title: APOBR is downregulated in EBV+ tonsils of children with obstructive sleep-disordered breathing

city: Aurora

first: Regie Lyn

last: Santos-Cortez

state: CO

department: Otolaryngology-Head and Neck Surgery

institute: University of Colorado Anschutz Medical Campus, School of Medicine

summary: Obstructive sleep-disordered breathing (oSDB) is a heterogeneous phenotype that is increasing in prevalence worldwide and has many potential co-morbidities that could severely affect quality of life. There is a need to identify biomarkers for oSDB and its co-morbidities to improve clinical management, particularly in children. We performed bulk mRNA-sequencing, differential expression analysis, and qPCR replication of selected differentially expressed genes (DEGs) using RNA samples extracted from tonsils of children with oSDB. Two variables were used as classifier, namely detection of Epstein-Barr virus (EBV) in tonsils, and need for continuous positive airway pressure (CPAP) treatment. Standard statistical tests were used to determine associations across clinical, EBV and DEG variables. Nineteen genes were dysregulated in tonsils that are EBV+ or from children needing CPAP. Of these genes, APOBR was downregulated in both EBV+ and CPAP+ tonsils, and this downregulation was replicated by qPCR in an independent set of pediatric samples. In the tonsils of adult patients with oSDB, APOBR was positively correlated with age, and potentially with diastolic blood pressure. Taken together, APOBR and DEGs in tonsillar tissues may be useful as potential biomarkers of oSDB severity and co-morbidity across the lifespan, with APOBR levels being dependent on latent EBV infection.

overall_design: Differential expression analyses of (a) EBV+ vs EBV- and (b) CPAP+ vs CPAP- pediatric tonsils

first: Regie


title: Comparison of the transcriptome of KP4 controls or resistant to Folfirinox after 96h of treatment with Vehicule or Folfirinox

status: Public on Oct 31 2025

city: Montréal

first: Paloma

last: Kalegari

state: Quebéc

address: 900 Saint Denis St

department: Biochemestry

country: Canada

institute: CRCHUM

type: Expression profiling by high throughput sequencing

summary: FOLFIRINOX induces senescence in pancreatic tumor cells. However, some cells can spontaneously escape this senescence. We wanted to characterize the escape mechanisms from FOLFIRINOX-induced senescence of pancreatic tumor cells. Our  in vitro adaptation model to FOLFIRINOX shows that cells that have already escaped 5 treatment cycles become less sensitive to FOLFIRINOX.

overall_design: RNA sequencing was performed to compare KP4 cells that were either untreated (DMSO) or treated with FOLFIRINOX for 4 days. Additionally, KP4 cells were analyzed after undergoing 5 cycles of the same treatment (DMSO or FOLFIRINOX).

first: Guillon

last: Jordan

first: Kalegari

last: Paloma

first: Gerardo

last: Ferbeyre


title: Identification of strong constitutive promoters in Burkholderia to activate natural product production in Gram-negative bacteria

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

summary: Gram-negative bacteria are an emerging source of natural products with pharmaceutical potential. However, the limited availability of essential genetic tools for drug discovery and sustainable production remains a challenge. Burkholderia serves as a promising source for such tools, as it produces diverse natural products and can be experimentally manipulated in the laboratory. Hence, this study aimed to identify strong and constitutive promoters from Burkholderia stagnalis TBRC 18363 for unlocking the potential of cryptic biosynthetic genes and enhance natural product production. Highly expressed genes were identified through transcriptomic analysis. Twenty-six promoters were evaluated in Escherichia coli and Pseudomonas putida reporter systems. Among all, promoters p2035 and p5642 exhibited superior performance in both systems. These promoters were selected for further investigation and were found to enhance the production titer of icosalide in B. stagnalis TBRC 18363 and FR900359, a Gq/11 protein inhibitor depsipeptide, in Chromobacterium vaccinii. This research emphasizes efficient promoters for target gene overexpression in Gram-negative bacteria.

overall_design: RNA of B. stagnalis TBRC 18363 was extracted using RiboPure™ RNA Purification Kit, bacteria (Invitrogen, U.S.A.). Cells were harvested from 250–600 microliter cultures in LS2 medium by centrifugation and resuspended with 300 microliter RNAwiz solution. Then, RNA extraction was performed following the kit protocol. RNA eluted from the kit columns were treated with DNaseI. Concentration and quality of RNA was measured by using nanodrop and 0.8% agarose gel electrophoresis, respectively. Approximately 6 microgram RNA of each samples was submitted for RNAseq analysis service at NovogeneAIT Genomics, Singapore. The integrity of RNA samples was analyzed by using Agilent 2100 bioanalyzer. The RNA sequencing was performed on Illumina NovaSeq 6000 with paired end 150 bp and acquired 3 GB data per samples.

first: Chayaphat

last: Wongsombat

first: Jindaporn

last: Kongsee

first: Thapanee

last: Pruksatrakul

first: Kitlada

last: Srichomthong

first: Pisut

last: Yotbuntueng

first: Piyanat

last: Charoenyingcharoen

first: Umaporn

last: Uawisetwathana

first: Pattaraporn

last: Yukphan

first: Vanicha

last: Vichai

first: Aiyada

last: Aroonsri


title: Nuclear body reorganization by the viral RNA kaposin promotes Kaposi-sarcoma associated herpesvirus gene expression

city: Calgary

first: Jennifer

last: Corcoran

state: AB

address: 3230 Hospotal Drive NW

department: Microbiology, Immunology, and Infectious Diseases

institute: University of Calgary

summary: Kaposin is the most abundantly expressed viral RNA in tumours caused by the oncogenic virus Kaposi-sarcoma associated herpesvirus (KSHV); however, its role in viral replication is not well understood. Here we show that during KSHV infection, kaposin acts as viral architectural RNA which reorganizes cellular nuclear speckles (NS) to sites proximal to the viral genome. We show kaposin is both necessary and sufficient for NS remodelling, making it the first example of an RNA capable of scaffolding NSs. When kaposin does not colocalize with NS, as during infection with kaposin-recombinant viruses, viral gene expression is crippled. Our data demonstrate that KSHV encodes an RNA that functions in cis as a scaffold, leveraging the capability of NS to boost the expression of genes in their proximity. These findings make kaposin an architectural RNA for NSs and an important regulator of KSHV gene expression and critical for KSHV-associated diseases.

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design: Comparative gene expression analysis between KSHV mutants as well as between latency and 48 hours post-reactivation

middle: A

first: Mariel

last: Kleer

first: Michael

middle: J

last: Johnston


title: EGR1 induction compromises the therapeutic efficacy of BET depletion in triple-negative breast cancer (RNA-Seq)

city: 长春市

last: Liu

state: 吉林省

address: 东民主大街519转化医学院

country: China

institute: 1st hospital

summary: Bromodomain and extraterminal domain (BET) proteins are epigenetic readers of acetylated lysine residues, which regulate gene expression and are involved in tumorigenesis. Over the past two decades, BET-bromodomain (BD) inhibitors and BET-targeting PROTAC degraders have been developed and clinically tested. BET protein depletion with PROTAC degrader is generally recognized to provide stronger outcomes compared to just inhibiting the binding of protein to acetylated lysine residues with competitive inhibitors. In this study, we found that the bivalent BET-BD inhibitor MS645 exhibited much more potent anti-proliferative activity than BET degraders, including ARV771, AT1, MZ1 and dBET1 in triple-negative breast cancer cells. MS645 treatment dissociated BET proteins from chromatin and decreased E2F1-3 expression, thus inhibited cell growth of TNBC. While ARV771 treatment didn't affect E2F1-3 expression though it displaced BET proteins from chromatin as well. We found knockdown of BRD4 or BRD4 depletion by ARV771 treatment dramatically induced EGR1 expression. EGR1 interacts with Septin complex and maintained its nuclear distribution. Septin complex is recruited by EGR1 to E2F1-3 gene loci to activate E2F1-3 transcription, thus maintained cell cycle progression.

overall_design: To investigate the differentially expressed genes in HCC1806 cells upon MS645 and ARV771 treatment, HCC1806 cells were treated with MS645 or ARV771 for 8h and RNA were isolated for RNA-sequencing

first: Deyu

last: Wang

first: Siwei

last: Zhang


title: Effect of HIPK3 depletion in tamoxifen-resistant EGFR-overexpressing MCF7 breast cancer cells

city: Leiden

first: Bob

last: van de Water

state: Leiden

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

summary: Overexpression and activation of EGFR in breast cancer can cause resistance to antiestrogen treatmen. Using high-throughput screening, we have identified HIPK3 as a mediator of tamoxifen resistance in MCF7 breast cancer cells. HIPK3 depletion re-sensitized cells to 4-hydroxytamoxifen under EGF-stimulated conditions. In this study, we investigated the transcriptomic responses to HIPK3 depletion, together with EGF stimulation and treatment with estradiol and 4-hydroxytamoxifen. RNA-sequencing demonstrated that depletion of HIPK3 caused increased expression of genes involved in mitotic signaling, oxidative damage, endoplasmatic reticulum stress and apoptosis in EGF, estradiol and tamoxifen treated MCF7 cells.

overall_design: We used MCF7 cells overexpressing EGFR to study (EGFR-mediated) tamoxifen resistance. The role of HIPK3  was investigated by performing siRNA knockdown of HIPK3 followed by gene expression profiling using RNAseq in EGFR-overexpressing MCF7 cells. Moreover, we studied the  responses to EGF and EGF, estradiol and 4-hydroxytamoxifen treatment in these cells, and how this is affected by HIPK3 knockdown, to understand potential mechanisms of drug resistance and sensitization.

first: Lynn

last: Wester

first: Peter

last: Bouwman

first: Vera

last: van der Noord


title: Ex vivo–expanded human regulatory T cells enhance cholesterol efflux and PON1 expression in oxLDL-exposed macrophages

city: London

first: Cristiano

last: Scotta

address: Kingston Lane

department: Life Science

country: United Kingdom

institute: Brunel University

summary:
Lipid-driven chronic inflammation is a primary driver of atherosclerosis progression. Enhancing the anti-inflammatory response by bolstering regulatory T cell (Treg) numbers or improving their function, holds promise for therapeutic control of the disease. We and others have previously demonstrated in clinical trials the safety and potential efficacy of adoptive Treg transfer in restoring immunological balance. This study investigates the capability of ex vivo expanded regulatory T cells to counterbalance pro-inflammatory signals and lipid accumulation in primary macrophages, thereby contrasting plaque formation and atherosclerosis progression.
To test this hypothesis, freshly isolated Tregs were ex vivo expanded into a clinical grade cell product before co-culturing with monocyte-derived M2-like macrophages. Macrophages were exposed to oxidised low-density lipoprotein (oxLDL) and co-cultured alone or in the presence of Tregs. Changes in macrophage phenotype, gene expression profile and functional properties such as the capacity to regulate the accumulation of cholesterol were analysed by flow cytometry, RNA sequencing and western blotting.
In the co-culture system, the study demonstrated a significant reduction in both pro-inflammatory effects of oxLDL and accumulation of modified cholesterol in macrophages when Tregs were present. We identified that Tregs through the transferring of cAMP into macrophages, could potentiate the ABCA1-mediated cholesterol efflux pathway, and crucially, elevate the anti-atherogenic activity by inducing Paraoxonase-1 expression.
The findings suggest a novel atheroprotective role for Tregs which supports the potential development of new experimental therapies for cardiovascular disease. By influencing macrophage function and cholesterol accumulation, Tregs present a promising avenue for mitigating atherosclerosis.

