title: scRNA-seq of the colon tissue in DSS-induced acute colitis

last: Zhao

summary: The complex inflammatory response regulatory network constructed by immune cells plays an important role in the occurrence and development of IBD.Neutrophils play a key role in IBD.Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool to deﬁne the heterogeneity of poorly classiﬁed tissue populations and disease-associated cell states. Here we apply scRNA-seq to generate a single-cell map of the colon tissue from mice with ulcerative colitis, and further conducted characteristic analysis of the functional subtypes of CXCR2 and CXCR4 neutrophils .

overall_design: Male mice were administrated with 2.5% DSS via drinking water to induce light colitis. scRNA-seq analysis of immune cells in normal colon tissue and colon tissue of mice with experimental colitis.

first: Tao

last: Wang

first: Guojian


title: Single-cell RNAseq analysis of  Nf1-deficient Prss56-derived cells from spinal columns of young and old mice

status: Public on Dec 30 2025

city: Créteil

first: Céline

last: Colnot

address: 8 rue du Général Sarrail

country: France

institute: INSERM

type: Expression profiling by high throughput sequencing

summary: Neurofibromatosis type 1 (NF1) is a genetic disorder affecting 1 in 3000 people due to heterozygous mutations in the NF1 gene. Patients with NF1 can develop multiple symptoms, such as neurofibromas, skin hyperpigmentation, and bone abnormalities, including tibial pseudarthrosis and spine deformity. Here, we aimed to elucidate the cellular origin and pathogenic mechanism of NF1 spine deformity. Prss56-Nf1 knockout (KO) mouse is a model that recapitulates neurofibromas and pseudarthrosis by carrying Nf1 gene inactivation in Prss56-expressing boundary cap (BC) cells, a neural crest subset, and their derivatives. Through transcriptomics analysis, we explored the molecular changes that occur through time in Prss56-derived cells populating the vertebral column of Prss56-Nf1 KO mice.

overall_design: Prss56-derived tdTom+ cells were isolated by FACS from digested vertebrae of  3 month-old or 12-16 month-old from Prss56Cre/Cre;R26tdTom/tdTom;Nf1fl/fl and Prss56Cre/+;R26tdTom/tdTom;Nf1+/+.

first: Franceska

last: Kovaci

first: Cassandre

last: Goachet


title: Single-cell transcriptome analyses reveal disturbed decidual microenvironment in women of advanced maternal age

city: Hangzhou

first: Hongliang

last: Xie

state: Zhejiang Province

address: 浙江省杭州市西湖区紫金港校区药学院

country: China

institute: Zhejiang University

summary: Background: Advanced maternal age (AMA) increases pregnancy risk. However, uterine-specific mechanisms independent of oocyte and embryo quality remain poorly defined. This study aimed to characterise the decidual microenvironment in women of AMA to identify key pathological changes and regulatory pathways. Methods and Results: Through integrated histology, organoid modelling, and high-resolution scRNA-seq of first-trimester decidua from women of AMA and controlled reproductive age, we uncovered a pathologically remodelled decidual microenvironment characterised by fibroblast expansion, immune depletion, and disrupted intercellular communication in the AMA decidua. Central to this pathology was hyperactivated TGF-β signalling, driving fibroblast-to-myofibroblast transition (FMT) and extracellular matrix overproduction, thereby fuelling fibrosis. Aberrant TGF-β further impaired decidual stromal cell (DSC) differentiation, causing failure of the essential mesenchymal-to-epithelial transition (EMT). We identified PRR15 as a novel DSC-specific regulator that is markedly suppressed in AMA. PRR15 deficiency unleashed hyperactive TGF-β/SMAD signalling, directly causing decidualization failure, enhanced fibrosis, and aborted DSC differentiation. Epithelial-mesenchymal transition and immune cell reprogramming towards profibrotic phenotypes further amplify the fibrotic pathology. Conclusion: This study established the aged decidual microenvironment, orchestrated by dysregulated TGF-β signalling and PRR15 loss, as a critical independent determinant of reproductive failure in AMA. Thus, it unveils novel diagnostic and therapeutic targets and strategies.

overall_design: This study investigated the impact of advanced maternal age (AMA) on the cellular and molecular composition of the human decidua during early pregnancy. Decidual tissue samples were collected from six women undergoing elective first-trimester surgical termination. The participants were stratified into two cohorts based on maternal age: the AMA group (35–49 years, n = 3) and a control (CTR) group of women of optimal reproductive age (22–30 years, n = 3). Women aged 31–34 years were excluded to avoid overlap between groups. All participants were clinically healthy, with no history of hormonal treatment, genetic abnormalities, reproductive disorders, or chronic systemic disease. Single-cell RNA sequencing (scRNA-seq) was performed on freshly isolated decidual tissue from each individual to characterize the cellular composition and transcriptional changes associated with AMA. The primary experimental variable under investigation was maternal age. The CTR group served as the baseline reference for identifying age-related alterations in cell populations, differentiation states, and intercellular communication. Each sample represents an independent biological replicate. The design enabled comparative analysis of decidual stromal cells, fibroblasts, and immune cells between the two age-defined groups.

first: Yu

last: Lu

first: Aoling

last: Zhang

first: Cuiyu

last: Yang

first: Aoyao

last: Li

first: Wenbo

last: Guo

first: Linhua

last: Hu

first: Xiaoling

last: Huang

first: ChiChiu

first: Songying

first: Xiaohui

last: Fan

first: Lu


title: RNA transcriptome analyses in Nup93R388W-knock in (KI) mice (strain: 129S1/SvlmJ)

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

country: USA

institute: UT Health Science Center at San Antonio

summary: To investigate the role of m6A in RNA export, we performed transcriptome profiling by high throughput sequencing.

