title: The transcription factors TCF1 and LEF1 promote B-1a cell homeostasis and regulatory function.

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

institute: Francis Crick Institute

summary: B cells are innate-like immune cells found abundantly in serosal cavities and their secreted antibodies are enriched for bacterial recognition1–5. The subset known as “B-1a” repress inflammation by production of regulatory molecules including IL-10 6–8. Unlike conventional B cells, which are produced daily in the bone marrow, B-1a cells are primarily generated from foetal precursors and maintained through self-renewal 9. The mechanisms regulating B-1a homeostasis and function are incompletely understood. Here we demonstrate that serosal cavity mouse and human B-1 cells as well as chronic lymphocytic leukaemia (CLL) B cells express the transcription factors TCF1 and LEF1, and circulating TCF1+LEF1+ B-1 cells increase significantly in patients with bacterial pleural infection. LEF1 is expressed from foetal B-1 progenitors, while TCF1 expression is higher in peripheral B-1a cells. TCF1 and LEF1 deficiency significantly reduces B-1a cells in mice. These transcription factors support B-1a turn-over regulating Myc targets and metabolic pathways. Upon B-1 cell activation, TCF1/LEF1 induce formation of a stem-like population, partly through IL-10 production. TCF/LEF1-deficient B-1 cells proliferate excessively, acquire an exhausted/senescent phenotype, express reduced IL-10 and PD-L1, and fail to suppress brain inflammation. These findings reveal a transcriptional program that links stemness and regulatory potential in B-1a cells.

overall_design: Total B cells (CD19+CD3-) from peritoneal cavity of  TCF1WTLEF1WT and TCF1ΔLEF1Δwere isolated by Fluorescence-activated cell sorting (FACS).

first: Qian

last: Shen

first: Carola

last: Vinuesa


title: The role of RUNX2 and BHLHE40 in pathologically relevant  CD4-positive tissue-resident T-cells in Crohn's disease. (RNA-seq, CD4+ T cell, part2)

status: Public on Aug 14 2025

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

type: Expression profiling by high throughput sequencing

summary: Tissue-resident T-cells (TRM) are deeply involved in immune memory at the site of inflammation. Here, we identified two key transcription factors, RUNX2 and BHLHE40 as regulators of pathologically relevant CD4-positive TRM in the inflamed gut mucosa of Crohn’s disease patients.

overall_design: CD4+ CD103+ HLA-DR+ and HLA-DR- T cells were sorted from mononuclear cells derived from surgically resected fresh gut specimens by flow cytometry. Total RNA was extracted using TRIzol reagent and subjected to RNA-sequencing.

first: Mitsuru

last: Arase

first: Mari

last: Murakami

last: Okuzaki

first: Kiyoshi

last: Takeda


title: ATOR-4066, a Neo-X-Prime bispecific antibody targeting CD40 and CEACAM5, induces strong myeloid and T cell dependent tumor immunity

city: Lund

first: Peter

last: Ellmark

address: Scheelevägen 2, Medicon Village

country: Sweden

institute: Alligator Bioscience AB

summary: ATOR-4066 is a bispecific antibody that targets CD40 and CEACAM5 developed for immunotherapy of cancer using the Neo-X-Prime platform. ATOR-4066 shows potent CEACAM5-dependent activation in vitro with ability to activate intratumoral immune cells from patient derived material. In vivo, ATOR-4066 induced superior anti-tumor activity compared to CD40 mAb in MC38-CEA tumors and cured mice with well-established tumors with a heterogeneous CEACAM5 expression. Using RNA sequencing, we show that ATOR-4066 promotes immune cell trafficking to tumors and activates both myeloid cells and T cells within the tumor microenvironment, with limited immune activation in the periphery.

overall_design: RNAseq of lymph nodes, blood, whole tumors and CD45+Ly6G- cells from tumors from hCD40tg mice inoculated with MC38-CEACAM5 tumors and treated with either vehicle, CD40 mAb or ATOR-4066.

first: Hampus

last: Andersson

first: Malin

last: Lindstedt


title: The transcription factors TCF1 and LEF1 promote B-1a cell homeostasis and regulatory function

country: United Kingdom

summary: B-1 cells are innate-like immune cells found abundantly in serosal cavities and their secreted antibodies are enriched for bacterial recognition1–5. The subset known as “B-1a” repress inflammation by production of regulatory molecules including IL-10 6–8. Unlike conventional B cells, which are produced daily in the bone marrow, B-1a cells are primarily generated from foetal precursors and maintained through self-renewal 9. The mechanisms regulating B-1a homeostasis and function are incompletely understood. Here we demonstrate that serosal cavity mouse and human B-1 cells as well as chronic lymphocytic leukaemia (CLL) B cells express the transcription factors TCF1 and LEF1, and circulating TCF1+LEF1+ B-1 cells increase significantly in patients with bacterial pleural infection. LEF1 is expressed from foetal B-1 progenitors, while TCF1 expression is higher in peripheral B-1a cells. TCF1 and LEF1 deficiency significantly reduces B-1a cells in mice. These transcription factors support B-1a turn-over regulating Myc targets and metabolic pathways. Upon B-1 cell activation, TCF1/LEF1 induce formation of a stem-like population, partly through IL-10 production. TCF/LEF1-deficient B-1 cells proliferate excessively, acquire an exhausted/senescent phenotype, express reduced IL-10 and PD-L1, and fail to suppress brain inflammation. These findings reveal a transcriptional program that links stemness and regulatory potential in B-1a cells.

overall_design: B-1 progenitors from fetal liver and bone marrow, B-1 cells from peritoneal cavity and spleen of  TCF1WTLEF1WT mice were isolated by Fluorescence-activated cell sorting (FACS) followed by hashtage with Cite-seq antibodies. B-1 cells from peritoneal cavity of TCF1ΔLEF1Δ mice  were isolated by Fluorescence-activated cell sorting (FACS).


title: Biallelic deleterious variants in SNAPIN, a retrograde dynein adaptor, cause a prenatal-onset neurodevelopmental disorder [1]

city: Chicago

first: Erica

last: Davis

state: IL

address: 225 E Chicago Avenue

department: Advanced Center for Translational and Genetic Medicine (ACT-GeM)

country: USA

institute: Ann & Robert H Lurie Children's Hospital of Chicago

summary: Fetal brain anomalies identified by prenatal ultrasound and/or magnetic resonance imaging represent a considerable healthcare burden with ~1-2/1,000 live births. To identify underlying etiology, trio prenatal exome sequencing or genome sequencing (ES/GS) has emerged as a comprehensive diagnostic paradigm with a reported diagnostic rate up to ~32%. Here, we report five unrelated families with six affected cases that presented neuroanatomical, craniofacial, and skeletal anomalies, all harboring rare, biallelic deleterious variants in SNAPIN, encoding SNARE-associated protein. SNAPIN is a ubiquitously expressed component of the autophagy-lysosomal pathway that catalyzes retrograde axonal transport and synaptic transmission. To investigate the role of SNAPIN in brain development, we generated zebrafish gene ablation models, which recapitulated human-relevant disease phenotypes. Two independent, genetically stable snapin mutants exhibited pre-adulthood lethality, reduced overall length, disproportionately smaller head size, and altered brain morphology. Transcriptomic profiling of snapin mutant zebrafish heads revealed an early and progressive transcriptomic shift marked by autophagy activation with concomitant downregulation of structural and neurodevelopmental genes. Assessment of brain cellular ultrastructure with electron microscopy and LC3-II immunoblotting revealed retrograde vesicle transport defects, with accumulation of late endosomes and autophagosomes. Together, these findings support SNAPIN as a likely causal gene for a severe neurodevelopmental syndrome and expand the growing list of autophagy-lysosome pathway regulators essential for human brain development.

overall_design: To investigate the impact of snapin dysfunction in an in vivo neurodevelopmental context, we performed transcriptomics studies using RNA isolated from heads of snapin 9bpdel-2bpins homozygous mutants and wild type zebrafish larvae at 10 dpf (two biological replicates each).

middle: E


title: Targeting ATF6 Reduces Pathological Neovascularization and Improves Visual Outcomes in Retinal Disease Models

city: Stanford

first: Allyssa

last: Bradley

address: 450 Jane Stanford Way

institute: Stanford University

summary: Pathological retinal neovascularization is a common mechanism for leading causes of vision loss including retinopathy of prematurity (ROP), diabetic retinopathy, and wet age-related macular degeneration. The Unfolded Protein Response (UPR) is an intracellular signal transduction mechanism controlled by the ER-resident proteins ATF6, IRE1, and PERK.  In response to endoplasmic reticulum stress, UPR activates downstream transcriptional and translational programs that upregulate many proteins, including key angiogenesis factors like VEGF and HIF1a.  This suggests an important role for UPR in developmental and pathologic retinal angiogenesis, but it is unclear which UPR regulatory genes are most important in these processes.  Here, we focused on the role of Activating Transcription Factor 6 (ATF6) in pathologic and developmental retinal angiogenesis. We induced pathologic retinal neovascularization in Atf6-/- mice using the oxygen-induced retinopathy (OIR) model of ROP and examined functional, histologic, and molecular consequences in the retina. we found significantly preserved visual function, accompanied by decreased retinal neovascularization, endothelial cell proliferation, and UPR and angiogenesis transcriptional programs in Atf6-/- mice after OIR. When we chemically blocked ATF6 signaling by intraocular injection of the small molecule Ceapin-A7, we also saw suppression of UPR and angiogenesis gene expression. Last, we examined very young Atf6-/- mice when the inner retinal vasculature is developing and found a significant defect in pruning and blood vessel extension to the periphery at P7, but this delay was transient and Atf6-/- blood vessels fully recovered at older ages of development. Together, our results demonstrate ATF6’s critical role in developmental and pathological angiogenesis and highlight its potential as a therapeutic target to mitigate pathological retinal neovascularization.

overall_design: RNA-seq profiling of Atf6-/- mouse retinas (C57BL/6J background) subjected to oxygen-induced retinopathy model of Retinopathy of Prematurity and wildtype mouse retinas subjected to intraocular injection of Atf6 inhibitor Ceapin-A7

first: Soyoung

last: Park

first: Soyeon

first: Kyle

last: Kim

first: Angela

last: Galdamez

first: Monica Sophia

last: Diaz-Aguilar

first: M

last: Hartnett

first: Eun-Jin

last: Lee

first: Jonathan

middle: H

last: Lin


city: Acton

first: Zhi-Ping

last: Feng

state: ACT

address:
131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University

country: Australia

institute: JCSMR

overall_design: RNA-seq profiling of B-1a cells sorted from peritoneal cavity from four different gentoypes: TCF1ΔLEF1Δ,TCF1Δ, LEF1Δ,TCF1WTLEF1WT

first: Qian

last: Shen

first: Hao

last: Wang

first: XiangPeng

last: Meng

last: Roco

first: Michale

last: Battaglia

first: Probir

last: Chakravarty


title: The transcriptome alteration of SCC15 cells after treatment with AOH1996.

city: Beijing

first: Yujia

address: 22 Zhongguancun South Avenue, Haidian District

country: China

institute: Peking University School and Hospital of Stomatology

summary: To explore the mechanism of AOH1996 therapeutic effect on SCC15 cells.

