n = 6) to euploid controls (D21, n = 6).

first: Brian

last: Niemeyer


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from adult WT and Dp16 mouse liver tissue

summary: Analysis of steady-state mRNA levels in mouse liver tissue at 19-26 weeks from wild-type C57BL/6J and Dp(16)1Yey mice.

overall_design: Comparison of wild-type (n=6) and Dp16 (n=6).


title: The gene expression profiles of HUVEC cells treated with LIMCH-overexpressed JAR cells-derived small extracellular vesicles.

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

summary: Preeclampsia is a major pregnancy complication leading to maternal and neonatal mortality, but the detailed pathogenesis remains unelucidated. Extracellular vesicles (EVs) contain proteins and nucleic acids inside and are responsible for intercellular communication. In this study, we investigated the roles of LIMCH1-containing EVs on vascular endothelial cells in vitro.

overall_design: We established LIMCH-1 overexpressed JAR cells and collected EVs using the ultracentrifuge. Then, HUVEC cells were treated with the EVs, and RNA sequencing was performed.

first: Seiko

last: Matsuo

first: Akira

last: Yokoi


title: scRNA-seq transcriptomic profiles of cochlear and vestibular hair cells from adult mice [10_weeks_CBAJ]

city: Omaha

first: David

last: He

state: NE

address: 2500 California Plaza

department: Biomedical Science

institute: Creighton University

summary: The cochlear and vestibular sensory epithelia contain four different hair cell (HC) types for detecting sound and motion. There are substantial differences in morphology and function among them. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of HCs in the inner ear.

overall_design: HCs from cochlear and vestibular sensory organs were isolated. cDNA library were constructed using the 10x Genomics Chromium Single Cell 3’ Reagent Kits V3.1.  7 mice were used for each biological replicate, and 6 biological replicates for cochlear sensory epithelium and 4 biological replicates vestibular sensory epithelia were prepared. Illumina NextSeq 6000 sequencer was used for sequencing.

first: Zhenhong

last: Xu

first: Samadhi

last: Kulasooriya

first: Huizhan

last: Liu


title: CSF1R marks a subset of foetal LMPPs with Acute Myeloid Leukaemia propagation properties in a KMT2A-MLLT3 mouse model

city: Edinburgh

first: Giuseppina

last: Camiolo

state: Edinburgh

address: EDINBURGH BIOQUARTER

institute: CENTRE FOR REGENERATIVE MEDICINE - THE UNIVERSITYOF EDINBURGH

summary: As KMT2A-MLLT3 oncoprotein can give rise to ALL and AML in infants, we investigated whether such choice could lie in two subsets of foetal LMPPs, that express or not CSF1R, and found that CSF1R mark a more potent subpopulation with leukaemic-initiating

overall_design: Murine CSF1R+/-LMPPs (Lin- Sca1+ ckit+ CD45+ Flt3+CSF1R+/-) were sorted from KMT2AMLLT3-expressing E14.5 foetal livers. Cell populations were analysed by bulk RNA-Seq

first: Katrin

last: Ottersbach


last: Jiang

overall_design: Total of 12 samples were analyzed, which included primed hPSCs, naive hPSCs and TLSCs. We conducted ATAC-SEQ  to analyzed the epigeneitc difference between different samples during the transition from primed hPSCs to TLSCs.

first: Bingqing

last: Xie


title: Sympathetic Neuron Hyperactivation Drives Hair Follicle Necrosis and T Cell Autoreactivity

city: Cambridge

first: Ya-Chieh

last: Hsu

state: MA

address: 7 Divinity Ave, sherman-fairchild

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Stress profoundly affects health, but the mechanisms driving stress-induced tissue changes remain poorly understood. Here, we show that strong acute stress drives rapid hair loss and initiates autoimmunity. Under stress, hyperactivated sympathetic nerves release excessive norepinephrine, causing necrosis in rapidly dividing hair follicle transit-amplifying cells (HF-TACs) while sparing most hair follicle stem cells (HFSCs). This differential sensitivity to stress stems from differences in cell death genes, metabolic strategies, and calcium homeostasis. Together, these factors render HF-TACs more vulnerable to the sudden calcium surges triggered by norepinephrine. HF-TAC necrosis releases cellular debris that triggers macrophage clearance and dendritic cell activation, ultimately leading to the activation and amplification of autoreactive T cells that can attack the hair follicle. Our findings reveal mechanistically how stress causes immediate tissue damage in the highly proliferative HF-TACs via sympathetic nerve-induced necrosis, which in turn fuels the activation of a T cell-mediated response against the hair follicle.