overall_design: Nuclear and total RNA etraction followed by high throughput sequencing (RNA-seq) in podocytes isolated from Nup93 wild-type (Nup93 +/+) and Nup93 homozygous R388W mutant (Nup93 RW/RW) mice

first: Zhang

first: Lee

last: Jihoon

first: Xu

last: Kexin


title: Dominant-negative TP53 mutations potentiated by the HSF1-regulated proteostasis network [2]

city: Cambridge

first: Vincent

last: Butty

state: MA

address: 77 Massachusetts Avenue 68-317A

department: Biology

institute: MIT

summary: Protein mutational landscapes are sculpted by the impacts of the resulting amino acid substitutions on the protein’s stability and folding or aggregation kinetics. These properties can, in turn, be modulated by the composition and activities of the cellular proteostasis network. Heat shock factor 1 (HSF1) is the master regulator of the cytosolic and nuclear proteostasis networks, dynamically tuning the expression of cytosolic and nuclear chaperones and quality control factors to meet demand. Chronic increases in HSF1 levels and activity are prominent hallmarks of cancer cells. One plausible explanation for this observation is that the consequent upregulation of proteostasis factors could biophysically facilitate the acquisition of oncogenic mutations. Here, we experimentally evaluate the impacts of chronic HSF1 activation on the mutational landscape accessible to the quintessential oncoprotein p53. Specifically, we apply quantitative deep mutational scanning of p53 to assess how HSF1 activation shapes the mutational pathways by which p53 can escape cytotoxic pressure conferred by the small molecule nutlin-3, which is a potent antagonist of the p53 negative regulator MDM2. We find that HSF1 activation broadly increases the fitness of dominant-negative substitutions within p53. This effect of HSF1 activation was particularly notable for non-conservative, biophysically unfavorable amino acid substitutions within buried regions of the p53 DNA-binding domain. These results indicate that chronic HSF1 activation shapes the oncogenic mutational landscape, preferentially supporting the acquisition of cancer-associated substitutions that are biophysically destabilizing. Along with providing the first experimental and quantitative insights into how HSF1 influences oncoprotein mutational spectra, these findings also implicate HSF1 inhibition as a strategy to alter the accessible mutational landscape of p53.

overall_design: We are testing three cell lines, parental A549, A549 cells expressing a consitutively active form of HSF1 (cHSF1) under a tet-repressor, and A549 cells expressing a dominant negative constitutively active form of HSF1 (dn-cHSF1) under a tet-repressor. A549 were treated with either DMSO (negative control) or Doxycycline (1 μg/mL dox for 24 h) while A549cHSF1 cells and A549dn-cHSF1 cells were treated with Doxycycline (1 μg/mL dox for 24 h) to activate the HSF1.  Differential gene expression was analyzed, with particular attention to upregulation of genes involved in the heat shock response.

first: Stephanie

last: Halim

first: Matthew

middle: D

last: Shoulders


title: The intrinsic impact of mechanical stress on the maintenance of oocyte dormancy

city: Suita

first: Katsuhiko

last: Hayashi

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

country: Japan

institute: The University of Osaka

summary: In the mammalian ovary, most oocytes remain dormant, and their dormant status plays a central role in maintaining the reservoir population of the female germ line. The equilibrium between the dormant and active states, the latter of which is responsible for producing mature oocytes, is therefore crucial for ensuring the sustained reproductive capability of females. We have previously reported that mechanical stress in the ovary plays a crucial role in oocyte dormancy. However, the mechanism underlying this relation remains unclear. Here we demonstrated that the mechanical stress is directly transduced into the oocytes, rather than to surrounding granulosa cells. Culture experiments and live-imaging analysis revealed the nuclear localization of FOXO3, a hallmark of oocyte dormancy, within oocytes cultured alone in response to mechanical stress. Interestingly, we discovered that the cytological response to mechanical stress was accompanied by ligand-independent internalization of the c-kit receptor, which dampens intracellular signaling and prevents oocyte activation. These results shed light on the relation between mechanical stress and oocyte dormancy and provide clues toward a greater understanding of female reproductive capability.

overall_design:
After culturing female mouse embryonic ovary under an external pressure (33.3 kPa), Stella-CFP- positive cells were isolated by fluorescence-activated cell sorting (FACS) and analyzed using RNA sequencing (RNA-seq).

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

first: Nagamatsu

last: Go

first: Shirane

last: Kenjiro

first: Hayashi

last: Katsuhiko


title: Peripheral Blood tRNA-derived Fragments as Novel Noninvasive Biomarkers for Diagnosis and Prognostic Stratification in Multiple Myeloma

city: Changde

first: Ming

last: Lei

state: Hunan

address: No. 818 Renmin Road, Wuling District

institute: The First People’s Hospital of Changde City

type: Non-coding RNA profiling by high throughput sequencing

summary: Transfer RNA-derived small RNAs (tsRNAs) have recently emerged as critical regulators in cancer biology, yet their expression profiles and clinical relevance in multiple myeloma (MM) remain poorly defined. Here, we employed high-throughput sequencing to comprehensively characterize tsRNA expression in peripheral blood mononuclear cells (PBMCs) from 22 newly diagnosed MM patients and 19 healthy controls. This analysis delineated a global tsRNA expression landscape, revealing distinct subtype distributions and length profiles of tRFs and tiRNAs.     Following stringent screening and RT-qPCR validation, eight candidate tsRNAs were identified, among which Other-1_19-tRNA-SeC-TCA-1 and Other-13_30-tRNA-Lys-CTT-1-M2 constituted a central regulatory module. Integrative prediction using miRanda and TargetScan uncovered 5,009 shared target genes, enabling construction of a tsRNA–mRNA interaction network comprising 11,141 edges and exhibiting a power-law topology with hub genes such as SRSF10. Functional enrichment analyses (GO and KEGG) indicated significant involvement of target genes in TGF-β, PI3K–Akt, AMPK, cell adhesion, and thyroid hormone signaling pathways.     Notably, elevated expression of Other-22_52-tRNA-Gly-GCC-1-M3 correlated strongly with renal impairment in MM, underscoring its potential as a noninvasive biomarker for renal risk assessment. Moreover, Other-36_54-tRNA-Met-CAT-2-M4 and Other-1_19-tRNA-SeC-TCA-1 demonstrated excellent diagnostic performance (AUC > 0.95). Correlation analyses further supported the diagnostic and prognostic relevance of these tsRNAs across multiple clinical parameters.     Collectively, our findings reveal a distinct imbalance in tsRNA expression in MM, suggesting that specific tsRNA fragments contribute to disease progression and renal injury through multifaceted signaling networks, thereby providing novel molecular insights for early diagnosis and risk stratification.

