title: Transcriptional and epigenetic landscape of the mouse intestine during aging identifies key molecular drivers of aging -associated dysfunctions and diseases. [WGBS]

first: Seyed Mohammd Mahdi

last: Rasa

summary: Aging is a complex multifactorial process leading to the loss of tissue/organ functionality and to an increase in disease risk. Aging-related intestinal dysfunctions include loss of barrier integrity, altered stress responses, nutrient malabsorption, and cancer formation. Many molecular mechanisms related to dysfunction and diseases are well-known (e.g. in cancer), however how aging impact on them before the occurrence of dysfunctions and diseases is poorly understood.  In this study, we applied a multi-layered omics-approach to characterize the transcriptional and the epigenetic landscape of mouse intestinal epithelium during aging. We found gender and cell-type specific transcriptional and epigenetic alterations on key pathways and genes linked to intestinal dysfunctions, stem cell aging, organismal lifespan and cancer. Moreover, we identified a switch in the composition of the old intestinal stem cell subpopulations, represented by a drift towards a more secretory lineage committed (and less stem) state accompanied by functional epigenetic alterations.

overall_design: Transcriptional and epigenetic landscape of the mouse intestine during aging.

first: Anna

last: Krepelova

first: Mahdi

first: Olena

last: Husak

first: Omid

last: Omrani

first: Dovydas

last: Sirvinskas

first: Suneetha

last: Nunna

first: Lisa

last: Adam

first: Sandra

last: Käppel

first: George

last: Garside

first: Farzaneh

last: Pourmasoumi

first: Ying-Pei

last: Huang

first: Hajo

last: Kries

first: Karl

last: Rudolph

first: Francesco

last: Neri


title: Transcriptional and epigenetic landscape of the mouse intestine during aging identifies key molecular drivers of aging -associated dysfunctions and diseases [RRBS]

status: Public on Sep 25 2025

city: Kiel

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

type: Methylation profiling by high throughput sequencing

middle: L


title: Egr1 is a sex-specific regulator of neuronal chromatin, synaptic plasticity, and behaviour [ATAC-Seq]

city: Bronx

first: Marija

last: Kundakovic

state: NY

address: 441 E. Fordham Road

department: Biological Sciences

country: USA

institute: Fordham University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Sex differences are found in brain structure and function across species, and across brain disorders in humans. The major source of brain sex differences is differential secretion of steroid hormones from the gonads across the lifespan. Specifically, ovarian hormones oestrogens and progesterone are known to dynamically change structure and function of the adult female brain, having a major impact on psychiatric risk. However, due to limited molecular studies in female rodents, very little is still known about molecular drivers of female-specific brain and behavioural plasticity. Here we show that overexpressing Egr1, a candidate oestrous cycle-dependent transcription factor, induces sex-specific changes in ventral hippocampal neuronal chromatin, gene expression, and synaptic plasticity, along with hippocampus-dependent behaviours. Importantly, Egr1 overexpression mimics the high-oestrogenic phase of the oestrous cycle, and affects behaviours in ovarian hormone-depleted females but not in males. We demonstrate that Egr1 opens neuronal chromatin directly across the sexes, although with limited genomic overlap. Our study not only reveals the first sex-specific chromatin regulator in the brain, but also provides functional evidence that this sex-specific gene regulation drives neuronal gene expression, synaptic plasticity, and anxiety- and depression-related behaviour. Our study exemplifies an innovative sex-based approach to studying neuronal gene regulation in order to understand sex-specific synaptic and behavioural plasticity and inform novel brain disease treatments.

overall_design: Male and ovariectomized, or intact proestrus female C57BL/6J mice underwent stereotaxic surgery at 7 weeks of age and received either Egr1 overexpression (AAV9-hSYN-Egr1-IRES-eGFP-WPRE3), Egr1 knockdown (AAV9-hSYN-Egr1-shRNA-eGFP-WPRE),  eGFP control (AAV9-hSYN-eGFP-WPRE), or scrambled shRNA control (AAV9-hSYN-scramble-eGFP-WPRE) AAV targeted to the ventral hippocampus to determine the sex-dependent effects of Egr1 overexpresssion or knockdown on the neurons in this brain region. Following 3 weeks of incubation, mice were sacrificed at 10-11 weeks of age and bilateral ventral hippocampi were flash frozen in liquid nitrogen. Nuclei were then extracted from frozen tissue and neuronal nuclei were obtained by FACS using an antibody targeting the neuronal nuclei-specific NeuN protein. The ATAC-seq libraries were prepared from 50,000 NeuN+ nuclei for each sample. 150 bp, paired-end sequencing was performed in one lane of an S1 flow cell on the NovaSeq 6000 instrument, yielding 40-75 million reads per sample.

first: Devin

last: Rocks

first: Luisa

last: Demarchi

first: Eric

last: Purisic

first: Heining

last: Cham

first: Eduardo

last: Gallo

first: John

middle: M

last: Greally

first: Masako

last: Suzuki


title: Cell passage number: an intrinsic factor influencing the reproducibility of cell experiments

status: Public on Sep 24 2025

city: Shenzhen

first: Wei

last: Yang

address: Shenzhen 6082 longgang Road

country: China

institute: Shenzhen Longgang Central Hospital

type: Expression profiling by high throughput sequencing

summary: The reproducibility of scientific research has been increasingly challenged in recent years. While extrinsic factors (e.g., cross-contamination, mycoplasma infection, serum variability) are well-studied, the role of intrinsic attributes like cell passage number remains underexplored. Using two tumor cell lines (ACHN and Renca), we employed RNA sequencing to analyze transcriptomic dynamics across passages (P3 to P39). Results revealed a nonlinear transcriptomic shift: mid-passage cells (P10/P11, P17) showed heightened activity in cell cycle, metabolism, and stress response, whereas low (P3) and high passages (P24/P39) exhibited stable and similar profiles. KEGG analysis indicated significant alterations in signaling, immune, and metabolic pathways during passaging. This study demonstrates that passage number shapes transcriptional landscapes and impacts experimental reproducibility. We advocate for strict passage control and explicit reporting of passage information to enhance reliability. These findings underscore the need for standardized cell culture practices to improve research reproducibility.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In this study, we focus on cell passage number to investigate its potential impact on the reproducibility of cell-based experimental results. We selected two commonly used tumor cell lines, Renca and ACHN, as research models. After thawing from cryopreservation (designated as P0), cells were continuously passaged at a 1:4 ratio up to P39. During this process, we collected cells at passages P3, P10/11, P17, P24, and P39 for RNA sequencing analysis.

first: Shuai

last: Liu

first: Hailun

last: Peng

first: Junyan

last: Meng

first: Liyuan

last: Zhuo

first: Shaoping

last: Fu


title: Single-cell RNA sequencing reveals cellular heterogeneity in lineage specification of MC38 subcutaneous tumor cells with either SPP1 overexpression or vector control

city: Beijing

first: Shengde

address: 38 Xueyuan Rd , Haidian District

institute: Peking University Health Science Center

summary: SPP1 (secreted phosphoprotein 1), also known as osteopontin, has emerged as a pivotal factor in the tumor microenvironment (TME) across various cancers. It has been reported that SPP1-positive macrophages are associated with immunosuppressive activity and poor prognosis in colorectal cancer (CRC). The increasing proportion of SPP1-positive macrophages contributes to immune suppression and immune desert by inhibiting T cell function in liver metastatic lesions. However, the role of SPP1 in colorectal cancer liver metastasis (CRLM) remains incompletely understood. Therefore, the impact of tumor-secreted SPP1 on the CRC microenvironment warrants further investigation. To explore the effect of SPP1 on diverse TME cell populations, we conducted single-cell RNA sequencing on MC38 xenografts. Our results revealed an increase in fibroblasts and a concurrent decrease in T cells following SPP1 overexpression, suggesting that SPP1 promotes cancer-associated fibroblast (CAF) infiltration into the CRC TME.

overall_design: First, a stable MC38 cell pool expressing SPP1 or vector was established using lentiviral transduction, and Western blotting was performed to verify the successful expression of SPP1. These cells were then subcutaneously inoculated into C57BL/6 mice for tumor formation. Seven days later, mice in the OE-SPP1 and OE-vector groups were intraperitoneally injected with anti-PD1 (10 mg/kg, twice a week). After two weeks of treatment, the mice were sacrificed, and subcutaneous tumors from one mouse in each group were selected for single-cell RNA sequencing. Finally, single-cell sequencing data analysis was conducted to identify the specific cell populations within the tumor microenvironment whose proportions were altered by OE-SPP1.

first: Zizhen

last: Zhang

first: Lin

last: Shen


title: Real-time quantitative PCR analysis of human pancreatic ductal adenocarcinoma cell lines treated with oxaliplatin or cisplatin

city: Heidelberg

first: Dirk

last: Theile

address: Im Neuenheimer Feld 410

institute: Heidelberg University

summary: AsPC-1 and BxPC-3 cells were treated for 4 h with oxaliplatin (AsPC-1 176 µM; BxPC-3 150 µM) or cisplatin (AsPC-1 150 µM; BxPC-3 65 µM) leading to similar intracellular platinum concentrations (662 pg Pt/µg protein), or left untreated (controls)

overall_design: Three independet replicates were each treated as described above.

first: Beate

last: Köberle


title: Single-cell gene expression profiling of a murine cell line with and without heat stress.

city: Kobe

first: Katsuyuki

last: Shiroguchi

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

summary: As a proof of concept of our approach to finding differentially expressed genes between cell fates predicted by image-based deep learning, we predicted the fates (survival and death) of heat-stressed cells and acquired those gene expression profiles.

overall_design: We temporally heated the mouse acute myeloid leukemia cell line C1498 at 45°C for 10 min and subsequently performed time-lapse imaging. We picked the imaged cells at -1, 1, 5, 10, and 15 h after heating completion using our developed Automated Live-imaging and cell Picking System (ALPS) and obtained those gene expression profiles. As a control experiment, we heated cells at 37°C instead of 45°C.

first: Tomoaki

last: Okaniwa


title: Expansion of a pivotal functional genomics resource identifies novel regulators of temperature-dependent fitness in the fungal pathogen Candida albicans

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

institute: Freie Universität

summary: Functional genomic screens in Candida albicans are fundamental to uncover novel gene functions and the molecular mechanisms of virulence. In this study, expansion of the Gene Replacement and Conditional Expression (GRACE) library, covering now ~73% of the C. albicans genome, revealed genes relevant for fitness at cold or heat stress. From an initial screen at 30°C and 39°C, strains with moderate to severe growth defects were further assayed for growth under six different temperatures. Assessment of growth scores revealed enrichment of genes associated with RNA metabolism and regulatory-related processes as important during cold stress, whereas genes involved in cell cycle, filamentation and stress response were essential during elevated temperature. Here, we describe the function of cold-essential gene C1_11680C (or YSF3), which is involved in splicing and branchpoint recognition. RNA-Seq was conducted for functional analysis of C1_11680C, by investigating transcriptomic changes upon deletion at host (37°C) and cold stress (22°C) temperatures. This revealed major global splicing defects and confirmed its identity as  the homolog of S. cerevisieae Ysf3 (Yeast splicing factor 3). We also found particular importance of this gene for splicing of introns with non-consensus branchpoints. In summary, this study describes the temperature-dependance of previously uncharazterized genes through a significant expansion of a pivotal genomics resource.

