title: HIV-1 Nef programs long-lasting innate immune memory in hematopoietic stem and progenitor cells in a mouse model

city: Melbourne

first: Andrew

last: Fleetwood

address: 75 Commercial Road

institute: Baker Heart and Diabetes Institute

summary: The HIV infection is accompanied by chronic inflammation and inflammation-related co-morbidities, even when viral replication is effectively supressed by therapy. It is often assumed that a complete cure would resolve this inflammation; however its origin and mechanisms may be more complex and not entirely dependent on the continuous presence of the virus. To investigate whether inflammatory programming can be imprinted in hematopoietic cells, we treated mice with extracellular vesicles containing the HIV protein Nef (exNef), a major viral pathogenic and inflammatory factor. Using a multi-omics approach, we found that haematopoietic cells exposed to exNef displayed epigenetic modifications and reprogramming of energy and lipid metabolism pathways characteristic of trained innate immunity (TRIM).

overall_design: Wild-type (C57BL/6) mice were administered either exNef or control exGFP exosomes over 2 weeks. Total bone marrow cells were collected from mice and stained with a mixture of antibodies to isolate LSKs, cKit+ and monocytes by FACS-sorting. Multiome-seq: Single nuclei were extracted from LSK, cKit+ and monocytes and joint snRNA- and scATAC libraries were prepared using 10x Genomics platform.

first: Nigora

last: Mukhamedova

first: Dragana

last: Dragoljevic

first: Man K

last: Lee

first: Yangsong

last: Xu

first: Malathi S

last: Dona

first: Ian

last: Hsu

first: Camila

last: Bertuzzo Veiga

first: Fumihiko

last: Takeuchi

first: Alex

last: Pinto

first: Michael

last: Bukrinsky

last: Murphy

first: Dmitri

last: Sviridov


title: IL-9 and Blimp-1 protects the transcriptional identity of group 2 innate lymphocytes in allergic asthma

status: Public on Apr 16 2026

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

country: USA

institute: University of Pittsburgh

type: Expression profiling by high throughput sequencing

summary: Allergic asthma is driven by type 2 immune responses, including those mediated by type 2 innate lymphoid cells (ILC2s). Although ILC2s are activated by the tissue alarmins IL-33 and IL-25, these signals do not intrinsically enforce type 2 identity, and the mechanisms that maintain type 2 cytokine expression remain unclear. Here we show that allergen-induced IL-33 and IL-25 rapidly induce IL-9, which in turn upregulates the transcriptional repressor Blimp-1 in ILC2s. Blimp-1 sustains type 2 immunity by directly repressing type 1 inflammatory programs, including expression of IFNg and TNF. Deletion of Blimp-1 in ILC2s increased type 1 cytokine production and reduced IL-5 and IL-13 expression, eosinophil recruitment, and mucus production in the lung. In contrast, IL-9 expression was enhanced in the absence of Blimp-1, leading to increased mast cell recruitment. Together, these findings identify Blimp-1 as a key regulator of ILC2 transcriptional fidelity that stabilizes type 2 inflammation while constraining divergent inflammatory programs during allergic responses.

overall_design: Control or Blimp-1 knockout mice were treated with either PBS, papain or Alternaria intranasally daily for 3 days. ILC2s were flow sorted from lungs

first: Yijia

last: Chen

first: Yibo

last: Zheng

first: Shilpi

last: Giri

first: Abbe

last: Pannucci


title: Steroid hormone antagonism affords vascular protection in a mouse model of Vascular Ehlers-Danlos Syndrome

city: Baltimore

first: Leda

last: Restrepo

state: MD

address: 733 N Broadway, Miller Research Building

department: Human Genetics

institute: Johns Hopkins

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Aortic dissection or rupture is a leading cause of mortality in vascular Ehlers-Danlos syndrome (VEDS), a disorder caused by mutations in the COL3A1 gene. Col3a1G938D/+ mice recapitulate features of VEDS, including high risk of aortic rupture. As in people with VEDS, aortic risk in this model accelerates at the onset of puberty, especially in males. We identify developmentally regulated gene programs associated with this vulnerability and that are targeted by treatments that mitigate aortic risk. Both genetic and pharmacological inhibition of the androgen receptor (AR) eliminated survival differences between sexes, while treatment with a dual AR and mineralocorticoid receptor (MR) antagonist provided near-complete and durable protection in both sexes. Pathways targeted by dual AR/MR inhibition, including those related to extracellular matrix (ECM) organization and cell-ECM interactions, largely overlapped with those also modulated by isolated MR antagonism. Selective targeting of MR signaling emerged as an effective therapeutic strategy in both sexes that avoids sexual side effects in males.

overall_design: ATAC-seq was performed on mouse aortic tissue at 60 days of age to compare chromatin accessibility between Col3a1+/+ (WT) and Col3a1G938D/+ (VEDS model) mice. Each library represents pooled aortic tissue from two age- and sex-matched animals per genotype. Libraries were prepared using the 10x Genomics Chromium Single Cell ATAC workflow, sequenced paired-end and analyzed in aggregate per library.

first: Emily

middle: E

last: Juzwiak

first: Caitlin

middle: J

last: Bowen

first: Rhiannon

last: Edwards

first: Serena

first: Cassie

last: Parks

first: Anthony

last: Zeng

first: Maya

middle: M

last: Black

first: Oscar

last: Reyes Gaido

last: Bramel

first: Dustin

middle: T

last: Shigaki

middle: A

last: Beer

first: Chiara

last: Bellini

first: Harry

middle: C

last: Dietz

first: Elena

last: Gallo MacFarlane


title: small RNA-seq of Extraceullular Vesicles derived from human immortalized podocytes treated with glucose and RabGTPase silenced

city: Valencia

first: Ana

last: Ortega

state: VALENCIA

address: Av. Menendez Pelayo 4

country: Spain

institute: Incliva Health Research Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Diabetic nephropathy (DN) is a major cause of end-stage renal disease and is characterized by early podocyte injury, leading to progressive glomerular dysfunction. Increasing evidence highlights extracellular vesicles (EVs) as crucial mediators of intercellular communication in the diabetic kidney, transferring bioactive molecules such as non-coding RNAs (ncRNAs) that modulate cellular responses and contribute to disease progression. The molecular mechanisms governing the selective packaging of ncRNAs into podocyte-derived EVs under hyperglycaemic stress, as well as the role of vesicle trafficking regulators such as RAB GTPases, remain poorly understood. In this study, conditionally immortalized human podocytes were exposed to high glucose conditions to model the diabetic environment. To investigate the contribution of vesicular trafficking to EV release, the small GTPases RAB27A and RAB3A were silenced using siRNA. EVs were isolated and their small RNA content was profiled by next-generation sequencing followed by RT-qPCR validation. The results demonstrated that both hyperglycaemia and RAB GTPase knockdown significantly modified the ncRNA composition of podocyte-derived EVs, indicating that glucose stress and vesicular trafficking pathways jointly shape the extracellular RNA landscape. These findings provide new insights into how RAB GTPase–dependent mechanisms regulate EV-mediated communication in podocytes during diabetic injury, potentially influencing key signaling pathways involved in disease progression.

overall_design: small RNA-seq of Extraceullular Vesicles from human immortalized podocyte cell line subjected to silencing and/or glucose treatment. Groups: silenced Rab (siRab), scramble (scr), NG (normal glucose) and HG (high glucose)

first: Olga

last: Martinez-Arroyo

last: Flores-Chova

first: Lesley

last: Escriva

first: Marta

last: Mendez-Debaets

first: Maria

last: Forner

first: Josep

last: Redon

first: Raquel

last: Cortes


title: Differential transcriptomic response of Atlantic salmon to fermented sunflower meal under commercial seawater farming conditions

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

summary: The study focused on the differential transcriptome of immune organs (i.e., head kidney and spleen) from farmed Atlantic salmon (Salmo salar) fed fermented sunflower meal (FSFM) at 5% and 10% in two commercial farms (CS: coast and FD: fjord location). Data showed that both head kidney and spleen (from  fish fed FSFM5% at CS) up-regulated mRNA biogenesis (linked to lipid metabolism and mRNA surveillance) as well as glycosyltransferases (associated with vitamin B6 and lipoic acid metabolism, or pantothenate and CoA biosynthesis). Regarding FD, head kidney from FSFM10% group had up-regulated enzymes (related to lysosome, glutathione metabolism, ribosomes and fatty acid elongation) and the downregulation of transcription machinery and DNA repair/recombination proteins (involved in nucleocytoplasmic transport or spliceosome)

overall_design: RNA-seq profiling of head kidney and spleen from Atlantic salmon (Salmo salar) fed one of three diets (Diet 1: 5% sunflower meal, Diet 2: 5% fermented sunflower meal, Diet 3: 10% fermented sunflower meal) at two farming sites (CS: Coast, FD: fjord).

first: Margareth

last: Øverland


title: Spatial and genetic constraints govern transcription-translation coupling and mRNA degradation in bacteria

city: Urbana

first: Yan

last: Zhang

state: IL

address: 600 S Mathews Ave Roger Adams Laboratory

department: Biochemistry

institute: University of Illinois Urbana-Champaign

summary: Bacterial gene expression is thought to involve tightly coupled transcription, translation, and mRNA degradation. However, recent work has indicated that this is not always the case, leaving the generality and regulation of this coordination unclear. Here, we use genetic, kinetic, and spatial analyses in Escherichia coli to show that transcription–translation coupling requires high translational activity and that nearly half of the transcriptome exhibits signatures consistent with partial uncoupling. We find that co-transcriptional mRNA degradation is rare due to membrane localization of RNase E, except for transcripts encoding inner membrane proteins. Our results show that translation efficiency determines the level of premature transcription termination, which in turn shapes mRNA degradation patterns and kinetics. Comparative analyses in Bacillus subtilis and Caulobacter crescentus also reveal gene- and species-specific coordination strategies. This challenges the universality of co-transcriptional coupling and defines how spatial and genetic features coordinate bacterial gene expression.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Rif-seq of E. coli MG1655 wild-type cells in MOPS rich defined media at 37˚C: mRNA sequencing (mRNA-seq) and total RNA sequencing (total RNA-seq) of samples collected at time points t = 0, 0.5, 1, 2, 3, 4, 5, 6, 8, 10 min following treatment with the transcription initiation inhibitor rifampicin (Rif-seq)

first: Seunghyeon

last: Kim

first: Xiangwu

last: Ju

first: Albur

last: Hassan

first: Yu-Huan

last: Wang

first: Shixin

last: Liu

first: Sangjin


title: L1CAM generates SOX2+ metastatic progenitors through planar cell polarity signaling in lung adenocarcinoma

city: New York

first: Jin Suk

last: Park

state: NY

address: 417 East 68th St

institute: MSKCC

summary: Lung adenocarcinoma (LUAD) is a leading cause of cancer-related deaths worldwide, with most fatalities attributed to metastasis. A primitive SOX2+ progenitor state, rare in primary tumors, becomes prominent in LUAD metastatic lesions and exhibits metastasis-initiating capacity. The signals that determine the emergence of SOX2+ progenitors are unknown. We report that the cell adhesion molecule L1CAM, a marker of metastasis-initiating regenerative progenitors, plays a crucial role in the emergence of LUAD SOX2+ progenitors. Mechanistically, L1CAM induces the planar cell polarity (PCP) complex to activate c-Jun, which in turn interacts with the chromodomain helicase CHD1 to drive Sox2 transcription and generate metastasis-initiating regenerative progenitors. Treatment with an L1CAM antibody drug conjugate (ADC) effectively eliminates these LUAD cells and eradicates patient-derived xenograft metastases. Our findings identify L1CAM/PCP signaling as a driver of the SOX2+ LUAD metastatic progenitor state and provide an approach to treating metastasis by targeting L1CAM+ LUAD progenitors.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For scRNA-seq data, mouse lung cancer cells were generated from KrasG12D;TP53-/- (KP) mice and submitted for single-cell sequencing after fresh tumor dissociation (day 0) or grown as tumoroids in Matrigel before submitted for single-cell sequencing (day 7). For ChIP-seq analysis, protein bound chromatin was precipitated using anti-CHD1, anti-cJun or IgG control using H23 cells.