overall_design: Peripheral blood mononuclear cell (PBMC) samples were collected from newly diagnosed multiple myeloma (MM) patients and age- and sex-matched healthy controls. Three samples were randomly selected from each group for RNA sequencing (RNA-seq) analysis.

first: Bi

middle: Y

last: Yi

first: Yan

last: Gao

middle: Z

first: Kai

first: Rong

last: Liu

first: Meng

last: Zeng

first: Han


title: KNSTRN knockdown impairs autophagy flux and inhibits bladder cancer progression through ROS- mediated lysosomal dysfunction

city: nanchang

first: Yaoyi

last: Xiong

state: jiangxi

address: No. 17 Yongwai Zhengjie, Donghu District, Nanchang City, Jiangxi Province, China

institute: Nanchang University

summary: Bladder cancer (BLCA) is a prevalent cancer affecting the urinary tract, the mitochondria-localized Astrin-binding protein (KNSTRN) has been shown to be strongly associated with the development of several cancers. In addition, abnormal levels of autophagy have been shown to have a dramatic impact on tumor development. However, the potential mechanisms of BLCA autophagy regulation by KNSTRN remain poorly understood. In this research, we found that knockdown of KNSTRN inhibited the autophagic flux of BLCA. Mechanistically, knockdown of KNSTRN leads to reactive oxygen species (ROS)-dependent disruption of the lysosomal acidic environment and reduction of protease activity, hindering autophagosome-lysosome fusion. Clioquinol reactivates lysosomal activity by normalizing lysosomal pH, which in turn reinstates autophagic flux. Intracellular ROS production is also critical for this process, as ROS scavengers (NAC) reverse lysosomal dysfunction and reactivate autophagic flux. Additionally, the autophagy activator rapamycin (Rapa) effectively protected against KNSTRN knockdown-induced cell death in vitro and in vivo. Thus, we demonstrate that knockdown of KNSTRN leads to intracellular ROS accumulation and lysosomal dysfunction, which impairs autophagic flux and inhibits BLCA progression.

overall_design: T24 cells were inoculated into 6 cm dishes and cultured for 24 hours until the cells were fully adherent to the wall, then treated with si-NC or si-KNSTRN for 24 h. subsequently, total RNA was extracted using RNA extraction solution and transcriptome sequencing was performed. Three biological replicates per group.

first: Xianbin

last: Huang


title: The Role of Placental DNA Methylation in the Pathogenesis of Chronic Intervillositis of Unknown Etiology

city: Boston

first: Maitreyi

last: Mazumdar

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

type: Methylation profiling by genome tiling array

summary: Objectives: Chronic intervillositis of unknown etiology (CIUE) is the pathological influx of maternal inflammatory cells into the intervillous space of the placenta without demonstrable cause. CIUE is associated with placental damage and increased risk of pregnancy loss, fetal demise, and growth restriction. The pathogenic mechanism is unclear, and we lack biomarkers for detection, and treatments to prevent recurrence. DNA methylation (DNAme) is a biomarker altered in association with many disease states. We hypothesized that CIUE may be associated with a distinct signature placental DNAme signature.    Methods: DNAme was profiled using the Illumina Infinium MethylationEPIC v2.0 array on fresh-frozen placental tissue. After quality control, data were available for 24 CIUE (14 high grade, 10 low grade) and 27 non-CIUE placental samples, plus six independent decidua samples. CIUE was confirmed and graded by a perinatal pathologist. Contamination was assessed using the 65 array genotyping probes, placental cell composition and epigenetic age were estimated. After processing, DNAme data were available at 855,732 CpGs.    Results: Several lines of evidence indicated maternal DNA in CIUE placentas. Genetic contamination metrics were higher in CIUE than non-CIUE cases. In XY samples, X chromosome copy number increased with CIUE grade, suggesting XX contaminating DNA. Principal components analysis placed CIUE samples closer to decidua along PC1 than non-CIUE samples, cell composition showed elevated Hofbauer cells, monocytes, and neutrophils in CIUE. Epigenetic age was higher in CIUE versus non-CIUE samples. Together, these findings suggested an increased concentration of non-self XX DNA in CIUE cases, likely originating from an adult, macrophage-rich source, suggesting a maternal origin. An epigenome-wide association study found that all significant differentially methylated loci associated with CIUE were attenuated after adjusting for cell composition.     Conclusions: Our results illustrate that placental DNAme patterns in CIUE reflect signatures of maternal infiltration rather than intrinsic DNAme alterations. This study also highlights the value of integrating the diverse molecular data outputs of DNAme arrays to explore the presence of maternal cells in placental tissue.     ***************************************************************  IDAT files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable SNP genotyping data for open access but are available upon reasonable request to JT or WPR for research use.  ***************************************************************