overall_design: RNA-sequencing (RNA-seq) was performed in SCC15 cells after treatment with AOH1996.

first: Lingfei

last: Jia


title: Low-potassium triggers epithelial NLRP3/ASC-driven kidney inflammation independently of inflammasomes

city: Shimotsuke

first: Takanori

last: Komada

state: Tochigi

address: 3311-1, Yakushiji

department: Center for Molecular Medicine

institute: Jichi Medical University

summary: We have employed a single cell RNA sequencing analysis using 10x genomics scRNAseq to study the effect of potassium deficiency on the non-leukocyte kidney cells. Long-term potassium deficiency leads to kidney injury and inflammation. This study investigated a pro-inflammatory cascade in the kidney epithelial cells.

overall_design: Male C57BL/6J WT mice were fed with a normal potassium or low potassium diet for 4 weeks. To obtain non-leukocyte kidney cells, the whole kidneys were enzymatically digested and single cells were isolated by using Fluorescence-activated cell sorting (FACS) and analyzed by scRNA-seq.

first: Komada

last: Takanori

first: Matsumura

last: Takayoshi

first: Takahashi

last: Masafumi


title: A memory transcriptome time course reveals essential long-term memory transcription factors in Drosophila

city: Halifax

first: Spencer

middle: Gordon

last: Jones

state: NS

address: 5850 College St

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: In vivo CRISPR screens in Head and Neck Cancer reveal that Uchl5 modulates extracellular matrix deposition to promote immune evasion.

city: Cambridge

first: Robert

last: Manguso

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Recurrent/metastatic head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy with a high unmet need for enhancing immunotherapy given current modest responses. Here, we performed an in vivo CRISPR screen in a HNSCC mouse model to identify immune evasion genes. We identified several epigenetic regulators of immune checkpoint blockade (ICB) response, including the ubiquitin C-terminal hydrolase 5 (UCHL5). Loss of Uchl5 in tumors increased CD8+ T cell infiltration and improved ICB responses. Uchl5 deficiency reduced extracellular matrix (ECM) production and epithelial-mesenchymal-transition (EMT) transcriptional signatures, which contribute to stromal desmoplasia, a histologic finding associated with reduced anti-PD1 response in human HNSCCs. We identified a functional role for COL17A1, a collagen highly and specifically expressed in HNSCC, in Uchl5-mediated immune evasion. Our findings suggest an unappreciated role for UCHL5 in promoting EMT in HNSCC and highlight ECM modulation as a strategy to improve immunotherapy responses.

overall_design: The preclinical murine oral carcinoma MOC1-esc1 cell line were treated for 24h with either DMSO or 10ng/ml IFNγ. Cells were collected for RNA-seq after 24h treatment.

first: Cong

last: Fu

first: Ashwin

middle: V

last: Kammula

first: Sarah

middle: Y

last: Kim

first: Ravindra

last: Uppaluri

middle: T


title: Junctional epithelial Plakoglobin facilitates intestinal inflammation by p38MAPK-dependent activation of the inflammasome

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

country: Germany

institute: University Hospital Würzburg

summary:
Desmosomes play an underexplored role in intestinal homeostasis and are linked to the pathogenesis of inflammatory bowel diseases. We found a novel function of the desmosomal plaque protein Plakoglobin (JUP) in initiating the innate immune response to facilitate intestinal inflammation.
Tissue samples from Crohn’s disease (CD) patients revealed a loss of JUP, which was mirrored in a mouse model of dextran sodium sulfate-induced (DSS) colitis. Inducible intestinal epithelial-specific knock-out of Jup (iVilCreERT2Jupfl/fl) in mice resulted in increased submucosal infiltration of macrophages and neutrophils, along with activation of the inflammasome. This was paralleled by p38MAPK phosphorylation, while loss of intestinal epithelial barrier function was absent. In DSS-colitis, epithelial Jup-deficiency impaired recovery and enhanced IL23/IL17-signaling. Intestinal organoids lacking Jup demonstrated NLRP1 inflammasome activation, indicated by increased IL1β and IL18 levels, which was attenuated by p38MAPK inhibition. In silico analysis and co-immunoprecipitation confirmed a direct interaction between JUP and p38MAPK, revealing a regulatory mechanism where JUP limits inflammasome signaling in intestinal epithelial cells. These effects were blunted by NLRP1/3 inhibitor ADS032.
These findings identify JUP as a critical modulator of epithelial innate immunity in the gut. The loss of JUP in tissues from CD patients underscores its potential relevance in disease pathology.

overall_design:
We generated single-cell transcriptome data from single cells purified from the adult mouse colon with the following experimental conditions: untreated wildtype mice, untreated JUP-KO mice, DSS-treated wildtype mice, and DSS-treated  JUP-KO mice.
Please note that processed data generated from each replicate is linked to the corresponding GEX sample records.

first: Matthias

last: Kelm

first: Natalie

last: Burkhard

first: Marius

last: Hörner

first: Catherine

last: Kollmann

first: Christoph

last: Otto

first: Babak

last: Saravi

first: Anna C.

last: Seubert

first: Friedrich

last: Forchel

first: Brenda

last: Gerull

first: Rebecca

last: Springer

first: Stefanie

last: Kampmeier

first: Vera

last: Rauschenberger

first: Nikita

last: Deoghare

first: Christoph-Thomas

last: Germer

first: Panagiota

last: Arampatzi

first: Daniela

last: Kugelmann

first: Alexander

last: García-Ponce

first: Jens

last: Waschke

first: Sven

last: Flemming

first: Nicolas

last: Schlegel


title: Targeted transcriptomics on the effects of genetic and pharmacological microglial depletion using Nanostring nCounter SPRINT

city: San Antonio

first: Xianlin

last: Han

state: TX

address: 7703 Floyd Curl Drive

department: Barshop Institute

institute: UT Health San Antonio

summary: Abnormal lipid metabolism in Alzheimer’s disease (AD) was first documented by Alois Alzheimer in his early observations of patients with a then unrecognized brain disease, which he noted was characterized by a significant presence of adipose inclusions or lipoid granules. Despite this early recognition, until recently the significance of abnormal lipid metabolism in AD has been largely overlooked by the scientific community for decades, highlighting a critical gap in our understanding of this complex disease. In the past decade, numerous loci and genes with genome-wide significant evidence of affecting AD risk have been reported. Notably, a significant portion of these AD risk genes are either preferentially or exclusively expressed by microglia in the brain and/or code for enzymes that directly or indirectly regulate lipid metabolism. This suggests a major, yet uncharacterized, role of microglia in modulating brain lipid metabolism under AD pathological conditions. In our study, we dissected microglia-dependent and independent regulation of lipid metabolism in an AD-like mouse model of amyloidosis, 5xFAD, taking advantage of pharmacological and genetic interventions to eliminate microglia. Using multidimensional mass spectrometry-based shotgun lipidomics (MDMS-SL), we identified overt changes in a number of AD-associated lipids (ADALs) in postmortem patient brains and mouse models of amyloidosis. This included bis(monoacylglycerol)phosphate (BMP), a lipid class enriched in endosomal/lysosomal compartments, and the two most abundant classes of lysophospholipids: lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE), which are commonly associated with inflammation. Our findings revealed that microglial depletion prevented the accumulation of arachidonic acid-containing BMP species, which are associated with lysosomal activation induced by amyloidosis via a mechanism that involves progranulin, coded by AD risk gene GRN, as shown by targeted transcriptomics, immunoblotting, and immunofluorescence. Surprisingly, AD-associated LPC and LPE accumulation was not driven by microglia. Instead, LPC accumulation correlated with astrocytic activation, while LPE accumulation seems to be associated with oxidative stress. In summary, we uncovered novel microglia-dependent and independent mechanisms that drive lipid dysregulation in AD. These findings may be mechanistically linked with the early glial lipoid deposits described by Dr. Alzheimer.

overall_design: Total 26 samples were included for genetic depletion cohort including both sexes in 4 groups. Total 12 samples were included for pharmacological depletion cohort in 3 groups with only male.

first: Ziying

last: Xu

first: Sepideh

middle: K

last: Shabestari

first: Savannah

last: Barannikov

first: Kevin

middle: F

last: Bieniek

first: Mathew

last: Blurton-Jones

first: Juan

middle: P

last: Pablo


title: A memory transcriptome time course reveals essential long-term memory transcription factors in Drosophila [RNA-Seq]

first: Spencer

last: Jones

summary: We have analyzed transcript level changes in nuclei isolated from the adult mushroom body (MB) of Drosophila melanogaster, as well from whole-head (WH) nuclear extracts, both during and after long-term courtship memory formation. MB and WH nuclei were isolated at eight time-points across a 24-hour period.

overall_design: Transcript levels were examined in mushroom body (MB) and whole-head (WH) nuclei isolated from adult wild-type flies at eight time points over a 24-hour period, both during and after long-term courtship memory training. Genetic material was collected from pools of 50–60 fly heads, with 2–3 replicates per condition

first: Jones

middle: G

last: Spencer

first: Kramer

middle: M

last: Jamie


title: The role of RUNX2 and BHLHE40 in pathologically relevant  CD4-positive tissue-resident T-cells in Crohn's disease. (scMultiome)

first: Daisuke

last: Motooka

overall_design: CD4-positive T cells were sorted from mononuclear cells derived from surgically resected gut specimens by flow cytometry. Nucei were extracted from  CD4-positive T cells and subjected to scMultiome analysis.

first: Mitsuru

last: Arase

first: Mari

last: Murakami

last: Okuzaki

first: Kiyoshi

last: Takeda


title: The role of RUNX2 and BHLHE40 in pathologically relevant  CD4-positive tissue-resident T-cells in Crohn's disease.

overall_design: RUNX2 and/or BHLHE40 were overexpressed on CD4-positive  T cells derived from human blood. Cells were stmulated by  PMA/ionomycin, followed by RNA extraction for bulk RNA-seq analysis.


title: The role of RUNX2 and BHLHE40 in pathologically relevant  CD4-positive tissue-resident T-cells in Crohn's disease. (CITE-seq, CD4+ T cell)

overall_design:
CD4+ T cells were sorted from mononuclear cells derived from surgically resected fresh gut specimens by flow cytometry. Each specimen was labeled with HTO antibodies and subjected to single-cell CITE-seq analysis
details of the HTO antibodies: Totalseq-C Human Universal Cocktail (supplementary file: TotalSeq_C_Human_Universal_Cocktail_v1_137_Antibodies_Barcodes.xlsx, BioLegend) was used.

first: daisuke


title: The G-Protein-Coupled Receptor Kinase 2 (GRK2) Orchestrates Hair Follicle Homeostasis