first: Yasemin

last: Kaygusuz

first: Carson

last: Kenum

first: Mohamed

last: Gatie

first: Lan

last: He

first: Roshan

last: Sharma

first: Ronan

last: Chaligné

first: Abdul

last: Khan

first: Mary Ann

last: Pohl

first: Thomas

last: White

first: Paul

last: Balderes

first: Ivo

last: Lorenz

first: Tuomas

last: Tammela

first: Anna-Katerina

last: Hadjantonakis

first: Karuna

last: Ganesh

first: Charles

last: Rudin

first: Joan

last: Massagué


title: Perception of a bacterial quorum sensing signal activates a tripartite plant immune strategy

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

country: China

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

summary: Bacterial quorum sensing (QS) during pathogenesis is an indicator of increasing danger. How sessile plants perceive QS for defense is unclear. Here, we show that Arabidopsis thaliana perceives 2'-aminoacetophenone (2’-AA), a volatile QS signal from Pseudomonas aeruginosa, through cell surface pattern recognition receptor (PRR) complexes, resulting in multistrategic defense and disease resistance. The 2’-AA-induced plant immunity requires chemical and genetic specificity. 2’-AA binds to the cytoplasmic domain of BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) and induces the formation of PRR complexes that initiate the plant immune responses. 2’-AA stimulates plant exudation of acetic acid, a volatile compound that effectively quenches QS and inhibits P. aeruginosa virulence. Plants exposed to 2’-AA reshaped the root microbiome by suppressing the abundant Pseudomonad taxa with increased bacterial diversity. These results illustrate the ability of plants to perceive and respond to pathogen QS.

overall_design: The aim of this experiment was to study the effect of acetic acid on the gene expression of Pseudomonas aeruginosa. Acetic acid/water was added to Pseudomonas aeruginosa bacteria solution with OD=0.01, and the final concentration of acetic acid was 0.00% in the control group and 0.04% in the treatment group. Bacteria were collected after 4 hours of treatment, with 3 replicates in each group

first: Danxia

first: Yang

last: Zhou

first: Wenjia

last: Yu


title: Ovarian transcriptomic profiling of fitness-related genes in F4 inbred mice and to validate differentially expressed genes using qRT-PCR

city: Bareilly

first: Pushpendra

last: Kumar

state: Uttar pradesh

address: Izatnagar

department: Animal Genetics

country: India

institute: ICAR-IVRI

summary:
Purpose: To investigate the differentially expressed genes in high litter size samples v/s low litter size samples of F4 inbred Swiss albino mice using RNA-Seq and to validate some identified differentially expressed genes using qRT-PCR.
Methods: Intact ovarian tissue samples were obtained from six F4 female [from two groups i.e. three from high litter size group (HLS; n=3) and three from low litter size group (LLS; n=3)] inbred mice, after assessment of estrous phase of ovarian cycle by vaginal cytology smear technique (Byers et al., 2012). After sacrifice of mice, their intact ovaries were rapidly harvested and immediately preserve in RNAlater (Invitrogen). The QC passed libraries were subjected to RNA sequencing by use of HiSeq X10 of Illumina® platform. The paired ends (2 X 150 bp) reads were sequenced and about 3GB raw data were generated for both high and low groups, separately. The provided raw data were processed with trimgalore for quality purpose and kallisto pipeline to get transcript abundances. Tximport was used to generate gene counts and DESeq2 was performed on gene count data of RNA-Seq experiment to get DEGs. DEGs in HLS v/s LLS groups in Swiss albino mice were subjected to functional enrichment using bioinformatics tools, eg: Profiler and GSEA. The interaction of important DEGs having fold change ≥ ± 1.5 and Padj ˂ 0.05 was studied using Network Analyst 3.0. A total 5 DEGs identified through RNA-Seq in high and low litter size groups were validated by quantitative real time PCR (qRT-PCR).
Results: All QC passed transcriptomic libraries were sequenced in paired end read sequencing platform and on an average 49.7 million reads of 150bp per sample were generated. All six samples produced a total of 44.7 GB of data, with an average Phred score of more than 35 per sample. All six samples yielded a total of 42.23 GB of trimmed data. The average mapping percentage was 78.5. The average GC percent and unique reads percent for clean data samples were 50 and 55.66, respectively. DESeq2 analysis yielded the 1018 genes under R environment with 5 % FDR. 347 genes were found to be up regulated, and about 671 genes were found to be down regulated out of 1018 genes. Based on functional enrichment analysis of 659 DEGs with fold change ≥ ± 1.5 and Padj ˂ 0.05, 166 significantly enriched gene ontology (GO) classes were identified. Out of 166 categories, 17, 109, 28, and 12 were significantly enriched in molecular function (MF), biological process (BP), cellular component (CC), KEGG, and REAC, respectively.
Conclusion: In the present analysis of ovarian transcriptome, cell–cell signaling and metabolic related pathways were significantly enriched in HLS as compare to LLS group of F4 inbred Swiss albino mice. In these pathways, TP63, SLC16A10, APOD, S100A8, LRRK2, GPD1, CNR1, HDAC9, WNT11, LPIN1, SLC5A7, KLB, GNAI1, IRS2, TIMP4, PRKAR2B, SLC1A3, GSTZ1, FAH, CLYBL, SYNGR1, FAT4, CIDEA, ECHDC1, FMO5, GPT and ALDH1A1genes were significantly up-regulated in HLS group of inbred mice.

overall_design: Ovarian transcriptomic profiling of estrous-phased ovary to identify DEGs related to fitness in F4 inbred mice and to validate differentially expressed genes using qRT-PCR.

first: Amit

first: B

middle: L

last: Saini


title: Low-Strength Type I Interferon Signaling Promotes CAR T-Cell Treatment Efficacy

city: Chicago

first: Erting

last: Tang

address: 5640 S Ellis Ave

institute: the University of Chicago

summary: CD19-directed chimeric antigen receptor (CAR) T-cell therapy has significantly advanced the treatment landscape for relapsed/refractory diffuse large B-cell lymphoma (r/r DLBCL). However, up to 60% of patients do not achieve a complete response. In this study, we analyzed the infusion products of eight r/r DLBCL patients with distinct clinical responses to axicabtagene ciloleucel using single-cell transcriptomics. Compared to patients with progressive disease, infusion products of complete responders demonstrated stronger signatures of type I interferon (IFN-I) signaling and cytotoxicity. Based on these findings, we developed a novel strategy to improve CD19-directed CAR T-cell treatment efficacy by incorporating IFN-I during the ex vivo manufacturing process. While high-strength IFN-I signaling increases both CAR T-cell cytotoxicity and apoptosis, low-strength IFN-I signaling selectively enhances CAR T-cell cytotoxicity without compromising viability. Our manufacturing method leverages an existing FDA-approved pharmacophore to improve CAR T-cell efficacy without altering CAR expression or current manufacturing protocols. This study demonstrates proof-of-principle for IFN-I as a modulator to enhance CAR T-cell treatment efficacy in vivo, showcasing its translational potential for improving CAR T-cell therapy.

overall_design:
Single-cell RNA sequencing (scRNA-seq) was performed to profile cells in the infusion products (IPs) from eight relapsed/refractory diffuse large B-cell lymphoma (r/r DLBCL) patients treated with Axicabtagene Ciloleucel. Five of these patients achieved a complete response (CR), and three experienced progressive disease (PD). The raw sequencing data for the CR IPs (GSM7505070, GSM6281133, GSM6281134, GSM7505071, GSM6281135) were previously reported under accession number GSE207192 by an earlier study from our lab. In this study, we re-analyzed the raw data to generate processed data. All data pertaining to the PD IPs were newly generated for this study.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
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first: Yifei

last: Hu

first: Jun

last: Huang


title: Mast cells selectively deliver extracellular vesicle-encapsulated mRNA to colorectal cancer cells

status: Public on Apr 15 2026

city: Bloomington

first: Heather

last: O'Hagan

state: IN

address: 1001 E 3RD ST

department: School of Medicine

institute: Indiana University

summary: Mast cells (MCs), a type of granulocytic immune cell, exert contrasting effects on tumorigenesis. The anti- or pro-tumorigenic activity of MCs depends on the cancer type, tumor microenvironment, as well as MC localization within the tumor. Consequently, their role remains controversial and poorly understood across multiple cancer types, including colorectal cancer (CRC). Most proposed mechanisms underlying MC activity in CRC have focused on MC secretion of biological factors. In this study, we demonstrated that MCs transfer extracellular vesicles containing mRNAs and proteins to CRC cells. This process occurs through a tightly regulated mechanism that requires direct cell-cell contact, calcium signaling, and integrin-mediated interactions. Such requirements resemble the aspects of an immunological synapse observed between lymphocytes and cancer cells. The novel mode of intercellular communication between MCs and cancer cells described here may help refine our understanding of MC functions in cancer biology.

overall_design: Gene expression profiling analysis of RNA-seq data for LAD2 cell-derived extracellular vesicles

first: Rosie

last: Lanzloth


title: Recognition and silencing of a new transposable element

city: Planegg

first: Luca

last: Salvi

state: Please select

address: Semmelweisstr. 3

country: Germany

institute: ViGeneron GmbH

summary: Genomes constantly face threats from transposable elements (TEs) and other genomic parasites. While the silencing of existing TE has been well studied, little is known about how cells recognize new invading TEs that they have not previously encountered. Here we explore this question by inserting a foreign sequences into S. pombe. Our data revealed that the newly invading TE tj1 is recognized and targeted for silencing by RNAi and heterochromatin. The efficiency of recognition, as well as the degree and stability of silencing, depends on the copy number and insertion location of the TE. We demonstrated that RNA, rather than DNA, is sensed, and that the efficiency of TE recognition correlates with levels of RNA antisense to the TE, generated from upstream transcripts. We also show that various genes of non-transposable nature can initiate silencing. Our data show that silencing may not require recognition of specific elements in the transposon by the host defense systems, and suggest that disruption of host transcription patterns can trigger recognition of TE.