overall_design: Cell type: FACS purified cells from mouse skin; 3 conditions: 12H, and 72H RTX treated vs control; 2 replicate for each condition.

first: Emily

last: Scott-Solomon

first: Shlomi

last: Brielle


title: Integrative Spatial Multi-Omics Reveal Niche-Specific Inflammatory Signaling and Differentiation Hierarchies in Acute Myeloid Leukemia

city: Houston

first: Hussein

last: Abbas

state: Texas

address: 1515 Holcombe Blvd

institute: The University of Texas at MD Anderson Cancer cent

summary: Acute myeloid leukemia (AML) is a clonal disorder characterized by immature blasts and arrested differentiation that primarily affects the bone marrow (BM) and occasionally presents as extramedullary (EM) disease. EM manifestations highlight AML’s adaptability to distinct microenvironments, which we examined using spatial analyses of medullary and EM tissues. We describe a workflow for Visium-based spatial transcriptomics in medullary and EM AML, revealing insights into cell-cell communication and the spatial organization of AML hierarchies. In BM, monocytes and granulocyte-monocyte progenitors colocalized with leukemic populations, sharing molecular signatures with those in EM sample. CXCL12-CXCR4-mediated communication correlated with PI3K/AKT/mTOR signaling in inflammatory niches. Trans-differentiation signals concentrated in AML-infiltrated regions; committed-like AML cells resided in inflammatory niches distant from trabeculae, while primitive-like cells localized near the endosteal niche. GeoMX digital spatial profiling and Opal multiplex fluorescent immunohistochemistry provided orthogonal validation. Overall, our study offers a valuable multimodal resource for exploring AML spatial biology with potential applications in other BM malignancies.

overall_design: Bone Marrow (BM) and Extramedularry (EM) tissue biopsies were routinely collected before treatment initiation from 2 patients with newly diagnosed AML. The samples were formalin fixed, and BM samples were decalcified using 10% formic acid. Following fixation and decalcification, the samples were embedded in paraffin and stored at room temperature before they were cut into 4-µm sections. Visium Spatial Gene Expression (Direct placement; v1) and Visium CytAssist Spatial Gene Expression (CytAssist-enabled; v2) protocols apllied on each BM and EM samples. Libraries sequenced using Illumina NovaSeq 6000.

first: Enes

last: Dasdemir


title: A late cytoplasmic surveillance pathway ensures ribosome integrity

status: Public on Nov 24 2025

city: Austin

first: Can

last: Cenik

address: 2500 Speedway

department: Department of Molecular Biosciences

institute: University of Texas

summary: Errors in ribosome assembly can produce defective subunits that can lead to aberrant translation events. How faulty ribosomes are recognized and whether they are recognized during assembly or translation remains poorly understood. We utilized a mutation in the ribosomal protein uL16 to track defective 60S subunits through the biogenesis and translation pathways. This mutation deletes a critical loop in the P site and arrests pre-60S particles during late cytoplasmic maturation. However, simultaneous mutations in the late biogenesis factors Nmd3 and Tif6 bypass this block, releasing defective ribosomes into the translational pool. Cryo-EM and selective ribosome profiling reveal that these ribosomes can form peptide bonds, but stall predominantly at the first few codons. We show that the uL16 mutant ribosomes are detected and targeted for degradation during biogenesis and that they escape degradation if they enter translation. We identify Reh1 as a non-canonical ribosome assembly factor that is required for this surveillance pathway.

overall_design: Selective ribosome profiling of  uL16-loop mutant ribosomes in S.cerevisiae.

first: Ruta

last: Chitale

first: Kaoling

last: Guan

first: Shilpa

last: Rao

first: Caroline

last: Wang

last: Taylor

first: Arlen

last: Johnson


title: Transcriptional profiling of HYF1 overexpression strain.