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary: Tightly regulated cell-cell and cell-niche intercommunications via intertwined signaling networks are involved in maintaining normal hair follicle (HF) homeostasis, cycling and cell fate determination. However, knowledge of specific mechanisms by which hair loss takes place under pathological situations is needed. Using a keratinocyte-specific knockout mouse model, we uncover that the G-protein-coupled receptor kinase 2 (GRK2) signaling node plays a key role in HF homeostasis. Epidermal GRK2 ablation causes alterations during anagen induction, giving rise to abnormal cyst-like structures. HF-linked cysts display aberrant growth and differentiation patterns as well as lineage infidelity, displaying features of abortive HFs unable to fully acquire canonical hallmarks. Cysts triggered by GRK2 deletion displace the dermal papilla away from the bulge and promote irreversible changes in HF stem cell architecture, leading to bulge destruction and hair loss. Our data provide unforeseen roles of GRK2 in epidermal physiology and uncover mechanisms linking dystrophic follicular cysts formation with hair loss, with potential connections to pathogenic processes operating in immune-mediated alopecias.

overall_design:
Comparative gene expression profiling analysis of bulk RNA-seq data obtained from 8-month-old whole mouse skin tissue lysates
Comparative gene expression profiling analysis of bulk RNA-seq data obtained from 8-month-old HFSCs

first: Alejandro

last: Asensio

first: Federico

last: Mayor Jr

first: Catalina

last: Ribas


title: A memory transcriptome time course reveals essential long-term memory transcription factors in Drosophila [ATAC-seq]

summary: We have analyzed regions of accessible chromatin in adult mushroom body neurons of Drosophila melanogaster of a control genetic background using ATAC-seq.

overall_design: Examination of accessible chromatin regions in the adult mushroom body of Drosophila melanogster in a control genetic background using ATAC-seq. Genetic material was extracted from 1/3rd of mushroom body nuclei isolated from pools of 50-60 fly heads in two biological replicates. Timing of material extraction corresponds to one hour after the onset of courtship training, one hour prior to the light period.


title: The role of RUNX2 and BHLHE40 in pathologically relevant  CD4 positive tissue-resident T-cells in Crohn's disease. (CITE-seq, CD4+ CD103+ T cell)

overall_design: CD4+CD103+ T cells were isolated from frozen gut specimens by flow cytometry, and each specimen was labeled with HTO antibodies before performing scRNA-seq analysis.


title: An mRNA-based broad-spectrum antiviral inspired by ISG15 deficiency protects against viral infections in vitro and in vivo II

status: Public on Aug 13 2025

city: New York

first: Dusan

last: Bogunovic

address: 650 W 168th Street

department: Pediatrics

institute: Columbia University

summary: Type I interferons (IFN-I) are cytokines with potent antiviral and inflammatory capacities. IFN-I signaling drives the expression of thousands of IFN-I stimulated genes (ISGs), whose aggregate function results in the control of viral infections. A few of these ISGs are tasked with negatively regulating the IFN-I response to prevent overt inflammation. ISG15 is a negative regulator whose absence leads to persistent, low-grade elevation of ISG expression and concurrent, often self-resolving, mild autoinflammation. The limited breadth and low-grade persistence of ISGs expressed in ISG15 deficiency are sufficient to confer broad-spectrum antiviral resistance. Inspired by the antiviral state of humans with ISG15 deficiency, we identified a nominal collection of 10 ISGs that recapitulated the broad antiviral potential of the IFN-I system, which typically induces the expression of thousands of ISGs. The expression of this 10-ISG collection in an IFN-I non-responsive cell line increased cellular resistance to Zika virus, vesicular stomatitis virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A lipid nanoparticle-encapsulated mRNA formulation of this 10-ISG collection significantly reduced IAV plaque size in vivo in mice when given prophylactically. Moreover, when used collectively and delivered prophylactically, 10-ISG was able to protect hamsters against a lethal SARS-CoV-2 challenge, in contrast with the lack of efficacy when mRNAs were delivered individually. These findings suggest that these 10 ISGs have potential as a broad-spectrum antiviral prophylactic.

overall_design: RNA sequencing on lung tissues from Syrian golden hamsters treated with PBS or modRNA-LNP formulations on day -1 and evaluated 4 days following SARS-CoV2 infection

first: Yemsratch

last: Akalu

first: Roosheel

middle: S

last: Patel

first: Justin

last: Taft

first: Brad

middle: R

last: Rosenberg


title: Effect of PRLX-93936 treatment on gene expression of PANC-1 cells

city: Palo Alto

first: Steven

last: Corsello

state: California

address: 240 Pasteur Drive

department: Stanford School of Medicine

summary: PRLX-93936 is an optimized derivative of erastin. To determine the downstream effects of PRLX-93936 on gene expression, we performed mRNAseq of PANC-1 cells treated with the drug or vehicle control.

overall_design: PANC-1 cells were seeded in 6-well plates. The following day, cells were treated in triplicate with 0.5 uM PRLX-93936, 5 uM PRLX-93936, or DMSO vehicle control for 2 hours and 6-hours. RNA was isolated using RNeasy Mini Kit (QIAGEN) with DNase treatment. RNA QC, library preparation, and Novaseq sequencing were performed by Genewiz. Gene-level expression was quantified from RNA-seq using the nf-core/rnaseq pipeline (version 3.12.0). Salmon (version 1.10.1) was used to generate gene-level read counts.

first: Nick

middle: A

last: Phillips


title: Spatially-patterned and functional kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling [hKPA_invivo_data]

city: Los Angeles

first: Zhongwei

last: Li

state: CA

address: 1425 San Pablo St

department: Keck medicine

institute: University of Southern California

summary: The paired kidneys are the central organs of homeostasis for our body systems, the sophisticated structure and complex cells composition underpins kidneys’ functions. Here we reported the generation of human kidney progenitor assembloid (KPA) with expandable nephron progenitor cells (NPC) and ureteric bud (UB). These generated hSK showed patterned structure and included nephron, collecting duct and interstitium. More importantly, after transplantation hKPA developed more mature features and vasculature, and transplanted PKD2 hKPA developed abundant cysts, which shared some common features with human ADPKD kidney

overall_design: Cell populations profiling analysis of transplanted hKPA collected at around 1-month and 2-month time points through 10x Genomics snRNA-Seq assay

first: Biao

last: Huang

first: Pedro

last: Medina

first: Jincan

last: He

first: Zipeng

last: Zeng

first: Janet

last: Romo

first: Sunghyun

last: Kim

first: Kari

last: Koppitch

first: Chennan

last: C. Zhang

first: Nils

last: O. Lindström

first: Cizhong

last: Jiang

first: Andrew

last: P. McMahon


title: BMAL1 represses transposable elements independently of CLOCK in pluripotent cells

city: Granada

first: Ivan

middle: Fernández

last: Rengel

address: Avenida de la Ilustración 114

institute: GENyO


title: An mRNA-based broad-spectrum antiviral inspired by ISG15 deficiency protects against viral infections in vitro and in vivo

first: Dusan

last: Bogunovic

overall_design: RNA sequencing on fibroblasts from ISG15-/- and healthy individuals under two conditions: unstimulated and IFN-I exposed (12-hour IFN-I stimulation followed by 24-hour rest).

first: Yemsratch

last: Akalu

first: Roosheel

last: Patel

first: Justin

last: Taft


title: Targeting an essential viral oncoprotein with an IL-7-enhanced mRNA vaccine induces durable immunity to Merkel cell carcinoma

city: New Haven

first: Jeffrey

last: Ishizuka

state: CT

address: 300 George Street

institute: Yale University

summary: mRNA technologies have reinvigorated cancer vaccine development, but the optimal antigenic targets remain unclear. Further, generation of memory CD8+ T cell responses, critical for durable immunity, remains a challenge. We identified the Merkel cell carcinoma (MCC) Large T Antigen (LTA) as an exemplar target antigen, required for tumor cell survival and immunogenic in a cancer with rising incidence and high unmet need. We developed an mRNA vaccine to MCC-LTA in murine studies and MCC patient samples and showed that antigen loss developed rapidly and caused resistance when the antigen was not essential for tumor survival. To improve T cell response quality and durability, we co-encoded LTA and IL-7, co-localizing proliferative and memory signals spatially and temporally with antigen exposure. IL-7-containing mRNA vaccines enhanced T cell expansion, memory differentiation and sustained tumor control. We propose that antigen essentiality and signal co-encoding may be adapted to improve the efficacy of mRNA therapeutics.

overall_design: scRNAseq, CITE-seq, TCRseq; MCC patient T cells were cultured in IL-2+IL-7 for 25 days. Every 7 days they were stimulated with monocyte-derived DCs either expressing the LTA vaccine or with placebo lipid nanoparticles. On the day prior to sequencing, T cells were stimulated with either placebo DCs, LTA-DCs or matched primary tumor cells prior to sequencing using the 5' 10x Genomics platform. Cell hashing / HTOs were used to distinguish experimental conditions.


title: ARID1A recruits non-homologous end joining factors to DNA breaks induced by G4 ligands

city: London

first: Karen

last: Lane

address: 237 Fulham Road

institute: Institute of Cancer Research

summary: ARID1A, a subunit of the BAF chromatin remodeler, is frequently mutated in cancer. Predicting how ARID1A loss impacts cancer therapy response is challenging because it influences many cellular pathways. G quadruplex (G4) binding ligands, such as pyridostatin, show anticancer effects, but the genetic determinants influencing the response to G4 ligands are not fully understood. Here, we show that ARID1A-deficient cells are selectively sensitive to pyridostatin compared to isogenic controls. This was apparent in ovarian and colorectal cancer cell line models, and in vivo studies suggest that G4 ligands hold promise for ARID1A-deficient cancers. While ARID1A modulates pyridostatin-induced transcriptional responses, we show that toxicity in ARID1A-deficient cells arises from the defective repair of topoisomerase-induced breaks. Notably, these cells fail to efficiently accumulate non-homologous end joining proteins on chromatin following pyridostatin exposure. These data uncover a role for ARID1A in the cellular response to G4 ligands, linking remodeling to G4 ligand-induced responses.

overall_design: RNA-seq of TOV21G cells - parental [ARID1A deficient] and 2 independent biological clones stably expressing exogenous ARID1A [ARID1A proficient]. Cells were untreated or treated with 10uM PDS and harvested after 4hrs

first: Susana

last: Simões-Sousa

first: Alison

last: Harrod

first: Jessica

last: Downs


title: Priming with DNMT inhibitors potentiates PD-1 immunotherapy by triggering viral mimicry in relapsed/refractory NK/T-cell lymphoma

city: Guangzhou

first: Jianfeng

last: Chen

address: 651East Dongfeng Road

institute: SYSUCC

summary: Anti-PD-1 immunotherapy has demonstrated significant anti-tumor efficacy in treating relapsed or refractory natural killer/T cell lymphoma (R/R NKTL). However, both intrinsic and acquired resistance remain a substantial challenge. DNA hypermethylation serves as a critical epigenetic modifier influencing anti-tumor immunity in NKTL. Here, we evaluate the efficacy and safety of combining DNA methyltransferase (DNMT) inhibitors with anti-PD-1 monoclonal antibody (mAb) as salvage therapy in 21 patients with R/R NKTL who had previously failed frontline immunotherapy. This combination therapy achieved an objective response rate (ORR) of 66.7% (14/21), with a complete response (CR) rate of 47.6% (10/21), and a 2-year overall survival (OS) rate of 50.2%. To investigate the mechanisms underlying the therapeutic efficacy of this combination, we established a preclinical xenograft model of acquired resistance to anti-PD-1 therapy. Our findings revealed that resistance to anti-PD-1 treatment was characterized by the absence of CD8+ T-cell infiltration and the inactivation of interferon pathways. In contrast, DNMT inhibitors restored CD8+ T-cell infiltration, and sensitized tumors to anti-PD-1 therapy. Mechanistically, DNMT inhibitors induced DNA demethylation of endogenous retroviral elements (ERVs), leading to the upregulation of endogenous nucleic acid expression and the activation of a viral mimicry response. This response subsequently triggered the type I interferon pathway, thereby enhancing anti-tumor immunity in both murine and human T-cell lymphoma models. Collectively, our study highlights the potential of DNMT inhibitors in restoring tumor sensitivity to anti-PD-1 therapy and provides compelling evidence for combining DNMT inhibitors with anti-PD-1 mAb as a promising therapeutic strategy for R/R NKTL.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 1.RNA-seq for EL4-P0 and EL4-P3 tumors. 2. RNA-seq for EG7-OVA cells after DMSO, azacytidine(AZA) or decitabine(DAC) treatment. 3. RNA-seq for NKYS cells after DMSO, azacytidine(AZA) treatment.