overall_design: We compare mRNA expression and splicing changes in different growth conditions (cold stress at 22°C, host temperature at 37° C) of Candida albicans wild-type and the GRACE strain tetO-YSF3/Δ upon induction (with Doxycycline) resulting in YSF3 depletion, and without.

first: Ci

first: Emily

middle: H

last: Xiong

first: Livia

last: Kupczok

first: Linda

middle: S

last: Archambault

first: Timothy

last: Wang

first: Caitlin

last: Holleran

first: Ting Xuan

last: Zhuang

first: Haoyang

first: Kevin

last: Chen

first: Daniel

last: Anderson

first: Bonnie

last: Yiu

first: Zhongle

first: Duncan

last: Carruthers-Lay

first: Zhen-Yuan

last: Lin

first: Cassandra

middle: J

last: Wong

first: Anne-Claude

last: Gingras

first: Nicole

last: Robbins

first: Leah

middle: E

last: Cowen


title: Seizure evolution in a mouse model of West syndrome involves complex and time-dependent 4 synapse remodeling, gliosis and alterations in lipid metabolism

city: Seoul

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

country: South Korea

institute: Korea University College of Medicine

summary: To investigate molecular changes in the hippocampus of Cyfip2 Arg87Cys knock-in mice at the cell-type-specific manner, we conducted single-nucleus transcriptomic analysis at postnatal weeks 28.

overall_design: We dissected the hippocampus from both hemispheres of each mouse. WT and Cyfip2 Arg87Cys knock-in mice were littermates, with two mice (replicates) prepared for each age-genotype group. After dissection, tissue samples were stored at -80°C before being processed further for single-nucleus isolation.

first: Ruiying

last: Ma

first: Muwon

last: Kang

first: Seungji

first: Seungsoo

last: Kim

first: Eunjoon

first: Kihoon

last: Han


title: Brain transcriptome analysis in the cortex and hippocampus of Cyfip2 Arg87Cys knock-in mice at four different postnatal stages

address: 73, Inchon-ro

institute: Korea University

summary: To investigate age-dependent molecular changes in the cortex and hippocampus of Cyfip2 Arg87Cys knock-in mice, we conducted transcriptome analysis at postnatal weeks 1, 7, 14, 28.

overall_design: We dissected the frontal cortex and hippocampal regions from both hemispheres of each mouse. WT and Cyfip2 Arg87Cys knock-in mice were littermates, with four mice (replicates) prepared for each age-genotype group. After dissection, tissue samples were stored in RNAlater at 4°C overnight and then at -80°C before being processed further for RNA extraction.

first: Hyojin


title: Egr1 is a sex-specific regulator of neuronal chromatin, synaptic plasticity, and behaviour

first: Marija

last: Kundakovic

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

overall_design: Refer to individual Series


title: Brain transcriptome analysis in the cortex and hippocampus of Cyfip2 heterozygous mice at three different postnatal stages

summary: To investigate age-dependent molecular changes in the cortex and hippocampus of Cyfip2 heterozygous mice, we conducted transcriptome analysis at postnatal weeks 1, 7, and 14.

overall_design: We dissected the frontal cortex and hippocampal regions from both hemispheres of each mouse. WT and Cyfip2 heterozygous mice were littermates, with four mice (replicates) prepared for each age-genotype group. After dissection, tissue samples were stored in RNAlater at 4°C overnight and then at -80°C before being processed further for RNA extraction.


title: Endothelial RNF20 Suppresses Endothelial-to-Mesenchymal Transition and Safeguards Physiological Angiocrine Signaling to Prevent Congenital Heart Disease [Day07_EC_Cd31po_polyARNA-Seq]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Heart morphogenesis and function rely on intricate communication among distinct cardiac cell types. How their co-development and crosstalk are coordinated is largely unexplored. Our study unveils the functions of the histone H2B ubiquitin (H2Bub1) ligase RNF20 in second heart field development and cardiac endothelial cells. We demonstrate that RNF20 promotes Nrg1 expression through a RNF20-H2Bub1-dependent mechanism and restrains TGF-β signaling by influencing RNA polymerase II pause release at TGF-β target genes in endothelial cells. While heightened TGF-β signaling following RNF20 loss results endothelial-to-mesenchymal transition (EndMT), both impaired Nrg1 signaling and elevated TGF-β activity contribute to abnormal cardiomyocyte proliferation and contractility.  Importantly, RNF20 expression is significantly reduced in cardiac endothelial cells from congenital heart disease patients showing a positive correlation with oxygen saturation and a negative correlation with key components and downstream effectors of TGF-β signaling. In summary, our work identifies a crucial role for RNF20 in safeguarding endothelial identity and physiological angiocrine signaling, thereby ensuring proper heart development and function.

overall_design: Differenciated EC cells were collected at Day7 of differentation after viral transfection at Day3.7 either by empty Vector Plko or ShRNF20. Total RNA was extracted for polyA RNA-seq

first: Julio

middle: D

last: Cordero Henriquez

first: Nalan

last: Tetik-Elsherbiny


title: Highlighting zoonotic importance of synanthropic fleas through microbiome analysis

city: Seville

first: Angela

middle: M.

last: García Sánchez

address: Profesor García González, 2

country: Spain

institute: Universidad de Sevilla

summary: The role of domestic and peridomestic animals in vector-borne diseases is very  important as they share a common environment with people having the potential to  extend the network of pathogen transmission to humans. The most significant  vector-borne infectious diseases that are shared by man, domestic and peridomestic animals are leishmaniosis, borreliosis, bartonellosis, ehrlichiosis, rickettsiosis and anaplasmosis with fleas acting as main vectors in the transmission of some of these diseases. Flea-borne diseases which are relevant in Europe include plague (caused by Yersinia pestis), murine typhus (caused by Rickettsia typhi), flea-borne spotted fever (Rickettsia felis), and cat scratch disease (Bartonella henselae).  In the present study, mNGS was applied to detect and understand the composition of the microbial communities of five different species of fleas (Archaeopsylla erinacei, Ctenocephalides felis, Spilopsyllus cuniculi, Pulex irritans and Ctenocephalides canis) collected on dogs, cats and hedgehogs from Andalusia (Spain) to know the prevalence of pathogenic bacteria among synanthropic fleas. Based on our results, we could conclude that Pulicidae family encompassed those flea species with a close contact with humans and therefore more involved in the potential transmission of infectious diseases. The higher relative abundance of the Phylum Pseudomanadota was mainly due to the presence of the endosymbiont Wolbachia, as well as to notice a high relative abundance of both genera Rickettsia and Bartonella in all flea species. For the first time, we detected Babesia sp. in all species tested, especially with higher abundance in S. cuniculi collected from cats emphasizing the need for further investigation into its potential implications as vectors. Our results also demonstrate that the microbiota composition of fleas is largely influenced by the host they parasitize. Lastly, statistical analyses of microbiota allowed for the ecological separation of flea species, with individuals from these five species clustering distinctly each other.

sample_organism:
Ctenocephalides felis
Archaeopsylla erinacei
Ctenocephalides canis
Pulex irritans
Spilopsyllus cuniculi

overall_design: mNGS was applied to study the composition of the microbial communities of adults of different species of fleas collected on dogs, cats and hedgehogs from Andalusia (Spain)

first: Cristina

last: Cutillas

first: Ignacio

last: Trujillo

first: Antonio

last: Zurita

last: García-Sánchez


title: Differentially Expressed Genes Between High-Metastatic LOVO-HM and Wild-Type LOVO Colorectal Cancer Cell Lines

first: Shengde

last: Liu

summary: Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality globally, with 30-40% of cases developing metastasis, primarily to the liver (CRLM). While immunotherapy has shown promise for the treatment of CRC, CRLM patients still experience limited therapeutic benefits potentially due to an immunosuppressive tumor microenvironment (TME). Therefore, it is urgently needed to elucidate the key-players that drives CRLM and potentiates immunotherapeutic resistance. In this study, we started from establishing a liver-metastatic subline of LoVo cells through continuous passaging in vivo, allowing the screening of RNA expression profiles associated with CRLM. Combining spatial-transcriptomic sequencing and single-cell analysis, we demonstrated a significant upregulation of SPP1 (secreted phosphoprotein 1) expression and secretion in CRLM, and potentiated its contribution to immunotherapeutic resistance. By applying patient-derived xenograft/organoid models and various syngeneic culturing systems, we discovered that SPP1 manipulates the production of CXCL12 by cancer-associated fibroblasts (CAFs) through activating the β-catenin/HIF-1α-related transcription, thus drives a feedback loop for cancer development, shapes an immunosuppressive landscape and contributes to primary/acquired resistance against immunotherapy. Our study underscores the potential of targeting SPP1 and CAFs as a strategy to overcome immunotherapeutic resistance in CRC, especially for CRLM. By providing robust preclinical evidence, we advocate for further investigation into SPP1 as a biomarker and a druggable target for precision cancer treatment. This research contributes critical insights into the intricate interactions within the TME and offers promising avenues for enhancing therapeutic outcomes in CRC patients facing liver metastasis.

overall_design: RNA-seq profiling of wildtype LoVo cells and high-metastatic LoVo cells (LoVo-HM)

first: Zizhen

last: Zhang

first: Lin

last: Shen


title: NGS analysis of small RNA level derived from barley shoots exposed to different duration of high temperature.

city: Poznan

first: Andrzej

last: Pacak

address: Uniwersytetu Poznanskiego 6

country: Poland

institute: Adam Mickiewicz University, Poznan

summary: Two-week-old barley plants were exposed to high and control temperature.

overall_design: RNA was isolated from 100 mg of barley shoots. Barley were exposed to high temperature (35.5°C) and control temperature (21°C).

first: Katarzyna

last: Kruszka

first: Zofia

last: Szweykowska-Kulińska


title: The GPR43-mediated function of eosinophils in asthma

city: Daejeon

first: Jihyun

last: Yu

address: 291 Daehak-ro, Yuseong-gu

institute: KAIST

summary: GPR43 is a short-chain fatty acid receptor exerting anti-inflammatory functions in various inflammatory diseases. Even though eosinophils are one of the cell types highly expressing GPR43, the role of GPR43 in regulating eosinophils has not been studied. In this experiment, we induced asthma in control (Epx-Cre/+) mice and eosinophil-specific GPR43-deficient (Epx-Cre/+GPR43fl/fl) mice using house dust mite extracts and compared the immune cell landscape in the asthmatic lungs of each group using single-cell RNA sequencing.

overall_design: Cells were extracted from asthmatic lungs of control and eosinophil-specific GPR43-deficient mice (3 mice for each group) and pooled. Dead cells and FSC(hi)SSC(hi) cells were excluded by fluorescence-activated cell sorting (FACS).