overall_design: DNA sequencing to map transposition loci, ChIP sequencings to asses chromatin states, total and polyA RNA sequencing to asses transcriptional silencing, experiments in wild type cells and different S. pombe mutants

first: Yinxia

last: Yan

first: Mario

last: Halic


title: Transcriptomic signatures of Trichomonas vaginalis isolates that exhibit low, intermediate, and high resistance to metronidazole in vitro

city: Birmingham

first: Keonte

middle: Jamel

last: Graves

state: AL

address: 1900 University Blvd, THT 230

department: Medicine-Infectious Diseases

institute: The University of Alabama at Birmingham

summary: As part of efforts to identify genes associated with Trichomonas vaginalis resistance to 5-nitroimidazole drugs, thirty cryopreserved T. vaginalis isolates were revived and grown using Diamonds TYM medium. Minimum lethal concentrations (MLCs) for metronidazole (MTZ), tinidazole (TDZ), and secnidazole (SEC) were determined using a drug susceptibility assay. Transcriptome profiling was performed for 15 MTZ-sensitive (MTZ-S, MLC < 50µg/mL) and 15 MTZ-resistant (MTZ-R, MLC ≥ 50µg/mL) isolates using next generation RNA-sequencing. Bioinformatics analyses identified differentially expressed genes (DEGs). Among MTZ-R isolates, 6 exhibited MLCs of 50µg/mL, 5 had MLCs between 100-200 µg/mL, and 4 had MLCs ≥ 400 µg/mL. The low-, intermediate-, and high-level MLC resistant isolates were compared to the MTZ-S isolates and transcriptomic profiling identified 154, 425, and 175 DEGs respectively. MTZ-resistant T. vaginalis isolates exhibited altered expression of virulence factor genes compared to sensitive isolates, with variations in gene expression observed across different MLC levels.

overall_design: RNA sequencing, bioinformatics, and biostatistical analyses were performed to identify differentially expressed genes (DEGs) in the MTZ-resistant vs. sensitive T. vaginalis isolates.

first: Colin

last: Reily

first: W

last: Secor

first: Jan

last: Novak

first: Christina

last: Muzny


title: Murine modeling of IDH-mutant 1p/19q-codeleted oligodendroglioma reveals genotype specific phenotypes

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

summary:
Background: Oligodendroglioma is a primary central nervous system tumor classified by the presence of isocitrate dehydrogenase (IDH) mutations and codeletion of 1p/19q. A lack of faithful preclinical model systems for this disease has limited progress in understanding the biology of this genetically unique subtype of adult diffuse-type glioma and in developing new effective therapies. To address this unmet need, we sought to establish a mouse model that faithfully recapitulates the genetic and phenotypic features of human IDH-mutant 1p/19q codeleted oligodendroglioma.
Methods: We performed in utero electroporation to introduce distinct combinations of genetic alterations and evaluated their potential to form tumors. Resulting tumors were characterized by histology, metabolite profiling, RNA-sequencing and single cell RNA-sequencing.
Results: We identified co-expression of IDH1R132H and PIK3CAE545K together with loss of Cic, Fubp1 and Cdkn2a (termed OligoCdkn2a) as the optimal genetic combination to drive fully penetrant tumors that histologically resemble human grade II/III IDH-mutant 1p/19q-codeleted oligodendroglioma. Substituting Cdkn2a loss with Trp53 deletion decreased latency and shifted tumors toward high-grade astrocytoma histology. OligoCdkn2a tumors displayed metabolic and transcriptional changes associated with IDH and CIC mutations, and single cell sequencing identified a bias towards oligodendrocyte differentiation compared to an IDH wild-type glioblastoma mouse model.
Conclusions: To our knowledge, OligoCdkn2a tumors represent the first autochthonous, genetically engineered mouse model to recapitulate the genetic, histological and transcriptional features of human IDH-mutant 1p/19q-codeleted oligodendrogliomas. This model will provide a valuable platform to further dissect mechanisms of tumorigenesis and test novel therapeutic strategies for this molecularly distinct glioma subtype.

overall_design:
Bulk RNA-sequencing was performed to analyze tumor endpoint tissue and primary murine cell lines across three distinct genetic models (Oligo Cdkn2a, Oligo Trp53, IDHWT GBM). For the tumor endpoint tissue cohort, 7 to 10 biological replicates per genetic condition were analyzed. For the primary cell lines, each genetic condition had one cell line with three technical replicates that was used for analysis.
!Series_overall_design = Oligo Cdkn2a primary murine line was treated with 1 μM Vorasidenib or DMSO vehicle for 14 days with serial passaging and media/drug refresh routinely. Cells were collected for RNA extraction and bulk RNA-seq at Day 14. Six samples total; 3x DMSO control and 3x Vorasidenib treated.

middle: N

first: Ipsita

middle: G

last: Kundu


title: A community machine learning challenge to predict the effects of gene perturbations on T cell differentiation for cancer immunotherapy

city: Cambridge

first: Jiaqi

last: Zhang

state: MA

address: 75 Ames St

institute: MIT; Broad Institute

summary: Perturbations of genes with functional importance in T cells could be used to change the distribution of CD8 T cell states to enhance anti-tumor functions for cancer immunotherapies. We launched a world-wide computational challenge to predict the effects of gene perturbations and to devise objective functions for prioritizing gene perturbations that lead to desired T-cell state distributions. We supported the challenge by generating a single-cell Perturb-seq dataset profiling the effect of knocking out 73 individual expert-defined genes in T cells transferred into a mouse melanoma model. We compared the top algorithms developed by participants, and found that performance was primarily determined by the prior data used for gene feature representation, with perturbational data derived features, proving most effective. Experimental validation of the top 61 genes nominated by the algorithms revealed that perturbation of Ndufv2 and Dimt1 reached the defined objective and biased differentiation toward desired states.

overall_design:
We used in vivo CRISPR to knockout each of 73 genes in naïve CD8+ T cells, followed by transfer of perturbed cells into mice. We restricted the CD8+ T cell repertoire using OT-1 TCR transgenic mice, in which CD8+ T cells express a TCR specific for the ovalbumin-derived peptide OVA257-264 (SIINFEKL) presented by H-2kb, enabling recognition of B16-OVA melanoma cells that express ovalbumin. Naïve Cas9-expressing OT1+ CD45.2+ CD8+ T cells were transduced with a library of 257 single guide RNAs (sgRNA). After five days, the modified naïve T cells were adoptively transferred to congenic CD45.1+ mice, which were then subcutaneously injected with B16-OVA melanoma cells 1 day after T cell transfer to examine how the individual loss of genes would affect T cells in the tumor microenvironment. The tumor-infiltrating perturbed T cells were then collected after 14 days (when exhausted T cells accumulate) and analyzed by single-cell RNA sequencing.

In the follow-up screen, we selected 57 target genes and designed 3 guides per gene. We performed a Perturb-seq of sgRNA knockouts following the same protocol and then the same steps as before, with additional hashtag staining to enable multiplexing of samples from individual mice.

first: Marc

last: Schwartz

first: Mohammed

last: Mutaher

first: Oluwatomisin

last: Olajide

first: Yuri

last: Pritkyin

first: Orr

last: Ashenbrg

first: Nir

last: Hacohen

first: Caroline

last: Uhler


title: Shared anti-biofilm targets of biofilm regulators Wor3 and Bcr1 in Candida albicans RPMI

city: Athens

first: Katharina

last: Goerlich

state: GA

address: 120E Green St

department: Microbiology

institute: University of Georgia

summary:
Candida albicans is an opportunistic fungal pathogen and a natural component of the
human microbial flora. One central C. albicans virulence trait is the ability to produce a
biofilm, which is regulated by several transcription factors. Mutations of some biofilm
transcriptional regulators cause the same severe biofilm-defective phenotype in multiple
clinical isolates. Mutations of others, such as Wor3, Bcr1, Ndt80, and Ume6, have mild
or variable phenotypes among clinical isolates. We hypothesized that Wor3 may have a
shared function with one of the other variable-phenotype biofilm regulators. This
hypothesis predicts that a double mutant lacking Wor3 and the shared-function
regulator will have a severe biofilm defect in all clinical isolates. We observed that a
wor3Δ/Δ bcr1Δ/Δ has a severe biofilm defect in vitro in 5 strain backgrounds tested. It
also has a severe oral biofilm defect in a mouse oropharyngeal candidiasis model in the
SC5314 reference strain background. RNA-seq data indicate that 5 genes encoding
cell surface/secreted proteins are upregulated in wor3Δ/Δ, bcr1Δ/Δ, and wor3Δ/Δ
bcr1Δ/Δ strains: CWH8, DAG7, JEN2, PGA6, and YWP1. Deletion mutations of CWH8,
DAG7, PGA6, or YWP1 enables biofilm formation in vitro in an SC5314-derived
wor3Δ/Δ bcr1Δ/Δ strain, and deletion of YWP1 enables biofilm formation in vitro in
wor3Δ/Δ bcr1Δ/Δ strains from 4 other genetic backgrounds. YWP1 has been shown to
have anti-biofilm activity previously, but CWH8, DAG7, and PGA6 are newly described
anti-biofilm genes. Our study illustrates the value of strain variation considerations for
gene function analysis and the importance of repression targets of biofilm regulators. In
addition, our results expand the number of anti-biofilm genes.

overall_design: RNA-seq profiling of WT (SC5314 A22) C. albicans cells and their mutant derivatives (wor2△/△, bcr1△/△, wor2△/△bcr1△/△, wor3△/△, andwor3△/△bcr1△/△). Cells were grown for 4h at 37C in RPMI.

first: Aaron

middle: P

last: Mitchell


title: ATRX inactivation disrupts global chromatin state and topology to dysregulate neurodevelopmental pathways in glioma cells of origin

city: Houston

first: Anand

last: Singh

address: 1901 East Road

institute: MD Anderson Cancer Center

summary: To investigate the role of cohesins in murine neuroprogenitor model (Tp53-/-, Atrx+; Tp53-/-, Atrx -/-)

overall_design: SMC1 CUT&TAG was performed on murine progenitor models

first: Prit Benny

last: Malgulwar

first: Annette

last: Machado

first: Jason

last: Huse

first: Kunal

last: Rai

middle: K

first: Ajay

last: Saw


title: Conserved metanephric kidney development and genome methylation in the red-eared slider turtle (Trachemys scripta elegans)

city: Memphis

first: Troy

last: Camarata

state: TN

address: 1003 Monroe Avenue

department: Biomedical Sciences

institute: Baptist University College of Osteopathic Medicine

type: Methylation profiling by high throughput sequencing

summary: Mammals and reptiles possess a metanephric kidney as the terminal renal organ for homeostasis of solutes and waste products. The development of the metanephric kidney has primarily been studied in mammalian model systems. Little is known about the conservation of metanephric kidney formation in non-mammalian species such as reptiles. Uniquely, reptiles maintain kidney progenitor cell populations throughout life and continually develop new nephrons, the functional unit of the kidney. The red-eared slider turtle, Trachemys scripta elegans, was utilized to investigate the conservation of reptilian metanephric kidney development. The nephron progenitor cell (NPC) marker, Six2, was detected in whole-mount turtle kidneys in a similar pattern to mammals. However, there were differences in progenitor cell niche morphology where turtle NPC populations formed distinct elongated rows instead of the rosette-like morphology found in the mouse. The pattern of NPC populations in the embryonic turtle kidney was maintained in the adult turtle. Whole-genome bisulfite sequencing was performed on cortical tissue containing the NPC populations from adult turtle kidneys and compared to those of adult mice. Significant conservation of gene methylation was detected in adult cortical tissue between the two species, although unique signatures were detected in turtle samples related to DNA repair and β-catenin signaling. This suggests a high level of conservation of metanephric kidney development at the genetic level.

sample_organism:
Mus musculus
Trachemys scripta elegans

platform_organism:
Mus musculus
Trachemys scripta elegans

overall_design: Whole genome bisulfite sequencing of adult renal cortical tissue isolated from Trachemys scripta elegans (red-eared slider turlte) and Mus musculus.