first: Cheng

last: Huang

first: Jing

last: Tan


title: Spatially-patterned and functional kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling [hKPA_TT_data]

first: Zhongwei

last: Li

summary: The paired kidneys are the central organs of homeostasis for our body systems, the sophisticated structure and complex cells composition underpins kidneys’ functions. Here we reported the generation of human kidney progenitor assembloid (KPA) with expandable nephron progenitor cells (NPC) and ureteric bud (UB). These generated hKPA showed patterned structure and included nephron, collecting duct and interstitium. More importantly, the application of TTNPB revealed the critical role of RA (retinoic acid) signaling pathway in hKPA generation.

overall_design: Cell populations profiling analysis of hKPA treated with complete Stage I medium or TT removal medium, collected on day 5 time point through 10x Genomics snRNA-Seq assay

first: Biao

first: Pedro

last: Medina

first: Jincan

last: He

first: Zipeng

last: Zeng

first: Janet

last: Romo

first: Sunghyun

last: Kim

first: Kari

last: Koppitch

first: Chennan

last: C. Zhang


title: Age-linked DNA Methylation and Gene Expression in Head and Neck Alveolar Rhabdomyosarcoma [RNA-seq]

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

summary: Alveolar rhabdomyosarcoma (ARMS) primarily affects children in the first decade of life, but it can also occur during adolescence, typically with a more favorable prognosis. This study aimed to explore DNA methylation (DNAm) and gene expression differences that could explain the poorer prognosis in younger patients. Whole-genome DNAm and transcriptome analyses were conducted on 10 head and neck ARMS samples, including 4 from patients under 1 year old and 6 from those over 10 years old. Although DNAm profiles were similar across age groups, significant differences in gene expression were identified. These findings suggest potential age-related molecular mechanisms and highlight candidate genes for further investigation as novel therapeutic targets. Notably, CDK9 emerged as a promising target, warranting further exploration in the context of ARMS treatment.

overall_design:
Patients were divided in two age groups. Then we performed differential expression analysis between patients under one year of age (group A) and over 10 years of age (group B)

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************


title: The noncoding circular RNA circHomer1 regulates synaptic development and experience-dependent plasticity in mouse visual cortex

city: Shatin

first: Yao

last: Zhu

address: CUHK

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) are a class of closed-loop, single stranded RNAs whose expression is particularly enriched in the brain. Despite this enrichment and evidence that the expression of circRNAs are altered by synaptic development and in response to synaptic plasticity in vitro, the regulation by and function of the majority of circRNAs in experience-dependent plasticity in vivo remain unexplored. Here, we employed transcriptome-wide analysis comparing differential expression of both mRNAs and circRNAs in juvenile mouse primary visual cortex (V1) following monocular deprivation (MD), a model of experience-dependent developmental plasticity. Among the differentially expressed mRNAs and circRNAs following 3-day MD, the circular and the activity-dependent mRNA forms of the Homer1 gene, circHomer1 and Homer1a respectively, were of interest as their expression changed in opposite directions: circHomer1 expression increased while the expression of Homer1a decreased following 3-day MD. Knockdown of circHomer1 delayed the depression of closed-eye responses normally observed after 3-day MD. circHomer1-knockdown also led to a reduction in average dendritic spine size prior to MD but critically there was no further reduction after 3-day MD, consistent with impaired structural plasticity. circHomer1-knockdown also prevented the reduction of surface AMPA receptors after 3-day MD. Thus, the expression of multiple circRNAs are regulated by experience-dependent developmental plasticity, and our findings highlight the essential role of circHomer1 in V1 synaptic development and experience-dependent plasticity.

overall_design: mRNA and circular RNA sequencing of the left and right V1 in wild-type C57BL/6J mice at P28 after 3-day MD.


title: Spatially-patterned and functional kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling

summary: The paired kidneys are the central organs of homeostasis for our body systems, the sophisticated structure and complex cells composition underpins kidneys’ functions. Here we reported the generation of human kidney progenitor assembloid (hKPA) with expandable nephron progenitor cells (NPC) and ureteric bud (UB). These generated hKPA (in vitro) showed patterned structure and included nephron, collecting duct and interstitium.

overall_design: Cell populations profiling analysis of human kidney progenitor assembloids (hKPAs) collected at Day 25 time point through 10x Genomics Multiome (scRNA/scATAC-seq) assays

middle: C

last: Zhang

first: Nils

middle: O

last: Lindström

first: Cizhong

last: Jiang

first: Andrew

last: McMahon


title: Unbiased and comprehensive identification of viral encoded circular RNAs in a large range of viral species and families

city: Namur

first: Damien

last: Coupeau

address: Rue de Bruxelles, 61

department: Namur Research Institute for Life Sciences

country: Belgium

institute: University of Namur

summary: Non-coding RNAs play a significant role in viral infection cycles, with recent attention focused on circular RNAs (circRNAs) originating from various viral families. Notably, these circRNAs have been associated with oncogenesis and alterations in viral fitness. However, identifying their expression has proven more challenging than initially anticipated due to unique viral characteristics. This challenge has the potential to impede progress in our understanding of viral circRNAs. Key hurdles in working with viral genomes include: (1) the presence of repetitive regions that can lead to misalignment of sequencing reads, and (2) unconventional splicing mechanisms that deviate from conserved eukaryotic patterns. To address these challenges, we developed vCircTrappist, a bioinformatic pipeline tailored to identify backsplicing events and pinpoint loci expressing circRNAs in RNA sequencing data. Applying this pipeline, we obtained novel insights from both new and existing datasets encompassing a range of animal and human pathogens belonging to Herpesviridae, Retroviridae, Adenoviridae and Orthomyxoviridae families. Subsequent RT-PCR and Sanger sequencings validated the accuracy of the developed bioinformatic tool for a selection of new candidate viral encoded circRNAs. These findings demonstrate that vCircTrappist is an open and unbiased approach for comprehensive identification of virus-derived circRNAs.

sample_organism:
Gallus gallus
Homo sapiens
Bos taurus
Ovis aries

overall_design:
To test our bioinformatics pipeline, we gathered samples from diverse viral infections : Bovine Leukemia Virus (BLV, 3 cell lines), Human T-Lymphotropic Virus 1 (HTLV-1, 2 cell lines), Alcelaphine Herpesvirus 1 (AlHV-1, 2 infected calves), Human Adenovirus C5 (hAdV-C5, 3 time points) and Gallid Herpesvirus 2 (GaHV-2, 1 infected cell line).
We extracted RNAs from the infected cell lines and treated them with RNase R before sending them for paired-end RNA sequencing at Novogene.
We processed the data through vCircTrappist to identify candidate circRNAs.

first: Alexis

last: Chasseur

first: Maxime

last: Bellefroid

first: Mathilde

last: Galais

first: Meijiao

last: Gong

first: Pierre

last: Lombard

first: Sarah

last: Mathieu

first: Amandine

last: Pecquet

first: Estelle

last: Plant

first: Camille

last: Ponsard

first: Laure

last: Vreux

first: Carlo

last: Yague-Sanz

first: Benjamin

last: Dewals

first: Nicolas

last: Gillet

first: Benoît

last: Muylkens

first: Carine

last: Van Lint


title: Role of reactive oxygen species on the intestinal macrophages development

city: Freiburg

first: Zohreh

last: Mansoori Moghadam

address: Breisacher Str. 115

institute: UNIVERSITÄTSKLINIKUM FREIBURG Center for Chronic Immunodeficiency

summary: Chronic granulomatous disease (CGD) is an immunodeficiency disease caused by defects in any one of the five structural components of the NADPH oxidase enzyme, i.e. X-linked reces-sive mutations in CYBB (gp91phox), or autosomal recessive mutations in CYBA (p22phox), NCF1 (p47phox), NCF2 (p67phox), NCF4 (p40phox). CGD results from reduced or absent reactive oxygen species (ROS) production. ROS play a crucial role in phagocytes; therefore, CGD patients are less capable to kill pathogens. I addition, and at the heart of this project proposal,   around 50 % of patients with CGD suffer from severe intestinal inflammation which shares features with inflammatory bowel disease, according to a report of the National Institutes of Health. However, the molecular and cellular mechanisms underlying CGD colitis are largely unknown. Our hypotheses is that CGD is associated colitis involves dysregulation of resident intestinal macrophages.

overall_design: Sorted the lamina propria macrophages (Ly6Clow MHC-II+) from 6 weeks old WT, p47phox-/-, and gp91phox-/- mice.


first: Zhongwei

last: Li

summary: The paired kidneys are the central organs of homeostasis for our body systems, the sophisticated structure and complex cells composition underpins kidneys’ functions. Here we report the generation of mouse kidney progenitor assembloid (KPA) with expandable nephron progenitor cells (NPC) and ureteric bud (UB). Unexpectedly, versatile renal interstitial cells can be induced in kidney progenitor assembloids. Mechanistically, some NPC can be transdifferentiated into interstitial progenitor cells (IPCs) in KPA context, then induced IPCs differentiate into various renal interstitial cells. These kidney progenitors-based KPA highly resembled postnatal mouse kidneys with well pattern and showed essential renal physiological functions.

overall_design: E12.5 mouse kidneys and expandable kidney progenitors-derived mouse kidney progenitor assembloids (KPA) were cultured under optimized stage-based media-v2, and collected at different time point. RNA samples were extracted and then subjected to bulk RNA-Seq analysis.

first: Biao

last: Huang

first: Zipeng

last: Zeng

first: Jincan

last: He

first: Pedro

last: Medina

first: Sunghyun

last: Kim

first: Kari

last: Koppitch

first: Jinjin

last: Guo

first: Chennan

last: Zhang

first: Nils

last: Lindström

first: Andrew

last: McMahon


summary: The paired kidneys are the central organs of homeostasis for our body systems, the sophisticated structure and complex cells composition underpins kidneys’ functions. Here we report the generation of mouse kidney progenitor assembloid (mKPA) with expandable nephron progenitor cells (NPC) and ureteric bud (UB). Unexpectedly, versatile renal interstitial cells can be induced in kidney progenitor assembloid. Mechanistically, some NPC can be transdifferentiated into interstitial progenitor cells (IPCs) in KPA context, then induced IPCs differentiate into various renal interstitial cells. These kidney progenitors-based KPA highly resembled postnatal mouse kidneys with well pattern and showed essential renal physiological functions.