first: Seongryong

last: Kim

first: You-Me


title: The role of GPR43 in regulating asthmatic lung eosinophils

summary: GPR43 is a short-chain fatty acid receptor exerting anti-inflammatory functions in various inflammatory diseases. Even though eosinophils are one of the cell types highly expressing GPR43, the role of GPR43 in regulating eosinophils has not been studied.   In this experiment, we compared transcriptomic profiles of control (Epx-Cre/+) and GPR43-deficient (Epx-Cre/+GPR43fl/fl) eosinophils purified from asthmatic lungs using bulk RNA sequencing.

overall_design: We induced allergic airway inflammation in control mice (n=5) and eosinophil-specific GPR43-deficient mice (n=4) using house dust mite extracts (HDM). Eosinophils were purified from the lungs of each group by FACS sorting, and their gene expression profiles were compared.


title: A multimodal cross-species comparison of pancreas development [ChIP-Seq]

city: Cincinnati

first: Daniel

middle: O.

last: Kechele

state: OH

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Human pancreas development remains incompletely understood due to limited sample access constrained by ethical and practical considerations. Here we investigate whether pigs resemble humans in pancreas development more closely than rodents, and as such, offer a valuable alternative large-animal model. As pig pancreas organogenesis is unexplored, we first annotated developmental hallmarks and lineage markers of pancreas differentiation and morphogenesis throughout the 114-day gestation. Building on this detailed roadmap, we further constructed a pig single-cell multiome atlas capturing temporal resolution across all three trimesters. Cross-species comparisons with human and mouse time-resolved integrated pancreas atlases accentuated that pig closely resembled human in developmental tempo, epigenetic and transcriptional regulation, gene expression patterns and gene regulatory networks (GRNs). Specifically, pig mimicked the dynamics of progenitor status, differentiation trajectories and GRNs governing endocrine fate acquisition in human. In pig multiome GRN, over 40% of transcription factors targeted by NEUROG3, the endocrine master regulator, were confirmed in human stem cell models. Most notably, we uncovered beta-cell heterogeneity arising during embryonic development, owing to endocrine induction in pancreatic progenitors with temporally altered epigenetic and transcriptional identity. Overall, our work lays the foundation for using pigs to model human pancreas biology and provides unprecedented insights into developmental principles and mechanisms across species.

overall_design: ChIP-seq for NEUROG3 binding in hPSC-derived endocrine progenitors (day 9) generated from NEUROG3-/- line rescued with tetracycline-inducible wild-type NEUROG3

first: Kaiyuan

last: Yang

first: Hannah

last: Spitzer

first: Michael

last: Sterr

first: Karin

last: Hrovatin

first: Sean

last: de la O

first: Xinghao

first: Eunike

last: Sawitning Ayu Setyono

first: Minhaz

last: Ud-Dean

first: Thomas

last: Walzthoeni

first: Krzysztof

last: Flisikowski

first: Tatiana

last: Flisikowska

first: Angelika

last: Schnieke

first: Katharina

last: Scheibner

first: James

last: Wells

first: Julie

middle: B

last: Sneddon

first: Barbara

last: Kessler

first: Eckhard

last: Wolf

first: Elisabeth

last: Kemter

first: Fabian

last: Theis

first: Heiko

last: Lickert


title: Oncogenic DEAD-box ATPase DDX41 establishes transcript ensembles via CLK3-dependent and -independent mechanisms

city: MADISON

first: Siqi

last: Shen

state: WI

address: 425 Henry Mall

institute: University of Wisconsin - Madison

summary: Post-transcriptional diversification of RNA transcripts mediated by complex processing machinery, including DEAD-box ATPases, establishes and maintains cellular phenotypes. For example, DDX41 controls RNA splicing, innate immune signaling, and genome stability. Although heterozygous DDX41 germline genetic variation occurs in familial myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), the DDX41 contribution to splicing globally, biological processes, and pathogenic mechanisms are incompletely defined. Using a genetic rescue system with Ddx41+/- myeloid progenitors, we established global wildtype DDX41 and pathogenic variant mechanisms. Differing from pathogenic variants of other RNA splicing regulators, DDX41 deficiency compromised multiple splicing steps. DDX41-regulated transcripts encoded factors controlling RNA splicing, including Cdc2-like kinase 3 (CLK3). DDX41 regulated Clk3 transcripts, and elevated CLK3 during myeloid differentiation. Loss-of-function analysis revealed that the majority of transcript regulation mediated by DDX41 requires CLK3, but splicing-related transcripts remain regulated upon CLK3 depletion. Thus, through a dual mechanism, with or without a splicing factor kinase that itself is DDX41-regulated, DDX41 establishes transcript ensembles in myeloid progenitors.

overall_design: GFP- or GFP-DDX41 expressing retrovirus was infected to Clk3+/+;Ddx41+/-  or Clk3-/-;Ddx41+/- cells. GFP positive cells were sorted by flow cytometry and total RNA was subjected to RNA-sequencing.

first: Jeong-Ah

last: Kim

first: Emery

last: Bresnick

first: Sunduz

last: Keles


title: A multimodal cross-species comparison of pancreas development

first: Daniel

last: Kechele


title: Endothelial RNF20 Suppresses Endothelial-to-Mesenchymal Transition and Safeguards Physiological Angiocrine Signaling to Prevent Congenital Heart Disease [polyAbulkRNA_seq_Cd31_pos_EC_Rnf20_het]

first: Gergana

last: Dobreva

overall_design: ESC from WT and Rnf20 heterozygous were differentiated at day 3.7 towards Endothelial cells (EC). At day10, cells were FACS sorted and only positive Pecam1 (CD31) were selected for RNA extraction and further sequencing.

first: Julio

last: Cordero Henriquez

first: Nalan

last: Tetik-Elsherbiny


title: Endothelial RNF20 Suppresses Endothelial-to-Mesenchymal Transition and Safeguards Physiological Angiocrine Signaling to Prevent Congenital Heart Disease

overall_design: Single cells were isolated from E10.5 hearts from Isl1_ctr and Isl1cre_Rnf20_fl_fl to be barcoded with 10X genome (Chromium Next GEM Single Cell 3' Kit v3.1).

first: Yanliang

last: Dou


title: Effect of MDM2 overexpression on response to etoposide treatment

status: Public on Sep 23 2025

city: Zurich

first: Jonas

last: Fullin

address: Rämistrasse 100

department: Department  of Medical Oncology and Hematology

country: Switzerland

institute: University of Zurich

summary: We aimed to study the effect of non-mutational p53 inactivation on the response of hematopoietic progenitor cells to genotoxic treatment. In order to study this in vitro, we generated HSPC lines by enforced ER-Hoxb8 expression in bone marrow cells derived from transgenic Trp53-fl-R245W-GFP mice. In the absence of Cre-mediated recombination, these cells are wild-type for Trp53. We additionally transduced these cells lentivirally with a construct overexpressing murine Mdm2 or a control vector. This leads to non-mutational inactivation of functional p53. Thereby, we aimed to compare the transcriptional response to genotoxic treatment in Trp53 wild-type cells with or without non-mutational p53 inactivation through Mdm2 overexpression

overall_design: Hoxb8 cells, immunophenotypically resembling murine granulocyte-macrophage progenitor cells, were transduced with either an Mdm2 overexpressing or a control vector. These cells were treated with 10 uM etoposide for 3 hours, after which RNA was isolated and subjected to bulk RNA sequencing.


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues [mRNA-seq]

city: La Jolla

middle: A

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: Plant Molecular and Cellular Biology

institute: Salk Institute for Biological Studies

summary: DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to anther or ovule tissues. We designate these factors as REM INSTRUCT METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. Furthermore, we demonstrate that mis-expression of RIM12 is sufficient to initiate siRNA production at ovule targets in anthers. These findings reveal a critical role for genetic information in targeting DNA methylation in reproductive tissues, expanding our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

overall_design: 24 mRNA-seq libraries were sequenced.

first: Guanghui

last: Xu

first: Yuhan

last: Chen

first: Laura

last: Martins

first: En

last: Li

first: Fuxi

last: Wang

first: Tulio

last: Magana

first: Junlin

last: Ruan


title: Single cell RNA sequencing for non-cardiomyocytes in healthy, adaptive hypertrophy, and heart failure hearts of C57BL/6JJcl mice.

city: Shinjuku-ku

first: Toshiomi

last: Katsuki

state: Tokyo

address: Shinanomachi 35

department: Cardiology

institute: Keio University Hospital

summary: Single cell RNA sequencing for non-cardiomyocytes derived from healthy, adaptive hypertrophy, and heart in healthy (Control), adaptive hypertrophy (post TAC 2W), and heart failure (post TAC 12W) hearts of C57BL/6JJcl mice.

overall_design: mRNA profiles of unselected non-cardiomyocytes isolated from hearts. One experiment for each time phase.

first: Yutaka

last: Suzuki


title: Neuronal type-specific modulation of cognition and AP-1 signaling by early-life rearing conditions. [RNA-Seq]

city: San Juan de Alicante (Alicante)

first: Miguel

last: Fuentes-Ramos

address: Av. Santiago Ramón y Cajal s/n

institute: Instituto de Neurociencias (UMH/CSIC)

summary: Environmental conditions profoundly influence cognitive development, particularly during early life. Transcriptional and epigenetic mechanisms may serve as molecular substrates for the lasting effects of environmental enrichment (EE) and impoverished environment (IE) on cognitive abilities and hippocampal function. However, the specific gene programs driving these changes remain largely unknown. In this study, we employed EE and IE paradigms to modulate cognitive abilities in opposing directions in mice. By combining hippocampal microdissection and genetic tagging of neuronal nuclei with genome-wide analyses of gene expression, chromatin accessibility, histone acetylation, and DNA methylation, we uncovered cell type-specific genomic changes induced by EE and IE in CA1 pyramidal neurons and dentate gyrus (DG) granule neurons. This multiomic screen identified the activity-regulated transcription factor AP-1 as a crucial mediator of neuroadaptation to environmental conditions during early life in both neuronal populations, albeit through distinct downstream mechanisms. Conditional deletion of Fos, a core AP-1 subunit, in excitatory neurons hampered EE-induced cognitive enhancement, further underscoring the pivotal role of this transcription factor in neuroadaptation.

overall_design: Nuclear RNA-seq profiling in two types of hippocampal excitatory neurons of adult mice raised in different environmental conditions: environmental enrichment (EE), standard cage (SC), and impoverished environment (IE).

first: Marta

last: Alaiz-Noya

first: Federico

last: Miozzo

first: Angel

last: Barco


title: Neuronal type-specific modulation of cognition and AP-1 signaling by early-life rearing conditions.


title: A multimodal cross-species comparison of pancreas development [ATAC-Seq]

first: Daniel

last: Kechele

overall_design: ATAC-seq in hPSC-derived endocrine progenitors generated from NEUROG3-/- line with and without rescue with tetracycline-inducible wild-type NEUROG3 for 8 hr or 24 hr. ATAC was performed 8 hr, 24 hr, or 3 d post induction.