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

summary: Heritable phenotypic switches are fundamental to the ability of cells to respond to specific conditions. Such switches are key to the success of environmental pathogens, which encounter disparate conditions as they transition between the environment and host. We determine that the copy number of chromosome seven in the thermally dimorphic fungus Histoplasma dramatically affects the rate of transition. Though Histoplasma is haploid, a second copy of this chromosome is present in natural isolates of multiple Histoplasma species and is gained and lost at a high rate. Cells carrying two copies of this chromosome exhibit aspects of the environmental transcriptome even under host-like conditions and have a competitive advantage in the transition to the environmental form. Conversely, these cells are considerably less virulent than euploid cells and have a competitive disadvantage in the mouse model of infection. Chromosome seven contains a previously unstudied transcription factor that, when overexpressed in euploid Histoplasma, is sufficient to promote some of the key phenotypes of aneuploidy. We hypothesize that rapid gain and loss of this chromosome benefits Histoplasma by increasing phenotypic variation, thus helping populations of cells survive abrupt transitions between environment and host.  This series contains expression profiling of increased copy number constructs for the HYF1 and HYF2 transcription factors.

overall_design: Three replicates for each of two genotypes for yeast cultures with or without a two day shift from 37°C to 25°C for a total of 12 samples.

first: Sarah

last: Heater

first: Anita

last: Sil


title: RNA-seq analysis of human cells overexpressing a novel short XIST transcript isoform

city: Bronx

first: Kevin

middle: Sean

last: O'Leary

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: We identified a novel short XIST isoform (sXIST) that is expressed in both male and female peripheral glia specifically. To study its functions, we overexpressed a fragment of it in the human HEK293T cell line and performed RNA-seq analysis of the sXIST overexpressing cells and GFP controls. We found that the up-regulated genes were enriched in pathways related to cilia functions and many share miRNA binding sites with the sXIST.

overall_design: HEK-293T cells were transfected with a sXIST construct or GFP. mRNA from the virus-infected cells was iisolated and analyzed by RNA-seq.

first: Meng-Yen

last: Li

first: Elena

last: Ezhkova

first: Deyou

last: Zheng


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: Single cell fixed RNA profiling from 4-month old WT and Dp16 mouse liver tissue

first: Matthew

last: Galbraith

summary: Analysis of single cell steady-state mRNA levels in fixed cells from mouse liver tissue at 4 months from wild-type C57BL/6J and Dp(16)1Yey mice.

overall_design: Comparison of cells from wild-type (n=4) and Dp16 (n=4) animals.

first: Kelly

last: Sullivan

first: Lauren

last: Dunn

first: Ariel

last: Timkovich


title: Global analysis of Arabidopsis thaliana DICER-LIKE1 RNA substrates

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

institute: ETH

summary: By introducing point mutations in the RNAse III domains of plant DCL1 we generated Catalytically inactive (ci) DCL1. Plant expressing DCL1ci show an increase stability of the RNA/DICER complexes and therefore represent an innovative strategy to perform a direct and systematic analysis of DCL1 substrates.

overall_design: Triplicates of pDCL1-DCL1ci-HA/dcl1-7 and respective dcl1-7 control plants RIP-seq

first: Nicolas

last: Bologna

first: Olivier

last: Voinnet


title: Critical role for a high-plasticity cell state in lung cancer

first: Jason

middle: Earl

last: Chan

address: 1275 York Ave, Box 20

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

summary: Plasticity—the ability of cells to undergo phenotypic transitions—drives cancer progression and therapy resistance. Recent studies have suggested that plasticity in solid tumors is concentrated in a minority subset of cancer cells, yet functional studies interrogating this high plasticity cell state (HPCS) in situ are lacking. Here, we develop mouse models enabling detection, longitudinal lineage tracing, and ablation of the HPCS in autochthonous lung tumors in vivo. Lineage tracing reveals that the HPCS cells possess high capacity for cell state transitions, giving rise to both early neoplastic (differentiated) and progressed lung cancer cell states in situ. Longitudinal lineage tracing using secreted luciferases reveals HPCS-derived cells harbor high capacity for growth when compared to bulk cancer cells or another cancer cell state with features of differentiated lung epithelium. HPCS ablation in early neoplasias abrogates benign-to-malignant transition, whereas ablation in established tumors by suicide gene or CAR T cells robustly reduces tumor burden. We further demonstrate that the HPCS gives rise to therapy-resistant cell states, whereas HPCS ablation suppresses resistance to chemotherapy and oncoprotein-targeted therapy. Interestingly, an HPCS-like state is ubiquitous in regenerating epithelia and in carcinomas of multiple other tissues, revealing a convergence of plasticity programs. Our work establishes the HPCS as a critical hub enabling reciprocal transitions between cancer cell states. Targeting the HPCS in lung cancer and in other carcinomas may suppress cancer progression and eradicate treatment resistance.