overall_design: Cell populations profiling analysis of mouse kidney progenitor assembloids collected at Day 24 time point through 10x Genomics Multiome (scRNA/scATAC-seq) assays


title: Chromosome segregation dynamics during the cell cycle of Staphylococcus aureus

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: Research on chromosome organization and cell cycle progression in spherical bacteria, particularly Staphylococcus aureus, remains limited and fragmented. In this study, we established a working model to investigate chromosome dynamics in S. aureus using a Fluorescent Reporter Operator System (FROS), which enabled precise localization of specific chromosomal loci. This approach revealed that the S. aureus cell cycle and chromosome replication cycle are not coupled, with cells exhibiting two segregated origins of replication at the start of the cell cycle. The chromosome has a specific origin-terminus-origin conformation, with origins localizing near the membrane, towards the tip of each hemisphere, or the “cell poles”. We further used this system to assess the role of various proteins with a role in S. aureus chromosome biology, focusing on the ParB-parS and SMC-ScpAB systems. Our results demonstrate that ParB binds five parS chromosomal sequences and the resulting complexes influence chromosome conformation, but play a minor role in chromosome compaction and segregation. In contrast, the SMC-ScpAB complex plays a key role in S. aureus chromosome biology, contributing to chromosome compaction, segregation and spatial organization. Additionally, we systematically assessed the impact of proteins linking chromosome segregation to cell division—Noc, FtsK, SpoIIIE, and XerC—on origin and terminus number and positioning. While these proteins have been studied previously, our work uniquely standardizes comparisons by using the same strain background, growth conditions, and analytical approaches for all mutants. This work provides a comprehensive study of the factors governing chromosome dynamics and organization in S. aureus, contributing to our knowledge on chromosome biology of spherical bacteria.

overall_design: Hi-C and whole genome sequencing expriments were performed on wild type and mutant cells of Staphylococcus aureus JE2 growing in TSB.


title: NSABP B-41: A Study of AC Followed by a Combination of Paclitaxel Plus Trastuzumab or Lapatinib or Both Given Before Surgery to Patients With Operable HER2 Positive Invasive Breast Cancer [B41_27_POST]

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Background: We studied the effect on tumour response to neoadjuvant therapy of the substitution of lapatinib for trastuzumab in combination with weekly paclitaxel after doxorubicin plus cyclophosphamide treatment, and of the addition of lapatinib and trastuzumab combined after doxorubicin plus cyclophosphamide treatment in patients with HER2-positive operable breast cancer to determine whether there would be a benefit of dual HER2 blockade in these patients.  Methods: For this open-label, randomised phase 3 trial we recruited women aged 18 years or older with an ECOG performance status of 0 or 1 with operable HER2-positive breast cancer. Each received four cycles of standard doxorubicin 60 mg/m(2) and cyclophosphamide 600 mg/m(2) intravenously on day 1 every 3 weeks followed by four cycles of weekly paclitaxel (80 mg/m(2)) intravenously on days 1, 8, and 15, every 4 weeks. Concurrently with weekly paclitaxel, patients received either trastuzumab (4 mg/kg load, then 2 mg/kg intravenously) weekly until surgery, lapatinib (1250 mg orally) daily until surgery, or weekly trastuzumab plus lapatinib (750 mg orally) daily until surgery. After surgery, all patients received trastuzumab to complete 52 weeks of HER2-targeted therapy. Randomisation (ratio 1:1:1) was done centrally with stratification by clinical tumour size, clinical nodal status, hormone-receptor status, and age. The primary endpoint was the pathological complete response in the breast, and analysis was performed on an intention-to-treat population.  Findings: Patient accrual started on July 16, 2007, and was completed on June 30, 2011; 529 women were enrolled in the trial. 519 patients had their pathological response determined. Breast pathological complete response was noted in 93 (52·5%, 95% CI 44·9-59·5) of 177 patients in the trastuzumab group, 91 (53·2%, 45·4-60·3) of 171 patients in the lapatinib group (p=0·9852); and 106 (62·0%, 54·3-68·8) of 171 patients in the combination group (p=0·095). The most common grade 3 and 4 toxic effects were neutropenia (29 [16%] patients in the trastuzumab group [grade 4 in five patients (3%), 28 [16%] in the lapatinib group [grade 4 in eight patients (5%)], and 29 [17%] in the combination group [grade 4 in nine patients (5%)]) and grade 3 diarrhoea (four [2%] patients in the trastuzumab group, 35 [20%] in the lapatinib group, and 46 [27%] in the combination group; p<0·0001). Symptomatic congestive heart failure defined as New York Heart Association Class III or IV events occurred in seven (4%) patients in the trastuzumab group, seven (4%) in the lapatinib group, and one (<1%) in the combination group; p=0·185).  Interpretation: Substitution of lapatinib for trastuzumab in combination with chemotherapy resulted in similar high percentages of pathological complete response. Combined HER2-targeted therapy produced a numerically but insignificantly higher pathological complete response percentage than single-agent HER2-directed therapy; these findings are consistent with results from other studies. Trials are being undertaken to further assess these findings in the adjuvant setting.  Trial registration: ClinicalTrials.gov NCT00486668.

first: Sandra

last: Swain

first: Gong

last: Tang


title: RNA-seq analysis of the effect of mitochondrial glutamine transporter inhibitor treated pancreatic cancer cells

city: Yeonsu-gu, Incheon

first: Yulseung

last: Sung

address: Room-317-3, Veritas Hall D, Yonsei University, 85 Songdogwahak-Ro

department: College of Pharmacy

country: South Korea

institute: Yonsei University

summary: The aim of this study is to evaluate data by comparing transcriptome profile (RNA-seq) of pancreatic cancer cells treated with mitochondrial glutamine transporter allosteric inhibitor. The global impact of the chemical inhibition of mitochondrial glutamine transporter is assessed to understand the change in metabolism related genes and difference in any other categories to fully comprehend the result of the chemical treatment.

overall_design: Expression profile by high throughput sequencing is conducted on pancreatic cancer cell line with the treatment of vehicle or mitochondrial glutamine transporter inhibitor

first: Jung Min

last: Han


title: Suppression of 6-pyruvoyl-tetrahydropterin synthase promotes remyelination in multiple sclerosis

city: shanghai

first: Yongshun

institute: ION

summary:
Background: Multiple sclerosis (MS) is a CNS autoimmune disease that is characterized by demyelination, neuroinflammation, and neuronal loss. Although current chemotherapies and immunotherapies for MS efficiently mitigate disease activity and relief clinical symptoms, neuroprotection targeting axon/neurons remains therapeutically challenging. Accumulating evidence has suggested that poor oligodendrocyte precursor cell (OPC) proliferation and subsequent migration/differentiation significantly impedes remyelination during MS. However, the molecular mechanisms underlying OPCs dysfunction during MS remain elusive.

Methods: Re-analysis of single cell sequencing data from human and mouse oligodendrocyte lineage cells (OLCs), along with staining results from brain sections of MS patients, was conducted to investigate the role of 6-pyruvoyl-tetrahydropterin synthase (PTS) in determining oligodendrocyte fate. To assess PTS function in MS, conditional knockout mice targeting OLCs were employed. Transcriptomic analyses further illuminated the molecular mechanisms through which PTS influences the disease process.

Results: PTS in OPCs is a suppressor of OPC proliferation that contributes to demyelination in MS. We found that PTS expression in OPCs was aberrantly increased in patients with MS. Mice lacking Pts specifically in OPCs displayed ameliorated experimental autoimmune encephalitis (EAE) severity, a mouse model of MS, which were accompanied by attenuated demyelination. Moreover, selective suppression of Pts in OPCs facilitated OPC proliferation and remyelination during EAE. Mechanistically, the knockdown of Pts activated the cholesterol biosynthesis pathway leading to enhanced OPC proliferation.

Conclusions: Our findings suggest that PTS is a negative regulator of OPC proliferation, and its disinhibition could offer a potential therapeutic target for MS.

overall_design: To investigate the underlying mechanism of PTS-mediated inhibition of OPC proliferation during EAE, we performed RNA sequencing (RNA-seq) analysis on the spinal cord tissue on day 17 following EAE induction.

first: Hui

last: Xiao

first: Yue

last: Wu

first: Yanqing

last: Yin

first: Jiawei

last: Zhou


title: DNA-hypermethylated human gastric cancer circumvents apoptosis in the absence of TP53 mutation.

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: This study was designed to identify genetic mutations specific for DNA methylation epigenotypes using exome targeted sequencing combined with genome-wide DNA methylation analysis on specimens from patients with gastric cancer. Comprehensive DNA methylation profile by Infinium 450k indicated that gastric cancer was clustered into four methylation epigenotypes (MEs): extremely high-ME (E-HME), high-ME (HME), low-ME (LME), and extremely low-ME (E-LME).

overall_design: Bisulphite converted DNA from the 35 gastric cancer cases were hybridised to the Infinium HumanMethylation450 BeadChip.

first: Keisuke

last: Matsusaka

first: Yasunobu

last: Mano

first: Masayuki

last: Urabe

first: Bahityar

last: Rahmutulla

first: Hiroyuki

last: Abe

first: Yasuyuki

last: Seto

last: Aburatani

first: Masashi

last: Fukayama

first: Atsushi

last: Kaneda


title: DNA-hypermethylated human gastric cancer circumvents apoptosis in the absence of TP53 mutation (RNA-Seq)

summary: Comprehensive gene expression analysis by RNA-seq was performed in various cell lines  after p53-MDM2 inhibitor treatment or knockdown of the target genes for novel cancer therapeutic strategies.

overall_design: Nutlin-3 and RG7388 were used as p-53-MDM2 inhibitor.  Knockdown of target genes (MDM2, TP53) and control (shNT: Non Target) were perfomed by pLKO.1 lentivirus system in various cell lines.

first: Motoaki

last: Seki

first: Kazuko

last: Kita

first: Genki

last: Usui

first: Ryoji

last: Fujiki

first: Hisahiro

last: Matsubara

first: Tetsuo

last: Ushiku


title: Cell-type and locus-specific epigenetic editing of memory expression [scATAC_data]

status: Public on Aug 12 2025

city: Lausanne

first: Johannes

last: Gräff

address: Station 19

department: SV BMI

country: Switzerland

institute: EPFL

summary: With their Janus-faced property of being at once dynamic and stable, epigenetic mechanisms have for long been proposed to act as potential molecular mnemonics, but a cell type-specific, locus-restricted and temporally controllable interrogation thereof has thus far been lacking. Over the past years, accumulating evidence has shown that memories are likely encoded in sparse populations of brain cells, so-called engrams, which have, with few exceptions, received little molecular attention. Here, we combine c-Fos driven engram tagging with CRISPR-based epigenetic editing in vivo to assess whether and the extent to which the epigenetic regulation of a single locus within engram cells can contribute to memory formation and storage. Focusing on the promoter region of Arc, a master regulator of learning and synaptic plasticity, we find that its temporally restricted epigenetic regulation within engram cells in the mouse dentate gyrus is both necessary and sufficient for memory retention after learning as well as for memory maintenance after recall. Furthermore, such epigenetic editing and its behavioral consequence is reversible, and capable of bidirectionally altering memory capacities even outside the labile phase of memory consolidation. Together, these findings suggest that epigenetic mechanisms are causally involved in regulating memory expression

overall_design: 10x single nuclear ATAC-seq for dCas9-KRAB-MeCP2 targeting Arc or non-targeted in hippocampus dentate gyrus

first: Davide

last: Coda

first: Lisa

last: Watt

first: Lilliane

last: Glauser

first: Mykhailo

last: Batiuk

first: Allison

last: Burns

first: Cora

middle: L

last: Stahl


title: Nociceptor neurons control pollution-mediated neutrophilic asthma; Expression profile of vagal nociceptor neurons in air pollution-exacerbated allergic airway inflammattion