first: Kaiyuan

last: Yang

first: Hannah

last: Spitzer

first: Michael

last: Sterr

first: Karin

last: Hrovatin

first: Sean

last: de la O

first: Xinghao

last: Zhang

first: Eunike

last: Sawitning Ayu Setyono

first: Minhaz

last: Ud-Dean

first: Thomas

last: Walzthoeni

first: Krzysztof

last: Flisikowski

first: Tatiana

last: Flisikowska

first: Angelika

last: Schnieke

first: Katharina

last: Scheibner

first: James

last: Wells

first: Julie

last: Sneddon

first: Barbara

last: Kessler

first: Eckhard

last: Wolf

first: Elisabeth

last: Kemter

first: Fabian

last: Theis

first: Heiko

last: Lickert


title: Epigenetic regulation of chromosomal instability by EZH2 methyltransferase [RNA-seq]

city: NY

first: Yang

last: Bai

address: 1300 York Ave

department: Cardiothoracic Surgery

institute: Weill Cornell Medicine

summary: Chromosomal instability (CIN) and epigenetic alterations, major drivers of tumor evolution, contribute to breast cancer metastasis. Whether CIN is epigenetically regulated in metastatic cells is poorly understood. Here we show that EZH2 expression is highly correlated with genomic copy number alterations across human breast tumors. Consistently, increased expression of EZH2 histone methyl transferase is associated with elevated CIN in triple negative breast cancer (TNBC) metastasis initiating cells. Genetic or pharmacological inhibition of EZH2 suppresses CIN whereas forced overexpression of EZH2 in otherwise non-transformed cells promotes chromosome segregation errors. Integrated global chromatin and transcriptome profiling identified Tankyrase (TNKS), a multifunctional poly (ADP ribose) polymerase (PARP), as a direct target of EZH2 transcriptional suppressive activity. Strikingly, depletion of TNKS was sufficient to abrogate the ability of EZH2 inhibition to suppress CIN. EZH2-mediated suppression of TNKS induced centrosome amplification and multipolar mitosis which often clustered into pseudo-bipolar mitotic spindles exhibiting chromosome segregation defects. Our work establishes a previously unappreciated epigenetic regulatory mechanisms of CIN and suggests that CIN suppression might be an important component of epigenetic modifying therapies such as EZH2 inhibitors which are currently in clinical use.

overall_design: RNA sequencing of sorted EO771.ML1 EZH2 high and EZH2 low cells are treated with either DMSO or 5uM EZH2 inhibitor for 7 days.

first: Liron

last: Yoffe


title: Quorum-sensing control of sepsis in the coagulase-negative staphylococcal species Staphylococcus haemolyticus

city: Bethesda

first: Gordon

middle: Yiu Chong

last: Cheung

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: In many pathogens, quorum-sensing systems regulate virulence. Quorum-sensing is therefore often proposed as a target for antivirulence drug development. Coagulase-negative staphylococci are leading causes of nosocomial blood infections and of mortality due to sepsis as the most extreme consequence of such infections. However, there is a severe lack of understanding how virulence and especially quorum-sensing affects coagulase-negative staphylococcal sepsis. Using a mouse systemic infection model, we here show that the staphylococcal Agr quorum-sensing system has a strong impact on mortality from sepsis caused by the exemplary coagulase-negative staphylococcal species Staphylococcus haemolyticus. To that end, we analyzed the mechanism and regulon of S. haemolyticus Agr, which revealed a strong focus of quorum-sensing regulation of phenol-soluble modulin toxins. Our results further indicate that PSMs are the virtually exclusive mediators of the Agr effect on S. haemolyticus sepsis and suggest that the predominant underlying mechanism is cytolytic capacity of PSMs. These findings imply that Agr and PSMs represent promising targets for antivirulence drug development targeting sepsis caused by coagulase-negative staphylococci. This contrasts quorum-sensing targeted efforts to control S. aureus blood infections, for which such approaches are considered less promising - a difference our results suggest is due to the much more focused role of Agr control in coagulase-negative staphylococci, where among toxins, Agr exclusively and exceptionally tightly controls PSMs.

platform_organism:
Coxiella burnetii
Rickettsia rickettsii
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: Staphylococcus haemolyticus wt vs. mutant at 4hr and 8hrs.

middle: Y

first: Fei

last: Da

first: Emilie

last: Fisher

first: Amer

last: Villaruz

first: Katherine

last: Le

first: Ryan

last: Liu

first: Ji

last: Lee

first: Daniel

last: Sturdevant

first: Hwang-Soo

last: Joo

first: Henning

last: Büttner

first: Holger

last: Rohde

first: Michael

last: Otto


title: Endothelial RNF20 Suppresses Endothelial-to-Mesenchymal Transition and Safeguards Physiological Angiocrine Signaling to Prevent Congenital Heart Disease [Heart_scRNAseq_E11_5_Cdh5cre_Rnf20KO]

first: Gergana

last: Dobreva

overall_design: Single cells were isolated from E11.5 hearts from Cdh5cre_wt and Cdh5cre_Rnf20_fl_fl to be barcoded with 10X genome (Chromium Next GEM Single Cell 3' Kit v3.1).

first: Julio

last: Cordero Henriquez

first: Yanliang

last: Dou


title: Epigenetic regulation of chromosomal instability by EZH2 methyltransferase [CUT&RUN]

first: Yang

last: Bai

overall_design: Cut and Run sequencing of sorted EO771.ML1 EZH2 high and EZH2 low cells are treated with either DMSO or 5uM EZH2 inhibitor for 7 days.

first: Cem

last: Meydan


title: The LINC01612-DVL2-WNT axis promotes human endoderm differentiation

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

summary: Long noncoding RNA in gene desert regions are largely uncharacterized despite their potential regulatory roles in cell differentiation. Here, we identify LINC01612 as a crucial modulator of human definitive endoderm differentiation. LINC01612 exhibits stage-specific expression without protein coding ability during endoderm differentiation. Depletion of LINC01612, through either shRNA-mediated knockdown or promoter deletion, severely disrupts human endoderm differentiation. Mechanistically, LINC01612 interacts with DVL2, a WNT regulator essential for early development, and stabilizes DVL2 protein level by reducing its ubiquitination. Loss of LINC01612 or DVL2 impairs WNT signaling, while both WNT activation and DVL2 overexpression could restore endoderm differentiation capacity due to the absence of LINC01612. These findings reveal LINC01612 as a key regulator in human definitive endoderm differentiation through stabilizing DVL2 protein level and modulating WNT activity.

overall_design: In this study, we utilized RNA sequencing (RNA-seq) to investigate the functional impact of LINC01612 on definitive endoderm (DE) differentiation. To achieve this, we compared transcriptomic profiles between LINC01612 knockout (LINC01612-KO) DE samples and wild-type DE controls. Additionally, to further elucidate the underlying mechanisms, we performed RNA-seq on DE cells with DVL2 knockdown (DVL2-KD) alongside control DE cells. Our analysis identified significant expression changes.

first: Wei

last: Jiang

first: Chenchao

last: Yan

first: Mao

last: Li


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues [small RNA-seq]

first: Julie

last: Law

type: Non-coding RNA profiling by high throughput sequencing

overall_design: 148 smRNA-seq libraries were sequenced.

first: Guanghui

last: Xu

first: Yuhan

last: Chen

first: Laura

last: Martins

first: En

first: Fuxi

last: Wang

first: Tulio

last: Magana

first: Junlin

last: Ruan


title: Gene expression profile on pons and medulla of maternal immune activation model rat

city: Tsu

first: Takeshi

last: Ohkawara

department: Developmental and Regenerative Medicine

institute: Mie University

summary: We created two-hit immune activation model by inducing a pseudo-bacterial infection (administration of lipopolysaccharide (LPS)) on postnatal (P) 11 in pups born to rats infected with a pseudo-virus (administration of polyinosinic-polycytidilic acid (poly I:C)) during pregnancy of day 10. Our model rats showed increased mortality rate due to LPS administration on P11 and abnormal blood biochemical test results. Next, we examined the gene expression in pons and medulla oblongata of our model rats on P11 by DNA microarray and found that a number of genes showed more than a 2-fold change in expression.

overall_design: Pregnant Wistar rat was injected intrapenitorially 10 mg/kg poly I:C or PBS at GD10. On P11, we administered 0.25 mg/kg LPS or PBS to male pups. After 4 hours, pons and medulla were collected.


title: Neuronal type-specific modulation of cognition and AP-1 signaling by early-life rearing conditions. [ATAC-Seq]

first: Miguel

last: Fuentes-Ramos

overall_design: ATAC-seq profiling in two types of hippocampal excitatory neurons of adult mice raised in different environmental conditions: environmental enrichment (EE), standard cage (SC), and impoverished environment (IE).

first: Marta

last: Alaiz-Noya

first: Federico

last: Miozzo

first: Angel

last: Barco


title: A. thaliana XVE_mTCP3 ER 16hr vs. XVE_mTCP3 DMSO 16hr

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: Cell expansion is crucial for organ morphogenesis in multicellular organisms. Plant cells are surrounded by rigid cell walls and turgor pressure drives cell expansion at a rate that is limited by the mechanical property of cell wall. The regulation of cell wall-loosening underlies the mechanism of cell expansion, but the integration of this regulation with organ morphogenesis is still elusive. In this study, we demonstrate that TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTORs (TCPs) transcription factors integrate cell wall loosening and organ morphogenesis in Arabidopsis thaliana. We observed that TCPs stimulated cell expansion and exaggerated elongation of hypocotyls. The atomic force microscopy analysis demonstrated that TCPs decreased the stiffness of cells, indicating the roles of TCPs to regulate the mechanical properties of cell wall. The gene expression analyses found that TCPs regulated the genes for both cell wall loosening and apoplast acidification such as SMALL AUXIN UP RNAs (SAURs). Because apoplast acidification induces cell wall loosening, we conducted western blot and pharmacological analyses and revealed that TCPs activated a plasma membrane-localized H+-ATPase responsible for apoplast acidification. Monitoring the apoplast pH at cellular resolutions indicated that TCPs stimulated apoplast acidification. Ectopic expression of a SAUR gene in a sextuple tcp mutant substantially recovered the hypocotyl morphology of the tcp mutant, providing the genetic evidence of the TCP-mediated SAUR regulation. Altogether, we demonstrate that TCPs govern cell wall loosening for cell expansion and pave the way to modify plant architectures through the regulation of cell wall loosening.

overall_design: Two-condition experiment, ER treated vs. DMSO treated. Biological replicates: 3 ER-treated replicates, 3 DMSO-treated replicates.

first: Tomotsugu

last: Koyama


title: A multimodal cross-species comparison of pancreas development [RNA-Seq]

first: Daniel

last: Kechele

overall_design: Bulk RNA-seq in hPSC-derived endocrine progenitors generated from NEUROG3-/- line with and without rescue with tetracycline-inducible wild-type NEUROG3. RNA-seqq was performed 8 hr, 24 hr, 48 hr, or 72 hr post induction.