overall_design:
DNAme data for 51 fresh-frozen placental (chorionic villi)  samples was profiled with the Illumina Infinium MethylationEPIC v2.0  array in Vancouver, Canada. DNAme data from raw IDAT files were read into R and processed with the minfi and ewastools packages. Methylated intensity, unmethylated intensity, and detection p values were calculated for all probes. The raw data (meth/unmeth/detp) is available, as are the full beta value matrices after data processing. H&E-stained slides of correlated formalin fixed paraffin embedded tissue for each CIUE sample were reviewed by a perinatal pathologist (JT) to ensure accurate diagnosis. CIUE was defined as low grade if between 5-50% of the placental intervillous space was occupied by histiocytes (with or without associated fibrin) and high grade if 50% or more of the space was involved, as previously described. IFNγ protein level expression status (positive/negative) was assessed  in all samples. For cases in this study, aneuploidy was determined by a combination of (i) clinically performed quantitative fluorescent polymerase chain reaction (ii) chromosomal microarray performed on a research basis, and (iii) copy-number analysis performed on the DNAme data with the conumee 2.0 R package. Because placental samples used for DNAme arrays were obtained from a single small sampling location, we were unable to distinguish between whole-placenta aneuploidy and confined placental mosaicism, and all aneuploid samples were annotated with the understanding that they may in some cases be mosaic.
*** IDAT files were not available due to patient privacy concerns***

first: Amy

middle: M

last: Inkster

first: Maria

middle: S

last: Peñaherrera

first: Wendy

middle: P

last: Robinson

first: Jefferson

last: Terry


title: Generation of a Comprehensive Epigenomic Atlas in Clear Cell Renal Cell Carcinoma Informs Kidney Cancer Progression and Heritability

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: By generating 194 epigenomic and transcriptomic profiles datasets from 57 human tissue samples, using H3K27ac and HIF2α chromatin immunoprecipitation sequencing (ChIP-seq), ATAC-seq, and RNA-seq, we provide a comprehensive integrated characterization of clear cell renal cell carcinoma (ccRCC) across normal, tumor, and metastatic states. Our epigenomic analyses reveal insights into various aspects of ccRCC biology. First, we show that significant enhancer reprogramming (H3K27ac) and shifts in the transcription factor HIF2α cistrome and chromatin accessibility landscape occur during the transition from normal to tumor; by contrast, there areis no significant differences between localized tumors and metastatic samples. Second, we show that fetal kidney-specific developmental pathways are reactivated to drive malignancy. Third, we performed the first cistrome cistrome-wide association study (CWAS) in ccRCC, validating five established RCC risk loci and identifying six novel regions associated with RCC risk, including a significant association on 12q24 linked to the SCARB1 gene that was functionally validated. These datasets provide new perspectives on the role of developmental pathways in ccRCC tumorigenesis and metastasis, insights into epigenetic mechanisms of ccRCC heritability, and a comprehensive epigenomic atlas for the research community.

overall_design: We performed H3K27ac ChIP-seq, HIF2α ChIP-seq, ATAC-seq, and RNA-seq on 57 independent tissue samples (194 total datasets), spanning 32 individuals diagnosed with clear-cell renal cell carcinoma. We also generated H3K27ac ChIP-seq, HIF2α ChIP-seq, ATAC-seq, and RNA-seq on 5 human clear-cell renal cell carcinoma cell lines.

first: Sarah

last: Abou Alaiwi

first: Ziwei

last: Zhang

first: Toni

middle: K

last: Choueiri

first: Sylvan

middle: C

last: Baca

first: Matthew

middle: L

last: Freedman


title: Differential Epithelial Responses to GII.3 HuNoV Infection in Jejunal Human Intestinal Organoids (HIOs)

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

summary:
We performed RNA-seq to compare the epithelial transcriptomic response to GII.3 HuNoV infection to gamma-irradiated inactivated HuNoV (gGII.3) and media controls in parental HIE lines (J2 and J4) and genetically modified HIOs (J2STAT1-KO and J4FUT2-KI), which support enhanced viral replication due to STAT1 knockout and FUT2 knock-in, respectively.  HIEs were harvested and analyzed at 24 hours post-infection/treatment.

NCBI grant:
Grant ID: U19 AI144297
Consortium name: Texas Medical Center Genomic Center for Infectious Diseases (TMC GCID)
URL: https://gcid.research.bcm.edu/

overall_design: HIOs from two different individuals and their genetically modified counterparts were used for total RNA sequencing

first: Sue

middle: E

last: Crawford

first: Gurpreet

last: Kaur

first: Hoa

last: Nguyen-Phuc

first: Khalil

last: Ettayebi

first: Muzny

last: Donna

first: Doddapaneni

last: Harshavardhan

first: Cristian

last: Coarfa

first: Sasirekha

last: Ramani


title: Triple-gene knockout pig RBC transfusion induces iron-mediated liver ferroptosis in nonhuman primates

city: Jeongeup-Si

first: Ju Young

last: Lee

address: 30 Baekhak 1 Gil,

country: South Korea

institute: Korea institute of toxicology

summary: Following a worsening blood supply shortage, researchers are investigating the application of genetically modified pig blood for human transfusion. To overcome cross-species immunological barriers, researchers utilize gene editing to remove the expression of three major carbohydrate xenoantigens (α-Gal, Neu5Gc, and Sd(a)) and insert genes, such as human protective genes (hCD55 and hCD39). This study aimed to investigate the mechanisms underlying long-term hepatic injury following xenotransfusion of genetically modified pig red blood cells (pRBCs). We xenotransfused pRBCs genetically engineered with GGTA1-/-(α-Gal -); CMAH-/-(Neu5Gc-); β4GALNT2-/-(Sd(a) -); hCD55; hCD39 into a non-human primate (NHP) model of acute hemorrhage hemolysis and evaluated the long-term immune response to xenogeneic RBCs in the liver, a key organ for RBC metabolism. Immediately after xenotransfusion (D+1), significant elevations of liver enzymes (AST, ALT) and iron-related factors were observed in the serum levels of the recipients, which were normalized by D+21. However, long-term analysis revealed excessive accumulation of iron ions in the liver and decreased expression of antioxidant enzymes. The resulting endoplasmic reticulum stress (increased GRP78/BiP expression), lipid peroxide accumulation, and iron-dependent cell death (ferroptosis) persisted in the liver of the recipient. These results suggest that gene editing alone cannot completely block oxidative stress damage caused by impaired RBC lysis. Notably, transcriptomic and immunohistochemical analyses in the NHP model identified the direct role of ferroptosis in xenotransfusion-induced liver injury. Therefore, we propose that a multilayered approach, including blocking the ROS-Iron axis and administering ferroptosis inhibitors, is needed to ensure long-term safety in the clinical development of xenotransfusion.