overall_design:
KP mice with either Slc4a11-FSF-MCD/+ with either Hipp11-FSF-GGCB/+ or Rosa26-FSFmTmG/+ reporter alleles or Hopx-FSF-MACD/+ mouse model with either Hipp11-FSF-GGCB/+ or Rosa26-FSF-mTmG/+ alleles were infected by adenoviral CMV-FlpO or lentiviral PGK-FlpO recombinase. Mice with tumors were treated as indicated and tumor cells were hashed with TotalSeq B and then isolated for single-cell mRNA sequencing after FACS purification. One dataset is KP Rosa26-tdTomato/+ with tumors harvested 14 weeks post tumor initiation. One dataset is a KP Slc4a11-MCD/+ iRFP670-GLuc cell line transplant.
Please note that GSM9193561/GSM9193562 are biological replicate of GSM8529536/GSM8529537, sequenced on separate lanes and have different featureref.csv files.

first: Chunhao

last: Pan

first: Doron

last: Betel

first: Tuomas

last: Tammela


title: Spatial transcriptome analysis for placental tissue of preeclampsia

first: Kosuke

last: Yoshida

summary: Preeclampsia (PE) is a major pregnancy complication leading to maternal and neonatal mortality. To investigate the spatial gene expression profile of preeclampsia, we performed the Visium FFPE spatial transcriptome analysis.

overall_design: We used formalin-fixed paraffin embedded (FFPE) tissues of preeclampsia and normal placenta. Accoriding to the Visium FFPE protocol, the spatial transcriptome analysis was conducted by CyberomiX (Kyoto, Japan).

first: Seiko

last: Matsuo

first: Akira

last: Yokoi


title: Epigenetic profiling of prostate adenocarcinoma and neuroendocrine prostate cancer models to understand DNMT-EZH2 crosstalk. [Cut&Run]

city: Boston

first: Varadha Balaji

last: Venkadakrishnan

summary: EZH2-DNMT crosstalk is diverse across prostate adenocarcinoma and neuroendocrine prostate cancer.

first: Himisha

last: Beltran


title: Hic-5 drives epithelial mechanotransduction promoting a feed-forward cycle of bronchoconstriction.

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

summary: Mechanical forces are essential for organ function, but excessive or dysregulated forces can promote pathologic conditions. In asthma, bronchoconstriction narrows the airway, compressing the airway epithelium and activating mechanotransduction, yet key regulators of mechanotransduction remain unclear. Here we show that Hic-5, a focal adhesion adaptor, is a key regulator of epithelial mechanotransduction. In human airway epithelial cells at air–liquid interface exposed to mechanical compression that mimics bronchoconstriction, we find that compression induces Hic-5 expression in airway basal cells. We further validated these in vitro findings by reanalyzing single-cell RNA-seq data from patients with asthma undergoing bronchoconstriction after allergen challenge, which revealed increased Hic-5 expression in airway basal cells. Hic-5 knockdown in human airway epithelial cells markedly attenuates mechanoresponses to compression, including stress fiber formation, differential gene expression, and increased secretion of endothelin-1 (ET-1). Through secretion of ET-1, a potent bronchoconstrictor, Hic-5 drives epithelial mechanotransduction and promotes a feed-forward cycle of bronchoconstriction, thereby highlighting dysregulated mechanical forces as active drivers of human disease.