first: Kaiyuan

last: Yang

first: Hannah

last: Spitzer

first: Michael

last: Sterr

first: Karin

last: Hrovatin

first: Sean

last: de la O

first: Xinghao

last: Zhang

first: Eunike

last: Sawitning Ayu Setyono

first: Minhaz

last: Ud-Dean

first: Thomas

last: Walzthoeni

first: Krzysztof

last: Flisikowski

first: Tatiana

last: Flisikowska

first: Angelika

last: Schnieke

first: Katharina

last: Scheibner

first: James

last: Wells

last: Sneddon

first: Barbara

last: Kessler

first: Eckhard

last: Wolf

first: Elisabeth

last: Kemter

first: Fabian

last: Theis

first: Heiko

last: Lickert


title: Understanding Aquaporin-5 (Aqp5) functions in human gastric cancer organoids

city: Singapore

first: Grace

last: Lim

address: 61 Biopolis Drive, Proteos

department: IMCB

country: Singapore

institute: A*STAR

summary: To study Aqp5 functions in human gastric cancer organoids, we generated Aqp5 FLIP-Puro organoids allowing for inducible loss of Aqp5 expression upon Cre gesicle administration. We analysed transcriptomes of these organoids at various timepoints following loss of Aqp5 to elucidate potential functions of Aqp5 in this system.

overall_design: Untreated and Cre gesicle-treated Aqp5 FLIP-Puro organoids were collected at 4 different timepoints post treatment (12h, 24h, 2 days and 5 days), with 3 replicates per condition.

first: Hui Yi Grace

first: Swathi

last: Yada

first: Nick

last: Barker


title: Neuronal type-specific modulation of cognition and AP-1 signaling by early-life rearing conditions. [CUT&Tag]

first: Miguel

last: Fuentes-Ramos

overall_design: Cut and Tag profiling of two types of hippocampal excitatory neurons of adult mice raised in different environmental conditions: environmental enrichment (EE), standard cage (SC), and impoverished environment (IE).

first: Marta

last: Alaiz-Noya

first: Federico

last: Miozzo

first: Angel

last: Barco


title: Spatial transcriptomics reveals the cellular neighborhood of erythropoietin-producing cells in the mouse kidney

status: Public on Sep 22 2025

city: Zürich

first: Olga

middle: Maria

last: Lempke

address: Winterthurerstrasse 190

institute: Univeristy of Zurich

summary: The main source of circulating erythropoietin (Epo) in the adult are kidney Norn cells. To shed new lights on the mechanisms governing Epo production, we combined spatial transcriptomics, mRNA-FISH and sequential immunofluorescence, enabling the identification of the direct neighborhood of active REP cells. While in the hypoxic mouse kidney REP cells are closest to proximal tubule (PT) segments (S) S1 to S2/3 and endothelial cells, Epo is re-induced by HIF-stabilizers in damaged kidneys in REP cells in the vicinity of injured PT (but normal endothelial) cells.

overall_design: All tissues analyzed in this work were derived from re-used frozen kidneys originally reported by Dahl et al. Acta Physiol. (Oxf.) 234, e13768. Hypoxic stimulation by exposure to 0.1% CO for 4 hours, unilateral ureteral obstruction (UUO) for 7 days, and the treatment with FG-4592/roxadustat for 90 minutes were described therein.

first: Olga M.

first: Thomas

last: Knöpfel

first: Stellor Nlandu

last: Khodo

first: Roland H.

last: Wenger


title: Transciptomics analysis for alcoholic cardiomyopathy

city: Omaha

first: Saraswathi

last: Viswanathan

state: NE

address: 4101 Woolworth Ave

department: Internal Medicine

institute: University of Nebraska Medical Center

summary: The effects of chronic plus binge ethanol-det feeding on myocardium are assessed.

overall_design: C57BL/6 male mice were fed with 5% Ethanol diet or isocaloric control diet for ten days followed by one binge of ethanol or maltose-dextrin by oral gavage. Mice are divided into 2 groups: CONT and ET.

first: Weilun

last: Ai


title: Captopril Restores Microglial Homeostasis and Reverses ASD-like Phenotype in a model of ASD induced by exposure in utero to anti-Caspr2 IgG.

city: Manhasset

first: Lior

last: Brimberg

address: 350 Community Drive

institute: Feinstein Institutes for Medical Research

summary: We performed single-cell RNA sequencing (scRNA-seq) of hippocampal microglia to define transcriptional changes induced by prenatal exposure to maternal anti-Caspr2 antibodies and their modulation by treatment (Captopril). Male offspring were analyzed across four main groups: (1) Saline-treated Controls, (2)Captopril treated Controls, (3) Anti-Caspr2, saline-treated, and (4) Anti-Caspr2, Captopril-treated . scRNA-seq revealed a Captopril (blood–brain barrier-permeable ACE inhibitor)-responsive microglial subcluster in Anti-Caspr2 mice with dysregulated translation (eIF2 signaling) and metabolic pathways (mTOR, oxidative phosphorylation) relative to controls. Captopril reversed these pathway alterations and restored a homeostatic microglial transcriptional state. These data provide a single-cell transcriptomic resource linking prenatal anti-Caspr2 exposure to persistent microglial dysfunction and demonstrate pathway normalization with BBB-permeable ACE inhibition.

overall_design: Hippocampal  brain macrophages (CD45+, CD11b++) were isolated from P42-P45 mice, and sorted on a BD FACSAria III. scRNA analysis included three mice from each group (Control Saline, Control Captopril, Anti-Caspr2 Saline, and Anti-Caspr2 Captopril), each representing a unique litter. Single-cell cDNA libraries were prepared according to the manufacturer’s instructions (Next GEM Single Cell 3′GEM v.3.1 protocol, 10x Genomics).

first: Benjamin

last: Spielman

first: Ciara

last: Bagnall-Moreau

first: Frank

last: Chen

first: Crystal

last: Balvuena

first: Christian

last: Cruz

first: Joseph

last: Carrion

first: An

last: Vo

first: Arnon

last: Arazi

last: brimberg


title: Cross-species blood transcriptional correlates of BCG-mediated protection against tuberculosis include innate and adaptive immune processes

city: Worcester

first: Richard

last: Baker

state: MA

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

summary: The immune mechanisms induced by the Bacillus Calmette-Guérin (BCG) vaccine, and the subset of which mediate protection against tuberculosis (TB), remain poorly understood. This is further complicated by difficulties to verify vaccine-induced protection in humans. Although research in animal models, namely mice and non-human primates (NHPs), has begun to close this knowledge gap, discrepancies in the relative importance of biological pathways across species limit the utility of animal model-derived biological insights in humans. To address these challenges, we applied a systems modeling framework, Translatable Components Regression (TransCompR), to identify human blood transcriptional variability which could predict Mtb challenge outcomes in BCG-vaccinated NHPs. These protection-associated pathways included both innate and adaptive immune activation mechanisms, along with signaling via type I interferons and anti-mycobacterial T helper cytokines. We further partially validated the associations between these mechanisms and protection in humans using publicly available microarray data collected from BCG-vaccinated infants who either developed TB or remained healthy during two years of follow-up. Overall, our work demonstrates how species translation modeling can leverage animal studies to generate hypotheses about the mechanisms that underlie human infectious disease and vaccination outcomes, which may be difficult or impossible to ascertain using human data alone.

overall_design:
Diversity Outbred (DO) mice were vaccinated intradermally with 105 CFU of BCG, and at 8 weeks challenged by aerosol with M. tuberculosis Erdman. Ninety-nine animals, representing a spectrum of outcomes regarding lung and spleen Mtb burden, lung histopathology, and early moribund, were chosen for further study. Gene expression was profiled by blood RNA-seq from samples collected 14 days before and 14 days after vaccination.

This work was supported by NIH contract 75N93019C00071 to CMS and DAL; NIH grant AI181898 to CMS, TJS, and DAL; and the Army Institute for Collaborative Biotechnologies collaborative agreement W911NF-19-2-0026 to DAL. Work by KB was supported in part by the NIEHS Training Grant in Environmental Toxicology (Grant # T32-ES007020).

first: Kate

last: Bridges

first: Denis

last: Awany

first: Anele

last: Gela

first: Temwa-Dango

last: Mwanbene

first: Sherry L

last: Kurtz

first: Richard E

first: Karen L

last: Elkins

first: Christopher M

last: Sassetti

first: Thomas J

last: Scriba

first: Douglas A

last: Lauffenburger


title: Toll-like Receptor 4 Induces Trained Innate Immune Tolerance in the Heart in a Model of Stress-induced Cardiomyopathy [ATAC-seq]

city: St. Louis

first: Douglas

last: Mann

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis

summary: This study aimed to determine the mechanism by which TLR4 activation establishes cardiac protection in mice subjected to isoproterenol-induced cardiac injury. We performed bulk ATAC sequencing to determine if this was set up through epigenetic means, which would suggest a mechanism consistent with trained innate immune tolerance.

overall_design: Female 10-wk old wild-type (C57BL/6J) mice were treated with lipopolysaccharide (LPS; 2.5 mg/kg), 1 ug recombinant interferon-b1/10 ug recombinant interferon-y (IFN), isoproterenol (ISO; 300 mg/kg), or diluent. Mice were then euthanized 7 days later (n=3/group) with bone marrow aspirates collected and used for bulk ATAC sequencing.

first: Kenji Rowel

middle: Q

last: Lim


title: Revealing tumour cell heterogeneity in an Aqp5-APK mouse pyloric tumour model

first: Grace

summary: The cell lineages present within the healthy gastric epithelium have been well delineated. However, tumour cell lineages within the stomach are less understood. To dissect the heterogeneity within pyloric tumours in the mouse stomach, we performed scRNAseq on an Aqp5-APK mouse pyloric tumour to resolve the diversity of cell populations present within these tumours.

overall_design: An Aqp5-eGFP-ires-CreERT2; Apcfl/fl; Ptenfl/fl; KrasG12D/+ mouse was induced with two doses of 4mg tamoxifen and the resultant tumours harvested after 10 weeks. Tumours were dissociated to single cells and processed for scRNAseq.

first: Hui Yi Grace

first: Swathi

last: Yada

first: Nick

last: Barker


title: Transcriptional memory of tomato plants using ultrasound and drought stress stimuli [RNA-seq]

city: Nyíregyháza

first: Judit

last: Dobránszki

state: Szabolcs-Szatmár-Bereg

address: Westsik Vilmos út 4-6.

department: Centre for Agricultural Genomics and Biotechnology

country: Hungary

institute: University of Debrecen

summary: Plant memory is a tool for plants that they can use to increase their fitness and cope with adverse environmental stresses. In this study, mRNA-seq., WGBS and RT-qPCR methods were applied for evaluating formation and maintenance of somatic transcriptional memory after treatment with ultrasound and drought stimuli in tomatoes. In addition, effects of repeated stimuli, as well as association-forming ability of plants were studied when they were trained previously with combined stimuli.  48 h after exposure to the two stimuli applied alone or in combination, significantly altered gene transcription and DNA methylation were revealed but there was no correlation between these changes. Using four selected target genes, we have proven that plants memorized stimuli for 5 to 10 days, in a gene-, and stimulus-dependent way. The repeated application of the stimuli caused altered behavior, such as habituation, sustained induction or modified re-induction, depending on the genes and physiological ages of plants. Plants were able to use one conditioned stimulus as a predictor of the other, unconditioned one, after conditioning in the case of 3 out of 4 target genes, and use their transcriptional memory associatively.