overall_design: To investigate DEG profiles of liver of Triple-gene KO pig RBC transfused-NHPs

first: Ha-Young

last: Shin

first: Young-Jin

last: Jang

first: Hyung-Sun

last: Kim

first: Seon-Ryoung

last: Park

first: Goo-Hwa

last: Kang

first: Joohyun

last: Shim

first: Nayoung

last: Ko

first: Jeong Ho

last: Hwang


title: LXR agonism elicits a pre-effector state in naïve CD8+ T cells [RNA-seq]

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

country: Germany

institute: Charité University Medicine

summary: Here, we analyze transcriptional profiles of naïve CD8+ T cells with versus without exposure to the synthetic LXR agonist RGX-104 in the absence of TCR stimulation.

overall_design: Differential gene expression analysis of naïve CD8+ T cells after 24 hours of treatment with the  synthetic LXR agonist RGX-104 versus DMSO.


title: Uterine histotroph and conceptus development. V. Comparative analysis of arginine-mediated transcriptomic reprogramming in conceptus trophectoderm of pigs and sheep

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Arginine (Arg) is an essential functional amino acid necessary for the survival and growth of both porcine and ovine conceptus trophectoderm cells. In this study, we report transcriptome sequencing of porcine and ovine conceptus trophectoderm cells following 48 hours of incubation with or without Arg treatment.

sample_organism:
Sus scrofa
Ovis aries

platform_organism:
Sus scrofa
Ovis aries

overall_design: An established porcine trophectoderm (pTr2) cell line isolated from Day 12 porcine conceptuses, as well as an established ovine trophectoderm (oTr1) cell line isolated from Day 15 ovine conceptuses were used to determine response to Arg at the physiological concentration of 0.2 mM in a 48 h culture.

first: Sudikshya

last: Paudel

first: Xiukun

last: Wang

first: Hongyao

last: Yu

first: Guang

last: Hu

first: Xiaoqiu


title: Chromatin Accessibility Dynamics Suggest Immune-Modulatory Effects of Vitamin D3 In Vivo

city: Olsztyn

first: Maciej

last: Rybiński

state: Warmian-Masurian Voivodeship

address: Trylińskiego 18

country: Poland

institute: Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences.

summary: Vitamin D₃ is a key micronutrient known to support innate immunity and modulate adaptive responses, with in vitro studies suggesting the involvement of epigenetic mechanisms. However, in vivo evidence remains limited. In this study, we investigated genome-wide epigenomic responses to vitamin D₃ supplementation in a cohort of 38 individuals from a Polish population. Peripheral blood mononuclear cells (PBMCs) were collected at baseline (day 0) and 24 hours after supplementation (day 1). ATAC-seq analyses revealed widespread vitamin D₃-induced changes in chromatin accessibility.

overall_design: ATAC-seq libraries of PBMCs obtained from a Polish cohort of 38 individuals before supplementation (day 0) as well as 24 hours after (day 1).

first: Rybiński

last: Maciej

first: Carlberg

last: Carsten


title: A SWI/SNF -specific Ig-like domain, SWIFT, is a transcription factor binding platform

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary: Mammalian SWI/SNF (BAF) chromatin remodeling complexes modulate DNA accessibility and gene expression, however, the mechanisms by which they are targeted on chromatin remain incompletely understood. Here, we define SWIFT (SWI/SNF Ig-Fold for Transcription Factor Interactions), found on the SMARCD family of subunits within the core module as an evolutionarily conserved, broad transcription factor (TF) binding platform. SWIFT is necessary and sufficient for direct interaction with the transactivation domain of a lineage-specific TF, PU.1, in vitro and in cells, with a single amino acid mutation in SWIFT able to disrupt PU.1-mSWI/SNF binding, inhibit site-specific complex targeting and activity, and attenuate oncogenic gene expression and proliferation of PU.1-dependent cancer cells. Dominant expression of SWIFT in isolation across cell types sequesters mSWI/SNF-interacting TFs and poisons TF-addicted cancer cells. Finally, TFs interact with SWIFT in a SMARCD paralog-specific manner, informing approaches for modulation of cell type- and disease-specific transcription.

overall_design: First, cells (hMSC, BIN-67, and U2OS) were transducted to express a given transcription factor, and ATAC-seq (in replicate) and chromatin profiling was performed. In another set of experiments, cells (hMSC, BIN-67, MOLM-13, and U-2 OS) were transducted to express both a given transcription factor and mSWI/SNF chromatin remodeling complex subunit either wild-type or mutated) and chromatin profiling, RNA-seq (in replicate), and ATAC-seq (in replicate) was again performed. Finally, transduction of the SMARCD2-SWIFT domain was performed in U-2 OS and CUT&RUN and ATAC-seq (in replicate) was performed.