title: Identification of aging and senescence markers of male African turquoise killifish livers

city: Bunkyo-ku

first: Satoshi

last: Kofuji

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Institute of Science Tokyo

summary: Vertebrates grow and mature with age after birth (aging change), deteriorate (senescence), and eventually die. However, many aspects remain unclear regarding the distinction between aging change and senescence at the body, organ and cell levels. In this study, we aimed to isolate molecular markers distinguishing aging change from senescence in the short-lived vertebrate African Turquoise killifish (N. furzeri). First, the lifespan of N. furzeri was divided into growth (young), mature (adult), and senescent (old) stages. Changes between young and adult were defined as “aging change”, while changes between adult and old were defined as “senescence”. Metabolome and gene expression analyses of the liver identified several metabolites and genes as aging and senescence markers. These results indicate that molecular markers reflecting aging change and senescence at the organ levels can be isolated using N. furzeri.

overall_design: RNA-seq data for the livers of Nothobranchiu furzeri (GRZ strain) at young, adult, and old stages.

first: Hiroshi

last: Nishina


title: Distinct nociceptor roles in inflammation and itch revealed by subset-specific transcriptomic adaptation

city: Toulouse

first: Lilian

last: Basso

address: INSERM UMR1291 – CNRS UMR5051 - University Toulouse III CHU Purpan – BP 3028

country: France

institute: INFINITY INSERM U1291

summary: This study identifies two distinct subsets of sensory neurons that separately regulate itch and inflammation in allergic contact dermatitis. MrgprD⁺ nonpeptidergic neurons adopt a transient regenerative program during inflammation and are essential for itch behavior, while Trpv1⁺ peptidergic neurons limit inflammation by restraining neutrophil infiltration. These findings uncover parallel, nonredundant neuronal circuits that independently control inflammatory and pruritic responses in the skin.

overall_design: We induced a mouse model contact dermatitis in GINIP-DTR mice where GINIP+ neurons were depleted.

first: Tiphaine

last: Voisin

first: Nadine

last: Gheziel


title: Age- and Sex- Driven Transcriptional and Metabolic Diversity in Myeloid-Derived Suppressor Cells After Mouse Sepsis

city: Gainesville

first: Jaimar

last: Rincon

state: FL

address: 1600 SW Archer Road

department: Departament of Surgery

institute: University of Florida

summary: Sepsis induces profound immune dysregulation, often resulting in chronic critical illness characterized by persistent immunosuppression and poor outcomes. Myeloid-derived suppressor cells (MDSCs) are central mediators of this immunosuppressive phenotype, yet the influence of age and sex on their transcriptional and metabolic states remain poorly understood. Here, we employed single-cell RNA sequencing of splenic leukocytes from young (3-4 months) and older (18-24 months) adult male and female mice subjected to a clinically relevant murine sepsis model to define age- and sex-specific MDSC phenotypes. We identified significant differences regarding age and sex in MDSC expansion, transcriptome, canonical pathway activation, RNA velocity, mitochondrial metabolism, and predicted cell-cell communication after sepsis. Using drug2cell analysis of total leukocytes we also identified cohort-specific drug target profiles. These findings underscore the importance of age and sex in shaping sepsis-induced MDSC biology and suggest that personalized immunomodulatory strategies targeting MDSCs could improve sepsis outcomes.

overall_design: scRNA sequencing was performed on young and older, male and female B6 mice after sepsis (CLP+daily chronic stress for 7 days) as well as in age and sex matched naïve mice.

first: Christine

last: Rodhouse

first: Dayuan

last: Wang

first: Hongru

last: Tang

first: Valerie

last: Polcz

first: Miguel

last: Hernández-Ríos

first: Xuanxuan

last: Yu

first: Leandro

last: Balzano-Nogueira

first: Angel

last: Charles

first: Seiichiro

last: Fujishima

first: Quan

last: Vo

first: Marvin

last: Dirain

first: Ricardo

last: Ungaro

first: Dina

last: Nacionales

first: Leilani

last: Zeumer-Spataro

first: Larissa

last: Langhi Prata

first: Shawn

middle: D

last: Larson

first: Gemma

last: Casadesus

first: Feifei

last: Xiao

first: Shannon

last: Wallet

first: Maigan

last: Brusko

first: Tyler

last: Loftus

first: Letitia

last: Bible

first: Alicia

last: Mohr

first: Paramita

last: Chakrabarty

first: Michael

last: Kladde

first: Clayton

last: Mathews

first: Lyle

last: Moldawer

first: Robert

last: Maile

first: Guoshuai

last: Cai

first: Philip

last: Efron


title: Mapping self-associating chromatin hubs identifies Id proteins as key determinants of exhausted T cell fate

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

summary: The goal of this study is to determine how transcription cofactors, Id2 and Id3, mediate differential regulation  of exhausted CD8 T cell fate decision and differentiation at the early stage of responses to chronic viral infection.

overall_design: Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) was performed on sort-purified antigen-specific CD8+ T cells on day 8 post-infection with LCMV clone 13.

first: Hu

last: Wei

last: Sheng'en

first: Zang

last: Chongzhi

first: Xue

last: Hai-Hui


title: Fecal Metagenomic Signatures of Lifespan Variation in Dogs: Findings from the Dog Aging Project

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

institute: Arizona State University

summary: Dog Aging Project fecal metagenomic data from the Precision Cohort

overall_design: Dog Aging Project Dogs  sampled to define aging in the gut microbiome.

first: Daniel

last: Promislow

first: Elhanan

last: Borenstein


title: Thre impact of Akkermansia muciniphila on Group B Streptococcus gene expression during infection of human vaginal epithelial cells.

city: Aurora

first: Kelly

middle: S.

last: Doran

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: Group B Streptococcus (GBS) is an opportunistic pathogen that colonizes the vaginal tract and can be transmitted to the fetus or newborn resulting in infection. Previously we identified that Akkermansia muciniphila alters the dynamics of GBS vaginal colonization. Here we determine that A. muciniphila promotes GBS aggregation and attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis revealed that A. muciniphila changed expression of 258 unique GBS genes during hVEC colonization, with many involved in cell wall/membrane/envelope biogenesis. We demonstrate that A. muciniphila-mediated increases in GBS aggregation and attachment to hVECs are dependent on GBS capsule and pili, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results highlight the dynamic impact of a commensal organism on GBS colonization, as well as demonstrate the probiotic potential of A. muciniphila in the vaginal environment.

sample_organism:
Streptococcus agalactiae
Homo sapiens
Akkermansia muciniphila

overall_design: RNA-seq profile of Streptococcus agalactiae or Group B Streptococcus  (Strain: COH1) during mono- and co-infection of human vaginal epithelial cells.

first: Stephanie

last: Marroquin

first: Shirli

last: Cohen

first: Melody

last: Neely

middle: S


title: PGC-1alpha pathway dysregulation disrupts myofiber specification in a mouse model of SBMA [snRNA-Seq]

city: Ann Arbor

first: Andrew

last: Lieberman

state: MI

address: 1150 W Medical Center Dr.

institute: University of Michigan

summary: Skeletal muscle pathology is a critical but poorly understood contributor to neuromuscular degeneration in spinal and bulbar muscular atrophy (SBMA), a CAG/polyglutamine (polyQ) expansion disorder caused by mutation in the androgen receptor (AR). Using a gene-targeted SBMA mouse model, we applied single-nucleus RNA sequencing to identify a previously unrecognized, disease-specific population of skeletal muscle myonuclei that replace normal myonuclear subtypes. This transition was driven by dysregulation of the PGC-1α pathway, a central regulator of myofiber specification and metabolic identity. PGC-1α dysfunction in SBMA muscle was age-, hormone-, and polyQ length–dependent and was partially rescued by subcutaneous delivery of AR-targeted antisense oligonucleotides. Integrated ChIP-seq and RNA-seq analyses revealed that aberrant PGC-1α activity promoted the expression of a distinct set of myofiber specification genes while downregulating those defining healthy Type IIb and Type IIx myonuclei. We propose a model in which this dysfunction arose downstream of polyQ-mediated sequestration of PGC-1α cofactors MEF2, CREB, and CBP, leading to transcriptional reprogramming and cellular dysfunction. These findings implicate PGC-1α dysregulation as a key event linking AR polyQ expansion to skeletal muscle degeneration and suggest a shared mechanism for polyQ-mediated muscle pathology across related neurodegenerative diseases.

overall_design: Nuclei were extracted from tibialis anterior (skeletal muscle) of 52-week WT or AR113Q male mice using the 10X Chromium Nuclei Isolation kit, for comparison of gene expression at the single nucleus level using the 10X Genomics platform.

first: Curtis

last: Kuo

first: Laura

middle: B

last: Chopp

first: Zhigang

last: Yu

first: Luhan

last: Ni

first: Hien

last: Zhao

first: Janghoo

last: Lim


title: PGC-1alpha pathway dysregulation disrupts myofiber specification in a mouse model of SBMA [ChIP-Seq]

overall_design: Chromatin was extracted from pooled tibialis anterior, totaling 200 mg per genotype, from WT and AR113Q. This was then immunoprecipitated with an antibody against PGC-1alpha (Novus NBP1-04676) and peaks were identified by ChIP-seq.


title: PGC-1alpha pathway dysregulation disrupts myofiber specification in a mouse model of SBMA [AR113Q RNA-Seq]

overall_design: RNA from tibialis anterior was extracted and sequenced from mice at 5, 26, or 52 weeks comparing WT and AR113Q knock-in tissue at each age. For the 52 week cohort, an additional included group of AR113Q mice received weekly subcutaneous injections of an anti-sense oligonucleotide directed against AR starting at 26 weeks.


title: Folate Receptor Beta Regulates Macrophage NLRP3 Inflammasome Activation and Pyroptosis in a Folate-Independent Manner [methylation array]

city: Indianapolis

first: David

last: Aronoff

state: Indiana

address: 545 Barnhill Dr. EH 305

department: Department of Medicine

institute: Indiana University School of Medicine

type: Methylation profiling by genome tiling array

summary: Folate receptor beta (FRb), encoded by FOLR2, is selectively expressed in monocytes and macrophages, yet its function in innate immune signaling remains poorly defined. Here, we identify FRb as a novel regulator of NLRP3 inflammasome activation and pyroptosis in human THP-1 macrophages. Using CRISPR/Cas9-mediated gene deletion, we show that loss of FOLR2 impairs caspase-1 activation, gasdermin D cleavage, and IL-1b release in response to multiple NLRP3 stimuli, without altering pro-IL-1 b induction. These defects were not rescued by exogenous folate and were independent of extracellular folate concentrations. Mechanistically, FOLR2 deletion reduced potassium efflux and downregulated multiple potassium channel genes. Single-cell RNA sequencing revealed broad transcriptional repression in FRb-deficient macrophages, including genes involved in inflammasome signaling and ion transport. Genome-wide methylation profiling showed increased CpG hypermethylation in FOLR2-deficient cells, consistent with reduced transcriptional activity. Our findings indicate that FRb promotes NLRP3 activation in a folate-independent manner by regulating transcription and K⁺ efflux in macrophages. These data reveal a previously unrecognized immunoregulatory role for FRb with implications for host defense, autoimmunity, and macrophage function in tissue microenvironments such as the tumor or placenta.

overall_design: Following treatment with phorbol 12 myristate 13 acetate (PMA) THP-1 WT or FOLR2 KO cells were rested in T-75 tissue culture flasks at 37C for 24 hours. Cells were then harvested from tissue culture flasks, plated in 6-well tissue culture plates at 5e6 cells/well with 2 mL of media and rested at 37C for 24 hours. Cells were harvested and DNA extracted with Qiagen QIAamp DNA Mini kit. DNA amounts were quantified via Nanodrop and stored at -20C until being run on Illumina Infinium MethylationEPIC v2.0 BeadChip microarray.