overall_design: Two stimuli were applied in the experiments, ultrasound and drought stress, separately and in combination. They were applied at the onset of the experiments (initial stimuli; Treatment I), and then 5 and 10 days after the initial stimuli in the first and the second series of experiments (Treatment II), respectively. Changes in gene transcription and DNA methylation in response to US, D and US+D treatments 48 h after the treatments were investigated.

first: Dóra

last: Farkas

first: Anita

last: Király

first: Viktor

last: Ambrus

first: Bianka

last: Tóth


title: Transcriptional memory of tomato plants using ultrasound and drought stress stimuli [WGBS]


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues [methylC-seq]

first: Julie

last: Law

overall_design: 30 methylC-seq libraries were sequenced.

first: Guanghui

last: Xu

first: Yuhan

last: Chen

first: Laura

last: Martins

first: En

last: Li

first: Fuxi

last: Wang

first: Tulio

last: Magana

first: Junlin

last: Ruan


title: Evaluating Aquaporin-5 (Aqp5) functions in mouse pyloric cancer stem cells

first: Grace

summary: To study Aqp5 functions in pyloric cancer stem cells, we isolated GFP+ putative stem cells and GFP- tumour epithelial cells from Aqp5 wildtype and Aqp5 knockout pyloric mouse tumours to understand the functions of Aqp5 in these cancer stem cells.

overall_design: Aqp5-eGFP-ires-CreERT2; Apcfl/fl; Ptenfl/fl; KrasG12D/+ mice with and without an Aqp5 KO allele were induced with two doses of 4mg tamoxifen and the resultant tumours harvested after 10 weeks, with 3 mice analysed per condition. FACS was performed to isolate GFP+ and GFP- tumour epithelial cell populations from each sample for RNAseq.


title: Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation [CUT&Tag]

city: Hangzhou

first: Hongtao

last: Yu

state: Zhejiang

address: Dunyu Street

institute: Westlake University

summary: Human neuroepithelial cells are the earliest neural progenitor cells (NPC) during brain development. The cell cycle is fundamental for cell proliferation and differentiation. How the cell cycle is linked to the differentiation process from embryonic stem cells (ESC) in blastocytes to neuroepithelial cells, however, is still unclear. In this study, using an in vitro ESC-to-NPC differentiation system and PAX6 as an NPC cell fate indicator, we discovered that the neural cell fate was transited, PAX6 expression exhibiting an incremental rise, during the G2 phase. For the mechanism, the loss of -401 bp to -450 bp from the transcription start site (TSS) of PAX6 efficiently blocked the cell cycle-dependent expression of PAX6. In addition, we found that using hydroxyurea to arrest the cell cycle of differentiating NPC could prevent NPC differentiation. Overall, this study reported the first scenario to link cell cycle and cell fate transition during early neurogenesis.

overall_design: PAX6 Cleavage Under Targets & Tagmentation of neural progenitor cells (NPC) at Day0 and Day3 during the process of NPC differentiation from embryonic stem cells

first: Song

last: Hu

first: Rongao

last: Kou

first: Zhuojie

last: Su

first: Guanchen

first: Haishan

last: Gao

first: Shutao

last: Qi


title: Organoid Modeling of Mouse Anterior Tongue Epithelium Reveals Regional and Cellular Identities

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

summary: The tongue is essential for swallowing, taste perception, and mechanosensation. The anterior and posterior parts of the tongue have region-specific developmental origins and are maintained by adult epithelial stem/progenitor cells. In vitro models that can be used to investigate anterior tongue biology have been lacking. Here, we develop a protocol to generate a long-term expanding organoid model from adult mouse dorsal anterior tongue. Anterior tongue organoids consist of Lgr6+ cells, Sox2+ stem/progenitor cells, and Hoxc13+ filiform papillae progenitor cells. Furthermore, anterior tongue organoids share region-specific transcriptomic profiles, gene regulatory networks, and signaling pathways with anterior tongue tissue. Anterior tongue organoids can be differentiated into various epithelial cell types including Merkel-like cells, keratinocytes, and taste bud cells. Gene regulatory network analysis reveals transcriptional programs associated with Krt8+ cell and Krt23+/Sbsn+ keratinocyte differentiation in the organoids. Together, this study provides an in vitro model of mouse dorsal tongue epithelium.

overall_design:
Tongues were collected from 20 BL/6 mice. CvP and FoP were collected using tweezers under stereomicroscope. Tissues were minced and treated with TrypLE containing 10 μM Y-27538 for up to 30 minutes. During the enzymatic digestion process, every 5 minutes, tissues were pipetted several times using a 1000 uL pipette tip. Single cells and small tissue clumps were collected in cold medium and fresh TrypLE + 10 uM Y-27538 was added to further digest the remaining tissues. In brief, 300 – 400 μL of 1 mg/mL collagenase/dispase solution was injected under the lingual epithelium using a 27G needle and tongues were incubated at 37°C for 20 to 25 minutes. Then, the epithelium was peeled off and digested with TrypLE containing 10 µM Y-27538 in the same manner as CvP and FoP tissues. ATEM and ATDM were collected and processed in the similar manner as the tissues. Single cells were washed twice with cold FACS buffer containing 1% FBS, 0.1 mM EDTA, and PBS. Cell pellets were resuspended in 500 μL cold FACS buffer, filtered through a 70 μm cell strainer and then through a 40 μm FACS tube. Cells were stained with 5 μM Draq5 (424101; Biolegend) and 1 μM 4′,6-diamidino-2-phenylindole (DAPI, D9542; Sigma-Aldrich) according to the manufacturer’s protocols. Viable single cells (Draq5+/DAPI-) were collected in PBS containing 1% BSA and 10 μM Y-27538 using the SH800S Cell Sorter (Sony Biotechnology, CA, USA). Cell numbers were counted using a hemocytometer before and after cells were washed with PBS containing 1% BSA and 10 μM Y-27538.

ATDM: Anterior tongue organoids in differentiation medium.
ATEM: Anterior tongue organoids in expansion medium.
PTEM: Posterior tongue organoids in expansion medium.

first: Seok-Young

last: Kim

first: Laurens

last: Verweij

first: Lin

last: Lin

first: Johan

last: van Es

first: Jay

last: Slack

first: Chris

last: Winkel

first: Tito

last: Candelli

first: Philip

last: Lijnzaad

first: Thanasis

last: Margaritis

first: Gerben

last: Breimer

first: Karin

last: Sanders

first: Marc

last: van de Wetering

first: Hans

last: Clevers


title: Low-input unstranded RNA sequencing on FACS isolated tdTomato positive cells from the sternocleidomastoid muscles of aP2-Cre;R26tdTomato and Cdh5-Cre;R26tdTomato animals

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: Gene expression of tdTomato positive FACS isolated sternocleidomastoid msucles from aP2-Cre;R26tdTomato and Cdh5-Cre;R26tdTomato animals for ssGSEA analysis

overall_design: We performed RNA sequencing on FACS isolated tdTomato positive cells from the sternocleidomastoid muscles of aP2-Cre;R26tdTomato and Cdh5-Cre;R26tdTomato animals

first: Katherine E

last: Gadek

first: Mark E

last: Hatley


title: Toll-like Receptor 4 Induces Trained Innate Immune Tolerance in the Heart in a Model of Stress-induced Cardiomyopathy [Multiome]

first: Douglas

last: Mann

summary: This study aimed to determine the mechanism by which TLR4 activation establishes cardiac protection in mice subjected to isoproterenol-induced cardiac injury. We performed Multiome sequencing to determine if this was set up through epigenetic means, which would suggest a mechanism consistent with trained innate immune tolerance.

overall_design: Female 10-wk old wild-type (C57BL/6J) mice were treated with lipopolysaccharide (LPS; 2.5 mg/kg), b-glucan (1 mg/mouse), 1 ug recombinant interferon-b1/10 ug recombinant interferon-y (IFN), isoproterenol (ISO; 300 mg/kg) or diluent. Mice were then euthanized 7 days later (n=3/group) with hearts collected and used for nuclei isolation and Multiome sequencing (10x Genomics). Nuclei from all hearts belonging to the same group were pooled prior to submission.

first: Kenji Rowel

last: Lim


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues [WGS]

city: La Jolla

first: Julie

last: Law

address: 10010 North Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to male or female reproductive tissues. We designate these factors as REM INSTRUCT METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. These findings not only reveal RIMs as the first sex-specific RdDM proteins but also establish a critical role for genetic information in targeting DNA methylation. This novel mode of targeting expands our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

overall_design: 6 whole genome sequencing libraries were sequenced.

first: Guanghui

last: Xu


title: Distinct lung functional, histological and cell senescence signatures in the single vs repetitive bleomycin mouse model of idiopathic pulmonary fibrosis

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

summary: To address the gap between acute bleomycin-induced fibrosis in mice and the chronic nature of human IPF, we performed RNA-seq on lung tissue from single-dose and repetitive bleomycin models of idiopathic pulmonary fibrosis (BLEO-IPF).  We find that the repetitive BLEO-IPF model recapitulates the key features of progressive fibrosis and senescence, offering a relevant pre-clinical platform for studying chronic IPF pathology and evaluating anti-fibrotic interventions.

overall_design: We performed RNA-seq on poly(A)-enriched RNA isolated from the inferior lung lobes of four mouse cohorts: healthy controls (n = 20), mice with single-dose BLEO-IPF (n = 14), mice with repetitive-dose BLEO-IPF (n = 10), and a matched baseline group for the repetitive model (n = 9).

first: Jamal

last: Bousamaki

first: Emma

last: Rørbeck


title: The interplay between hormonal vitamin D and lipopolysaccharide signaling on human neutrophil transcriptional responses

city: Montreal

first: Aiten

last: Ismailova

address: 3655 Sir William Osler

country: Canada

institute: McGill University

summary: Introduction: Biologically active vitamin D (1,25-dihydroxyvitamin D or 1,25D) has emerged as a key regulator of human innate immunity. 1,25D signaling in macrophages strongly induces the expression of neutrophil chemoattractants, such as IL-8/CXCL8. Meta-analysis of vitamin D-regulated expression profiles has suggested that 1,25D may regulate granule formation in granulocytic cells. Here, we have examined the effects of 1,25D signaling on human neutrophil gene expression, alone and in combination with the inflammatory signal lipopolysaccharide (LPS). These studies are of interest because, whereas 1,25D signaling boosts innate immunity, it is anti-inflammatory. Methods and results: We determined the effects of 1,25D alone and in combination with LPS on gene expression of primary human neutrophils by RNAseq. LPS did not affect or slightly enhanced the expression of several well-characterized 1,25D-target genes, but strongly suppressed that encoding the 1,25D catabolic enzyme CYP24A1. Chromatin immunoprecipitation (ChIP) assays revealed that 1,25D- dependent vitamin D receptor (VDR) binding to the major CYP24A1 enhancer was eliminated in neutrophils treated with LPS, whereas binding to other 1,25D-target genes was unaffected. Notably, LPS induced binding of transcriptional repressors MAFF and BACH1 to the major CYP24A1 enhancer region. In other studies, pathway analyses revealed that 1,25D suppressed LPS-induced genes encoding inflammatory proteins. In addition, RNAseq and confirmatory RT/qPCR studies revealed that 1,25D, both on its own and in combination with LPS, increased mRNA expression of genes encoding antimicrobial components of secretory granules, including that encoding cathelicidin antimicrobial peptide (CAMP). Consistently, exposure of neutrophils to 1,25D enhanced bacterial killing, as revealed by a 20-25% reduction in E. coli colonies incubated with 1,25D-treated neutrophil conditioned media. The increased bacterial killing by 1,25D is mediated by 1,25D- induced secretion of cathelicidin, as an antibody against LL-37, the active form of cathelicidin, blocked antimicrobial activity. Discussion: Collectively, the data suggest that LPS prolongs vitamin D signaling by suppressing expression of the 1,25D catabolic enzyme CYP24A1. 1,25D signaling in the presence of LPS attenuates the expression of several genes associated with LPS inflammatory responses, whereas 1,25D in the absence or presence of LPS enhances the release of antibacterial proteins secreted by neutrophils in response to infection.