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

institute: Queen's University

summary: Sequencing of TRPV1+ neurons in jugular-nodose complex (JNC) in a mouse model of air pollution-exacerbated allergic inflammation.

overall_design: TRPV1-cre/wt::tdTomato-fl/wt mice were sensitized via intraperitoneal injection with a mix of grade V OVA (200 µg/dose; Sigma-Aldrich A5503) and Imject® Alum (1 mg/dose; ThermoFisher 77161) on days 0 and 7. Subsequently, they underwent intranasal challenges with OVA (50 µg/dose), with or without fine particulate matter (FPM; 20 µg/dose; NIST 2786), from day 14 to 16. Control mice were sensitized but not challenged. The mice were euthanized on day 17, jugular-nodose complex (JNC) were collected, and tdTomato+ cells from naive, OVA-challenged, and OVA-FPM co-exposed mice were sroted by FACS.

first: Theo

last: Crosson

first: Katiane

last: Roversi

first: Jo-Chiao

last: Wang


title: Hypomethylation of thrombospondin-1 promoter region is associated with reduced aqueous humor flow

city: Hung Hom

first: Samantha SW

last: Shan

address: 1 Yuk Choi Road

department: School of Optometry

institute: The Hong Kong Polytechnic University

type: Methylation profiling by high throughput sequencing

summary: Prolonged use of dexamethasone (DEX) elevates intraocular pressure (IOP) and increases the risk of developing glaucoma. In a previous study, we demonstrate that DEX stimulates the expression of thrombospondin-1 (THBS1) in primary human trabecular meshwork (hTM) cells, and that inhibiting THBS1 expression prevents DEX-induced elevation of IOP in mice. Therefore, we investigate the mechanism by which DEX regulates THBS1 expression. Treatment with the DNA methylation inhibitors, 5-azacytosine or 5-aza-2’-deoxycytidine, upregulates THBS1 protein levels in vitro and in vivo, reduces outflow facility in perfused mouse eyes, and elevates IOP in mice. In primary hTM cells, 7-day DEX treatment results in hypomethylation of the THBS1 promoter region and reduces transcript levels of 2 DNA methyltransferases (DNMTs), DNMT1 and DNMT3A. Taken together, we show that DEX reduces expression of DNMTs and DNA methylation of the THBS1 promoter region, supporting a critical role for THBS1 in DEX-induced outflow reduction.

overall_design: To study the effect of dexamethasone (DEX) on DNA methylation in primary human trabecular meshwork (hTM) cells (n = 3 different cell strains, two male, one female), we treated hTM cells with 300 nM  DEX or PBS (as vehicle-control) for 7 days, extracted the genomic DNAs and submitted to BGI (China) for whole genome bisulfite sequencing (WGBS).

first: Kit-ying

last: Choy

first: Wei-ying

last: Yang

first: Choi-ying

last: Ling

first: King-kit

last: Li

first: Karena

middle: H

first: Hong-lok

last: Lung

first: Chi-ho

last: To

first: W

middle: D

last: Stamer

first: Chi-wai

last: Do

first: Samantha


title: Neoadjuvant immunotherapy promotes the formation of mature tertiary lymphoid structures in a remodeled pancreatic tumor microenvironment

city: Baltimore

first: Dimitrios

last: Sidiropoulos

state: MD

address: 1650 Orleans St

department: Oncology

institute: Johns Hopkins University

summary: Pancreatic adenocarcinoma (PDAC) is a rapidly progressing cancer that responds poorly to immunotherapies. Intratumoral tertiary lymphoid structures (TLS) have been associated with rare long-term PDAC survivors, but the role of TLS in PDAC and their spatial relationships within the context of the broader tumor microenvironment remain unknown. Here, we report the generation of a spatial multi-omics atlas of PDAC tumors and tumor-adjacent lymph nodes from patients treated with combination neoadjuvant immunotherapies. Using machine learning–enabled hematoxylin and eosin image classification models, imaging mass cytometry, and unsupervised gene expression matrix factorization methods for spatial transcriptomics, we characterized cellular states within and adjacent to TLS spanning across distinct spatial niches and pathologic responses. Unsupervised learning identified TLS-specific spatial gene expression signatures that significantly associated with improved survival in PDAC patients. We identified spatial features of pathologic immune responses, including intratumoral TLS–associated B-cell maturation colocalizing with IgG dissemination and extracellular matrix remodeling. Our findings offer insights into the cellular and molecular landscape of TLS in PDACs during immunotherapy treatment.

overall_design:
Spatial transcriptomics with Visium (10x Genomics) was performed on surgical specimens obtained from patients with pancreatic ductal adenocarcinoma.

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Submitter states that missing raw data are being made available for controlled access in dbGaP.
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first: Luciane

last: Kagohara

first: Elana

last: Fertig


title: Combinatorial effect of serotonin and indole on enterohemorrhagic Escherichia coli (EHEC) transcriptome

city: Madison

first: Vanessa

last: Sperandio

state: WI

address: 1550 Linden Dr

department: Medical Microbiology & Immunology

institute: University of Wisconsin - Madison

summary: Previous studies have shown serotonin and indole downregulate expression of virulence genes in EHEC, here we demonstrate the combinatorial effect of serotonin and indole on EHEC transcriptome

overall_design: EHEC strain 86 24 was used for this study. WT EHEC was grown with 10 µM serotonin, 500 µM indole or both of them together in low-glucose DMEM until late log phase under aerobic conditions. RNA was extracted from these samples. The experiment was conducted with three biological replicates.

first: Mehmet Ali

last: Hoskan


title: Cell-type and locus-specific epigenetic editing of memory expression [parseRNA_data]

first: Johannes

last: Gräff

overall_design: single nuclear Parse sequencing for dCas9-KRAB-MeCP2 targeting Arc or non-targeted in hippocampus dentate gyrus

first: Davide

last: Coda

first: Lisa

last: Watt

first: Lilliane

last: Glauser

first: Mykhailo

last: Batiuk

first: Allison

last: Burns

first: Cora

last: Stahl


title: Cell-type and locus-specific epigenetic editing of memory expression

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

overall_design: Refer to individual Series


title: Cell-type and locus-specific epigenetic editing of memory expression [ChIP_data]

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for dCas9-KRAB-MeCP2 targeting Arc or non-targeted in N2A cells


title: Single-cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway

city: Houston

first: Angela

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Bacillus Calmette-Guérin (BCG) is the mainstay of treatment for intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC), yet recurrence rates remain high. To improve the efficacy of BCG, a better understanding of the immune landscape underlying BCG resistance is critical. Here, we performed single-cell RNA-sequencing (scRNA-seq) and whole-exome sequencing on tumors from NMIBC patients before and after BCG treatment. Our analysis revealed a marked increase in CD6/ALCAM interactions between T cells and urothelial cells in BCG recurrent tumors. CD6-high T cells were enriched in recurrent tumors and exhibited downregulation of activation-related genes, indicative of functional impairment. These observations were supported by analysis of an independent BCG-treated NMIBC cohort, in which CD6/ALCAM signaling was correlated with shorter recurrence-free survival (p = 0.00059). Our findings reveal a previously unrecognized association between CD6/ALCAM signaling and BCG resistance in NMIBC patients and highlight this pathway as a potential therapeutic target to enhance response to BCG.

overall_design: Single cell rna sequencing of Non-muscle invasive bladder cancer (NMIBC)  samples comparing BCG naïve and recurrent samples. Samples names starting with BC indicate bladder cancer and the _# indicates sample ID.  Samples names starting with BN indicate bladder normal where samples were taken from bladder regions away from any tumors.

first: Byron

last: Lee

first: Ivan

last: Juric

first: Tyler

last: Alban

first: Emily

middle: E

last: Fink

first: Arvind

last: Ravi

first: Mark

last: Holton

first: Vladimir

last: Makarov


title: Histone modification cross-talk and protein complex diversification confer plasticity to Polycomb repression

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

institute: Max Planck Institute of Biochemistry

summary: Polycomb chromatin domains are chromosomal regions decorated with histone H2A monoubiquitination at lysine 119 (H2Aub1) and histone H3 tri-methylation at lysine 27 (H3K27me3). These domains are dynamically shaped through the actions of different Polycomb group protein complexes to control gene expression during development. To assess how different Polycomb group subcomplexes contribute to these histone-modification profiles in Drosophila embryos, we utilized mutants that abrogate their function. While canonical Polycomb Repressive Complex (PRC) 1 deposits low levels of H2Aub1 solely at Polycomb target genes, variant PRC1 generates the bulk of H2Aub1 genome-wide. In late-stage embryos, PR-DUB-mediated deubiquitination effectuates a uniform low-level H2Aub1 profile across the genome. The combined activities of PRC2.1 and PRC2.2 drive formation and maintenance of most H3K27me3 domains but PRC2.1 is the limiting enzyme for creating such domains at HOX genes. Surprisingly, reduction in the H3K27me3 level and repression defects caused by removing PRC2.1 were largely rescued in animals also lacking PR-DUB, which showed extensive H2Aub1 accumulation at Polycomb targets that promoted compensatory H3K27me3 deposition by PRC2.2. Diversification of Polycomb protein complexes combined with feedback-loop mechanisms involving histone modification cross-talk equip the system with the plasticity, adaptability, and buffering capacity needed to safeguard cell fate decisions during development.

overall_design:
Analyses of ChIP-seq profiles generated from wild-type and mutant late stage Drosophila embryos.