first: Lisa

last: Rogers

first: Kyle

last: Firestone

first: Riya

last: Chinni

first: Anna

last: Branco

first: Kayla

last: Wrobleski

first: Teresa

last: Chou

first: Jeffery

last: Goldstein

first: Xiaoping

last: Gu

first: Emily

last: Mason

first: Shaoyou

last: Chu

first: Michael

last: Rubart-von der Lohe

first: Philip

last: Low


title: Impaired taurine transport contributes to the development of bronchopulmonary dysplasia

city: Milwaukee

first: Masaki

last: Lin

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

summary: Sprague-Dawley rat pups were used to study the effect of taurine supplementation on hyperoxia-exposed lungs. The study, which was conducted with meticulous attention to detail, found significant effects of taurine supplementation. Rat pups were randomly assigned to room air (NOX) and >90% oxygen (HOX) from postnatal day 1 (P1) to P10. Half of the pups of each group received a daily taurine (100 mg/kg) intraperitoneal injection or an equal volume of PBS (two by two design). The four groups were NOX-PBS, NOX-taurine, HOX-PBS, and HOX-taurine. At P10, a comprehensive range of methodologies was employed, including morphometrics, histology, metabolomics, and immunoblots. Two pups, one male and one female, were randomly selected for single-cell RNA sequencing at P10

overall_design: Lung cells from each pup, a total of eight pups, were barcoded before combing for sc-RNAseq run through the Chromium platform at 25 billion reads.

first: Xigang

last: Jing

first: Yekai

last: Wang

first: Mark

last: Roethle

first: Shuang

last: Jia

first: Michelle

last: Teng

first: Ganesh

last: Konduri

first: Martin

last: J. Hessner

first: Kirkwood

last: A. Pritchard

first: Billy

middle: W

last: Day

first: Yan

last: Jin

first: Stephen

last: Naylor

first: Chien-Wei

first: Haiwei

first: Jianhai

last: Du

first: Ru-Jeng


title: Global transcriptome of Arabidopsis mutants nac42-L1 and nac42-L2 inoculated by the fungal pathogen Sclerotinia sclerotiorum following temperate and mediterranean acclimation

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

institute: INRAE

summary: The short-term, reversible process that allows plants to cope with immediate environmental fluctuations is often referred to as acclimation. Plant acclimation help maintain the balance of natural systems, supporting biodiversity and the services that ecosystems provide, such as carbon sequestration and water regulation. With climate change modifying the distribution area of plants and causing more frequent and severe weather events, knowledge of how plants acclimate can inform strategies to manage ecosystems and agriculture. Analyses of plant immune responses under abiotic constraints generally focus on pathogen inoculation under prolonged and stable abiotic conditions. Daily fluctuations of the environment may alter plant metabolism, growth and flowering as well as gene regulation and invasive growth of fungal pathogens. Yet, how plant immunity acclimates to daily temperature fluctuations remains largely unexplored. To study the molecular bases of quantitative disease resistance acclimation, we performed a global transcriptome analysis of Arabidopsis thaliana accessions Col-0, Rld-2 and Sha grown in temperate, continental and Mediterranean climates, followed or not by Sclerotinia sclerotiorum inoculation.

overall_design: Periphery of S. sclerotiorum disease lesions collected 24 hours post-inoculation on detached leaves of A. thaliana mutants. Plants were previously acclimated under two different day/night temperature regimes. Samples were collected in three independent replicates of the experiment.

first: Marie

last: Didelon

first: Florent

last: Delplace


title: Folate Receptor Beta Regulates Macrophage NLRP3 Inflammasome Activation and Pyroptosis in a Folate-Independent Manner

first: David

last: Aronoff

overall_design: Following treatment with phorbol 12 myristate 13 acetate (PMA) THP-1 WT or FOLR2 KO cells were rested at 37C for 24 hours. Cells were then harvested from tissue culture flasks, removed dead cells with magnetic bead based separation and fixed according to 10x Genomics FLEX protocol. Cells were then submitted for scRNA-seq.

first: Lisa

last: Rogers

first: Kyle

last: Firestone

first: Riya

last: Chinni

first: Anna

last: Branco

first: Kayla

last: Wrobleski

first: Teresa

last: Chou

first: Jeffery

last: Goldstein

first: Xiaoping

last: Gu

first: Emily

last: Mason

first: Shaoyou

last: Chu

first: Michael

last: Rubart-von der Lohe

first: Philip

last: Low


title: Shared anti-biofilm targets of biofilm regulators Wor3 and Bcr1 in Candida albicans

first: Katharina

last: Goerlich

overall_design: RNA-seq profiling of WT C. albicans cells and their mutant derivatives (wor3△/△, bcr1△/△, and wor3△/△bcr1△/△). Cells were grown for 4h at 37C in RPMI+10%FBS.

first: Aaron

last: Mitchell


title: Rhinolophus sinicus limb embryonic development single cell transcriptome

city: KunMing

first: Xue

last: Lv

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology, CAS

summary: Bats are the only mammals capable of true flight, possessing unique wings primarily composed of elongated digits and interdigital membranes.  However, the developmental coordination between digit elongation and interdigital membrane expansion remains poorly understood.  Here, we conduct a single-cell analysis of developing bat limbs of Chinese horseshoe bat and for key development stages of limb. Within the sequenced 30 thousand cells, we identify a specific population of mesenchymal progenitors in the bat forelimb that express high levels of PDGFD.  This cell population has the potential to differentiate into the interdigital membrane and release growth factors that promote the proliferation of bone-related cells.  Compared to hindlimbs, the developing bat forelimbs undergo prolonged chondrogenesis and delayed osteogenesis, resulting in more chondrocytes and fewer osteoblasts.  The bone-related cells also can release growth factors that facilitate the proliferation of skin-related cells.  Our findings suggest that interactions mediated by growth factors among different cell populations play a vital role in coordinating the development of digit elongation and interdigital membrane expansion in bat forelimbs.

sample_organism:
Mus musculus
Rhinolophus sinicus

platform_organism:
Mus musculus
Rhinolophus sinicus

overall_design: Following the pipeline described by (Rosenberg et al. 2018), we generated single-nucleus RNA-seq libraries of bat forelimbs and hindlimbs from R. sinicus embryos at CS16, CS18, and CS20, as well as the forelimbs of mouse embryos at the matched developmental stages: E13.5, E14.5 and E16.5.

first: Zhen

last: Liu

last: Lyu

first: Jing

last: Bai


title: Gene expression profile of nociceptors innervating the skin at a single cell level at steady state and in a Contact hypersensitivity model

first: Lilian

last: Basso

summary: Changes in Gene expression in skin-innervating nociceptor during contact hypersenisitivity are unknown. We sorted skin-innervating nociceptors at steady state, after sensibilization and at D1 and D4 after allergen skin challange.

overall_design: Back -skin innervating nociceptors were retrograddly stained with DiI and sorted by FACS and subsequently sequenced.

first: Basso

last: Lilian

first: Gheziel

last: Nadine

first: Voisin

last: Tiphaine

first: Gaudenzio

last: Nicolas


title: Anueploidy selects for the acquisition of driver genes in breast cancer

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

summary: Chromosome instability is highly prevalent in cancer and drives large scale chromosomal imbalances, known as aneuploidies. How aneuploidy contributes to tumorigenesis remains difficult to study due to the vast numbers of genes affected. Here, we established a CRISPR Knock Out and Activation Linked Assay (CRISPR-KOALA), enabling high-throughput bidirectional genetic screens in immune-competent mouse models of cancer. We developed a compendium of the ten most frequent human chromosome arm-level alterations in basal-like breast cancer (BLBC), a disease type driven by large copy number alterations (CNAs).  Using CRISPR-KOALA, we screened the mouse orthologs of all 3,752 genes on these arms and identified 90 cancer driver genes, the vast majority of which have hitherto unknown functions in cancer. These genes drive distinct signalling pathways including MAPK, Hippo and WNT, reflecting the high degree of BLBC heterogeneity. Manipulating the identified cancer driver genes overcomes the need for CNAs in p53-mutant BLBC mouse models. Mechanistically, we uncover PLGRKT as a potent oncogene that lies on chromosome 9p and show that its tumor-promoting activity is associated with highly stress-resistant mitochondria and an increased capacity to detoxify reactive oxygen species. Together, our findings reveal that arm-level CNAs can function to select specific driver genes to promote heterogeneous biological processes.

overall_design: To investigate the transcriptomes of FACS-purified Tigre-, Hipp11-, Fbxw7-, Csnk1a1-, and Mettl14-knockout and HA, Tigre-, Hipp11,  Plgrkt-, including plasminogen-binding deficient mutant, overexpressing mammary tumor cells, generated by lentiviral CRISPR-knockout, CRISPR-activation or open reading frame injections directly in the mammary epithelium of tumor prone Pten;P53;Cas9 compound mutant mice. At least 3 independent tumors were processed and analyzed for each group and directly compared to their respective controls, which were Tigre, Hipp11 for CRISPR-knockout and activation, or HA for open reading frame experiments.

first: Khalid

last: Al-Zahrani

first: Ellen

middle: R

last: Langille

first: Jocelyn

last: Nurtanto

first: Andreea

last: Obersterescu

first: Katie

last: Teng

first: Christopher

last: Lowden

first: Julien

last: Dessapt

first: Cynthia

middle: H

last: Chiu

first: Lauren

middle: V

last: Caldwell

first: David

last: Cook

first: Miguel

last: Pérez-Castro

first: Jacob

last: Berman

first: Ricky

last: Tsai

first: Alexander

last: Bahcheli

first: Geraldine

last: Mbamalu

first: Shifei

last: Wu

first: Masahiro

last: Narimatsu

first: Adele

last: Lopes

first: Iosifina

last: Fotiadou

first: Kin

last: Chan

first: Linkang

last: Zhang

first: K.W. Annie

last: Bang

last: Parsons

first: Larissa

last: Mourao

first: E. Idil

last: Temel

first: Liddy

last: McCulla

first: Palavalasa

last: Sravya

first: Li

first: Peter

last: Sajjakulnukit

first: Costas

last: Lyssiotis

last: Borowsky

first: Colinda

last: Scheele

last: Wahl

first: Hartland

last: Jackson

first: Katherine

last: Stewart

first: Elaine

last: Fuchs

first: Sean

middle: E

last: Egan

first: Miguel Angel


title: Location matters: spatial-dependent effects of myofibroblasts determine survival in breast cancer

city: Singapore

first: Kanaga

last: Sabapathy

state: --None--

address: 11 Hospital Crescent

department: Division of Cellular & Molecular Research

country: Singapore

institute: National Cancer Centre Singapore

summary: While cancer-associated fibroblasts (CAFs) have been historically considered pro-tumorigenic, several studies found that myofibroblast-like CAFs (myCAFs) may have tumor-restraining properties. In our previous study (PMID: 37863888), we performed multi-regional bulk transcriptomics profiling of 8 ER+/PR+/HER2- breast tumors and matched peri-tumoral tissues. We identified an adipose-enriched peri-tumoral subtype which was significantly associated with poorer overall survival in breast cancer patients, in contrast to a myofibroblast-enriched subtype. Here, we performed single-nucleus RNA-sequencing of  2 ER+/PR+/HER2- invasive breast carcinomas and their matched peri-tumoral tissues (1-7 cm from tumor margins), as well as 1 reduction mammoplasty (RM) sample. We identified tumor-induced changes in the peri-tumoral adipocytes compared to RM adipocytes, as well as a high abundance of myCAFs in the larger tumor, whereas a distinct myofibroblast-like subpopulation was found in the peri-tumoral tissues of the smaller tumor. Together with deconvolution analyses of TCGA data and 3D co-culture experiments, we show that that myofibroblasts have both tumor-promoting or -restraining roles depending on their location within or surrounding the tumor.