overall_design: RNA-seq profiling of primary human neutrophils treated with or without 100nM 1,25D, and in the presence or absence of 100ng/ml LPS for 6 hours.

first: John

last: White


title: Transcriptomic analysis of NGO (nano-graphene oxide) treated human PBMCs

city: Seoul

first: Aaron

last: Yu

address: Gwanak-ro 1

institute: Seoul national university

summary: We isolated PBMCs from human peripheral blood. To understand the effect of NGO on hPBMCs, we treated hPBMCs with NGO and analyzed changes in the transcriptome.

overall_design: To investigate the effect of NGO on hPBMCs in a T cell-activated condition, we activated T cells with CD3/28 Dynabeads and IL-2, and treated hPBMCs with NGO.

first: Kyung-Rok

first: Hyun Sung

last: Park

first: Mi-Kyung

last: Oh

first: Soon Won

last: Choi

first: Jaechul

last: Ryu


title: Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation

first: Hongtao

address: No.600 Dunyu Road, Xihu District

overall_design:
scRNA sequencing for gene expression profiles of neural progenitor cells isolated nuclei during the time series of differentiation
scATAC sequencing for chromatin accessibility profiles of neural progenitor cells isolated nuclei during the time series of differentiation
Please note that HDF5 files (containing filtered cell barcode × feature matrices for both gene expression and chromatin accessibility) are direct outputs of Cell Ranger ARC count command (v1.0.1) and are linked to the corresponding scATAC-seq sample records.

first: Song

last: Hu

first: Rongao

last: Kou

first: Zhuojie

last: Su

first: Guanchen

last: Li

first: Haishan

last: Gao

first: Shutao

last: Qi


title: Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation [ATAC-seq]

overall_design: Chromatin accessibility profiling of neural progenitor cells (NPC) at cirtical timepoints (Day0, 1, 2, 3, 6) during the process of NPC differentiation from embryonic stem cells


title: Transcriptomic analysis of NGO (nano-graphene oxide) treated acute GVHD or nonGVHD patients' PBMC

summary: We obtained and collected PBMCs from patients with acute GVHD (aGVHD) and non-GVHD patients who did not develop aGVHD after HSPC transplantation, provided by Asan Medical Center. To understand the effect of NGO on aGVHD/nonGVHD patient's PBMCs, we treated PBMCs with NGO and analyzed changes in the transcriptome.

overall_design: To investigate the effect of NGO on aGVHD/nonGVHD patient's PBMCs in a T cell-activated condition, we activated T cells with CD3/28 Dynabeads and IL-2, and treated PBMCs with NGO.

first: Eun-Hye

last: Hur

first: Je-Hwan

last: Lee


title: IL-2/IL-15 signaling induces NK cell production of FLT3LG which augments anti-PD-1 immunotherapy

city: Seattle

first: Kevin

last: Barry

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: Natural killer (NK) cells play a critical role in anti-cancer immunity through their direct cytotoxicity and production of cytokines, such as Flt3L. NK cell production of Flt3L controls conventional type I dendritic cell (cDC1) abundance in the tumor and promotes protective immune responses. Here, we show that NK cell production of Flt3l in the tumor is regulated by activation, and that activation by IL-2 and IL-15 uniquely induces Flt3L expression in NK cells. IL-2 signaling in NK cells leads to more Flt3L production, increased cDC1 abundance in the tumor, and increased activity of anti-PD-1 immunotherapy in melanoma. Further, NK cell subsets differentially regulate Flt3L in the tumor, with CD11b–CD27+ NK cells in mouse tumors enriched for IL-2-family signaling and upregulating Flt3l upon activation. Further, human CD56brightCD16– NK cells more strongly correlate with cDC1 and FLT3LG levels than other NK cell subsets across multiple human melanoma datasets and cancer indications. This mechanistic insight into NK cell regulation of FLT3LG and control of the NK cell-cDC1 axis provides insights and novel strategies for the development of more effective cancer immunotherapies.

overall_design: RNAseq of 4 NK cell populations sorted from day 14 B16F10 tumors subcutaneously implanted into the flanks of female B6 mice. N = 6. NK cell populations: CD11b+CD69-, CD11b+CD69+, CD27+CD69+, CD27+CD69-

first: Avanessian

last: Shayan C.

first: van den Bijgaart

last: Renske J.E.

first: Chew

last: Nayvin W

first: Tang

last: Thao T.

first: Abe

last: Kokoro

first: Gauthier

last: Jordan

first: Barry

last: Kevin C.


title: Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation [RNA-seq 2]

first: Hongtao

last: Yu

overall_design: RNA-seq profiling of neural progenitor cells (NPC) with/without cell cycle synchronization at the S phase during the process of differentiation


title: CRISPRa-mediated activation of genes associated with inherited retinal dystrophies in human cells for diagnostic purposes

city: Schlieren

first: Elvir

last: Becirovic

state: Zurich

address: Wagistrasse 14

department: Department of Ophthalmology

institute: University of Zurich

summary: Many patients suffering from inherited diseases do not receive a genetic diagnosis and are therefore excluded as candidates for treatments, such as gene therapies. Analyzing disease-related gene transcripts from patient cells would improve detection of mutations that have been missed or misinterpreted in terms of pathogenicity during routine genome sequencing. However, the analysis of transcripts is complicated by the fact that a biopsy of the affected tissue is often not appropriate, and many disease-associated genes are not expressed in tissues or cells that can be easily obtained from patients. Here, using CRISPR/Cas-mediated transcriptional activation (CRISPRa) we developed a robust and efficient approach to activate genes in skin-derived fibroblasts and in freshly isolated peripheral blood mononuclear cells (PBMCs) from healthy individuals. This approach was successfully applied to blood samples from patients with inherited retinal dystrophies (IRD). We were able to efficiently activate several IRD-linked genes and detect the corresponding transcripts using different diagnostically relevant methods such as RT-(q)PCR, long- and short-read RNA sequencing. The detection and analysis of known and unknown mRNA isoforms demonstrates the potential of CRISPRa-mediated transcriptional activation in PBMCs. These results will contribute to ceasing the critical gap in the genetic diagnosis of patients with IRD or other inherited diseases.

overall_design: PacBio Revio RNA long-read sequencing of human retinal organoids (n=3 per sequencing, age = 230 days).

first: Valentin

last: Weber

first: Alice

last: Reschigna

first: Maximilian

last: Gerhardt

first: Thomas

last: Heigl

first: Klara

last: Hinrichsmeyer

first: Sander

last: Engel

first: Zoran

last: Gavrilov

first: Dina

last: Otify

first: Frank

last: Blaser

first: Isabelle

last: Meneau

first: Christian

last: Betz

first: Hanno

last: Bolz

first: Martin

last: Biel

first: Stylianos

last: Michalakis


title: TGFβ activation and inhibition of Wnt and MAPK signaling pathways promote the specification of joint lineage cells in vitro and ex vivo

city: Boston

first: April

last: Craft

address: 320 Longwood Ave

department: Orthopedic Surgery

institute: Harvard Medical School

summary: The developmental processes of synovial joint initiation and subsequent differentiation of progenitor cells towards anatomically and functionally distinct joint tissues are not well understood. Here we quantified the induction of cells expressing growth and differentiation factor 5 (Gdf5), an early marker of joint formation, and Prg4, a proteoglycan found in the superficial zone of articular cartilage and other joint tissues, utilizing a dual reporter mESC line and directed differentiation methodologies. We found TGF signaling to be necessary and sufficient for the induction of Gdf5-RFP and Prg4-GFP. Inhibition of either canonical Wnt signaling or MAPK signaling significantly increased the induction of Gdf5-RFP and chondrogenesis, while activation of either pathway prohibited this. Activation of MAPK significantly promoted the emergence of Prg4-GFP-expressing cells and elevated levels of tendon-ligament fibroblast genes such as Tnmd. We used single cell transcriptomics to determine the cellular composition of these cultures and determined that Gdf5+ cells are chondrogenic in both in vitro cultures and in mouse E12.5 and E14.5 limb bud cells. We validated the joint cell- promoting role of Wnt and MAPK inhibition in both systems. In summary, we used a novel ESC model to elucidate the roles of TGF, Wnt and MAPK signaling in the specification and differentiation of joint lineage cells.

overall_design: Mouse embryonic limb buds were isolated, sequenced, and comparied to in vitro derived chondrocytes and connective tissue

first: Suyash

last: Raj

last: Cutia

first: Stefano

last: Menghini

first: Mireia

last: Ribes

first: Junming

last: Cai

first: Mariel

last: Young

first: Terence

last: Capellini


title: Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation [RNA-seq 1]

first: Hongtao

last: Yu

overall_design: RNA-seq profiling of neural progenitor cells (NPC) at cirtical timepoints (Day0, 1, 2, 3, 6, 18 and 35) during the process of NPC differentiation from embryonic stem cells

first: Song

last: Hu

first: Rongao

last: Kou

first: Zhuojie

last: Su

first: Guanchen

last: Li

first: Haishan

last: Gao

first: Shutao

last: Qi


title: Tuberous Sclerosis Complex Regulates Progenitor Balance and Upper Layer Neuronal Generation During the Development and Evolution of the Cerebral Cortex

first: Jeremy

last: Simon

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

summary: Radial progenitors serve to coordinate the generation and placement of appropriate numbers and types of neurons in the developing cerebral cortex. Radial progenitors divide asymmetrically to generate neurogenic intermediate progenitors (IPs) and the symmetric proliferation of IPs rapidly expands cortical neuronal population. The temporal maintenance of a balanced diversity of cortical progenitors and the resultant generation, placement, and connectivity of appropriate numbers of different classes of neurons serve as a blueprint to guide the formation of a properly wired cerebral cortex. Here, we show that Tuberous Sclerosis Complex proteins function to facilitate radial progenitor/intermediate progenitor balance and the generation of upper-layer neurons. Regulation of TSC expression levels during human brain evolution may lead to the expanded generation of upper-layer neurons necessary for higher-order brain functions in humans.

overall_design:
10x single-cell RNA-seq of P0 cerebral cortical neurons from control and TSC1/2 cKO mice, 3-4 biological replicates each.