first: Siddhant

middle: U

last: Jain

first: Alexander

middle: W

last: Ying


title: CD300e as a driver of immunosuppressive tumor microenvironment and colorectal cancer progression via macrophages reprogramming

city: Padova

first: Gaia

last: Codolo

state: Padova

address: via U. Bassi 58/b

department: Department of Biology

country: Italy

institute: University of Padova

summary: Colorectal cancer progression is strongly influenced by the tumor microenvironment, particularly by tumor-associated macrophages, which often acquire immunosuppressive features that dampen antitumor immunity. CD300e is a myeloid receptor known to modulate immune responses, but its role in CRC remains unexplored. Here, we show that CD300e is selectively upregulated in tumor-infiltrating monocytes and monocyte-derived macrophages in human CRC, displaying an immunosuppressive phenotype characterized by reduced antigen presentation. Using in vitro co-cultures of patient-derived tumor organoids and human monocytes, we demonstrate that tumor-derived signals are sufficient to induce CD300e expression and skew macrophages toward a pro-tumorigenic profile. To investigate the functional relevance of CD300e, we employed CD300e knockout mice in AOM/DSS-induced and MC38 subcutaneous CRC models. In both settings, CD300e deletion led to reduced tumor burden, enhanced major histocompatibility complex expression in TAMs, and improved T cell-mediated antitumor responses. Transcriptomic and functional analyses revealed that CD300e-deficient macrophages display increased phagocytic activity, upregulated antigen presentation pathways, and a greater ability to support T cell proliferation and cytotoxicity. Adoptive transfer experiments confirmed that CD300e expression on macrophages alone is sufficient to promote tumor growth and suppress effector T cell function. These findings identify CD300e as a key regulator of macrophage-mediated immune suppression in CRC and suggest that targeting CD300e may represent a novel strategy to reprogram TAMs and enhance the efficacy of cancer immunotherapy.

overall_design: Monocytes from CD300e+/+ and CD300e-/- mice were isolated from bone marrow.

first: Laura

last: Masatti

first: Enrica

last: Calura

first: Annica

last: Barizza


title: Inapparent maternal ZIKV infection impacts fetal brain development and postnatal behavior [SingleNuclei]

city: Piscataway

last: Daniels

state: NJ

address: 604 Allison Road

department: Cell Biology and Neuroscience

institute: Rutgers, The State University of New Jersey

summary: Zika virus (ZIKV) has emerged as a significant public health concern due to its association with severe neurological outcomes in infants, including microcephaly and congenital Zika syndrome (CZS). However, while the majority of ZIKV infections during pregnancy do not result in CZS, the potential long-term neurological effects of mild or inapparent maternal infections remain poorly understood. In this study, we adapted a model of maternal ZIKV infection in human STAT2 knock-in (hSTAT2) mice to investigate the effects of ZIKV infection during mid-gestation, aiming to mirror typical asymptomatic infections as they occur in humans. We found that maternal ZIKV infection at mid-gestation leads to vertical transmission without causing overt developmental deficits or clinical signs in dams or offspring. Despite the absence of immediate clinical signs, transcriptomic analyses revealed significant changes in the developing fetal brain, particularly in genes related to synaptic function and neuronal development. These molecular alterations were associated with increased synaptic density in the hippocampus and heightened susceptibility to chemically induced seizures in offspring, suggesting subtle yet significant long-term neurological consequences. Using motion sequencing (MoSeq), an unsupervised machine learning approach that profiles naturalistic motor behavior, we also identified persistent, sex-biased alterations in the content and structure of spontaneous behavior in offspring exposed to maternal ZIKV infection. Our findings highlight that even mild maternal ZIKV infections can disrupt fetal neurodevelopment, underscoring the need for enhanced monitoring and public health measures for children exposed to ZIKV in utero but who do not experience severe developmental alterations at birth. Additionally, our study provides a valuable animal model and comprehensive, cell type-specific transcriptomic datasets that will facilitate new lines of investigation into the impact of inapparent maternal ZIKV infections on fetal and childhood brain development.

overall_design: We performed single-nucleus RNA-seq on E18.5 fetal brains derived from human STAT2 knock-in (hSTAT2-KI) dams that were injected with either PBS or Zika virus at gestational day E12.5.

first: Tsui-Wen

last: Chou

first: Micheal

last: McCourt

first: Marissa

last: Lindman

first: Irving

last: Estevez

first: Benjamin

last: Buckley

first: Joshua

last: Thackray

first: Kailyn

last: Rodriguez

first: Marialaina

last: Nissenbaum

first: Cherul

last: Mishra

first: Colm

last: Atkins

last: Kusnecov

first: Max

middle: A

last: Tischfield


title: Intranasal mixed regimen with dNS1-based virus and STFKB vaccine could induce both system and mucosal humoral immunity

city: Xiamen

first: junyu

last: chen

state: Fujian

address: No.4221, South Xiang'an Road

department: School of Public Health

institute: Xiamen University

summary: This study demonstrates that an intranasal mixed vaccination regimen combining a dNS1-based live-attenuated virus and an STFKB subunit vaccine effectively induces robust humoral immunity at both systemic and mucosal sites. Compared to single-component regimens, the mixed approach elicited significantly higher levels of antigen-specific serum IgG antibodies, indicative of systemic immunity. Crucially, it also generated potent mucosal IgA responses in respiratory tissues (e.g., nasal washes, lung lavages) and distal mucosal sites. These findings highlight the potential of this combinatorial intranasal strategy to provide dual-layered immune protection against respiratory pathogens by simultaneously engaging systemic and local mucosal defenses.

overall_design: Mice were intranasally immunized in four groups: (1) dNS1-based live-attenuated virus alone, (2) STFKB subunit vaccine alone, (3) a mixture of dNS1-virus and STFKB vaccine, and (4) a negative control (vehicle). At defined post-immunization timepoints, Single-cell suspensions were prepared from lung tissues and subjected to single-cell RNA sequencing (scRNA-seq) to comprehensively profile the global transcriptional landscape of immune cells.