overall_design: Single-nucleus RNA sequencing was performed on 5 samples (2 breast tumor, 2 peri-tumoral stroma, 1 reduction mammoplasty).

first: Hannah

last: Si Hui Lau


title: RNA-seq analysis in progeny leaves on rice seed treatd with heat

city: Fukuoka

first: Yushi

last: Ishibashi

address: 744 Motooka

institute: Kyushu university

summary: We report the relationship between transgenerational growth and  transcriptome in progeny leaves on rice seeds treated with heat.

overall_design: Examination of RNA-seq in progeny leaves on rice seeds treated with heat.

first: Ishibashi

last: Yushi

first: Suriyasak

last: Chetphilin


title: Stem cell activity is linked to a transient acquisition of pluripotency during callus proliferation

city: Seoul

first: Soon Hyung

last: Bae

state: South Korea

address: Gwanak-ro 1, Gwanak-gu

country: South Korea

institute: Seoul National University

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

overall_design: Refer to individual Series


title: Primary Cilia Mediate Stress Vulnerability and Exercise Antidepressant Adaptation: Evidence for Ventral Hippocampal Astrocytic Ciliary Remodeling by Exercise

first: Dong-Joo

last: Hwang

address: 1239, Yangjae-daero, Songpa-gu

department: Institute of Sport Science

institute: Korea National Sport University

summary: Chronic stress engenders marked inter-individual heterogeneity in vulnerability to depression and anxiety, indicating that distinct neurobiological processes shape susceptibility and resilience. To identify the mechanisms underlying this divergence, mice subjected to chronic restraint stress (CRST) were stratified into stress-susceptible or resilient phenotypes using multidimensional behavioral clustering. To examine how exercise modifies these stress-defined endophenotypes, we used a graded treadmill paradigm in which low-, moderate-, and high-intensity exercises were parametrically defined relative to the ventilatory threshold (VT). Only low-intensity exercise performed below VT produced robust antidepressant and anxiolytic effects in susceptible mice. Whole-brain c-Fos mapping revealed the selective recruitment of the ventral hippocampus (vHPC) during low-intensity exercise. Chemogenetic silencing of vHPC neurons abolished these behavioral benefits, indicating that vHPC engagement is essential for exercise-induced resilience. Transcriptomic profiling of vHPC showed that this adaptive state was associated with the coordinated modulation of primary cilium-associated gene networks. Morphometric analyses confirmed that chronic stress-induced pronounced elongation of primary cilia, particularly in astrocytes, whereas low-intensity exercise restored both ciliary length and the proportion of ciliated astrocytes. These structural recalibrations coincided with reduced expression of proinflammatory cytokines, including IL-1α and fractalkine, suggesting that astrocytic cilia act as a key interface linking stress signaling to neuroimmune regulation. Collectively, these findings outline a mechanistic cascade in which exercise below the VT engages vHPC circuits, reorganizes cilia-related transcriptional programs, and restores astrocyte and inflammatory homeostasis, converting stress-susceptible states into resilient phenotypes.

overall_design: RNA-seq profiling of sedentary controls (SED), stress-susceptible animals (SUS), and stress-susceptible animals subjected to low-intensity exercise (SUS+LE)

first: Joon-Yong

last: Cho


title: Single-cell RNA-sequencing of calli harvested 7 and 12 days after incubation on callus-inducing medium

summary: Plant somatic cells can be reprogrammed to form a pluripotent cell mass, known as callus, which can be used to regenerate organs or an entire plant via de novo organogenesis. Exogenous treatment of tissue explants with a high auxin-to-cytokinin ratio stimulates callus formation. Here, we found that the pluripotency acquisition in the callus is transient during callus formation, independent of explant origin. Using single-cell transcriptome analysis of pluripotent and nonpluripotent calli, obtained at 7 and 12 days after incubation on callus-inducing medium (CIM), respectively, we found that root stem cell activity conferred by the WUSCHEL-RELATED HOMEOBOX5 (WOX5)-TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) module is diminished by the prolonged incubation of callus on CIM. The reduced root stem cell activity led to the differentiation mainly into mature lateral root cap (LRC)-like cells in callus. Concomitant with differentiation into LRC-like cells, epidermis-like cells accumulating very long chain fatty acids (VLCFAs) that promote cellular pluripotency are sloughed off. Additionally, stress responses that induce the loss of pluripotency are activated in the mature LRC-like cells and a sub-cluster of xylem pole pericycle cells. Taken together, our data indicate that callus formation is likely a continuous developmental program, in which stem cell activity is acquired then lost, resulting in the transient nature of cellular pluripotency in callus.

overall_design: Leaves of 2-week-old Arabidopsis thaliana seedlings were excised and incubated on callus-inducing medium. After 7 and 12 days of incubation, calli were collected to perform single-cell RNA-sequencing.

first: Soon

first: Ok-Sun

last: Park

first: Hun-Young

last: Lee

first: Kyounghee

first: Sangrea

last: Shim

first: Yoo-Sun

last: Noh

first: Pil

middle: J

last: Seo


title: Bulk RNA-sequencing of calli harvested 7 and 12 days after incubation on callus-inducing medium

overall_design: Leaves of 2-week-old Arabidopsis thaliana seedlings were excised and incubated on callus-inducing medium. After 7 and 12 days of incubation, calli were collected to perform bulk RNA-sequencing. Three biological replicates for each time point were generated.


title: JMJD1C-mediated epigenetic control of autoimmunity and HIT antibody production [RNA-seq]

status: Public on Apr 14 2026

first: Demin

last: Wang

state: WI

address: 8727 W Watertown Plank Rd

institute: 1Versiti Blood Research Institute

summary: Heparin-induced thrombocytopenia (HIT) is a common drug-induced immune disorder occurring in a subset of heparin-treated patients. Immune complexes comprising heparin, platelet factor 4 (PF4), and PF4/heparin-reactive antibodies are central to its pathogenesis. However, the role of epigenetic modification in HIT remains unexplored. Our study identified JMJD1C, a member of the lysine-specific histone demethylase 3 subfamily, as an essential regulator of PF4/heparin-specific antibody production. While JMJD1C was expressed throughout B-cell development and was dispensable for normal B-cell development, its deficiency disrupted immune tolerance and promoted production of self-reactive antibodies in systemic autoimmune diseases, including PF4/heparin-specific platelet-activating antibodies, a hallmark of pathogenic HIT antibodies. JMJD1C-deficient B cells were hyperresponsive, characterized by enhanced B-cell receptor (BCR)-induced proliferation. Transcriptomic analysis (RNA-Seq) revealed upregulation of pathways associated with BCR signaling, NF-kB activation, the cell cycle, and systemic lupus erythematosus (SLE). CUT&Tag profiling demonstrated that JMJD1C deficiency increased H3K36me1 modification at gene start sites in these pathways, indicating that epigenetic dysregulation drives B-cell hyperactivation. Importantly, transcriptional profiling and regulon analysis of B cells from HIT patients showed enrichment of BCR signaling, cell-cycle, NF-κB, and SLE-associated pathways, closely mirroring those in JMJD1C-deficient B cells. Epigenetic analyses further revealed enhanced promoter chromatin accessibility and elevated H3K36me1 deposition at promoter-TSS regions in HIT B cells. Together, these findings establish a strong molecular overlap between JMJD1C deficiency and human HIT B cells and reveal a previously unrecognized epigenetic mechanism underlying HIT pathogenesis. Our study provides the first evidence linking epigenetic regulation to HIT, offering new insights into its pathophysiology.

overall_design: Splenic FO B cells were sorted and stimulated with anti-IgM for 2 hours, then lysed in TRIzol for RNA extraction. mRNA was isolated (10 to 50 ng) using the NEBNext poly(A) mRNA Magnetic Isolate Module and converted into libraries with the NEBNext Ultra RNA Library Prep kit (New England Biolabs). Libraries were quantified using Qubit-Fluorometer and the Kapa Library Quantification Kit. Library size (150–900 bp) was determined with the D1000 ScreenTape system (Agilent).


title: T cell lymphoma associated STAT3 variants impose a type 1 regulatory phenotype

city: Maimi

first: Alejandro

last: Villarino

state: Florida

address: 1600 NW 10th Ave, Rosenstiel Medical Science Building (RMSB), Room 3152A

institute: University of Miami

summary: STAT3 signaling is fundamental to T cells, where it underlies basic cellular processes like metabolism and apoptosis, and specialized processes like differentiation and cytokine production. However, mutations of STAT3 are strikingly prevalent in T cell cancers and aberrant or excessive STAT3 signaling is thought to mobilize cellular pathways that encourage malignancy. To better understand how STAT3 mutations drive T cell cancers, we compared two frequent cancer-associated variants, Y640F and N647I, at cellular and molecular levels. Using a retrogenic system, we demonstrate that they are qualitatively similar yet quantitatively distinct; each bears a gain-of-function phenotype but Y640F has greater transcriptome-wide effects. We also discovered that these and other common STAT3 mutants invoke a T regulatory 1 (Tr1) gene program characterized by expression of IL-10 and other factors that dampen T cell responses, most notably LAG3 and CD39. Importantly, Tr1 ’skewing’ is evident in both mouse T cells expressing cancer-associated STAT3 variants and humans afflicted with T cell malignancies. These studies advance current understanding of how cancer-associated mutations impact STAT3 function and reveal anti-inflammatory properties that may help transformed T cells persist, expand and/or avoid eradication.

overall_design: bulk' RNA-seq and scRNA-seq analysis of transduced CD4+ and CD8+ T cells sourced from WT mice or mice lacking STAT3

first: Aaron

last: Schultz

first: Molly

last: Dalzell

first: Luis

last: Nivelo

first: Sarah

last: Henrickson


title: Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn’s Disease: a first in human trial

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

institute: Parean Biotechnologies

summary: A marked decrease in Faecalibacterium prausnitzii is a hallmark of Crohn’s disease (CD)-associated dysbiosis and predicts disease relapse. Here, we present the development and first-in-human evaluation of F. prausnitzii strain EXL01 for CD treatment. The EXL01-strain demonstrated anti-inflammatory effects in four models of colitis in rodents. A first-in-human, open-label, single-arm study of oral EXL01 was conducted in eight adult participants with mild to moderate CD, following corticosteroids-induced clinical response or remission. The primary endpoint was safety, and secondary endpoints included clinical, endoscopic, histological, molecular, and microbiome assessments. EXL01 was well-tolerated with no treatment-related adverse events. Six participants completed the study; two discontinued treatment due to disease flare. While gut microbiota composition remained largely stable, transcriptomic analyses revealed distinct changes in ileal gene expression following EXL01 treatment, notably modulation of immune-related genes and upregulation of energy metabolism pathways. Compared to participants who remained in remission, those who flared showed higher baseline systemic inflammation markers and innate immunity gene expression. These findings demonstrate that oral administration of EXL01 is feasible and well tolerated, and establishes proof-of-concept for F. prausnitzii as a first-in-class live biotherapeutic for CD. ClinicalTrials.gov registration: NCT05542355.