overall_design: To mimic bronchoconstriction, well-differentiated HBE cells were exposed to apical-to-basal pressure with a magnitude of 30cm H2O for 3 hrs, as previously described (11, 12, 49, 53). Time-matched control cells received 0cm H2O pressure. Cells and conditioned media were collected between 3 and 72 hrs. In experiments using recombinant human (rh) TGF-β1 (Cell Signaling Technologies, Danvers, MA), we spiked 10 ng/ml into the basolateral media of HBE cells in ALI cultures. Cells were collected between 24 and 72 hrs for further analysis. To determine the signaling pathways that regulate mechanical compression-induced Hic-5 protein expression, we used pharmacological inhibitors of the TGF-β receptor (SB431542; 10 µM, Tocris, Bristol, UK), MEK (U0126; 10 µM, Tocris), and EGFR (AG1478; 10 µM, Tocris). Each inhibitor was added to the basolateral media of HBE cells 1 hr prior to exposure to mechanical compression or TGF- β. As a control, 0.1% DMSO was used.To knock down Hic-5 expression in HBE cells, we used antisense oligonucleotides designed and provided by Ionis Pharmaceuticals. We initially tested five ASOs targeting TGFB1I1(denoted as Hic-5 ASO). Then, we  selected the most effective ASO and used for subsequent experiments. HBE cells maintained in ALI culture were treated with 10µM of either a non-targeting control (scrambled) ASO or Hic-5 ASO between ALI days 9 and 20 prior to the application of mechanical compression. We confirmed the knockdown efficiency of the Hic-5 ASO in well-differentiated HBE cells by RT-qPCR and western blot analysis.

first: Chimwemwe

last: Mwase

first: Wenjiang

last: Deng

first: Hyo-Jin

last: Kim

first: Jennifer

last: Mitchel

first: Thien-Khoi

last: Phung

first: Michael

last: O’Sullivan

first: Joel

last: Mathews

first: Jeffrey

last: Crosby

first: Christopher

last: Turner

first: Jin-Ah

last: Park


title: Bulk RNA sequencing analysis of human airway basal stem cells stimulated by BALF from mouse fibrotic lungs and normal lungs

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

summary: To understand how the microenvironment of fibrotic lungs affects the behavior of airway basal stem cells (BCs), we constructed a mouse model of pulmonary fibrosis using bleomycin induced injury, and collected bronchoalveolar lavage fluid (BALF) from the control group and bleomycin damaged mice on day 14 after injury. Then, human BCs were stimulated with control or bleomycin BALF in culture and subjected to bulk RNA sequencing. Transcriptomic analysis showed that basal stem cells stimulated with bleomycin BALF upregulated genes related to chemotaxis and migration, and activated the TGF-β pathway.

overall_design: Human BCs were stimulated with PBS or bleomycin BALF in culture for 48 hours and subjected to bulk RNA sequencing. Total RNA was extracted from Human basal cells using Trizol (15596018CN, Invitrogen), and RNA extraction was performed according to the manufacturer’s instructions. Subsequently, the extracted RNA was treated with Dnase I (Invitrogen, Life Technologies, USA) to remove any contaminating DNA. Utilize the Novogene platform for cDNA library construction and sequencing.

first: Tingting

last: Zou

first: Shiyu

last: Zhang

first: Mingzhe

last: Liu


title: Single-Cell Mapping of Alternative Splicing Linked to Checkpoint Immunotherapy Response

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

summary: Evidence suggests that alternative RNA splicing (AS) plays a critical role in tumor biology and may contribute to the generation of tumor antigens. Here, we develop a method to detect AS in short-read single-cell 5’-RNA-sequencing data, allowing us to uniquely characterize the heterogeneity and dynamic changes in AS in individual cell types within the tumor microenvironment. We identify numerous splicing events specific to either cancer cells or stromal cell types, or for triple-negative versus estrogen receptor-positive breast cancers. By correlating these splice events with expression of splicing regulators in individual cells, we also identify their potential mediators. For instance, we identify and functionally validate the Epithelial Splicing Regulatory Protein-1 (ESRP1) to drive AS in breast cancers responding to immune checkpoint blockade (ICB). Prioritization of splicing events based on their likelihood to represent tumor antigens reveals that their aggregated load also correlates with high immune activity in multiple cancers, while also predicting expansion of T-cells in breast cancers receiving ICB and prolonging long-term survival of cancer patients treated with ICB. Collectively, our method provides a framework for analyzing AS in single-cell data and defines a key role for AS in the response to ICB.

overall_design: RNA-seq profiling of widetype MCF-7 cells and their ESRP1 knockdown and overexpression derivatives, as well as widetype BT-549 cells and their NOVA1 knockdown derivatives.