first: Junyu

last: Chen

first: Yaode

first: Ruotong

last: Wu

first: Yangtao

first: Heming

first: Hualong

last: Xiong

first: Xijing

last: Wang

first: Xu

last: Zhang

first: Congjie

first: Xiangjie

first: Zhen

last: Lu

first: Tiangying

first: Quan

last: Yuan

first: Ningshao

last: Xia

first: Yixin


title: Inapparent maternal ZIKV infection impacts fetal brain development and postnatal behavior [BulkSeq]

first: Brian

last: Daniels

overall_design: We performed bulk RNA-seq on fetal brains and 3-week-old offspring brains derived from human STAT2 knock-in (hSTAT2-KI) dams that were injected with either PBS or Zika virus on indicated gestational days.

first: Tsui-Wen

last: Chou

first: Micheal

last: McCourt

first: Marissa

last: Lindman

first: Irving

last: Estevez

first: Benjamin

last: Buckley

first: Joshua

first: Kailyn

first: Marialaina

first: Charul

first: Colm

first: Alexander

first: Max


title: CD300e as a driver of immunosuppressive tumor microenvironment and colorectal cancer progression via macrophages reprogramming [scRNA-Seq]

first: Gaia

last: Codolo

overall_design: CD300e+/+ and CD300e-/- mice were subjected to AOM/DSS tumorigenesis. CD11b cells were isolated from colon adenomas by FACS sorting.

first: Laura

last: Masatti

first: Enrica

last: Calura

first: Annica

last: Barizza


title: Sox8 is essential for vertebrate gastrulation

city: Dresden

first: Elias

middle: H

last: Barriga

address: ArnoldStrasse 18

department: Cluster of Excellence Physics of Life

institute: TU Dresden

summary: Gastrulation is a fundamental developmental process during which germ layers are formed and the body axes are defined. In this study, we report that the transcription factor Sox8 is essential for gastrulation, as it contributes to the formation of ventral territories and the definition of the dorsoventral border in Xenopus laevis. Briefly, a combination of RNA sequencing with a newly developed CRISPR Cas7-11 mRNA knockdown approach revealed that Sox8 is essential for correct gastrulation. Mechanistically, we found that Sox8 directly regulates the expression of the Wnt inhibitor Kremen2. We also observed that sox8 or kremen2 knockdown results in an expansion of Wnt signalling activity towards ventral territories and a decrease in ventralizing BMP signalling activities in these tissues. Thus, we propose that Sox8 contributes to defining the ventral mesoderm by inhibiting Wnt signalling and, in turn, reinforcing BMP signalling in this region. Together, our data provide new insights into the molecular control of vertebrate gastrulation and invite researchers to assess whether this Sox8/Kremen2 regulatory axis is involved in other biological processes.

overall_design: We performed RNA-seq analysis of ventral tissue from control and sox8 CRISPR 7-11-treated Xenopus laevis embryos. The RNAseq experiment was performed and optimized by the Genomic Unit of Instituto Gulbenkian Ciência (IGC), Oeiras. mRNA libraries from ventrolateral mesoderm tissues were prepared using the Smart-seq2 protocol adapted from Macaulay et al, 2016 (https://doi.org/10.1038/nprot.2016.138). Two biological replicates from control and sox8 CRISPR were used for RNA seq analysis.

first: Sofia

middle: R

last: Moreira

first: Artemis

middle: G

last: Korovesi


title: The Breakome of BRCA1 and BRCA2 Mutation Carriers Reveals Early Processes in Breast Oncogenesis

city: Jerusalem

first: Rami

last: Aqeilan

address: Hadassah medical school

department: Immunology and Cancer Research

country: Israel

institute: Hebrew University

summary: DNA double-strand breaks (DSBs) can lead to genome instability in cancer. Cells rely on an efficient DNA damage response (DDR) to maintain their DNA integrity and prevent oncogenic transformation. However, the early events that connect recurrent DNA damage to oncogenesis are not yet fully understood. Here, we employed in-suspension Breaks Labeling in-situ and Sequencing (sBLISS) to identify DSBs in primary cells of non-malignant carriers of BRCA1 and BRCA2 mutations (BRCAmut), categorized as high-risk patients, to characterize the effects of homologous recombination (HR) loss on cancer initiation. We demonstrate that the landscape of physiological DSBs in BRCAmut samples differs from that in healthy controls, and resemble more the pattern observed in cancer cells. Our results reveal that proto-oncogenes and tumor suppressors contain more breaks in BRCAmut samples, and that highly broken genes tend to be more highly expressed.  These highly broken genes are also often mutated in breast cancer tumors. Finally, differentially broken genes in BRCAmut samples exhibit a strong correlation with homologous recombination repair. Together, our findings underscore the impact of BRCA loss on the early stages of carcinogenesis and highlight future possibilities for early cancer detection.

overall_design: sBLISS (in-suspension Breaks Labeling in-situ and Sequencing) of epithelial primary cells derived from non-malignant BRCA1 and BRCA2 mutation carriers at high risk of developing breast cancer or non-carrier average risk controls, and sBLISS of non-malignant and breast cancer cell lines. All samples are non-treated.