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

last: Bonnet


title: Single-cell sequencing of mouse lung epithelial cells after bleomycin injury and modulation of IRE1α

city: San Francisco

first: Vincent

last: Auyeung

department: Medicine

institute: University of California, San Francisco

summary: Epithelial cells that are committed to a differentiated state in homeostasis can change their identity in response to injury. In the lung, alveolar type 2 (AT2) cells are the resident secretory epithelial cells of the alveolus, and after injury can proliferate and differentiate into type 1 cells. This inducible plasticity is central to alveolar regeneration, fibrosis, and malignancy, but the regulatory pathways that govern the balance between fate maintenance and differentiation are incompletely understood.  Epithelial cells that are committed to a differentiated state in homeostasis can change their identity in response to injury. In the lung, alveolar type 2 (AT2) cells are the resident secretory epithelial cells of the alveolus, and after injury can proliferate and differentiate into type 1 cells. This inducible plasticity is central to alveolar regeneration, fibrosis, and malignancy, but the regulatory pathways that govern the balance between fate maintenance and differentiation are incompletely understood. IRE1α is an ER transmembrane protein conserved throughout eukaryotes that senses misfolded protein in the ER lumen and initiates cellular efforts to regain protein folding homeostasis through its cytosolic kinase and RNase domains. We previously showed that IRE1α pharmacologic or genetic loss of function decreased the accumulation of damage-associated transient progenitors (DATPs), and also promoted their differentiation into new alveolar epithelial cells. To further detail the functions of IRE1α after AT2 injury, we performed single-cell transcriptome profiling of the AT2-to-AT1 transition after bleomycin injury, with pharmacologic or epithelial-specific genetic loss of IRE1α function.

overall_design: This is single cell sequencing of mouse lung epithelial cells from a study with factorial design. The four groups are: wildtype mice exposed to saline; wildtype mice exposed to bleomycin; mice with conditional knockout of IRE1α in the lung epithelium -- Shh(Cre/+) Ern1(flox/flox) -- exposed to bleomycin; and wildtype mice exposed to bleomycin and treated daily with the IRE1a kinase inhibitor KIRA8. Lungs were harvested and dissociated on day 10 after bleomycin exposure, and sorted for live, CD45- CD31- Epcam+ single cells. Cells from multiple mice in each treatment group were pooled into a single GEM lane. Single-cell sequencing performed using 10X Single Cell 3' technology. The output of Cell Ranger software is provided in the processed data file.

first: Dean

last: Sheppard

first: Feroz

last: Papa


title: RNA-seq analysis of AhR-deficient monocytes in mouse

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

summary: We analyzed the transcriptome of steady-state bone marrow monocytes from mice deficient for AhR in monocytes (Ccr2*AhR KO) or WT littermates.

overall_design: Monocytes were extracted from the bone marrow.

first: Adeline

last: Cros


title: Deep Mutational Scanning Reveals EGFR Mutations Conferring Resistance to the 4th-generation EGFR tyrosine kinase inhibitor BLU-945

status: Public on Aug 11 2025

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

summary: Fourth-generation EGFR tyrosine kinase are in development to overcome common resistance mutations. We performed deep mutational scanning (DMS) of the EGFR kinase domain in the context of L858R by introducing a saturation library of ~17,000 variants into Ba/F3 cells. DMS library-expressing cells were exposed to osimertinib or BLU-945 to identify escape mutations. L718X mutations were enriched across all conditions. BLU-945 specific mutations included K714R, K716T, L718V, T725M, K728E, K754E/N, N771S/T, T783I, Q791L/K, G863S, S895N, K929I, and M971L. A secondary DMS screen combining osimertinib and BLU-945 exclusively enriched for L718X mutations. Clinically, L718X mutations emerged in two patients treated with BLU-945. One patient with baseline EGFR L858R and L718Q mutations experienced early progression. Another with baseline EGFR L858R, T790M, and C797S acquired an L718V mutation at progression. This study demonstrate how comprehensive resistance profiling of targeted therapies can predict clinically relevant mutations and guide rational combinations to delay or prevent resistance.

overall_design: The experiment was designed to profile resistance mutations to EGFR tyrosine kinase inhibitors osimertinib and BLU-945. A saturation mutagenesis library for the EGFR L858R kinase domain was generated and expressed in Ba/F3 cells. The library-expressing cells which depend on the transduced EGFR variant for survival in the absence of interleukin-3, were subjected to different drug treatment condition. Barcoded subamplicon sequencing was then used to identify which EGFR variants were enriched in the surivivng cell populations under the pressure, which enriched variants being inerpreted as candidate reisistance mutations.

first: Yueyang

last: Wang

first: Michela

last: Ranieri

first: Tigran

last: Abramyan

first: Lev

last: Tsidilkovski

first: Michelle

last: Hollenberg

first: Alfonso

last: Lopez

first: Xavier

last: Moore

first: Fiona

last: Sherman

first: Jiehui

last: Deng

first: Hayk

last: Saribekyan

first: Garegin

last: Papoian

first: Kwok-kin

last: Wong

first: Elaine

last: Shum

first: John

middle: T

last: Poirier


title: Transient tissue residency and lymphatic egress define human CD56bright NK cell homeostasis (scRNA-seq)

city: Huddinge

first: Dan

last: Sun

address: Alfred Nobels allé 8

department: MedH

institute: Karolinska Institutet

summary: Although human tissue-resident (TR) CD56bright natural killer (NK) cells can be identified based on integrins and chemokine receptors inferred from murine studies, many aspects of their homeostasis remain elusive. Here, we used an integrated approach of dynamic human, humanized mouse, and non-human primate models and sampling of efferent lymph fluid to determine recirculation and TR patterns of human NK cells. By intravascular labelling, we show that CD56bright access tissue niches at steady state. Furthermore, in human liver transplantation, donor-derived CD56bright NK cells represent the dominant TR NK cell population early after transplantation but were replaced over time by infiltrating recipient NK cells that established tissue-resident traits, a process partly regulated by Runx3. Transient TR CD56bright NK cells recirculated via lymphatics, displaying a consistent phenotype detectable in draining lymph nodes and efferent lymph fluid, and waned from peripheral blood upon lymph node egress blockade. Finally, CD56dim NK cells, constrained to vasculature at steady state, entered lymph nodes upon inflammation. Altogether, this study provides a mechanistic framework for the transient tissue-residency and recirculation patterns of human NK cell populations.

overall_design: We performed 10x 3' scRNAseq of total CD45+ cells from samples of four different transplant livers at six hours and one-year post transplantation.

first: Annika

last: Niehrs

first: Laura

last: Hertwig

first: Isabella

last: Nordström

first: Benedikt

last: Strunz

first: Christoph

last: Ziegenhain

first: Martin

middle: I

last: Ivarsson

first: Niklas

middle: K

last: Björkström


title: Allergen-specific mRNA-lipid nanoparticle therapy for prevention and treatment of experimental allergy in mice

city: Cincinnati

first: Yrina

last: Rochman

state: OH

address: 3333 Burnet Avenue

department: Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

summary: Allergic diseases have reached epidemic proportions globally, calling attention to the need for better treatment and preventive approaches. Herein, we developed allergen-encoding messenger RNA (mRNA)–lipid nanoparticle (LNP) strategies for both therapy and prevention of allergic responses. Immunization with allergen-encoded mRNA-LNPs modulated T cell differentiation, inhibiting the generation of T helper type 2 and type 17 cells upon allergen exposure in experimental asthma models induced by ovalbumin, and naturally occurring house dust mite (HDM) and the major HDM allergen Der p1. Allergen-specific mRNA-LNP treatment attenuated clinicopathology in both preventive and established allergy models, including reduction in eosinophilia, mucus production, and airway hypersensitivity, while enhancing production of allergen-specific IgG antibodies and maintaining low IgE levels. Additionally, allergen-specific mRNA-LNP vaccines in mice elicited a CD8+CD38+KLRG– T cell response as seen following SARS-CoV-2 mRNA vaccination in humans, underscoring a conserved immune mechanism across species, regardless of the mRNA-encoded protein. Notably, mRNA-LNP vaccination in combination with an mTOR inhibitor reduced the CD8+ T cell response without affecting the vaccine-induced anti-allergic effect in the preventive model of asthma. This technology renders allergen-specific mRNA-LNP therapy a promising approach for prevention and treatment of allergic diseases.

overall_design: Mice received 2 doses of empty LNP (LNP) or OVA-mRNA LNP vaccine (mRNA) on days 0 and 7. Everolimus (Ev. or EVL) was administered daily from day -2 to 12 post-vaccination. Mice were OVA + Alum sensitized on days 24 and 36 and subsequently OVA challenged for 4 consecutive days (days 48-51). Lung tissue were collected 2 days after the final challenge (day 53). Naïve mice served as unmanipulated controls.

first: Michael

last: Kotliar

first: Andrea

last: Klingler

first: Mohamed-Gabriel

last: Alameh

first: Garrett

last: Osswald

first: Julie

last: Caldwell

first: Mark

first: Jennifer

last: Felton

first: Lydia

last: Mack

last: Hargis

first: Jilian

last: Melamed

first: Ian

middle: P

last: Lewkowich

first: Artem

last: Barski

first: Drew

last: Weissman

first: Marc

last: Rothenberg


title: CUT&Tag Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays [CUT&Tag]

city: Rochester

first: Patrick

middle: J

last: Murphy

state: New York

address: 601 Elmwood Avenue

department: Biomedical Genetics and Genomics

institute: University of Rochester

summary: Determining the genomic localization of chromatin features is an essential aspect of investigating gene expression control, and ChIP-Seq has long been the gold standard technique for interrogating chromatin landscapes. Recently, the development of alternative methods, such as CUT&Tag, have provided researchers with alternative strategies that eliminate the need for chromatin purification, and allow for in situ investigation of histone modifications and chromatin bound factors. Mindful of technical differences, we set out to investigate whether distinct chromatin modifications were equally compatible with these different chromatin interrogation techniques. We found that ChIP-Seq and CUT&Tag performed similarly for modifications known to reside at gene regulatory regions, such as promoters and enhancers, but major differences were observed when we assessed enrichment over heterochromatin-associated loci. Unlike ChIP-Seq, CUT&Tag detects robust levels of H3K9me3 at a substantial number of repetitive elements, with especially high sensitivity over evolutionarily young retrotransposons.  IAPEz-int elements for example, exhibited underrepresentation in mouse ChIP-Seq datasets but strong enrichment using CUT&Tag.  Additionally, we identified several euchromatin-associated proteins that co-purify with repetitive loci and are similarly depleted when applying ChIP-based methods.  This study reveals that our current knowledge of chromatin states across the heterochromatin portions of the mammalian genome is extensively incomplete, largely due to limitations of ChIP-Seq. We also demonstrate that newer in situ chromatin fragmentation-based techniques, such as CUT&Tag and CUT&RUN, are more suitable for studying chromatin modifications over repetitive elements and retrotransposons.

overall_design: CUT&Tag and CUT&RUN sequencing and analysis for H2A.Z, H3K27ac, H3K27me3, and H3K9me3 in MEFs and mESCs.