first: Chen

last: Gu

first: Diether

last: Lambrechts


title: Bulk RNA sequencing analysis of Ctrl/PROTAC human airway basal stem cells stimulated by TGF-β

summary: To evaluate how TGF-β regulates human airway basal stem cells (BCs), we used PROTAC to inhibit TGF-β signaling in BCs and exposed Ctrl-BCs and PROTAC-BCs to recombinant TGF-β1 for 24 hours, followed by bulk RNA sequencing analysis. We found that multiple cell cycle related and proliferation related genes were upregulated in PROTAC-BCs compared to Ctrl-BCs, while the expression levels of cell migration related genes were reduced in the PROTAC-BCs group, and genes related to barrier formation and stem cell differentiation were also downregulated.

overall_design: Ctrl-BCs and PROTAC-BCs were stimulated with 10 ng/ml recombinant TGF-β1 in culture for 24 hours and subjected to bulk RNA sequencing. Total RNA was extracted from BCs using Trizol (15596018CN, Invitrogen), and RNA extraction was performed according to the manufacturer’s instructions. Subsequently, the extracted RNA was treated with Dnase I (Invitrogen, Life Technologies, USA) to remove any contaminating DNA. Utilize the Novogene platform for CDNA library construction and sequencing.


title: Microglial reactivity and neuroinflammation-driven in motivational behaviors are regulated by Orai1 channels

city: Chicago

first: Rogan

last: Grant

state: IL

address: 303 E Superior St, Simpson Querrey Biomedical Research Center 5-522

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

summary: Microglia are the primary immune cells of the central nervous system (CNS) and act as the first line of defense against disease and injury in the brain by releasing inflammatory molecules and clearing dead cells. Microglial functions are tightly regulated by dynamic transitions between homeostatic and reactive cell states, which can either exacerbate or resolve CNS inflammation. While Ca2+ signaling is known to regulate specific microglial functions such as phagocytosis, its role in controlling these critical state transitions remains poorly understood. Here, we identify the Orai1 Ca2+ channel as a key regulator of microglial plasticity and inflammation-induced behavioral dysfunction in mice. Transcriptomic and metabolomic analyses revealed that conditional Orai1 deletion in microglia suppressed proinflammatory programs linked to immunity and inflammation. Conversely, Orai1 knockout increased expression of growth factors and anti-inflammatory mediators, including BDNF, ARG1, and the mitochondrial metabolite, itaconate. In a model of CNS inflammation induced by peripheral inflammatory challenge with lipopolysaccharide (LPS), Orai1 deficiency attenuated microglial and astrocyte reactivity and reduced hippocampal levels of the cytokines IL-1β and IL-6. Consistent with these cellular changes, microglial Orai1 knockout mice were protected against LPS-induced changes in motivational, depression-like behaviors, including impairments in reward-seeking and escape responses. These findings establish Orai1 channels as central regulators of microglial cell plasticity and neuroimmune responses, highlighting their therapeutic potential for neuroinflammatory disorders.

overall_design: Primary microglia from Orai1fl/fl or Orai1fl/fl Cx3CR1-cre/ERT2 were cultured from neonates or FACS purified from adult animals and  treated with Tg+PDBu, LPS, or vehicle control  for 6h or 24h.

first: Kaitlyn

last: DeMeulenaere

first: Megan

last: Martin

first: Hiam

last: Valencia

first: Jelena

last: Radulovic

last: Salter

first: Murali

last: Prakriya


title: An integrated multi-omics and network analysis of neutrophil differentiation from initial- to late-stage

city: Beijing

first: Cheng

last: Li

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

summary: The goal of this study is to study the gene regulation mechanism during ATRA-induced HL-60 cell neutrophil differentiation especially in the early time-point. We demonstrated the striking early changes event that trigger the whole differentiation process. We also identified the pioneer TFs (Transcription factors) that ignite the differentiation process with the corresponding TF correlation networks.

overall_design: Genome-wide mapping of transcriptomic, chromatin accessibility, and chromatin interaction in differenti time-points during neutrophil differentiation.