overall_design: MAINTAIN was a Phase 1, 2-parts, randomised, parallel arm, placebo controlled, partially double-blind, multicentre study evaluating the safety and target engagement of EXL01 in adults with mild to moderate CD (Crohn Disease Activity Index (CDAI) 180-350) with ileal involvement who achieved corticosteroid (CS)-induced clinical response (CDAI decrease ≥70) or remission (CDAI <150).

first: Perle

last: Guarino-Vignon

first: Edouard

last: Louis

first: Hang-Phuong

last: Pham

first: Giovanna

last: Orianne

first: Emma

last: Tkacz

first: Loic

last: Brot

first: Eolia

last: Mazzetti

first: Delphine

last: Sedda

first: Pauline

last: Ruffié

first: Nathalie

last: Rolhion

first: Geert

last: D’Haens

first: Benjamin

last: Hadida

first: Philippe

last: Langella

first: Harry

last: Sokol


title: In planta transcriptome analysis of Pseudomonas syringae pv. tomato DC3000 two component regulator mutant cvsR during early infection and early exposure to pattern-triggered immunity in Arabidopsis thaliana

city: Athens

first: Brian

middle: Howard

last: Kvitko

address: 120 Carlton St.

department: Plant Pathology

institute: University of Georgia

summary: We extracted P. syringae transcriptome from infected A. thaliana tissue under naive or PTI preactivated tissue by flg22 treatment, through physical separation by low speed centrifugation at 5 hours post inoculation. We compared the transcriptome of wildtype strain and mutant strain of cvsR, a previous identified two component regulator. This study aim to understand bacterial response to PTI and the role of cvsR regulon in plant.

sample_organism: Pseudomonas syringae pv. tomato str. DC3000

overall_design: Bacteria extracted from naïve mock-treated leaves and immune activated leaves (flg22)  at 5 hours post inoculation. Bacterial initial inoculum as in vitro media-based sample (KB). Samples collected in triplicate on different days for each strain and treatment.

first: Hsiao-Chun

last: Chen

first: Brian Howard


title: RNA-seq analysis of soleus muscle from control and StarD7 mKO mice

city: Tochigi

first: Yasuhiro

last: Horibata

address: 880 Kitakobayashi

institute: Dokkyo Medical University

summary: RNA sequencing was performed on soleus muscle from control and StarD7 mKO mice to investigate transcriptional changes associated with mitochondrial lipid dysregulation.

overall_design: RNA-seq analysis was performed on soleus muscle from control and StarD7 mKO mice (n = 3 per group). Total RNA was extracted and poly(A)-selected libraries were prepared and sequenced using the Illumina NovaSeq 6000 platform with paired-end 50 bp reads. Differential gene expression between control and mKO mice was analyzed.


title: JMJD1C-mediated epigenetic control of autoimmunity and HIT antibody production

first: Demin

last: Wang

overall_design: CUT&Tag was performed as described68. Sorted FO B cells were stimulated with anti-IgM for 2 h, washed, bound to ConA-coated beads (Bangs Laboratories), and incubated overnight with anti-H3K36me1 (Abcam), followed by anti-rabbit IgG secondary antibodies (Antibodies Online). Samples were incubated with the pA-Tn5 adapter complex (Epicypher) for 1 h at room temperature and subjected to tagmentation at 37°C. DNA was extracted, PCR-amplified, and sequenced on an Illumina NextSeq 500 using the NextSeq 500/550 v2 kit.


title: Wnt-dependent ontogeny of acellular cementum-forming cementoblasts on the tooth root surface

city: Houston

first: Taishi

last: Komori

state: TX

address: 7500 Cambridge St #1210

institute: The University of Texas Health School of Dentistry

summary: Cementum is a specialized mineralized tissue that covers the tooth root surface and anchors the tooth to the surrounding periodontal ligament. The coronal acellular cementum (AC) is indispensable for periodontal attachment and represents a key target for periodontal regenerative therapies. However, the developmental origin and molecular identity of AC-forming cementoblasts remain poorly understood. Here, through an integrated spatial and single-cell transcriptomic analysis, we identify AC-forming cementoblasts as a distinct population of noncanonical mineralizing cells enriched for cell-matrix organization and Wnt signaling signatures, distinguishing them from cellular cementum-forming cementoblasts localized in the apical portion. Lineage tracing using a Wnt inhibitory factor 1 (Wif1-creER) demonstrates that AC-forming cementoblasts originate exclusively from peri-epithelial apical Wif1+ cells of the elongating tooth root via canonical Wnt signaling activation. Collectively, our findings uncover the unique ontogeny and molecular signature of acellular cementum, providing insights into the formation and maintenance of the periodontal attachment apparatus.

overall_design: We generated a cellular-resolution spatial transcriptomic map of the murine mandible at P25 to comprehensively define the transcriptomic landscape of cementoblasts.

first: Noriaki

last: Ono


title: Transcriptional profiling of L4-L6 DRGs in Twik-1 knockout mice following chronic constriction injury

city: Daegu

first: Myungin

last: Baek

address: Techno jungang Daero 333

department: Department of Brain Sciences

institute: DGIST (Daegu Gyeongbuk Institute of Science and Technology)

summary: To identify the molecular mechanisms of reduced pain response in Twik-1 knockout mice, we performed bulk RNA-sequencing on lumbar DRGs from WT and Twik-1 knockout mice. Thirty days after sciatic nerve injury, the ipsilateral L4-L6 DRGs were manually sectioned into ~150 µm slices using a razor blade. RNAs were extracted from the sliced DRGs using PicoPure™ RNA Isolation Kit. RNA libraries were constructed using the SMART-Seq v4 Ultra Low Input RNA Kit. High-quality libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads. Image analysis was performed using the NovaSeq 6000 Control Software (v1.8.2), and base calling data were demultiplexed using bcl2fastq (v2.20.0.422), generating FASTQ files. Raw sequencing reads were aligned to the Mus musculus reference genome (GRCm39) using STAR aligner (version 2.7.11a). The genome index was built from the primary assembly FASTA file (Mus_musculus.GRCm39.dna.primary_assembly.fa.gz) and the corresponding gene annotation file (Mus_musculus.GRCm39.113.gtf.gz), ensuring accurate mapping across exon–intron boundaries. Resulting SAM/BAM files were then processed, sorted, and indexed with Samtools (version 1.18). Gene-level counts were generated using htseq-count (version 2.0.3) with the corresponding GTF annotation file.

overall_design: Transcript profiles of lumbar (L4-L6) DRGs were generated using bulk RNA sequencing. The study utilized two variables: genotype (WT vs. Twik1-KO) and injury model (Sham vs. CCI). The data set comprises 17 samples divided into four groups: Sham-WT (n=5), CCI-WT (n=5), Sham-Twik1-KO (n=4), and CCI-Twik1-KO (n=3).

first: Seo Young

last: Yang

first: Tery

last: Yun

first: Junhee

last: Park

first: Hyosang

last: Lee


title: Multi-functional Small Molecule for Regenerative Healing of Avascular Meniscus Tears: Modulation of Inflammation, Differentiation, and Multi-Tissue Crosstalk

city: New York

first: Chang

middle: Hun

state: NY

institute: Columbia University

summary: Avascular meniscus tears are a major contributor to mechanical joint locking, compromised gait and function, and the initiation and progression of post-traumatic osteoarthritis. Unfortunately, the avascular meniscus tears hardly heal. Here, we report a novel small molecule, 4-PPBP, a sigma-1 receptor (σ1R) agonist, exhibiting significant potential to promote avascular meniscus healing by activating synovial mesenchymal stem cells (syMSCs) and modulating macrophage-regulated inflammation via multi-tissue crosstalk. In vivo, a single injection of 4-PPBP-loaded bioglue minimized meniscal gapping, with improved meniscus healing and gait performance. In contrast to the degenerative changes in the untreated control, 4-PPBP/bioglue application resulted in integrated fibrocartilaginous tissues. scRNA-seq and CellChat analyses revealed 4-PPBP-activated cell-cell communications leading to inflammatory regulation and cell differentiation. Macrophages showed a robust reduction in pro-inflammatory genes, and fibroblasts, chondrocytes, and fibrochondrocytes increased genes associated with differentiation and matrix synthesis in response to 4-PPBP. Anti-inflammatory cell-cell communication signals were significantly elevated between adipocytes and macrophages.

overall_design: Sprague-Dawley rats (250 to 275g, Charles River, Boston) were used approximately 1 week before the procedure to allow adequate animal acclimation. For surgeries, animals were placed in an induction chamber with isoflurane  administration at 4% for induction of anesthesia before placement on a surgical table. Sustained-release buprenorphine was administered before surgery. Continuous isoflurane administration at 1.5-2% was used for maintenance of anesthesia. The anesthetic state was assessed using a hind-limb toe pinch and respiratory observation. The state of anesthesia was continuously monitored (pinch reflex) throughout the procedure. The surgical site was shaved, prepped with povidone-iodine/ethanol, and draped in a sterile surgical manner. Each rat was positioned in the supine position to expose the meniscus after hair removal and 3 surgical disinfections. The right knee was shaved and prepped with povidone-iodine/ethanol and draped in a sterile surgical manner. Rats were placed on a warm water-flowing heating pad to maintain body temperature. A 1.5 cm vertical incision was made and then the medial joint capsule was sectioned. Before the defects were created, all menisci were confirmed to have a sufficient size for creating the planned defects. A 2 mm complete meniscus injury was performed in the inner two-thirds of the anterior portion of the medial meniscus. 20 μl bioglue was injected between the injury sites. The skin was sutured continuously with absorbable sutures. 2 rats per cage were housed under pathogen-free conditions. They were fed standard laboratory rodent and water ad libitum. Animals were maintained at a constant temperature of 25°C and kept on a 12-h light/dark cycle. Finally, rats were euthanized by carbon dioxide inhalation at each time point. At 2 weeks post-op, cells were isolated from whole knee joint tissues, including synovium, ligament, infrapatellar fat pad, cartilage, and medial meniscus. The harvested tissues were minced, followed by 5 mg/ml collagenase I and IV in serum-free DMEM for 2.5 h at 37°. After enzymatic digestion, an equal volume of 10% FBS in DMEM was added to neutralize the enzymes. Suspended cells were transferred to a 100 µm strainer, centrifuged at 1,600 rpm, and rinsed 3 three times using PBS with 10% FBS. All cells from three animals per group were combined for scRNA-seq analysis.

first: Meng

last: Feng

first: David

last: Pellei

first: Ming

first: Angelyn

last: Nguyen

first: Sarah

last: Ginsberg

first: Hun Jin

last: Jeong


title: Wnt-dependent ontogeny of acellular cementum-forming cementoblasts on the tooth root surface [scRNA-seq]

overall_design: Building on the spatial transcriptomic findings, we next investigated the ontogeny and hierarchy of the cementoblast lineage using single-cell transcriptomics. Pthrp-mCherry+ cells were isolated by fluorescent-activated cell sorting (FACS) at P15 (completion of AC formation), P25 (onset of CC formation), and 8 weeks (maturation), followed by single-cell RNA-sequencing (scRNA-seq). We then computationally integrated these datasets with a previously published Pthrp-mCherry dataset from P6.