first: Brandon

last: Park

first: Shan

last: Hua

first: Karli

last: Casler

first: Eric

last: Cefaloni

last: Ayers

first: Rahiim

last: Lake

first: Kristin

first: Paula

last: Vertino

first: Mitchell

last: O'Connell


title: Neanderthal-derived variants increase SOX9 enhancer activity in craniofacial progenitors that shape jaw development

city: Edinburgh

first: Hannah

last: Long

address: Crewe Rd South

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: Facial appearance is one of the most variable morphological traits in humans, influenced by both rare and common genetic variants that can impact facial form between individuals and in disease. Deletion of an enhancer cluster 1.45 megabases upstream of the SOX9 gene (EC1.45) results in Pierre Robin sequence, a human craniofacial disorder characterised by underdevelopment of the lower jaw and frequently associated with cleft palate. We reasoned that single nucleotide variants in EC1.45 may cause more subtle alterations to facial morphology. Here, we took advantage of recent human evolution, and the distinct morphology of the Neanderthal lower jaw, to investigate the impact of three Neanderthal-derived single nucleotide variants on EC1.45 function and jaw development. Utilising a dual enhancer-reporter system in zebrafish, we observed enhanced Neanderthal regulatory activity relative to the human orthologue during a specific developmental window. At this same stage, we show that EC1.45 appears to be selectively active in neural crest- derived progenitor cells which lie in close apposition with and are transcriptionally related to precartilaginous condensations that contribute to craniofacial skeletal development. To examine the potential consequences of increased SOX9 expression in this specific cellular population during jaw development, we overexpressed human SOX9 specifically in EC1.45-active cells and observed an increase in the volume of developing cartilaginous precursors. Taken together, our work implicates Neanderthal-derived variants in increased regulatory activity for a disease- associated enhancer with the potential to impact craniofacial skeletal development and jaw morphology across recent hominin evolution.

overall_design: To explore the relative activity and cell type specificity of the human versus Neanderthal EC1.45 Peak1-2 enhancers further, we performed single cell-RNA sequencing (scRNA-seq) for the two human-Neanderthal enhancer reporter lines at 2 dpf. Fluorescence-activated cell sorting (FACS) was used to isolate all cells that were eGFP-positive, mCherry-positive or double-positive from dissected embryonic cranial regions at 2 dpf. This resulted in 40,000 cells for the Tg(Hu:GFP;Ne:Ch) line and 10,000 cells for the Tg(Ne:GFP;Hu:Ch) line which were processed as two separate samples using the 10x Genomics Chromium single-cell 3′ gene expression technology (v3.1).

first: Kirsty

last: Uttley

last: Jüllig


title: RNAseq analysis of human CD14+ monocytes exposed to an agonist of Aryl Hydrocarbon Receptor

first: Elodie

last: Segura

summary: Aryl Hydrocarbon Receptor (AhR) is a ligand-activated transcription factor. To understand what genes are controlled by AhR in human monocytes, we performed transcriptomic analysis.

overall_design: Human CD14+ monocytes were cultured in presence of an AhR inhibitor (SR1) or agonist (FICZ) for 6h.

first: Alba

last: De Juan


title: Medium-chain triglycerides improve cognition and systemic metabolism in mouse models of Alzheimer's disease

city: Sherbrooke

first: Mariano

last: Avino

address: 3201 Jean Mignault

department: Biochemistry and Functional Genomics

institute: Sherbrooke University

summary: Lifestyle-based interventions, including dietary modifications, can reduce dementia risk. In this regard, dietary supplementation with medium-chain triglycerides (MCT) has shown potential therapeutic benefits in individuals with Alzheimer's disease (AD). These effects are widely presumed to be mediated by hepatic conversion of MCT into circulating ketones. However, the physiological and cellular mechanisms underlying the benefits of MCT remain understudied, particularly in the context of AD. Here, we investigated the cellular and molecular changes occurring in the brain and systemically in response to dietary supplementation with MCT versus a ketogenic diet (KD). The experimental design consisted of comparing a 70% carbohydrate control diet to either a control diet supplemented with 10% MCT or a carbohydrate-free high fat KD. Diets were tested in two AD mouse models, slow-progressing 3xTg-AD mice that model pre-symptomatic/early stages and rapidly-progressing 5xFAD mice that model late stages of the disease. We found that MCT supplementation and KD both improved hippocampal-dependent spatial learning and memory, increased dendritic spine density of hippocampal neurons, and modulated hippocampal expression of genes associated with mitochondrial functions, synaptic structure, and insulin signaling in AD mouse models. However, unlike KD, MCT supplementation did not elevate circulating ketones, suggesting different mechanisms. Indeed, MCT enhanced the peripheral insulin response of AD mice, while KD conversely unveiled their latent metabolic vulnerability, increasing their hyperglycaemia, body weight gain, and adiposity. The systemic metabolic disturbances of AD mice correlated with transcriptomic alterations in hepatic lipid metabolism and ketogenesis genes and increased lipid droplet accumulation. These liver metabolic abnormalities were partially reversed by both MCT supplementation and KD, but in distinct ways. Notably, KD selectively triggered hepatic neutral lipid depletion and prominent proinflammatory gene expression while MCT down-regulated expression of cholesterol-related genes. Collectively, these findings reveal that MCT supplementation in the context of AD improves cognition and systemic metabolism without elevating circulating ketone levels.

overall_design: Liver 3 months-old mice received for 6 months, either a Control diet (C, 70% carbohydrate, 20% long-chain triglycerides, 10% protein, 4.1 kcal/g, Research Diets), a Control diet enriched with medium-chain triglycerides (MCT or M, 70% carbohydrate, 10% long-chain triglycerides, 10% medium-chain triglycerides (C8:0-C10:0 ratio of 3:2), 10% protein, 4.1 kcal/g, Research Diets) or a carbohydrate-free high fat ketogenic diet (KD or K, 90% long-chain triglycerides, 10% protein, 6.7 kcal/g, Research Diets). WT and 3xTg-AD mice liver were used with a sample size of 4 mice per genotype/diet giving a total of 24 livers (WT-C=4, WT-K=4, WT-M=4, 3xTg-C=4, 3xTg-K=4, 3xTg-M=4).

first: Paule

last: M'Bra

first: Laura

last: Hamilton

first: Gaël

last: Moquin-Beaudry

first: Chenicka

last: Mangahas

first: Federico

last: Pratesi

first: Anne

last: Castonguay

first: Sophia

last: Mailloux

first: Manon

last: Galoppin

first: Jessica

last: Avila Lopez

first: Megan

last: Bernier

first: Marta

last: Turri

first: Marian

last: Mayhue

last: Aumont

first: Martine

last: Tétreault

first: Stephen

last: Cunnane

first: Karl

last: Fernandes


title: Widespread specific intron-retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts

city: Belo Horizonte

first: Izabela

last: Mamede

state: MG

address: Av. Pres. Antônio Carlos, 6627

department: Laboratory of Mucosal Immunology/Biochemistry And Immunology

country: Brazil

institute: Rockefeller University/Universidade federal de Minas gerais

summary: Many essential cellular processes require RNA to interact with protein(s) to form ribonucleic protein complexes (RNPs). For example, all cellular proteins are produced by the ribosome - a large and stable RNP, gene splicing requires a choreography of numerous small and large RNPs, even the replication of telomeric DNA requires an RNP. All these examples are stable RNPs that exhibit specific sedimentation rates (e.g., in a sucrose gradient) based on the composition of RNA and protein. In this study we aimed to identify RNAs components of RNPs on a transcriptome-wide scale. Using sucrose-gradient followed by sequencing we identified 1,057 RNA transcripts that are likely to be components of cellular RNPs. Our approach determined that RNP are not due to the cellular abundance nor length of the constituent RNA transcripts. The RNPs identified were predominantly nuclear, containing a specified retained intron and resistant to RNA degradation. Collectively our study reveals a widespread phenomena of a specific intron being retained in a stable nuclear RNP.

overall_design:
Gradient ultracentrifugation was performed at 30,000 rpm (SW41 rotor) for 18h at 4°C. Sucrose gradients were fractionated using ISCO gradient fractionation system (ISCO Model 160 Gradient Former Foxy Jr. Fraction Collector) into 12 fractions of 900 ul. RNA was purified from sucrose fractions using Directzol RNA Miniprep kit (ZymoResearch, R2062), following the manufacturer’s instructions.
Human IPSCs, various fractions.

first: Isabela

last: Pereira


title: Dual roles of DEAD-box RNA helicase Brr2 in genome stability

city: Chongqing

first: jin

last: you

address: Huxi Campus

institute: Chongqing University

summary: R-loop is a common chromatin feature consisting of a displaced single-stranded DNA and an RNA-DNA hybrid, and dysregulation of R-loop surveillance results in genomic and transcriptomic instability. Although the RNA moiety of most R-loops originates from linear transcripts, circular RNAs (circRNAs), outputs from back-splicing, can also hybridize with the complementary strand of a DNA duplex. However, how circRNA-associated R-loops (ciR-loops) are monitored remains elusive. Here, we identified the DEAD-box RNA helicase Brr2 as an evolutionarily-conserved ciR-loop repressor with dual roles in inhibiting circRNA generation and resolving harmful ciR-loops. Accumulation of ciR-loops caused by loss-of-function of this dual-action factor induces antisense transcription and premature transcription termination for many genes and generates significant DNA damage, which further leads to a series of defects in DNA replication, cell division and cell proliferation. We propose that functional integration of multilayered regulation by a single protein can be an efficient double protection against genome instability.

overall_design: To explore whether Brr2-mediated regulation represents a widespread mechanism for circRNA generation, total RNA samples from Brr2 KD and control cells were subject to Ribo-Zero Next-Generation Sequencing.

first: Jin

last: You

first: Chuan

last: Huang


title: Connexin 43 drives glioblastoma cancer stem cell phenotypes through a WNK lysine-deficient protein kinase 1-c-MYC signaling axis

city: Cleveland

first: Erin

last: Mulkearns-Hubert

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic

summary: The coordination of cellular processes such as growth and survival relies on communication between cells through gap junctions. Gap junction intercellular communication is driven by connexin proteins, which also mediate protein-protein interactions and communication with the extracellular space via hemichannels. Despite their essential roles, connexin function in cancer is context dependent, with connexin 43 (Cx43) reported to both promote and suppress tumor growth in glioblastoma, the most common primary malignant brain tumor. Here, we detect expression of Cx43 in glioblastoma patient-derived cancer stem cells and demonstrate that Cx43 is essential for their survival and self-renewal. Mechanistically, depletion of Cx43 reduces c-MYC expression through reduced levels of the upstream mediator WNK lysine-deficient protein kinase 1 (WNK1). Depletion of WNK1 phenocopies Cx43 knockdown and reduces MYC expression and tumor growth. Together, these results define a novel signaling axis downstream of Cx43 that promotes tumor growth and cancer stem cell phenotypes in glioblastoma.

overall_design: To establish the functional effects of Cx43 and WNK1 in glioblastoma cells, we reduced expression of Cx43 or WNK1 in DI318 glioblastoma patient xenograft model cells using shRNA.

first: Justin

last: Lathia


title: The role of Spp1 in pancreatic cancer

city: London

first: Huafu

last: Li

address: 237 Fulham Road, Fulham Road

institute: Institute of Cancer Research- Fulham Road (ICR)

summary: We performed RNA-seq analysis on Spp1 wild-type and CRISPR/Cas9-mediated Spp1 knock out pancreatic tumour organiod from Pdx1-Flp;KrasFSF-G12D;Trp53frt/frt; Vim-EGFP (KPFV) mice. We compared the transcriptome between these two groups of them with the aim to understand their molecular signatures and the relevance to human pancreatic ductal adenocarcinoma subtypes.

overall_design: Spp1 wild-type compare to Spp1 knock out pancreatic tumour organiod

first: Linxiang

last: Lan

first: Axel

last: Behrens