overall_design: To investigate the effect of regulatory T cell co-culture on the genetic profile of monocyte-derived M2-like macrophages.

first: Caraugh

last: Albany

first: Daniela

last: Mastronicola

first: Wladislaw

last: Stroukov

first: Rocio

last: Martinez-Nunez

last: Scottà


title: Comprehensive Mapping of Transcriptionally-active Enhancers During Murine Cardiogenesis at Single Cell Resolution

city: Stanford

first: Francisco

middle: Xavier

last: Galdos

state: CA

address: 265 Campus Dr.

department: Cardiovascular Institute

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: An in-depth understanding of the complex mechanisms that orchestrate normal embryonic heart development is required to disambiguate the origin of congenital heart disease. However, the epigenetic landscapes governing cell type-specific gene expression patterns during heart development at single cell resolution has yet to be revealed. Here we use simultaneous single cell RNA and assay for transposase accessible chromatin sequencing to construct a comprehensive multimodal map of embryonic murine heart development, profiling cell type- and timepoint-specific epigenetic regulatory elements as well as their gene targets. Furthermore, we compare these regulatory elements with published GWAS hits to map variants implicated in key developmental processes and clinical phenotypes to enhancers for genes that are actively transcribed during cardiac development. Taken together, our work provides a rich resource for the broader scientific community that empowers future studies in heart development and disease and offers a simple computational framework for integrating and profiling multiomic data in single cells.

overall_design: Mouse embryonic hearts were harvested at embryonic days 8.5, 10.5, and 16.5 and dissociated into single cells. Nuclei were extracted from cell suspensions and underwent ATAC transposition followed by single nuclei capture using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (CG000338 Rev F) protocol. ScRNA and scATAC libraries were generated using the 10X Genomics protocol. Subsequent sequencing was conducted using an Illumina NOvaSeq 6000 at 20,000 read pars per nuclei for the gene expression library and 25,000 read pairs per nuclei for the ATAC library.

middle: X

first: Carissa

last: Lee

first: William

last: Goodyer

first: Sidra

last: Xu

first: Tahmina

last: Samad

first: Sean

middle: M

last: Wu

first: Stella

last: Su


title: Quantitative transcriptome N6-methyladenosine profiling reveals the mechanism of far-red regulated anthocyanin homeostasis in Arabidopsis

city: Chicago

first: Shun

last: Liu

state: IL

address: 929 E. 57th. Street

department: Chemistry

institute: University of Chicago

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most abundant messenger RNA modification in higher eukaryotes. Functional studies of the RNA m6A modification in plants have been limited by mapping individual m6A-modified sites in whole transcriptomes. In this study, we introduce the method m6A-selective allyl chemical labeling and sequencing (m6A-SAC-seq) for quantitative whole-transcriptome profiling of m6A at single-nucleotide resolution under light and dark conditions in Arabidopsis. With this technology, we observed far-red but not red light, noticeably increase the m6A level. Further evidence showed that far-red light modulated mRNA stability and translation by m6A methylation. Additionally, our data uncovered that far-red light promoted m6A methylation of anthocyanin homeostasis related transcripts through the stabilization of FIONA1 (FIO1) and m6A methyltransferase complex, MTA (mRNA adenosine methylase A) and MTB, and the core component FIP37 (FKBP12 INTERACTING PROTEIN 37KD). Thus, with m6A stoichiometry information at single-base precision, we proposed a new mechanism for the regulation of anthocyanin accumulation under far-red light through m6A methylation.

overall_design: PolyA samples from twelve wild type (2 input and 2 MjDim1-treated in red light, far-red light and dark conditions, respectively), four fio1 mutant (2 input and 2 MjDim1-treated in far-red light), four mta mutant (2 input and 2 MjDim1-treated in far-red light) and four phyA mutant (2 input and 2 MjDim1-treated in far-red light) were collected for high-throughput sequencing.

first: Bochen

last: Jiang

first: Mengjie

last: Chen

first: Chuan

last: He


title: Gene expression changes in postnatal mouse brain Neural Stem Cells differentiated in the presence of platelets.

city: Patras

first: Adamantia

last: Kouvela

address: Asklipiou 1

country: Greece

institute: Department of Biochemistry, School of Medicine, University of Patras

summary: Whole transcriptome sequencing of postnatal mouse brain Neural Stem Cells (NSCs) cultured for three days in serum-free media, in the presence (proliferation conditions) or absence (differentiation conditions) of growth factors EFG and FGF2, as well as when co-cultured with mouse platelets (in a ratio of 75 platelets per NSC) in the absence of growth factors.

overall_design: Expression profiling by the Ion Torrent Genestudio S5 platform with Ion Chef (Ion torrent)

first: Maria

last: Anesti

first: Aggeliki

last: Dimopoulou

first: Dimitrios

last: Dimitrakopoulos

first: Constantinos

last: Stathopoulos

first: Ilias

last: Kazanis


title: Single-cell transcriptome sequencing provides insight into multiple chemotherapy resistance in a patient with refractory DLBCL: a case report

city: Wuhan

first: Zhao

middle: Ke

last: Wei

state: Hubei

address: 109 Machang Road, Jianghan District

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: Relapsed and refractory diffuse large B-cell lymphoma (DLBCL) is associated with poor prognosis. As such, a comprehensive analysis of intratumoral components, intratumoral heterogeneity, and the immune microenvironment is essential to elucidate the mechanisms driving the progression of DLBCL and to develop new therapeutics.

overall_design: Here, we used single-cell transcriptome sequencing and conventional bulk next-generation sequencing (NGS) to understand the composite tumor landscape of a single patient who had experienced multiple tumor recurrences following several chemotherapy treatments.

last: Kewei

first: Zhang

last: Liling


title: Effect of naringin in mouse lymph nodes

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

summary:
The induction of CD169-positive macrophages in lymph nodes may be a new therapeutic strategy to enhance cancer immunity in cancer immunotherapy. Naringin, a natural compound, was identified as a CD169 inducer in macrophages.
Naringin is a flavonoid glycoside found in citrus fruits, tomatoes, and legumes and has several functional activities, such as anti-oxidative and anti-inflammatory activities.

overall_design: Naringin (200 mg/kg per day) was mixed with food and administered daily, and then inguinal lymph nodes were resected.


title: Podocyte Twin in Culture: Patient-specific ex vivo Model of Genetic FSGS caused by an INF2 Mutation

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

country: Germany

institute: RWTH Aachen University Medical School

summary: We used an ex vivo cell culture model to generate patient-specific podocytes from a patient with genetic FSGS caused by an INF2 mutation. The patient's entire genetic background was maintained in all cell types of the protocol. Bulk RNA sequencing analysis was performed to first validate the outcome of the protocol by comparing the hiPSC-derived podocytes generated from a healthy donor with a conditionally immortalized podocyte cell line. Subsequently, the patient-specific hiPSC-derived podocytes holding the INF2 mutation were compared to the healthy hiPSC-derived podocytes and mutation specific phenotypic and functional alterations were investigated.

overall_design:
This study consists of bulk RNA sequencing samples from a conditionally immortalized podocyte cell line (M. Saleem) and from different steps of the differentiation protocol for the generation of podocytes derived from human induced pluripotent stem cells (hiPSC) in biological duplicates (n=2). The different steps include hiPSCs before differentiation, nephron progenitor cells and terminal differentiated hiPSC-derived podocytes generated from a healthy donor and a patient with genetic FSGS caused by an INF2 mutation.
***Submitter states that raw data are not available due to patient privacy concerns***

first: Janina

last: Müller-Deile

first: Victoria

last: Rose


title: Training-induced exosomal miR-136-3p modulates mitochondrial functions by targeting NRDC in human skeletal muscle.

city: Stockholm

first: Mutsumi

last: Katayama

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary:
The purpose of this study was to validate the role of abundant miRNA, miR-136-3p, in extra vesicles collected from serum after training. We transfected miR-136-3p into human skeletal muscle cells.
To search of targets genes of miR-136-3p, we performed transcriptome analysis to compare expression profiles between control and miR-136-3p transfected human skeletal muscle cells.

overall_design: We used microarrays to detail the global regulation of gene expression by miR-136-3p and identified up- and down-regulated genes by miR-136-3p in human skeletal muscle cells.

first: Anna

last: Krook


title: Putative indicators of thyroid hormone system disruption - a transcriptional footprint of developmental hypothyroidism in hippocampus

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: Thyroid hormone (TH) system disrupting compounds can impair brain development by perturbing TH action during critical life stages. Human exposure to TH system disrupting chemicals is therefore of great concern. To better protect humans against such chemicals, sensitive test methods that can detect effects on the developing brain are critical. Worryingly, however, current test methods are not sensitive and specific towards TH-mediated effects. To address this shortcoming, we performed Bulk-RNA-sequencing of rat brains developmentally exposed to two different thyroperoxidase (TPO) inhibiting compounds, the medical drug methimazole (MMI) or the pesticide amitrole.

overall_design: Pregnant and lactating rats were exposed to 8 and 16 mg/kg/day(d) MMI or 25 and 50 mg/kg/d amitrole from gestational day 7 until postnatal day 16. Bulk-RNA-seq was performed on hippocampus from the 16-days old male pups. MMI and amitrole caused pronounced changes to the transcriptomes; 816 genes were differentially expressed, and 425 gene transcripts were similarly affected by both chemicals. Functional terms indicate effects from key cellular functions to changes in cell development, migration and differentiation of several cell populations. Of the total DEGs, 106 DEGs appeared to form a consistent transcriptional footprint of developmental hypothyroidism as they were similarly and dose-dependently expressed across all treatment groups. Using a filtering system, we identified 20 genes that appeared to represent the most sensitive, robust and dose-dependent markers of altered TH-mediated brain development. These markers provide inputs to the adverse outcome pathway (AOP) framework where they, in the context of linking TPO inhibiting compounds to adverse cognitive function, can be used to assess altered gene expression in the hippocampus.

first: Louise

last: Ramhøj

first: Bertrand

last: Evrard


title: An IL-17-Ly6G+Polymorphonuclear Neutrophil (PMN) axis limits protective host responses against tuberculosis.