first: Minglei

last: Shi

first: Qing

last: Chen


title: Unbiased assessment of 2-Arachidonoylglycerol in cardiovascular inflammation and myocardial remodeling

city: Bonn

first: Susanne

middle: Viktoria

last: Schmidt

address: Venusberg Campus 1

country: Germany

institute: Institute of Clinical Chemistry and Clinical Pharmacology

summary: 2-arachidonoylglycerol (2-AG) is an endogenous modulator of inflammatory processes and ligand for the endocannabinoid system. Recent scientific investigations accumulated evidences for its key role in inflammatory cardiovascular diseases, like atherosclerosis and left ventricular remodeling. However, molecular mechanisms set in motion by 2-AG are still poorly understood and its role in cardiovascular inflammation is the matter of controversial debate. Yet, there is a dramatic need to understand local effects of 2-AG at the site of heart inflammation, and tissue injury and reconstruction to develop novel therapeutic strategies which modulate both processes for the better and a fast recovery. Myeloid cells, like tissue-resident macrophages and monocytes are central mediators of inflammatory processes and mediate cardiac adverse remodelling after an insult by myocardial infarction, myocarditis or chronic hypertension. In this study, we investigated the impact of 2-AG on the transcriptional programming of peripheral monocytes as model system for resident macrophages in heart tissue or monocytes which are recruited to the site of cardiac tissue remodelling. Data of RNA sequencing analysis and quantification cytokine expression we seeked to clarify the question, if 2-AG induces rather an inflammatory or a wound healing phenotype of monocytes recruited to the site of cardiac tissue injury.

overall_design: CD14+ primary human monocytes were isolated from peripheral blood of healthy donors and treated with 2-AG up to 24h. Genes differentially expressed between 2-AG treated monocytes and respective controls were determined by mRNA sequencing and used for bioinformatics analysis of changes in myeloid cell functions and cell signaling pathways.

first: Moritz

last: Nöthel

first: Susanne V.

first: Julian

last: Jehle

first: Franziska

last: Dorer

first: Alexandru

last: Odainic

first: Marie

last: Rüthing

first: Georg

last: Nickenig


title: Gene expression profile at single cell level of spinal cord infilitrating CD4 T cells at the peak of EAE disease

first: Drew

last: Pardoll

address: 1650 Orlean St.

department: Oncology

institute: Johns Hopkins Medical Institute

summary: We used single cell RNA sequencing to evaluate the molecular differences between WT and G123KO CD4 T cells in the context of EAE disesase.

overall_design: Immune cells were enriched from the spinal cord by a Percoll gradient protocol. Enriched cells were then further isolated to live CD4 T cells by fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Marisa

last: Mitchell-Flack

first: Hong

last: Yu


title: The Ionotropic AMPA receptor contributes to autoimmunity via altered regulatory T cell differentiation and function

summary: To investigate the differential gene expression profile of G123KO iTreg vs. WT iTreg.

overall_design: We performed the gene expression profile on day 3 differentiated WT and G123KO iTreg cells.


title: Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

institute: EPFL

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

overall_design: Refer to individual Series


title: An integrated multi-omics and network analysis of neutrophil differentiation from early- to late-stage

first: Wei


title: Pyruvate Kinase Muscle (PKM)-2 promotes CD4 T cell survival by regulating pyruvate oxidation during homeostasis and expansion

city: Frederick

first: Ian

last: Bettencourt

state: MD

address: 1050 Boyles Street Rm 31-16A

department: CIL

institute: NCI

summary: Glycolysis is an essential metabolic pathway for rapidly expanding T cells, but role of Pyruvate Kinase Muscle (PKM) 1 and 2 in regulating this process is underappreciated.  Here, using a pharmacological activator and targeted deletion of PKM2 in T cells we delineated distinct functions of PKM1 and 2 in regulating CD4 T cell survival during homeostasis and expansion.  Expanding PKM2-deficient CD4 T cells increased PKM1 expression with associated mitochondrial ROS-mediated cell death. Examination of T cell compartments revealed PKM2-deficient CD4 T cells were unaltered in the thymus but were significantly reduced in peripheral tissues as mice aged. The failure of PKM1 to protect CD4 T cells in the absence of PKM2 resulted in protection from T cell mediated colitis as pathogenic cell numbers were significantly reduced resulting in less severe disease compared to control cells. This study shows PKM2 is critical for CD4 T cell survival during expansion and homeostasis.

overall_design: Naïve T cells were isolated from spleen and lymph nodes of wild type or Pkm2 knockout mice.  Cells were cultured for 24 hours with IL7 alone (resting) or IL7 plus plate-bound aCD3 and aCD28 antibodies.

first: Jeff

last: Subleski

first: Erika

last: Palmieri

first: Jessica

middle: F

last: Walls

first: Steven

last: Hsu

first: Timothy

last: Gower

first: Scott

last: Durum

first: Daniel

last: McVicar