One animal in the control group of scRNAseq experiments was excluded based on poor RNA quality. TSC1_TSC2_control replicates 1, 3, and 4 were subsequently renamed to TSC1_TSC2_control_Rep1, TSC1_TSC2_control_Rep2, and TSC1_TSC2_control_Rep3, respectively, for publication.

first: Eva

last: Anton


title: Total stranded RNA sequencing on bulk tumor or FACS isolated tumor cells from  known rhabdomyosarcoma models

first: Hongjian

last: Jin

summary: Comparision of aP2-Cre, Myog-Cre and Cdh5-Cre SmoM2 driven tumors shows that Cdh5-Cre tumors express muscle markers but have unique gene expression profiles; Comparision of aP2-Cre SmoM2/tdTomato tumor cells and Cdh5-Cre SmoM2/tdTomato tumor cells isolated by FACS for CD31-/tdTomato+ cells reveals that Cdh5-Cre tumors are not rhabdomyosarcoma

overall_design: We performed RNA sequencing on bulk tumor from known rhabdomyosarcoma models to compare to our novel tumor.

first: Katherine E

last: Gadek

first: Mark E.

last: Hatley


title: Comparison of gene expression between human lung resident MSC subpopulations.

city: Los Angeles

first: Brendan

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

summary: Lung resident MSCs were isolated from a deidentified donor. After ~14-day culture, individual colonies were isolated using a cloning ring approach. Individual colonies were separately expanded and the cells at passage 4 were collected for total RNA isolation.

overall_design: RNA-seq profiling of cultured lung human MSC and grouping based on hierarchical clustering.

first: Danyi

last: Peng

first: Ke

last: Cao

first: Youngfeng

last: Luo

first: Matthew

last: E. Thornton

first: Elizabeth

last: P. Henske

first: Wei

last: Shi

last: H. Grubbs


title: Comparison of gene expression between mouse lung resident MSC subpopulations.

summary: Lung resident MSCs were isolated from the Tbx4-rtTA/TetO-Cre/mT-mG reporter mice at 3 months of age, in which embryonic lung mesenchymal cells are genetically marked by doxycycline induction from embryonic day 6.5 to postnatal day 1. The cultured MSCs at passage 2 were sorted by FACS and total RNA was isolated. Samples were from different isolations.

overall_design: RNA-seq of Mouse lung MSC isolated by use of a fluorecent reporter and flow cytometry


title: Effect on adult Human Nasal Organoid transcription of differentiation at 34°C vs. at 37°C vs. at 37°C followed by a 2 day shift to 34°C

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

summary: Physiological temperature in the human nasal passages peaks at ~34°C, which is lower than internal human body temperature. This experiment explored the effect on the transcriptome of Human Nasal Organoids (HNOs) based on differentiating at 34°C vs. 37°C for 21 days vs. 37°C for 21days followed by a shift to 34°C for 2 additional days. RNAseq was also performed on undifferentiated HNOs.

overall_design: Nasal organoids  from three independent individuals were used for total RNA sequencing.

first: Sarah

last: Blutt

first: Amal

last: Kamal

first: Katherine

middle: P

last: Lemon

first: Hoa

last: Nguyen-Phuc


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues

first: Julie

last: Law

summary: DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to anther or ovule tissues. We designate these factors as REM INSTRUCTS METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. Furthermore, we demonstrate that mis-expression of RIM12 is sufficient to initiate siRNA production at ovule targets in anthers. These findings reveal a critical role for genetic information in targeting DNA methylation in reproductive tissues, expanding our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

overall_design: Illumina sequencing of smRNA-seq, mRNA-seq, methylC-seq, and ChIP-seq datasets were generated in this study. For small RNA and mRNA sequencing experiments, three replicates for wild-type plants and two replicates for mutant plants were included.

first: Guanghui

last: Xu


title: single cell gene expression analysis of  aP2-Cre and Cdh5-Cre tdTomato labeled cells from multiple muscle [scRNA-seq]

first: Hongjian

last: Jin

summary: Comparison of aP2-Cre and Cdh5-Cre tdTomato labaled cells from hindlimb and SCM muscles shows they mark the same endothelial cell populations

overall_design: We perfromed single cell gene expression analysis of scRNA-seq data from aP2-Cre and Cdh5-Cre tdTomato labeled cells from multiple muscle groups

last: Gadek

first: Mark


title: Altered neuroinflammaory transcriptomic profile in the hippocampal dentate gyrus three weeks after lateral fluid percussion injury in rats

status: Public on Sep 21 2025

city: Cincinnati

first: Anthony

middle: Joseph

last: DeSana

state: Ohio

address: 231 Albert Sabin Way

department: Neurosurgery

institute: University of Cincinnati

summary: Traumatic brain injury (TBI) is a major source of disability worldwide with cognitive and memory deficits being pervasive after injury. The hippocampus, a major structure involved in learning and memory, is particularly vulnerable to TBI, and cellular dysfunction within the hippocampal dentate gyrus is believed to be a major contributor to cognitive deficits after TBI. However, there is a little known about the transcriptomic changes occurring directly within the dentate gyrus at subacute-to-chronic timepoints after TBI. To address this, we performed bulk RNA sequencing and single nuclei RNA sequencing of the isolated dentate gyrus three weeks after lateral fluid percussion injury in male rats. We report here that there is evidence of an ongoing neuroinflammatory response marked by increased neuroinflammatory genes that implicate various neuroinflammatory pathways that are associated with a subset of microglia and astrocyte populations. R-code available at "https://github.com/NgwenyaLab/DeSana_and_Alfawares_2025"

overall_design: Male sprague dawley rats received a traumatic brain injury by lateral fluid percussion injury and then were euthanized 3 weeks after injury. The brain was dissected out and ipsilateral dentate gyrus was isolated and processed for bulk RNA sequencing (n = 3/group) or single nuclei RNA sequencing (n = 2/group)

first: Yara

last: Alfawares

first: Roshni

last: Khatri

first: Tracy

last: Hopkins

first: Faith

middle: V

last: Best

first: Jennifer

middle: L

last: McGuire

first: Laura

last: Ngwenya


title: Provision of choline chloride to the bovine preimplantation embryo alters postnatal body size and DNA methylation.

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: Choline is a vital micronutrient that can be utilized in the formation of betaine and multiple phospholipids. In this study, we aimed to confirm, and expand on previous findings, how choline impacts embryos from the first 7 days of development to affect postnatal phenotype. Bos indicus embryos were cultured in a choline-free medium or medium supplemented with 1.8 mM choline. Blastocyst-stage embryos were transferred into crossbred recipients. Once born, calves were evaluated at birth, 94 d, 178 d and at weaning (average age=239 d). Following weaning, all calves were enrolled into a feed efficiency trial before being separated by sex, with males being slaughtered at approximately 580 d of age and females followed until their first pregnancy check. Results confirm that exposure of 1.8 mM choline chloride during the first 7 d of development alters postnatal characteristics of the resultant calves. Calves of both sexes from choline-treated embryos were consistently heavier through weaning. Males had heavier testes at 3 mo of age. There were sex-dependent alterations in DNA methylation in whole blood caused by choline treatment. After weaning, feed efficiency was affected by an interaction with sex, with choline calves being more efficient for females and less efficient for males. Calves from choline-treated embryos were heavier, or tended to be heavier, than calves from control embryos at all observations after weaning. Carcass weight was heavier for choline calves and the cross-sectional area of the Longissumus dorsi muscle was increased by choline. Few females became pregnant during the experiment although numerically more choline females were pregnant than control females. Results confirm that exposure of the preimplantation embryo to 1.8 mM choline altered phenotypes of the animal through the first 19 months after birth.

overall_design: Whole blood samples were collected from the jugular vein of a randomly selected subset of 6 animals from each treatment-sex subgroup (i.e., n=24 total, 6 females derived from control embryo, 6 males derived from control embryo, 6 females derived from cholin-treated embryo and 6 males derived from cholin-treated embryo) and used to determine DNA methylation using whole whole genome enzymatic methyl sequencing.

first: McKenzie

last: Haimon

first: Eliab

last: Estrada-Cortés

first: Thiago

middle: F

last: Amaral

first: Hélène

last: Martin

first: Pascal

last: Dufour

first: Surwich

last: Jeensuk

first: Jeremy

last: Block

first: Daniella

last: Heredia

first: Mauro

last: Venturini

first: Camlia

middle: S

last: Rojas

first: Angela

last: Gonella-Diaza

first: Nicolas

last: DiLorenzo

last: Scheffler

first: Ky

middle: G

last: Pohler

first: Peter

last: Hansen


title: Gene expression profiling in human primary hepatocytes and human induced pluripotent stem cell-derived hepatocytes before and after IL-1β Treatment

city: Cleveland

first: Xianfang

last: Wu

address: 9500 Euclid Avenue/NE20, Office NE2-308, Office NE2-308

department: Infection Biology

institute: Cleveland Clinic

summary: The shared transmission routes of hepatitis B virus (HBV) and hepatitis C virus (HCV) result in coinfections that accelerate and exacerbate liver disease. The clinical burden is further exacerbated in the era of direct-acting antivirals (DAAs) against HCV, where reports of HBV reactivation post-DAA treatment in coinfected patients have emerged. Beyond an HCV-induced canonical interferon (IFN) response, the mechanisms through which HCV suppresses HBV remain poorly understood. Here, we employ a multicellular liver culture system, co-culturing human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes, hepatic stellate cells and macrophages, that supports productive HCV and HBV infection and replicates clinical coinfection dynamics. We demonstrate that IL1β from macrophages activated by HCV modulates host factors involved in HBV infection independent of IFN signaling. By combining bioinformatic predictions with reporter assay validation, we identified the transcriptional mediators of these changes. Hepatocytes downregulate expression of HBV receptor SLC10A1  due to induction of a truncated C/EBPβ isoform, which negatively regulates the full-length variant’s activity. Simultaneously, IL1β induces the expression of ISG20, a known anti-HBV factor, through USF1 phosphorylation. Finally, we show that a modified treatment protocol combining DAA with an HBV entry inhibitor effectively prevents HBV reactivation. Our findings position this liver culture platform as a tool not only for detailed mechanistic dissection of the complex multicellular responses in HBV-HCV coinfection, but also for nominating and testing future therapeutic avenues for coinfected patients.

overall_design: To unravel the mechanisms underlying IL1β-induced suppression of HBV infection, we conducted transcriptomic analysis on primary human hepatocytes and human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes treated with two distinct IL1β concentrations (i.e., 10ng/ml and 20ng/ml) for a 24-hour duration. Our objective was to identify differentially expressed genes (DEGs) in hepatocytes regulated by IL1β and cross-reference these DEGs with known host factors that either promote or inhibit HBV infection.