city: New Delhi

first: DHIRAJ

last: KUMAR

state: Delhi

address: ARUNA  ASAF ALI MARG

department: Cellular Immunology

country: India

institute: ICGEB, New Delhi

summary: The protective correlates of Mycobacterium tuberculosis (Mtb) infection-elicited host immune responses are incompletely understood. Here we report pro-pathogenic crosstalk between IL-17, COX2, and Ly6G+Polymorphonuclear Neutrophils (PMNs). We show that most intracellular bacilli in the wild-type (WT) mice's lungs are Ly6G+PMN-resident. In BCG-vaccinated WT mice, Mtb continues to persist inside Ly6G+PMNs, which is sensitive to COX2 inhibition. Using a genetically susceptible IFNγ -/- mice model, we report that excessive neutrophil infiltration and corresponding bacteremia are dependent on Ly6G+PMN-derived IL-17. COX2 inhibition and IL-17 neutralization reverses Ly6G+PMN infiltration, associated pathology and death in IFNγ -/- mice. Inhibiting RORγT along with COX2 in Mtb-infected WT mice further demonstrates the pathological nature of the IL-17- Ly6G+PMN axis. Clinically, in a prospective cohort of pulmonary TB subjects, high neutrophil count and serum IL-17 levels precipitate adverse treatment outcomes. Therefore, targeting the pro-pathogenic IL-17- Ly6G+PMN axis could enhance TB prevention and therapy in normal and genetically vulnerable subjects.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from Polymorphonuclear Neutrophils of Mycobacterium tuberculosis infected mice treated with BCG and/or Celecoxib and uninfected mice

first: Priya

last: Sharma

first: Mrinmoy

last: Das

first: Dhiraj

last: Kumar

first: Amit

last: Singhal


title: Comprehensive bioinformatics analysis reveals the hub genes and pathways in a mouse model of Pierpont Syndrome

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

institute: Amsterdam University Medical Centers

summary: Unravelling molecular defects resulting from the missense mutation in TBL1XR1 using targeted mutant mice bearing the Tbl1xr1 Y446C/Y446C mutation. These mice used as an animal model of Pierpont syndrome have disturbed hearing and a trend for disturbed locomotor activity. RNA seq of cortex tissue has been performed to establish the transcriptome.

overall_design: mRNA profiles for cortex of wild type and Tbl1xr1Y446C/Y446C mice (6 mice for each genotype, 3 male and 3 female mice per genotype).

first: Yalan

last: Hu

first: Peter

last: Lauffer

first: Anita

last: Boelen


title: Gene expression of hippocampus from 17-month-old wildtype mice with sham/400 mGy X-ray irradiation treatment and 17-month-old 3xTg-AD mice with sham/400 mGy  X-ray irradiation treatment.

city: Hong Kong

first: MA

last: Chi Him Eddie

address: Tat Chee Avenue, Kowloon, Hong Kong

department: Department of Neuroscience

country: Hong Kong

institute: City University of Hong Kong

summary: Current study aimed to identify the 400 mGy X-ray irradiation-induced unique gene expression changes in the hippocampus of the 17-month-old 3xTg-AD mice.

overall_design: The 13.5-month-old 3xTg-AD mice and the age-matched wildtype mice received biweekly X-ray irradiation at 50 mGy/sham irradiation 8 times. When the mice reached 17 months old, the hippocampus from the different groups was harvested for bulk RNA sequencing (n=3-6 from each treatment group), and a total of 18 samples were analyzed.

first: Chi

middle: H

last: Ma

first: Yi

last: Xu

first: Tan

last: Wu

first: Xin

last: Wang


title: Thiolutin is a direct inhibitor of RNA Polymerase II

city: Boston

first: Chenxi

last: Qiu

state: MA

address: NRB 858, 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Thiolutin is a well-known and long-used natural product transcription inhibitor with an unresolved mode of action. Recent studies have identified Zn2+-chelation activity for both thiolutin and the related dithiolopyrrolone holomycin, with direct inhibition of RNA polymerases ruled out as a mode of action. However, negative results for direct transcription inhibition of RNA polymerases in recent studies are contradicted by previously observed thiolutin inhibition of extract fractions containing yeast RNA Polymerases I, II, and III. Here, we present chemical genetic and biochemical approaches to investigate the mode of action of thiolutin. We identify diverse classes of mutant that alter sensitivity to thiolutin. We functionally dissect the multidrug resistance and thioredoxin pathways controlling thiolutin sensitivity. We provide genetic evidence that thiolutin causes oxidation of thioredoxins in vivo and suggest that thiolutin both induces oxidative stress and alters Zn2+, Cu2+ and Mn2+ homeostasis in vivo, recapitulating previously observed thiolutin interactions with Zn2+. Finally, our results resolve contradictory biochemical results for thiolutin inhibition of transcription by direct demonstration of thiolutin inhibition of RNA polymerase II (Pol II) in vitro. Inhibitory activity requires both appropriate reduction of thiolutin and the presence of Mn2+. Thio/Mn2+ inhibition is abrogated when template DNA is pre-bound to Pol II or when excess DTT is present, and renders Pol II pause prone in elongation if initiation is bypassed using a pre-formed Pol II elongation complex. Together, we propose that thiolutin directly inhibits Pol II transcription through a novel mechanism distinct from known transcription inhibitors.

overall_design: This is a series of processed RNA polymerase II (Pol II) ChIP-seq data after thiolutin treatment to evaluate how Pol II occupancy over the gene changes upon thiolutin treatment at a genome-wide scale, as an approach to provide insight to the mode of action of thiolutin (initiation inhibition vs elongation inhibition). Input chromatin or Chromatin IP samples using FLAG M2 antibody (Sigma) for FLAG-tagged Rpb3 from control or thiolutin treated yeast chromatin. Cells were untreated, or treated with thiolutin (in DMSO) at 10 µg/mL final concentration in the medium for 1, 2, 4, or 8 minutes or with DMSO (vehicle for thiolutin) for 8 minutes. Chromatin samples included spike-in chromatin from Schizosaccharomyces pombe also including FLAG-tagged rpb3+.

first: Payal

last: Arora

first: Craig

middle: D

last: Kaplan


title: Gene expression of hippocampus from 9-month-old wildtype mice with sham/400 mGy X-ray irradiation treatment and 9-month-old 3xTg-AD mice with sham/400 mGy  X-ray irradiation treatment

summary: Current study aimed to identify the 400 mGy X-ray irradiation-induced unique gene expression changes in the hippocampus of the 9-month-old 3xTg-AD mice.

overall_design: The 5.5-month-old 3xTg-AD mice and the age-matched wildtype mice received biweekly X-ray irradiation at 50 mGy/sham irradiation 8 times. When the mice reached 9-month-old, the hippocampus from different treatment groups was harvested for bulk RNA sequencing (n=3 from each treatment group), and a total of 12 samples were analyzed.


title: Dual transcriptomics of host-pathogen interaction of neonatal sepsis/meningitis causing isolate Cronobacter turicensis z3032 with zebrafish larvae

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

summary: Cronobacter (C.) is an important emerging opportunistic foodborne pathogen representing  significant cause of mortality in neonatal patients with bacteremia and meningitis.  Knowledge on the pathobiology of Cronobacter mediated meningitis has to a large extend been explored using in vitro models. To explore the innate immune response against the neonatal sepsis/meningitis causing isolate C. turicensis z3032 in vivo, zebrafish larvae (Danio rerio) were used as infection model. Following establishment of infection in zebrafish larvae with z3032, dual RNA-sequencing of host-pathogen was undertaken to profile RNA expression simultaneously in the pathogen and the head region of the zebrafish host.

overall_design: returned to a petri dish with fresh embryo medium and incubated at 28 °C until development of typical signs of disease such as axis curvature and necrosis which was observed at approx. 36 h dpi. 60 randomly chosen zebrafish larvae from each group (infected, mock-infected) were euthanized by a prolonged immersion in an overdose of 50 mg/L Tricaine solution, followed by decapitation with a sharp blade, their heads collected and transferred into 1.5ml Eppendorf tubes Excess E3 medium was removed and   replaced by RNAlater (Ambion) and stored at 4°C until further processing. For the extraction of total RNA, RNAlater was replaced by 600 ull of Qiazol, and the tissue was homogenized using a pestle motor followed by drawing of sample with a needle until the tissue was completely homogenized. As a control, RNA was isolated from z3032 cultures grown in LB to stationary phase (18-24 h). For both the zebrafish and bacterial culture, RNA extractions were performed using the miRNeasy Mini kit (Qiagen) according to the manufacturer's protocols. An additional DNase treatment was performed with a TURBO DNA-free kit (Ambion) according to the manufacturer's protocols. The concentration of the extracted RNA was measured using a NanoDrop Spectrophotometer. The total RNA samples were subjected to ribosomal RNA (rRNA) depletion, zebrafish samples mock-infected with PBS were treated with Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina), zebrafish infected with C. turicensis were treated with Ribo-Zero rRNA Removal Kit (Gram-negative Bacteria) (Illumina) followed by Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) and the C. turicensis sample grown in LB was treated with Ribo-Zero rRNA Removal Kit (Gram-negative Bacteria). The depletion steps and subsequent 125 bp paired-end RNA Sequencing on a HiSeq2500 (Illumina) were performed at the Functional Genomic Center at University Zurich (FGCZ), Zurich, Switzerland.

first: Chiara

middle: C

last: Cosentino

first: Athmanya

middle: K

last: Eshwar

first: Francis

last: Muchaamba

first: Claudia

last: Guldimann

first: Roger

last: Stephan

first: Angelika

last: Lehner


title: EGR1 induction compromises the therapeutic efficacy of BET depletion in triple-negative breast cancer (ChIP-Seq)

last: Liu

address: 东民主大街519转化医学院

summary: Bromodomain and extraterminal domain (BET) proteins are epigenetic readers of acetylated lysine residues, which regulate gene expression and are involved in tumorigenesis. Over the past two decades, BET-bromodomain (BD) inhibitors and BET-targeting PROTAC degraders have been developed and clinically tested. BET protein depletion with PROTAC degrader is generally recognized to provide stronger outcomes compared to just inhibiting the binding of protein to acetylated lysine residues with competitive inhibitors. In this study, we found that the bivalent BET-BD inhibitor MS645 exhibited much more potent anti-proliferative activity than BET degraders, including ARV771, AT1, MZ1 and dBET1 in triple-negative breast cancer cells. MS645 treatment dissociated BET proteins from chromatin and decreased E2F1-3 expression, thus inhibited cell growth of TNBC. While ARV771 treatment didn't affect E2F1-3 expression though it displaced BET proteins from chromatin as well. We found knockdown of BRD4 or BRD4 depletion by ARV771 treatment dramatically induced EGR1 expression. EGR1 interacts with Septin complex and maintained its nuclear distribution. Septin complex is recruited by EGR1 to E2F1-3 gene loci to activate E2F1-3 transcription, thus maintained cell cycle progression.

overall_design: To investigate the genomic occupancy of BRD4, H3K27ac and EGR1 upon MS645 and ARV771 treatment, HCC1806 cells were treated with different chemicals and ChIP-seq was performed

first: Deyu

first: Siwei

last: Zhang


title: Ruxolitinib improves hematopoietic regeneration by retrieving mesenchymal stromal cell function in aGVHD

city: Tianjin

first: Quan

last: Gu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Tianjin, China

summary: Acute graft-versus-host disease (aGVHD) is a severe complication of allogeneic hematopoietic stem cell transplantation. Hematopoietic dysfunction accompanied by severe aGVHD, which may be caused by niche impairment, is a long-standing clinical problem. However, how the bone marrow (BM) niche is damaged in aGVHD hosts is poorly defined. To comprehensively address this question, we employed a haplo-MHC-matched transplantation aGVHD murine model and performed single-cell RNA sequencing of non-hematopoietic BM cells. Transcriptional analysis showed that BM mesenchymal stromal cells (BMSCs) were severely affected with a reduction in cell ratio, abnormal metabolism, compromised differentiation potential and defective hematopoietic supportive function, which were validated by functional assays.