title: Arid3b suppresses CD8+ T cell infiltration and function in microsatellite stable colorectal cancer via Runx3 [RNA-seq]

city: Beijing

first: Zhidong

last: Gao

address: No.11 Xizhimen South Street

institute: Peking University People’s Hospital

summary: Microsatellite stable/proficient mismatch repair (MSS/pMMR) colorectal cancer (CRC) is characterized by a cold tumor microenvironment, marked by sparse CD8⁺ T cell infiltration and resistance to immune checkpoint inhibitors (ICIs). To uncover regulators that limit CD8⁺ T cell infiltration in MSS CRC, we conducted an in vivo CRISPR/Cas9 screen targeting genes in CD8⁺ T cells using a CMT93 cell-derived tumor model. This screen identified Arid3b as a key negative regulator of CD8⁺ T cell tumor infiltration and antitumor activity. Genetic ablation of Arid3b in CD8⁺ T cells significantly enhanced their intratumoral accumulation and mediated robust tumor control. Mechanistically, Arid3b deficiency upregulated Runx3, promoting a tissue-resident memory phenotype and effector function. Notably, the benefits conferred by Arid3b knockout were abrogated by Runx3 deletion, indicating a Runx3-dependent mechanism. In summary, targeting ARID3B could offer a promising strategy to reshape the tumor microenvironment and sensitize MSS CRC to immunotherapy.

overall_design: RNA-seq profiling of Arid3b-KO or Control OT1 CD8+ T cells co-cultured with or without CMT93-OVA cells for 4 hours

first: Shuo

first: Sen

last: Hou

first: Ce

last: Luo

first: Yingjiang

last: Ye

first: Zexian

last: Zeng


title: Mitochondrial metabolism regulates the immunogenic responsiveness of dendritic cells

city: MADRID

first: Ignacio

last: Heras-Murillo

state: MADRID

address: c/Melchor Fernandez Almagro, 3

institute: CNIC

summary: Activation of dendritic cells (DCs) is linked to increased glycolysis. However, the role of the mitochondrial electron transport chain (ETC) in conventional DC subset function is poorly defined. Here, we revealed that immunogenic activation elevates late oxygen consumption in cDC1s, but not cDC2s. To investigate the relevance of the ETC in DC immunogenicity, we generated mice with impaired ETC complex III function in DCs. ETC complex III impairment attenuated poised or adjuvant-triggered cDC1 activation, migration and capability to prime T cells for anti-cancer immunity, while it had a mild effect on cDC2s. Mechanistically, loss of complex III in cDC1s led to a deregulated redox and metabolite balance causing DNA hypermethylation of PU.1-binding regions. This DNA hypermethylation diminished early stimulus-induced gene expression linked to immunogenic responsiveness of cDC1s, which was rescued via ectopic expression of alternative oxidase. Our findings show how the ETC differentially regulates the immunogenic function of cDC subsets.

overall_design: cDC1s from Uqcrqf/f,  Itgax-Uqcrqf/f, Uqcrqf/f AOX-Rosa26 and Itgax-Uqcrqf/f AOX-Rosa26 mice were FACS sorted and used for WGBS.

first: Josep

last: Calafell-Segura

first: Diego

last: Mañanes

first: Esteban

last: Ballestar

first: Stefanie

last: K. Wculek

last: Sancho


title: Arid3b suppresses CD8+ T cell infiltration and function in microsatellite stable colorectal cancer via Runx3

overall_design: ChIP-seq of HA or IgG in HA-tagged Arid3b-overexpressing CD8+ T cells

last: Wang

first: Yiteng

last: Jin


title: Systems-level investigation of mucopolysaccharidosis IIIA identifies deficient synaptic activity as a key driver of disease progression

city: Melbourne

first: Jan

last: Kaslin

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

summary: Mucopolysaccharidoses are lysosomal storage diseases that collectively represent a major cause of lethal, treatment-refractory childhood dementias. Clinically-useful interventions are hampered by an incomplete understanding of their neuropathological origins. Using the zebrafish sgshΔex5-6 model of mucopolysaccharidosis IIIA (MPS IIIA, Sanfilippo syndrome A), we conducted several ‘omics-based analyses to define important features in the progression of neurological disease. We find that the massive endolysosomal burden resulting from increased lysosomal storage of heparan sulfate and other secondarily accumulating substrates induces abnormal microtubule organisation and vesicle trafficking in neurons. This results in a gradual impairment of synaptic vesicle localisation at the presynaptic terminal and consequently impaired neuronal activity. Importantly, the endolysosomal phenotype in MPS IIIA zebrafish precedes the onset of molecular hallmarks of overt synaptic dysfunction, though the larval MPS IIIA brain was found to be more susceptible to perturbation than wild type siblings. Ubiquitous transgenic overexpression of sgsh in sgshΔex5-6 zebrafish corrected neuropathological features at the cellular and molecular level, but was associated with low but elevated rates of developmental malformation. Our findings provide mechanistic evidence linking the well-described lysosomal storage basis for MPS IIIA to its disproportionately neurological manifestations, facilitating development and refinement of future therapeutic interventions for this currently untreatable disorder.

overall_design: RNA-seq profiling of zebrafish of the following genotypes at the indicated stages/tissues: 1) wild type; 24 hpf whole embryos (n = 50 pooled), 5 dpf larval heads (n = 50 pooled), 2-month-old brain (n = 3 pooled), 3-month-old brain (n = 3 pooled), 18-month-old brain (n = 3 pooled). 2) sgshΔex5-6; 24 hpf whole embryos (n = 50 pooled), 5 dpf larval heads (n = 50 pooled), 2-month-old brain (n = 3 pooled), 3-month-old brain (n = 3 pooled), 18-month-old brain (n = 3 pooled). 3) wild type ubiquitously overexpressing wild type sgsh; 2-month-old brain (n = 3 pooled). 4) sgshΔex5-6 ubiquitously overexpressing wild type sgsh; 2-month-old brain (n = 3 pooled).

first: Alon

middle: M

last: Douek

first: Abbas

last: Salavaty

first: Mirana

last: Ramialison

first: Peter

last: Currie


title: Srrm2 haploinsufficiency drives SynGAP-γ reduction, Agap3 mis-splicing, and oligodendrocyte deficits in a genetic mouse model of schizophrenia

city: Cambridge

first: Sameer

last: Aryal

state: Massachusetts

address: 75 Ames St

institute: Broad Institute of MIT and Harvard

summary: To investigate the effects of loss of function of SRRM2, a risk gene for schizophrenia and developmental delay/intellectual disability (DD/ID), we performed bulk RNA sequencing of eight brain regions at 1 and 3 months of age. We also performed single-nucleus RNA sequencing of the prefrontal cortex and striatum at 1 month of age. Both experiments compared heterozygous Srrm2 mutant mice (Srrm2+/−) with wild-type littermate controls.

overall_design:
Bulk RNA-Seq of eight brain regions—cerebellar cortex (CC), cerebellar vermis (CV), prefrontal cortex (PFC), striatum (ST), hippocampus (HP), substantia nigra (SN), somatosensory cortex (SSC), and thalamus (TH)—from Srrm2 heterozygous mutant mice and wild-type littermate controls at 1 and 3 months of age.
Single nucleus RNA-Seq of two brain regions—prefrontal cortex (PFC), striatum (STR)—from Srrm2 heterozygous mutant mice and wild-type littermate controls at 1 month of age.


title: Characterization of a panel of mouse primary cell lines from Myc-driven mammary gland tumours and lung metastasis derived from them

city: London

last: Tarrago-Celada

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Triple negative breast cancer (TNBC) represents 15% of all breast cancer subtypes. It is the most aggressive type, with limited treatment options and is often associated with metastasis. TNBC are associated with high expression of an oncogene, c-Myc, driving metabolic to promote tumour growth and metastasis. To study the metabolic changes that allow cancer cells to become metastatic, we used MMTV-Myc mouse model (mouse mammary tumour virus – Myc) of mammary gland tumorigenesis to generate tumour cell lines either from primary mammary gland tumours or lung metastasis. “MYAZ16.1e”, “MYAZ6.6g”, and “MYAZ12.3i” are cell lines generated from primary MMTV-Myc mammary gland tumours (the number represents the I.D. of a tumour-bearing mouse). These cells have low metastatic capacity. “Myc310” is also a tumour cell line generated from one of the MMTV-Myc tumours, but which has higher metastatic capacity and forms visible metastatic lesions in the lung. To generate models with high metastatic capacity, tumour cells were isolated from the lungs of mice bearing mammary gland tumours generated by ectopic injection of Myc310 cells into the fat pad. These cell lines were named “LM1”, “LM2” and “LM3”. LMs cells were further injected in the fat pads of mice to generate mammary gland tumours. LMs cells showed higher metastatic capacity than Myc310 cells. Tumour cell lines isolated from the lungs of mice bearing LM1, LM2 or LM3 mammary gland tumours were named “LM1-LM”, “LM2-LM”, “LM3-LM”. We have demonstrated that that the metastatic cell lines, Myc310, LM and LM-LM are more dependent on extracellular cysteine/cystine to survive than non-metastatic MYAZ cell lines. We therefore performed transcriptomics of some of the generated cell lines in control and cysteine/cystine deprived conditions. To generate a non-tumourigenic control for in vitro experiments and analysis, normal mammary gland epithelial cells were immortalized by ectopic expression of p53DN and E1A and named “iMMEC” cell line (immortalized mouse mammary epithelial cells). To model the event during acute induction of c-MYC overexpression, we generated the “iMMEC+MYC”, iMMECs via transducing with a doxycycline inducible c-MYC construct.

overall_design: All cells were seeded at the same density (250,000 cells per well in 6-well plates) in DMEM:F12 (supplemented with 10% FBS, 1% P/S, 1% HEPES, insulin, hydrocortisone and EGF). For iMMECs+MYC, 500 ng/mL doxycycline was added to the media to induce MYC. After 24 hours media was changed for some of the cell lines (MYAZs, Myc310, LMs and LM1-LM models), to either control or cysteine/cystine deprived media for 6h. Then cells were collected and RNA extraction was performed with RNAeasy kit (QIAGEN 74104). Three technical replicates were done for each cell lines, and the rest of the cell lines have also three biological replicates except Myc310, iMMECs, and iMMEC+MYC.

first: Michael

last: Kossifos

first: Ersa

last: Gjelaj

first: Yulia

last: Panina

first: Tegan

last: Gilmore

first: Mariia

last: Yuneva


title: Condensin and topoisomerases cooperate to relieve topological stress at stalled replication forks

city: Montpellier

first: Mégane

last: Da Mota

address: 141 rue de la cardonille

institute: CNRS

summary: Resolving complex topological structures at replication forks is essential for faithful DNA replication, yet the underlying mechanisms remain poorly understood. Evidence from diverse eukaryotes suggests that condensin – best known for driving chromosome condensation in mitosis – may also operate during S phase to alleviate torsional stress in cooperation with topoisomerases. Here, we show in budding yeast and human cells that condensin binds stressed replication forks, where it cooperates with topoisomerases I and II to promote nascent DNA resection and restart replication. Our data indicate that condensin acts together with topoisomerase I at reversed forks to convert positive supercoils into topological DNA structures that are relaxed by topoisomerase II, enabling fork restart. These findings reveal an evolutionarily conserved role for condensin in resolving topological constraints at arrested forks, reminiscent of its function in chromosome segregation, and suggest that this activity helps prevent the formation of toxic chromosome structures during fork arrest and reversal.

overall_design: DNA Copy Number analysis and Chromatin immunoprecipitation DNA sequencing (ChiP-seq) for Brn1-PK9

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