overall_design: By combining scRNA-seq with functional assays, we revealed a novel mechanism underlying the effect of ruxolitinib on aGVHD niche components and broadened the BMSC-based therapy for aGVHD.


title: ChIP-Seq of MYC in MCF-7 cells with EPIC1 knockdown or overexpression.

city: Pittsburgh

first: Da

last: Yang

state: PA

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

summary: EPIC1 is reported to interact with MYC through and promote cell-cycle progression. EPIC1 regulate the occupancy of MYC to its target genes.

overall_design: Chromatin immunoprecipitation assays followed by sequencing (ChIP-Seq) of MYC in MCF-7 cells with EPIC1 knockdown or overexpression.

first: Zehua

first: Yifei

first: Sihan

last: Li


title: Loss of Twist impairs tentacle development and induces epithelial neoplasia in the sea anemone Nematostella vectensis

status: Public on Oct 30 2025

city: Vienna

first: Patricio

last: Ferrer Murguia

state: Vienna

address: Djerassiplatz 1

country: Austria

institute: University of Vienna

summary: The basic helix-loop helix transcription factor Twist plays diverse roles in mesodermal development across bilaterians, but its function in cnidarians remains unclear. Here, we investigate the role of Twist in tentacle morphogenesis and tissue homeostasis in the sea anemone Nematostella vectensis. Using a CRISPR/Cas9 generated knockout, we show that twist mutants exhibit impaired secondary tentacle formation, reduced proliferation in budding tentacles, and absence of micronemes, structures that demarcate tentacle boundaries-suggesting defects in spatial patterning. We demonstrate that twist expression is regulated by Wnt, BMP, and Notch signalling but is independent of MAPK and Hedgehog pathways. Loss of Twist disrupts expression of mesodermal transcription factors paraxis and tbx15 and perturbs the TOR-FGF signalling feedback loop necessary for normal tentacle growth. Moreover, starting at juveniles, mutants develop neoplasm-like epithelial overgrowth with tentacle-like molecular and morphological profiles, indicating a role for Twist in maintaining tissue homeostasis at the oral pole.  Together, our findings reveal that Twist integrates major signalling pathways to regulate secondary tentacle patterning and maintain spatial tissue organisation in the diploblastic Nematostella vectensis.

overall_design: CRISPR/Cas9-generated twist knockout mutants of Nematostella vectensis were raised to adulthood. Tissue samples from tentacles and neoplasm-like outgrowths were excised at defined developmental days and processed for RNA sequencing.

last: Ferrer Muguia

first: Ulrich

last: Technau


title: Transcription-Replication Conflict Resolution by Nuclear RNA Interference [dRNH ChIP-seq]

city: Cold Spring Harbor

first: Teri

last: Cheng

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: RNA interference (RNAi) plays an important role in the nucleus critical to genome maintenance and heterochromatin silencing. In the fission yeast Schizosaccharomyces pombe, Dicer (Dcr1) also plays a critical role in releasing RNA polymerase II (Pol II) to limit transcription-replication (T-R) stress, but a mechanistic insight is still lacking. Here, we show that Dcr1 resolves T-R conflicts by processing promoter-proximal co-transcriptional R-loops, facilitating replication progression and limiting DNA damage. We found in RNase H-deficient cells, which accumulated pathological R-loops, that further mutating Dcr1 caused hypersensitivity to genotoxic stress. Genetic evidence implicates Dcr1 in regulating nascent transcription, with the helicase domain providing an additional catalytic function in genome stability reminiscent of archaeal helicase homologs involved in replication. In the absence of Dcr1, DNA breaks accumulate around transcription start sites (TSSs), termination sites (TTSs) and pause sites, consistent with replication collision, and DNA replication processivity and speed are impaired in a manner dependent on transcriptional activity and directionality. Argonaute (Ago1) is implicated in dcr1Δ-induced genome instability, as its deletion suppressed the genotoxic stress phenotype of dcr1Δ. Our results demonstrate a novel nuclear function of Dcr1, likely ancestral to the RNAi pathway.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) of WT, dcr1Δ, rnh1Δ  rnh201Δ, and the triple mutant  rnh1Δ  rnh201Δ  dcr1Δ

first: Robert

last: Martienssen


title: Single cell sequencing revealed cell heterogeneity in rice infected with RRSV and RGSV

city: Fuzhou

first: Lu

last: Wang

state: Fujian

address: No.15 Shangxiadian road

department: College of Plant protection

institute: Fujian Agriculture and Forestry University

summary: Rice infection with RRSV and RGSV causes severe symptoms and is transmitted by the brown planthopper, which feeds on the base of the rice stem and spreads the virus. We analyzed cell heterogeneity at the base of the rice stem after virus infection by single cell RNA sequencing (scRNA-seq).

overall_design: We collected the stem base of healthy rice and rice infected by two viruses, and then intercepted the segmentation 1.5cm-2.5cm above node for protoplast dissociation, and scRNAseq was performed on the captured cells.


title: Genital herpes shedding episodes associate with alterations in the spatial organization and activation of mucosal immune cells

city: Seattle

first: Rachael

last: Zemek

state: Washington

address: 1100 Fairview Ave

institute: Fred Hutchinson Cancer Centre

summary:
Analysis of vaginal mucosa samples from patients that are HSV-2 seronegative or seropositive, with comparison of active vs inactive HSV-2 shedding (Anogenital Swab HSV-2 PCR Result). This unique dataset was used to define and spatially map immune cell subsets and localized gene expression via spatial transcriptomics.
Herpes Simplex Virus 2 (HSV-2) infection results in variable rates of local viral shedding in anogenital skin. The impact of episodic viral exposures on immune cells in adjacent mucosal tissues, including the genital tract, is unknown. However, any immune responses at this site could impact protective mucosal immunity, tissue homeostasis, and adverse health outcomes. To investigate the impact of HSV-2 on cervicovaginal tract immunity, we applied flow cytometry, immunofluorescent imaging, analysis of soluble immune factors, and spatial transcriptomics to cervicovaginal tissue and blood samples provided by a total of 232 HSV-2 seropositive and seronegative participants, with genital HSV-2 shedding evaluated at the time of biopsy. This unique dataset was used to define and spatially map immune cell subsets and localized gene expression via spatial transcriptomics. HSV-2 seropositivity alone was associated with minimal differences in cervicovaginal and circulating T cell phenotypes. However, the vaginal mucosa during active HSV-2 shedding was associated with alterations in T cell, macrophage, and dendritic cell localization and gene expression consistent with increased immune surveillance, with immune activating and suppressing signals potentially reinforcing mucosal tissue homeostasis.

overall_design: HSV-2 Seronegative: 6 samples. HSV-2 Seropositive: 5 samples (3 shedding, and 2 non-shedding)


title: Differential autophagy responses in macrophages in chronic inflammatory gastrointestinal disorders

first: Dhiraj

last: Kumar

address: Aruna Asaf Ali Marg

institute: International Centre for Genetic Engineering and Biotechnology

summary:
Background & Aims: Macrophages are critical to maintain intestinal homeostasis and contribute to localized inflammation, once dysregulated. How their responses across chronic gut pathologies like idiopathic inflammation or infection-mediated inflammation are regulated, is not known. This study aimed at understanding macrophage dysfunction in patients of chronic idiopathic gut inflammation [Crohn’s Disease (CD)] and chronic gut infection-related inflammation [Intestinal Tuberculosis (ITB)].
Methodology: Confirmed CD (n=42) and ITB (n=41) cases were recruited and whole blood samples were collected. PBMCs were enriched for CD14+ monocytes and differentiated into Monocyte-derived macrophages (MDMs), which were either left uninfected or infected ex vivo with Mycobacterium tuberculosis (Mtb). These MDMs were assessed for Mtb survival, gene expression by RNA-seq, mitochondrial function and autophagy flux assays.
Results: MDMs from both CD and ITB subjects were permissive to intracellular Mtb growth, however the bacteria showed significantly better survival in the CD MDMs. RNA-seq data demonstrated that inflammatory response and autophagy pathway genes (protein coding as well as long noncoding RNA genes) are differentially regulated among CD and ITB MDMs, either basally or upon Mtb infection. Indeed, CD MDMs when compared to ITB, showed significantly diminished autophagy flux.
Conclusions: Our results indicate an inherent impairment of autophagy process in CD MDMs when compared with ITB MDMs. We propose that the inability to maintain the autophagy process could contribute towards chronic idiopathic inflammation disorders of the gut.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from monocytes derived macrophages.

first: Sonakshi

last: Udinia

first: Mrinmoy

last: Das


title: Glioma immune microenvironment associated with malignant transformed cells  Transcriptome sequencing

city: suzhou

first: xiangtong

last: xie

address: wansheng street

institute: Suzhou Kowloon Hospital,Shanghai Jiao Tong University School of Medicine,Suzhou 215028

summary:
Ribonucleic acid sequencing (RNA-seq) of ihCTC, C12, ihDCTC, ihSTC-BM, precursor mesenchymal stem cells (MSCs) and myeloid-derived suppressor cells (MDSCs) was performed to establish a database of differentially expressed genes (DEGs).This paper intended to find the leader molecules for malignant transformation of these cells, thereby laying a foundation for the development of new molecular targeted therapy.The sequencing cell lines were established in the relevant references.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iTAMD cells (C12, ihCTC, ihDCTC, ihSTC_BM))and its precursor cells (MDSC and MSC).

first: Xiangtong

last: Xie

first: Ke

last: Yan

first: Xifeng

last: Fei

first: Chungang

last: Dai

first: Jie

last: Wu

first: Hanchun

last: Chen

first: Dongyi

last: Jiang

first: Haifeng

last: Zhao

first: Donghua

first: Wenyu

last: Zhu

first: Zhimin

first: Qiang

last: Huang


title: Transcriptomic Profiling of Bronchial Epithelium Reveals Dysregulated Interferon and Inflammatory Responses to Rhinovirus in Exacerbation-Prone Pediatric Asthma [scRNA-Seq]

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Host factors influencing susceptibility to rhinovirus-induced asthma exacerbations remain poorly characterized. Using organotypic bronchial epithelial cultures from well-characterized children with asthma and healthy children, this study investigated viral load kinetics and resultant host responses by bulk and single-cell transcriptomics and targeted protein analyses. Bronchial epithelium from exacerbation-prone children exhibited greater rhinovirus replication and a cascade of exaggerated downstream interferon (IFN), inflammatory, epithelial stress, and remodeling responses. These transcriptional patterns were confirmed and further refined using single-cell transcriptomics, revealing cell type-specific contributions—particularly from non-ciliated cell populations including secretory immune response, tuft, and basal cells. We observed that these post-infection differences were associated with lower pre-infection IFN-stimulated gene (ISG) expression and protein levels of the ISG CXCL10. Prophylactic IFN-β treatment reduced viral replication and normalized downstream responses, supporting low baseline (pre-infection) IFN tone as a modifiable causal determinant of host susceptibility to adverse rhinovirus-induced responses in exacerbation-prone children with asthma.

overall_design: We compared transcriptional responses across 3 donor groups, severe asthma (SE), non-Severe asthma (NSE), and healthy controls at baseline (uninfected) and post RV infection sampes.

first: Naresh

last: Doni Jayavelu

first: Jason

last: S. Debley

first: Matthew

last: Altman


title: ERAdP facilitates package  and biogenesis of dense core vesicles in Paneth cells to enhance intestinal antibacterial capacity

city: Beijing

first: Cunzhen

last: Li

address: No 15 Datun Road, Chaoyang District

institute: Chinese Academy of Sciences

summary: Analysis of gene expression profile in small intestine crypts(IEC) between Cnep1r1 knock out and wild type mice

overall_design: Total RNA was extracted from IEC between Cnep1r1 knock out mice and wild type mice and hybridization on Affymetrix microarrays.


title: Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [10xGermfree]

city: CAMBRIDGE

first: Jacques

last: Deguine

state: Massachusetts

address: 415 Main Street, 415M-7175 - Xavier lab

department: Immunology Program

institute: Broad Institute

summary: Enteric neurons are essential regulators of intestinal physiology, yet their responses to varying microbial and immune environments along the intestinal tract and or during challenges remain poorly understood. Here, we regionally profile enteric neurons across gnotobiotic, allergic and parasite-infected mice. We demonstrate that timing and complexity of microbial perturbations and type 2 inflammation result in motor neuron state shifts and alter multiple functionally distinct sensory neurons, including IL-13- and leukotriene-responsive Nmu-hi cells and Grp-hi neurons, which expand in germ-free colonic tissue and interact with Grpr+ interstitial cells of Cajal. Leveraging AAV-based Perturb-seq to define genetic controllers of inhibitory motor neuron state transition, we identified Edf1 and Mitf as controllers of this program and of gastrointestinal transit time, directly linking enteric neuron states to physiology.

overall_design: To understand the cellular context in which enteric neurons reside, large intestine tissues were harvested from a total of 6 mice for each group, germ free or SPF, and isolated cells were analyzed by droplet based single-cell RNA-seq.

first: Peng

last: Tan

first: Alok

last: Jaiswal

first: Shane

middle: P

last: Murphy

first: Eric

last: Brown

first: Hailey

last: Wheeler

first: Chien-Wen

last: Su

first: Emily

last: Finan

first: Guadalupe

last: Jasso

first: Hai Ning

last: Shi

first: Daniel

middle: B

last: Graham

first: Toni

last: Delorey

first: Ramnik

last: Xavier


title: Stability and Progressive Differentiation of Tfr cells are intrinsically and extrinsically controlled by Tfh programs [TCR-seq]

city: BOSTON

first: Jeong-Mi

last: Lee

state: MASSACHUSETTS

address: 221 Longwood Avenue, EBRC 3rd Floor

institute: Brigham and Women's Hospital

summary: Follicular regulatory T (Tfr) cells restrain follicular helper T (Tfh) cell-mediated B cell responses in the germinal center (GC) reaction to optimize humoral immunity while limiting autoimmunity.  The immune system partially regulates GC responses by controlling the stepwise differentiation of Tfh cells.  Whether Tfr cell development requires sequential developmental stages and how the immune system regulates these processes to control humoral immunity is poorly understood.   Here, we used longitudinal sampling of lymphoid organs along with fate mapping and matched single-cell RNASeq/TCRseq to assess developmental dynamics of Tfr cells. We found that Tfr cells undergo dynamic clonal expansion. During this process, Tfr cells also undergo progressive differentiation through progenitor-like, early effector, and late effector stages.  Late effector Tfr cells possess inherent instability, with a propensity to lose expression of the transcription factor FoxP3 to become ExTfr cells. ExTfr have unique features and can be redeemed to become suppressive Tfr cells.  Acquisition of a Tfh-like transcriptional program in Tfr cells was an intrinsic predictor of progeny instability.  Extrinsically, Tfh cells enhanced late effector Tfr cell differentiation by diverting early effector Tfr cells away from a default Blimp1-expressing pathway to a Bcl6-expressing one.  Moreover, Tfh induce Tcf7 in Tfr cells which promotes late effector Tfr differentiation. Together, these data indicate that Tfr cells are a dynamic and plastic cell subset, the progressive differentiation of which is controlled at later effector stages by intrinsic and extrinsic programs that work together to provide a negative feedback loop to control humoral immunity.

first: Peter

middle: T

last: Sage

first: Paulo

middle: L

last: Raeder


title: Stability and Progressive Differentiation of Tfr cells are intrinsically and extrinsically controlled by Tfh programs

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: T follicular regulatory cells from seconday lymphoid tissue


title: The transcription factor NFIL3 is necessary and sufficient to specify the ILC fate in lymphoid progenitors [CUT&RUN]

city: Nantes

first: Christelle

last: Harly

address: 8 quai Moncousu

institute: CNRS

summary: Helper innate lymphoid cells (ILC) play important functions in immunity and tissue homeostasis, but their development remains poorly understood. In this study, we identified NFIL3 as the earliest known requirement during ILC development. Forced expression of NFIL3 in mouse lymphoid progenitors in vitro triggered the staged expression of downstream transcription factors including Tcf7, Gata3, Zbtb16 and Id2 that are implicated in ILC development. Thus, NFIL3 resides at the apex of a hierarchy of transcription factors important for innate lymphocyte development, and is necessary and sufficient to impose the innate lymphoid cell fate.

overall_design: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) in lymphoid precursors transduced to express NFIL3-HA for specific binding, or NFIL3 for control background with the anti-HA antibody

first: Joseph

last: Léger

first: Eva

last: Artano

first: Delphine

last: Coulais

first: Naomie

last: Belletoise

first: Fadhloun

last: Raoudha

first: Devin

last: Kenney

first: Avinash

last: Bhandoola


title: The transcription factor NFIL3 is necessary and sufficient to specify the ILC fate in lymphoid progenitors [RNA-seq - Tox]

overall_design: Bulk RNA-seq comparing ILC precursors generated by forcibly expressing TOX or control GFP in lymphoid precursors


title: The transcription factor NFIL3 is necessary and sufficient to specify the ILC fate in lymphoid progenitors [RNA-seq - Il7rLT]

overall_design: Bulk RNA-seq comparing ex vivo early ILC intermediate progenitors using different sorting strategies


title: The transcription factor NFIL3 is necessary and sufficient to specify the ILC fate in lymphoid progenitors [RNA-seq - ex vivo, Nfil3]

overall_design: Bulk RNA-seq comparing ILC precursors generated by forcibly expressing NFIL3 in lymphoid precursors, and ex vivo isolated ILC precursors


title: Transcriptomic profiling of meningiomas reveals SMARCB1 mutation-driven immunosuppression via IL-17/CSF1 axis

city: Shanghai

first: Guanghui

last: Hu

state: Shanghai

address: NO.1279 Sanmen Road

department: Plastic and Reconstructive Surgery

institute: The Affiliated Shanghai Fourth People's Hospital of Tongji University

summary: Meningiomas with SMARCB1 mutations exhibit distinct immunosuppressive microenvironments. This study performed RNA-seq profiling of 13 human meningioma samples and 1 control sample to identify molecular mechanisms underlying immune evasion. We discovered that SMARCB1 loss upregulates the IL-17/CSF1 axis, leading to increased tumor-associated macrophage infiltration and CD8+ T-cell exhaustion. These findings provide new targets for immunotherapy in refractory meningiomas.

overall_design: RNA sequencing was performed on 14 FFPE-derived samples including 13 meningioma samples spanning WHO grades 1-3 and 1 dura mater control sample. Following RNA extraction from FFPE blocks with quality control (RIN assessment), libraries were prepared using SMARTer stranded total RNA-seq kit and sequenced on Illumina NovaSeq (PE150). Data were analyzed via STAR alignment to GRCh38 and FPKM quantification with featureCounts, focusing on a 14-gene immunogenic signature (including CSF1, IL17RA and CD163) to characterize SMARCB1-associated immune profiles through PCA and GSVA approaches.

first: Ben

last: Jin

first: Hao

first: Yanhua

last: Lu

first: Long

last: Zhang

first: Juxiang

last: Chen

first: Miaoxia

last: He


title: Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [10xPerturbSeq]

first: Jacques

last: Deguine

overall_design: Adeno-associated virus (AAV)-based gene delivery was used for CRISPR screening and retrograde labeling of projecting neurons. The AAV-PHP.S capsid, tailored to infect peripheral neurons, was used for  in vivo Perturb-seq access to the ENS. In addition, the piggyBac transposon element was used for AAV-mediated stable transgene expression . We generated separate pools of guide RNAs (gRNA) for the different classes of genes discussed above and stably introduced them in Cas9-expressing animals by injecting AAV PHP.S vectors encoding gRNAs with a tdTomato-KASH reporter, and the piggyBac transposon system. The latter was used to sort nuclei from infected cells. Four weeks after AAV infection, we isolated nuclei from infected submucosal and myenteric plexuses, and subjected them to single nuclei RNA-seq to generate transcriptome profiles and gRNA sequences for individual cells.

first: Peng

last: Tan

first: Alok

last: Jaiswal

first: Shane

last: Murphy

first: Eric

last: Brown

first: Hailey

last: Wheeler

first: Chien-Wen

last: Su

first: Emily

last: Finan

first: Guadalupe

last: Jasso

first: Hai Ning

last: Shi

first: Daniel

last: Graham

first: Toni

last: Delorey

first: Ramnik

last: Xavier


title: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations

city: La Jolla

first: Alon

last: Goren

address: 9375 Gilman Dr

department: Department of Medicine

institute: University of California San Diego

summary: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to study the genomic localization of DNA-associated proteins. However, conventional protocols include multiple manual steps that can introduce inconsistency and limit scalability, thereby restricting the inclusion of appropriate replicates and controls. Although the introduction of liquid handling platforms has improved reproducibility, most existing efforts have automated only a subset of the workflow, and extending automation to efficiently map non-histone proteins, such as chromatin regulators, remains challenging. Here, we present a fully automated implementation of our previously developed single-pot ChIP-seq protocol, named spa-ChIP-seq, which enables scalable processing of 8 to 96 ChIP-seq samples from crosslinked cells to sequencing-ready library in approximately three days with an estimated cost of $70 per sample. Benchmarking spa-ChIP-seq against manual ChIP-seq performed in parallel demonstrates comparable signal-to-noise ratio between the two workflows. Using spa-ChIP-seq, we systematically evaluate multiple parameters including shearing and crosslinking conditions, buffer compositions, and the ratio of antibody to cell-number. We find, for the first time to our knowledge, that weaker genomic localization signals are sensitive to changing the antibody to cell-number ratio, whereas the stronger signals remain unaffected. This finding underscores the importance of maintaining consistent antibody-to-cell-number ratio for comparative studies, such as treatment responses or chromatin-QTL mapping. The spa-ChIP-seq protocol is publicly available, including deck setups, operational parameters, and scripts. We envision that this robust, cost-efficient protocol will facilitate high-throughput, reproducible ChIP-seq analyses, supporting large-scale studies of antibody validation, compound screening, population genomics, and diagnostic frameworks.

overall_design: ChIP-seq of H3K27ac and H3K27me3 comparing crosslinking conditions (DSG+FA and FA only), lysis buffers for sonications (LB3 and EBB) while evaluating the automated workflow versus the manual workflow. We also evaluated the ratios of antibody to chromatin by performing titration ChIP-seq experiments with H3K9ac, BRD4, HA-tag, and P300 antibodies.

first: Yuwei

last: Cao

first: Lauren

last: Patel

last: Alcoser

last: Mendenhall

first: Christopher

last: Benner

first: Sven

last: Heinz


title: Comparative Single Cell RNA Sequencing of Notch2 and RBPJ-deficient mononuclear phagocyte cells and myeloid progenitors from the spleen and bone marrow

city: Hannover

first: Jaba

last: Gamrekelashvili

address: Carl-Neuberg-Str. 1

department: Nephrology

institute: MHH

summary: Mononuclear phagocytes and their myeloid progenitors are critical in various homeostatic processes as well as immune responses. We employed single-cell RNA sequencing to investigate myeloid progenitors and mononuclear phagocytic cell subsets, including monocytes, splenic red pulp macrophages and dendritic cells in the spleen and in the bone marrow, with a focus on how Notch2 and its nuclear mediator Rbpj regulate these subsets. Our study offers a comparative analysis of mononuclear phagocytes and their progenitors examining cells isolated from the spleens or bone marrow of myeloid Notch2 (N2ΔCx3cr1)-, and Rbpj (RbpjΔCx3cr1)-deficient mice or control animals. Our findings may provide further insights into the heterogeneity of the mononuclear phagocytic cells in the spleen and bone marrow and show the critical role of Notch signaling in their development.

overall_design:
Mononuclear phagocytic cells and their myeloid progenitors from Ctrl, Notch2- and Rbpj deficient mouse spleens or bone marrow (two mice of each genotype) were labeled with different HTOs, pooled as spleen or bone marrow, and isolated using fluorescence-activated cell (FACS)-sorting.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Florian P

last: Limbourg


title: Transcriptomic profile of IL-10-producing B cells (B10) in response to IL-2 signal in vitro

city: Rennes

first: Simon

last: Leonard

address: 2 avenue du Prof Léon Bernard

institute: Université Rennes

summary: IL-2 is one of the first cytokine discovered but its complex roles in T cell effector functions has shadowed its function in B cell responses. B cells transiently expressed IL-2 receptor upon activation but it is unclear whether all mature B cell subsets have an equal dependence upon IL-2 and how IL-2 dictates B cell fate. Using our newly generated B-cell-specific Il2rb conditional knockout (KO) model of mice lacking IL2RB signaling in mature B cells, our objectives were to: (1) transcriptionally characterize IL-10-producing B cells induced by IL-2 ; (2) explore a potential commitment of these IL-10-secreting B cells ; (3) decipher IL-2 mechanisms of action on B cells by identifiying signal transducers and/or transcriptional players mobilised in immunoregulatory polarization program iniated by IL-2 signaling. We found that IL-2 acts intrinsically on B cells to promote Maf and Il10 expression and engage B cells toward immunoregulatory profile. In parallele, we found that IL-2 promotes plasma cell reprogramming on IL-10-producing B cells.

overall_design: To investigate the role of IL-2 on IL-10-producing B cell, we recovered spleen from Ctrl mice, isolated B cells and cultured them 3 days with aBCR + IL-5 + IFNg + IL-2 (n=4). We then sorted CD25pos IL-10pos B cells (B10+) and CD25pos IL-10neg B cells (B10-) using FACS ARIA, extracted RNA and performed Bulk RNA-sequencing on these samples with illumina technology. We performed comparative gene expression profiling analysis of RNA-seq data.

first: Maxime

last: Maugendre

first: Juliette

last: Gauthier

last: Léonard

first: Celine

last: Delaloy


title: Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [Neuron SmartSeq2]

first: Jacques

last: Deguine

overall_design: Enteric neurons were isolated from submucosal and myenteric plexuses of duodenal-jejunal segments, ileum and colon from either germ free (GF), Bacteroides thetaiotaomicron (BT) colonized, altered Schaedler flora (ASF) rederived or specific-pathogen free (SPF) mice. In addition, we also examined the ENS response to a spectrum of type 2 inflammatory responses induced by food allergy or by infection with an enteric parasite.  For food allergy, mice were sensitized with ovalbumin (OVA) in alum administered intraperitoneally, and subsequently challenged by intragastric OVA. To examine responses to a parasite, we studied animals at 14 days post infection with the exclusively enteric parasite Heligmosomoides polygyrus (H. polygyrus), a helminth. We utilized the neuron-specific Uchl1 (also known as PGP9.5) reporter mouse Uchl1-H2B-mCherry/GFPgpi.

first: Peng

last: Tan

first: Alok

last: Jaiswal

first: Shane

last: Murphy

first: Eric

last: Brown

first: Hailey

last: Wheeler

first: Chien-Wen

last: Su

first: Emily

last: Finan

last: Jasso

last: Shi

last: Graham


title: Transcription-Replication Conflict Resolution by Nuclear RNA Interference [sRNA-seq]

first: Teri

last: Cheng

type: Non-coding RNA profiling by high throughput sequencing

overall_design: small RNA sequencing (sRNA-seq) of WT, dcr1Δ, rnh1Δ  rnh201Δ, and the triple mutant  rnh1Δ  rnh201Δ  dcr1Δ

first: Robert

last: Martienssen


title: Transcription-Replication Conflict Resolution by Nuclear RNA Interference [H2AX ChIP-seq]

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) of WT, dcr1Δ, rnh1Δ  rnh201Δ, and the triple mutant  rnh1Δ  rnh201Δ  dcr1Δ


title: Single-cell RNA sequencing reveals distinct senotypes and a quiescence-senescence continuum at the transcriptome level following chemotherapy

city: Boulder

first: Brianna

last: Fernandez

state: CO

address: 3415 Colorado Avenue

department: Biochemistry

institute: University of Colorado Boulder

summary: Quiescence (reversible cell-cycle arrest) and senescence (irreversible arrest) are challenging to distinguish due to a lack of specific biomarkers, yet both arise simultaneously after chemotherapy. While senescence suppresses tumors by limiting proliferation and recruiting the immune system, quiescent cancer cells evade future therapies and may resume proliferation. Here, we pair time-lapse imaging of cell-cycle dynamics with single-cell RNA-sequencing after etoposide treatment to differentiate these states, linking heterogeneous cell-cycle phenotypes to the transcriptomic landscape. We identify diverse senescent types (senotypes) and link them to two arrest pathways – a gradual path arising after a standard mitosis-to-G0 transition, and a rarer but direct path driven by a mitotic slip. Using pseudotime trajectory analysis, we find that senescent phenotypes begin to manifest early and gradually along the first trajectory, even in shallow quiescent cells. These data support a model wherein, following chemotherapy, quiescence and senescence exist on a continuum of cell-cycle withdrawal at a transcriptome-wide level.

overall_design: MCF10A cells were treated with 2.5, 10, or 25μM etoposide for 24 h. Cells were then washed twice with PBS before being returned to full-growth media. Full-growth media was refreshed every 3d during the drug recovery period. Cells were sequenced on day 6 following etoposide washout.

first: Victor

last: Passanisi

first: Humza

last: Ashraf

first: Sabrina

last: Spencer


title: In Vivo Imaging Reveals Exosome-Mediated Intercellular Communication in Lens Development

city: Guangzhou

first: jingyu

last: Ma

state: Guangdong

address: No. 7 Jinsui Rd

institute: SUN YAT-SEN UNIVERSITY

summary: The transparency of lens relies on proper intercellular communication. Exosomes are crucial mediators of intercellular communication and play a key role in organ homeostasis and development. However, their presence and dynamics in the lens remain unclear. This study aimed to investigate the existence of endogenous exosomes in the lens and explore their potential functions. Using the cryaa promoter to drive Cd63-AcGFP expression, we achieved lens-specific exosome labeling in zebrafish.  Live imaging revealed the presence of exosomes in lens cells during development and their movement trajectory under physiological conditions. Additionally, lens-derived exosomes (lens-Exos) facilitate communication not only between lens cells but also with surrounding tissues. We also identified that the biogenesis of Cd63+ exosomes in the lens is regulated by the Syntenin-a pathway. As knockdown of Syntenin-a in zebrafish resulted in delayed lens development, indicating a potential role for exosomes in normal lens development. Furthermore, in vitro hESC-lentoid induction showed that extracellular vesicles from ROR1+ lens progenitor cells (ROR1+ LPCs-EVs) promote lentoid differentiation. Proteomic analysis provided insights into the functions of ROR1+ LPCs-EVs. Overall, our study is the first to observe endogenous exosomes in the lens, providing new insights into lens pathophysiology and a potential strategy for modulating the lens microenvironment.

overall_design: ROR1+ cells were magnetically isolated at D30 from hESC-derived lentoid bodies induction system, and RNA-seq was performed on three biological replicates (Passage 0) for transcriptome profiling.

first: Jingyu

first: Qihang

last: Sun

first: Yijia

last: Chen

first: Jinyan

last: Li

first: Shuai

last: Ouyang

first: Shurui

last: Ke

first: Jiani

first: Huilin

last: Liang

first: Shuyi

first: Lixia

last: Luo


title: Complex DNA Structural Variant on Chromosome 2 in a Pediatric Patient with  Development Delay and Congenital Malformation

first: Jesse

last: Bengtsson

address: 720 Broadway

institute: Pacific Northwest Research Institute

summary: The 2q31 region is commonly associated with pathogenic alleles of the HOXD cluster leading to various clinical phenotypes related to skeletal development. We present a patient with short stature, tetralogy of Fallot, and multiple congenital anomalies. Initial array comparative genomic hybridization (aCGH) revealed a de novo complex genomic rearrangement (CGR) spanning 2q31 in proband characterized as a triplication (TRP)-duplication (DUP)-triplication (TRP). Subsequent analysis applying combined next-generation sequencing methodologies including whole-genome sequencing (WGS) short-reads, PacBio WGS long-reads, and optical genome mapping (OGM) indicated two additional duplications on each end of the rearrangement, consisting of DUP-TRP-DUP-TRP-DUP. This involves three breakpoint junctions, of which each were resolved down to a nucleotide level. This genomic catastrophic event includes many disease-causing genes, and analysis of each gene and its known disorders was required in order to connect genotype to phenotype in a unique CNV.

overall_design: This work was designed to determine the structure of copy number variants on chr2

first: Ming Yin

last: Lun

first: Claudia M.B.

last: Carvalho


title: Transcription-Replication Conflict Resolution by Nuclear RNA Interference

first: Teri

last: Cheng

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

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

overall_design: Refer to individual Series


title: Transcription-Replication Conflict Resolution by Nuclear RNA Interference [Ago1 ChIP-seq]

summary: RNA interference (RNAi) plays an important role in the nucleus critical to genome maintenance and heterochromatin silencing. In the fission yeast Schizosaccharomyces pombe, Dicer (Dcr1) also plays a critical role in releasing RNA polymerase II (Pol II) to limit transcription-replication (T-R) stress, but a mechanistic insight is still lacking. Here, we show that Dcr1 resolves T-R conflicts by processing promoter-proximal co-transcriptional R-loops, facilitating replication progression and limiting DNA damage. We found in RNase H-deficient cells, which accumulated pathological R-loops, that further mutating Dcr1 caused hypersensitivity to genotoxic stress. Genetic evidence implicates Dcr1 in regulating nascent transcription, with the helicase domain providing an additional catalytic function in genome stability reminiscent of archaeal helicase homologs involved in replication. In the absence of Dcr1, DNA breaks accumulate around transcription start sites (TSSs), termination sites (TTSs) and pause sites, consistent with replication collision, and DNA replication processivity and speed are impaired in a manner dependent on transcriptional activity and directionality. Argonaute (Ago1) is implicated in dcr1Δ-induced genome instability, as its deletion suppressed the genotoxic stress phenotype of dcr1Δ. Our results demonstrate a novel nuclear function of Dcr1, likely ancestral to the RNAi pathway.

first: Robert

last: Martienssen


title: mTORC1 controls ILC2 activation and allergic lung inflammation through NMUR1-mediated neuronal regulation

first: Dongdi

last: Wang

address: 227 South Chongqing Road, Shanghai, China

institute: Shanghai Jiaotong University School of Medicine

summary: Group 2 innate lymphoid cells (ILC2s) play critical roles in allergic lung inflammation through initiating and amplifying type 2 immune responses. However, the molecular mechanisms underlying pathogenic ILC2 activation remain largely unknown. Here, we show that lung ILC2s exhibit increased mTORC1 activation in allergic asthma. Genetic ablation of RAPTOR, an adaptor protein of the mTORC1 complex, results in reduced IL-5 and IL-13 production in ILC2s and protects mice from allergic inflammation. Pharmacological inhibition of mTORC1 by rapamycin also suppresses ILC2 pathogenic activation and ameliorates allergic lung inflammation. Mechanistically, mTORC1 signaling promotes ILC2 activation through metabolic regulation of epigenetics to maintain neurointerin U receptor 1 (NMUR1) expression, which mediates neural-ILC2 interaction via the NMU-NMUR1 axis. These findings identify mTORC1 as a novel regulator to control the neural-ILC2 interaction and highlight mTORC1 as a potential therapeutic target for allergic asthma.

overall_design: lung ILC2s mRNA profiles of PBS treated mice and Papain treated mice

first: Lei

last: Shen


title: Vascular regeneration with adenovirally reprogrammed endothelial cells and their long-term neovascularization effects

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

summary: Reprogrammed endothelial cells (rECs) have been generated directly from human fibroblasts for cell therapy by overexpression of a transcription factor, ETV2, through lentiviral vector. However, due to the nature of lentiviral vector, rECs induced with this vector system are less desirable. By using adenoviral vector, we sought to generate rECs with vascularizing and therapeutic potential in clinically more compatible manner. Furthermore, we aimed to enhance cell engraftment and neovascularization potential by encapsulating rECs with a peptide amphiphile (PA) nanomatrix gel. We employed adenoviral vector harboring ETV2 to reprogram human fibroblasts into ECs and examined characteristics and therapeutic effects of rECs induced with adenoviral ETV2 (Ad-ETV2). We found that Ad-ETV2 transduction into fibroblasts induced the expression of EC genes and repressed the expression of fibroblast-related genes. KDR expressing cells at D6 (Ad-rECs) displayed the EC functional phenotypes in vitro assays and expressed proangiogenic factors at high level. Transcriptomic analysis of Ad-rECs by RNA-seq confirmed the conversion into ECs by demonstrating that fibroblast-related genes were down-regulated whereas vascular development and angiogenesis-related genes were up-regulated in Ad-rECs. ETV2 transduction suppressed fibroblast characteristics and induced endothelial characteristics in fibroblasts during the reprogramming process. Transplantation of these Ad-rECs into ischemic hindlimb enhanced the recovery of blood flow and augmented capillary density. These Ad-rECs clearly contributed to new vessel formation through direct vascular incorporation and possibly vessel guidance over 12 months. Also, encapsulation of rECs into PA-RGDS enhanced Ad-rEC engraftment in the ischemic tissue and vessel incorporation. Here we demonstrate that, using clinically suitable adenoviral vector system transducing ETV2, human somatic cells can be directly reprogrammed to functional and therapeutically potent ECs. Ad-rECs were able to efficiently recover impaired blood flow and induce repair of ischemic tissue. Moreover, PA-RGDS nanomatrix gel improved engraftment and, consequently induced long-term, neovascularization effects or Ad-rECs. This PA-RGDS encapsulated Ad-rECs can serve as an efficient therapeutic platform for vascular regeneration.

overall_design: RNA-seq were generated by deep sequencing

first: Sang-Ho

last: Lee

first: Seongho

last: Bae

first: Young-sup

last: Yoon


title: The transcription factor NFIL3 is necessary and sufficient to specify the ILC fate in lymphoid progenitors [DNase-seq]

first: Christelle

last: Harly

overall_design: DNase-seq analysis of ILC precursors at different developmental stages

first: Joseph

last: Léger

first: Eva

last: Artano

first: Delphine

last: Coulais

first: Naomie

last: Belletoise

first: Fadhloun

last: Raoudha

first: Devin

last: Kenney

first: Avinash

last: Bhandoola


title: Trastuzumab Priming on aggregate formation, Intracellular signaling, and the Tumor Microenvironment

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: To investigate the imapct of trastuzumab priming on monolayer to spheroid formation

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AU565 cells in 2D and 3D models with and without Trastuzumab treatment

first: Cassandra

last: Roberge

last: Ramos

first: Margarida

last: Barroso

first: Christopher

last: James


title: CD94 deficiency or blockade unleashes the anti-tumor immunity in mice and humanized murine models

city: Hefei

first: Jiarui

last: Li

state: Anhui

address: Huangshan road #443

institute: University Of Science And Technology Of China

summary: NKG2 family members have emerged as promising targets in tumor immunotherapy. CD94 can dimerize with both inhibitory and activating NKG2 proteins, while the overall effect and value of targeting CD94 on anti-tumor immunity are unclear. We used single cell RNA-seq reveal a remodeled tumor microenvironment in CD94-KO mice, with a reduction in immunosuppressive cells and an increase in anti-tumor immune cells.

overall_design: CD45+  tumor‑infiltrating lymphocytes were sorted from subcutaneous tumor tissues of WT and CD94-KO mice and analyzed using scRNA-seq (per scRNA-seq data derived from 5 tumor-bearing mice).

first: Xianwei

last: Wang

first: Guoshuai

last: Cao

first: Yuwei

last: Wu

first: Ming

last: Cheng

first: Yawen

last: Chen

first: Haoyu

last: Sun

first: Rui

first: Hui

last: Peng

first: Zhigang

last: Tian


title: Transcriptional dysregulation in the spinal cord of SCA3 provides insights into disease mechanisms [KO_RNAseq]

status: Public on Oct 29 2025

city: Ann Arbor

first: Hayley

middle: S

last: McLoughlin

state: MI

address: 109 Zina Pitcher Pl

department: Neurology, Human Genetics

institute: University of Michigan

summary: Spinocerebellar ataxia type 3 (SCA3) is a neurodegenerative disease caused by polyglutamine repeat expansion in the ATXN3 gene. Despite the ubiquitous expression of ATXN3 throughout the body, SCA3 pathology is pronounced in select, vulnerable regions within the central nervous system (CNS). Notably, imaging studies of SCA3 patients have revealed spinal cord atrophy prior to ataxia symptom onset and progressing with disease severity. However, the molecular mechanisms underlying SCA3 pathology in the spinal cord remain largely unexplored. Here, we present, for the first time, a comprehensive analysis of the spinal cord transcriptome using SCA3 tissue from humans and mouse models. Our data demonstrates both early and progressive transcriptional dysregulation in the spinal cord, impacting key biological processes such as lipid metabolism, inflammation, cellular structure, and nucleic acid processing. Transcriptomic profiling of Atxn3 knockout mice revealed only weak transcriptional changes in the spinal cord, with minimal overlap compared to the robust alterations observed in SCA3 knock-in mice, indicating that the molecular signature of the disease in the spinal cord is likely not driven by ATXN3 loss of function. In addition, we identified aberrant RNA splicing, particularly affecting genes involved in cytoskeletal organization. Collectively, our findings indicate that SCA3-associated transcriptional dysregulation in the spinal cord contributes to canonical pathological mechanisms of SCA3 both early and progressively. These results underscore the central role of the spinal cord in SCA3 pathogenesis and advocate for its inclusion as a key therapeutic target.

overall_design: RNAseq of RNA collected from the spinal cord of Atxn3 KO and WT mice at 24 weeks of age.

first: Jacen

last: Emerson

first: Brianna

last: Nelthrope

first: Emma

last: Walker

first: Grace

last: Mao

first: Hannah

last: Shorrock


title: Transcriptional dysregulation in the spinal cord of SCA3 provides insights into disease mechanisms [Human_RNAseq]

overall_design: RNAseq of RNA collected from the spinal cord of Human SCA3 and age-matched control samples.


title: Transcription-Replication Conflict Resolution by Nuclear RNA Interference [Ago1-RIP-seq]

city: Cold Spring Harbor

first: Teri

overall_design: Ago1 RNA-immunoprecipitation sequencing (Ago1-RIP-seq) of WT, dcr1Δ, rnh1Δ  rnh201Δ, and the triple mutant  rnh1Δ  rnh201Δ  dcr1Δ.

first: Robert

last: Martienssen


title: The transcription factor NFIL3 is necessary and sufficient to specify the ILC fate in lymphoid progenitors [scRNA-seq]

first: Christelle

last: Harly

overall_design: scRNA-seq of ILC precursors at different developmental stages

first: Joseph

last: Léger

first: Eva

last: Artano

first: Delphine

last: Coulais

first: Naomie

last: Belletoise

first: Fadhloun

last: Raoudha

first: Devin

last: Kenney

first: Avinash

last: Bhandoola


title: The transcription factor NFIL3 is necessary and sufficient to specify the ILC fate in lymphoid progenitors


title: Transcription-Replication Conflict Resolution by Nuclear RNA Interference [RNA-seq]

last: Cheng

overall_design: RNA sequencing (RNA-seq) of WT, dcr1Δ, rnh1Δ  rnh201Δ, and the triple mutant  rnh1Δ  rnh201Δ  dcr1Δ.


title: Leukocyte-intrinsic ER stress responses contribute to chemotherapy-induced peripheral neuropathy.

city: Winston Salem

first: Ming

last: Leung

state: NC

address: 1 Medical Center Blvd

department: Comprehensive Cancer Center

institute: Atrium Health Wake Forest

summary: Chemotherapy-induced peripheral neuropathy (CIPN) is the most prevalent and limiting side effect of paclitaxel treatment in cancer patients. CIPN affects sensory neurons through neuroinflammatory mechanisms, but how immune cells sense and interpret systemic paclitaxel exposure during treatment is unclear. Here, we report that paclitaxel administration triggers the endoplasmic reticulum (ER) stress sensor inositol-requiring enzyme 1α (IRE1α) in circulating and dorsal root ganglia-resident myeloid cells, engendering an inflammatory milieu that promotes CIPN. Mechanistically, paclitaxel induced overproduction of mitochondrial-derived reactive oxygen species (ROS) that provoked ER stress and IRE1α hyperactivation in macrophages. This process reprogrammed macrophages towards a highly inflammatory state characterized by IRE1α-dependent production of TNF-α, IL-1β, PGE2, IL-6, IL-5, GM-CSF, MCP-1, and MIP-2. Ablation of IRE1α in leukocytes, or treatment with a selective IRE1α pharmacological inhibitor, prevented dorsal root ganglia neuroinflammation and CIPN-related pain behaviors in mice. Furthermore, the development and severity of CIPN in patients with gynecological cancer was associated with the status of IRE1α activation in their circulating leukocytes. Our study uncovers leukocyte-intrinsic IRE1α as a key mediator of CIPN and suggests that targeting its dysregulated activation could help mitigate CIPN in cancer patients receiving paclitaxel.

overall_design: To investigate whether paclitaxel might impact the global transcriptomic profile of myeloid cells via IRE1a activation, we performed gene profiling analysis using data obtained from RNA-seq of wild-type (WT) versus IRE1a-deficient (cKO) bone marrow differentiated macrophages exposed to paclitaxel (10 µM, n=4) or vehicle control (Dimethyl sulfoxide; DMSO, n=4) treated for 18 hours.

first: Miriam

last: Fonseca

first: Oriana

last: Gelblung

first: Sarah

last: Pennypacker

first: Taylor

last: Brooks

first: Michael

last: Limia

first: James

middle: W

last: Morgan

first: Xuewei

last: Zhu

first: Luis

last: Tovias-Sanchez

first: Alejandro

last: Pluma-Pluma

first: Ruth

last: Elena Martinez

first: Mathew

last: Eber

first: Sun

last: Park

first: Cristina

last: Furdui

first: Deepika

last: Awasthi

first: Alexander

last: Emmanuelli

first: Byuri

last: Cho

first: Chen

last: Tan

first: David

middle: I

last: Shalowitz

first: Samuel

last: Lentz

last: Kelly

first: Anderson

middle: O

last: Cox

first: Lindsay

last: Macnamara

first: Fang-Chi

last: Hsu

first: Yusuke

last: Shiozawa

first: Wesley

first: Takao

last: Iwawaki

first: Lance

last: Miller

first: Glenn

last: Lesser

first: Roy

last: Strowd

first: Juan

middle: R

last: Cubillos-Ruiz

first: Edgar

last: Romero-Sandoval


title: Dynamic neutrophil-keratinocyte communication network centered on IL-36/TNFSF15 responses characterizes inflammatory responses in generalized pustular psoriasis.

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: Generalized pustular psoriasis (GPP) is a severe subtype of psoriasis characterized by epidermal neutrophil infiltration, often presenting as acute, potentially life-threatening flares. However, the characterization of the immune micro-environment in GPP lesions remains largely unknown. Here, we used single-cell RNA profiling to interrogate the transcriptomes of 60,000 single cells from GPP lesional skin (n=13) and healthy adult skin (n=4), combined with spatial transcriptomics. We identified a unique neutrophil subset lacking CASP8 expression but exhibiting elevated levels of inflammatory pathway genes, including RIPK1, NFKB1, IL1B, CXCL1, and CXCL8 in GPP flares, illustrating neutrophil transition from pre-inflammatory to a pro-inflammatory state, and activation of a communication network between IL36G+ keratinocytes and neutrophils in GPP lesions, with TNFSF15 (TL1A) released from neutrophils exaggerating the inflammatory crosstalk. We further demonstrated that fibroblasts and capillary endothelial cells function as central communication hubs in GPP, through dynamic receptor-ligand interactions with several spatially proximate immune cells, including T cells, neutrophils, and macrophages. In this work, we provide an in-depth view of immune cell participation and highlight the role of neutrophil-keratinocyte crosstalk in GPP pathogenesis.

overall_design: To investigate changes in cell type composition and transcriptional profiles in lesional skin from GPP patients, compared with skin from healthy controls.

first: Johann

middle: E

last: Gudjonsson

first: Lam

last: Tsoi


title: Mitochondrial and lysosomal signaling orchestrates heterogeneous metabolic states of regulatory T cells

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital


title: Mitochondrial RNA cytosolic leakage drives the SASP [CRISPR/Cas9]

city: Rochester

first: Dominik

last: Saul

state: Minnesota

address: 200 First Street SW Rochester

institute: Mayo Clinic

summary: Senescent cells secrete proinflammatory factors known as the senescence-associated secretory phenotype (SASP), contributing to tissue dysfunction and aging. Mitochondrial dysfunction is a key feature of senescence, influencing SASP via mitochondrial DNA (mtDNA) release and cGAS/STING pathway activation. Here, we demonstrate that mitochondrial RNA (mtRNA) also accumulates in the cytosol of senescent cells, activating RNA sensors RIG-I and MDA5, leading to MAVS aggregation and SASP induction. Inhibition of these RNA sensors significantly reduces SASP factors. Furthermore, BAX and BAK play a key role in mtRNA leakage during senescence, and their deletion diminishes SASP expression in vitro and in a mouse model of Metabolic Dysfunction Associated Steatohepatitis (MASH). These findings highlight mtRNA's role in SASP regulation and its potential as a therapeutic target for mitigating age-related inflammation.

overall_design: RNA-seq profiling of proliferating and senescent fibroblasts lacking proteins associated with cytosolic RNA signaling, including DDX58 (RIG-I), IFIH1 (MDA5) and MAVS. Moreover, RNA-seq was also performed in fibroblasts lacking mitochondria, which were subsequently transfected with isolated mitochondrial RNA (mtRNA). Finally, RNA-seq analysis was performed in livers from liver-specific Bax Bak KO animals with diet-induced metabolic dysfunction-associated steatohepatitis (MASH).

first: Victorelli

last: Stella

first: Han

last: Yeaeun

first: Saul

last: Dominik

first: Passos

last: Joao


title: Single-cell spatial transcriptomic profiling defines a pathogenic inflammatory niche in chronic active multiple sclerosis lesions - Microglia cell culture

city: Munich

first: Ruoqing

last: Feng

address: Feodor-Lynen-Strasse 17

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Compartmentalized inflammation is considered a critical factor in driving the progression of multiple sclerosis (MS). Yet, the mechanisms sustaining its persistence remain poorly understood. A hallmark of this persistent and slowly evolving inflammatory process are chronic active MS lesions. In this study, we created a high-resolution, single-cell molecular and spatial atlas of chronic inflammation in MS. To accomplish this, we combined single-nucleus RNA sequencing (snRNA-seq) with single-cell spatial transcriptomics using multiplexed error-robust fluorescence in situ hybridization (MERFISH) to examine MS lesions, specifically focusing on those exhibiting chronic active immune pathology characterized by lymphocyte presence. Our integrative profiling uncovered the molecular landscape of glial and immune cells, their disease-associated states, and the surrounding microenvironments. Within the lesion rim, we identified CD8+ T cell niches with inflamed, foamy microglia, characterized by an interferon response and dysfunctional lipid metabolism. To investigate the function of these microglia, we deleted ATP-binding cassette transporters A1 and G1 (ABCA1/G1) in microglia of mice and induced experimental autoimmune encephalomyelitis (EAE). Our findings revealed that inhibiting cholesterol efflux increased the formation of lipid-storing phagocytes, which actively drove inflammatory processes in EAE. Moreover, we found that pharmacologically targeting sterol metabolism presents a promising therapeutic strategy for mitigating inflammation in EAE. Thus, we have created a high-resolution map of immune niches in chronic active MS lesions, leading to the discovery of lipid-associated microglia as key drivers of neuroinflammation.

overall_design: Primary mouse microglia were purified from early postnatal brains, seeded on coated slides in defined medium, and exposed to a myelin plus IFN-γ activation regimen. After fixation and permeabilization, a 500-gene MERFISH panel was applied to spatially resolve lipid-metabolism and inflammatory transcripts at single-cell resolution, enabling unbiased identification of distinct microglial states across the culture.

first: Janos

last: Groh


title: Transcription-Replication Conflict Resolution by Nuclear RNA Interference [PRO-seq]

first: Teri

last: Cheng

overall_design: Precision run-on sequencing (PRO-seq) of WT, dcr1Δ, rnh1Δ  rnh201Δ, and the triple mutant  rnh1Δ  rnh201Δ  dcr1Δ, as well as with various suppressors such as med20-1 (med20-Y44S), and rpb1-T481K, and single catalytic mutant of Dcr1-K38R/A.

first: Robert

middle: A

last: Martienssen


title: Protein Kinase Cι dictates tumor trajectory, cell state plasticity and immune surveillance in lung adenocarcinoma

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

summary: By genetically ablating oncogenic PKCι in a Kras/Trp53-driven lung adenocarcinoma mouse model, we identify two distinct tumor trajectories that resemble lung development and lung regeneration, respectively. Mechanistically, loss of PKCι expression leads to the accumulation of senescent tumor cells with transcriptional similarities to the pre-AT1 transitional cell state (PATS) observed during alveolar regeneration after injury. In addition to inhibiting cellular plasticity through stable proliferation arrest, senescent PATS-like tumor cells induce formation of large, organized aggregates of immune cells called tertiary lymphoid structures (TLS) within KPI tumors.

overall_design: Individual tumors were microdissected from ~30-week KP (KrasG12D/Trp53fl/fl) and ~40-week KPI (KrasG12D/Trp53fl/fl/Prkcifl/fl) animals (n = 5 tumors/animal; 2 animals/genotype). After removal of endothelial cells, red blood cells, and dead cells, scRNA-seq was performed on tumor samples containing both cancer and immune cells.

first: Duy

last: Nguyen

first: Luis

last: Prieto

first: Hu

last: Li

first: Darren

middle: J

last: Baker

first: Alan

last: Fields


title: mTORC1 controls ILC2 activation and allergic lung inflammation through NMUR1-mediated neuronal regulation [WT-KO ILC2s RNA-seq]

first: Dongdi

last: Wang

overall_design: lung ILC2s mRNA profiles of  R5/+ (WT) and R5/+Rptorf/f (KO) mice after papain treament

first: Lei

last: Shen


title: Transcription-Replication Conflict Resolution by Nuclear RNA Interference [GLOE-seq]

overall_design: GLOE-seq of WT, dcr1Δ, rnh1Δ  rnh201Δ, and the triple mutant  rnh1Δ  rnh201Δ  dcr1Δ.


title: v-ATPase-mediated buffering of mitochondrial dysfunction

city: Helsinki

first: Christopher

middle: B.

last: Jackson

state: - Select -

address: Hartmanninkatu 8

department: Department of Biochemistry and Developmental Biology

country: Finland

institute: University of Helsinki, Faculty of Medicine

summary: Mitochondrial dysfunction is implicated in a broad spectrum of human disease including primary mitochondrial disorders, neurodegeneration, cancer, and ageing. Cells have evolved several mechanisms in response to mitochondrial dysfunction to maintain cellular homeostasis and face fundamental challenges orchestrating the expression of the nuclear and mitochondrial genome. Here we used genome-wide CRISPR/Cas9 knockout screening in HEK293 to identify activated cell fitness pathways in response to distorted mitochondrial protein synthesis promoting cell survival upon mitochondrial dysfunction.

overall_design: HEK293 cells were treated with low doses of actinonin, chlormaphenicol and the combination over 15-days using the Brunello GeCKO library. The samples encompass day 15 sequencing results of EtOH-treated control and the respective treatments in independent replicates.

first: Geoffray

last: Monteuuis