first: Sara

last: Oster Flayshman

first: Osama

last: Hidmi

first: Jackelyn

last: Alva-Ornelas

first: Jonathan

last: Monin

first: Victoria

last: Seewaldt

first: Mark

last: LaBarge

first: Yotam

last: Drier

middle: I


title: The Nonamer Code for RAG1-mediated Recombination in vivo

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

institute: Bar-Ilan University

summary: V(D)J recombination, essential for adaptive immunity, is initiated by RAG1/2, which recognizes Recombination Signal Sequences (RSSs) flanking gene segments at Antigen Receptor (AgR) loci. RSSs comprise conserved heptamer and nonamer motifs separated by a 12/23-base spacer. While the first three heptamer nucleotides (5’-CAC) are strictly conserved, RSS promiscuity enables RAG “off-target” activity at RSS-like sequences, termed “cryptic RSSs” (cRSSs), contributing to chromosomal deletions and lymphoid tumorigenesis. Notably, the nonamer exhibits substantial sequence variability across physiological RSSs. In addition, many cRSSs lack a discernible nonamer-like sequence, limiting the ability to predict RAG targets based on RSS consensus. Using a high-throughput approach, we characterized here the nonamer properties supporting RAG-mediated recombination. While the consensus nonamer (5’-ACAAAAACC) exhibited strong functionality, numerous sequences significantly diverged from it promoted high recombination rate. These functional nonamers balance two, somewhat opposing, features: affinity for the RAG nonamer-binding domain (NBD) – primarily via a shared purine–weak–purine (RWR) motif at positions 4–6, and nucleosome repulsion. Moreover, nonamers of genomic cRSSs mimic canonical nonamers mainly through nucleosome-repelling sequences. This study provides a model for both physiological RAG activity and its off-target effects, enhancing our understanding of immune repertoire formation and the genetic basis of lymphoid cancers.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Recombination profiling of v-Abl pre-B cells transduced with randomized nonamer RSS library; includes pre- and post-recombination samples and pre-integration library control.

first: Wessal

last: Hanout-Chuiko

first: Sunil

last: Pachakar

first: Rawan

last: Foqara

first: Hadas

last: Sibony-Benyamini

first: Shira

last: Peretz

first: Nurit

last: Edri

first: Moshe

last: Dessau


title: Helicobacter pylori infection aggravates hepatic steatosis by lactylation-driven WTAP-mediated m6A modification

city: Nanjing

first: Han

last: Chen

state: Jiangsu

address: #300 Guzhou Road, Gulou District

institute: Nanjing Medical University

summary: Helicobacter pylori (H. pylori) infection has been investigated as a potential risk factor for extragastric diseases, including metabolic dysfunction-associated fatty liver disease (MASLD). However, the details of the underlying mechanisms remain inadequately understood. In this study, we elucidate that H. pylori infection exacerbates hepatic metabolic disorders both in vitro and in vivo, manifesting as increased lipid deposition and insulin resistance. Mechanistically, H. pylori infection further upregulates m6A content, particularly increasing the expression of one of the m6A methyltransferases, WTAP.

overall_design: The m6A-Seq analysis of the HepG2 cells co-cultivated with H.pylori and controls.


title: 3D genome landscaping of in vitro totipotent cellular models [RNA-seq]

city: Hangzhou

first: Zheting

last: Zhang

state: Zhejiang

address: Dunyu load

department: school of life science

institute: Westlake University

summary: Totipotent embryos lack higher-order genome architecture. In this study, we profile the 3D genome architecture of two putative totipotent cellular models, ciTotiSCs and TBLCs. Notably, both ciTotiSCs and TBLCs retain TADs and structurally resemble ICM/ESCs more closely than totipotent embryos. While TADs and compartmentalization are positionally conserved, they weaken upon acquisition of totipotency. Integrative analysis of epigenetic and Hi-C data further reveal that pluripotency genes undergo coordinated epigenetic landscape remodeling and contact domain reorganization, driving pluripotency suppression. Conversely, totipotency gene activation appears to operate through distinct, yet undefined mechanisms. This study establishes the first functional link between 3D genome folding and totipotency-pluripotency transitions while proposing a revised framework for evaluating in vitro totipotency models.

overall_design: RNA-seq libraries were prepared from the ESC and the two mouse 2C-like cell lines generated from it, the ciTotiSCs and the TBLCs.

first: Yu

last: Fu


title: Brainstem metabolic changes in a mouse model of Dravet Syndrome

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

summary: Dravet Syndrome (DS) is a severe genetic epileptic encephalopathy caused by mutations in the SCN1A gene that encodes the voltage-gated sodium channel (NaV1.1) subunit alpha. DS is characterized by intractable seizures, progressive developmental delay, cognitive impairment, and high mortality due to sudden unexpected death in epilepsy (SUDEP). Post-ictal apnea that precedes asystole has been observed to lead to SUDEP; however, the exact molecular underpinnings are unclear. Seizure-induced hippocampal metabolic alterations have been reported in DS mice. Whether such alterations occur in the brainstem, a master regulator of autonomic functions, thereby influencing morbidity, mortality/SUDEP, and seizure outcomes is unknown. We used Scn1aA1783V/WT DS mice and showed that there are temporal alterations in the brainstem metabolome which are distinct in comparison to the forebrain metabolome. Glycolytic, and pentose phosphate pathway intermediates were significantly elevated in the brainstem of DS mice during the period of enhanced susceptibility to mortality (post-natal day P20-30). Post P20-30, mitochondrial aconitate, and the antioxidant glutathione were significantly elevated. Single nuclei RNA sequencing (snRNA seq), and proteomic analyses revealed alterations in genes associated with neurotransmission, cellular respiration, protein translation, as well as systematic rewiring of protein kinase-mediated pathways that were specific to the brainstem. These findings suggest that there are widespread metabolic changes in the brainstem of DS mice that are associated with alterations in druggable molecular pathways.

overall_design: The goal of this study was to evaluate baseline differences in the brainstem transcriptomes of a mouse with Dravet Syndrome (Scn1aA1783V/WT, carries a knock-in missense mutation in the gene SCN1A that encodes for a voltage-gated sodium channel subunit alpha) compared to a wildtype (WT) C57Bl6 mouse. Brainstem tissue was collected from mice during post-natal days P40-50. This is the developmental time period where Dravet mice have survived past the critical period of enhanced susceptibility to mortality (P20-30). This study will help us understand what the brainstem (critical region for regulation of autonomic functions) transcriptome looks like and whether transcriptomic alterations could play a role in influencing seizures, morbidity, and mortality outcomes in Dravet Syndrome mice.

first: Cameron

last: Metcalf

first: Ashwini

last: Sri Hari


title: CBX7, a polycomb repressor, functions as a methylation-dependent transcriptional activator and cytosolic signaling regulator in lymphoid cells

city: Denver

first: Rafeul

last: Alam

state: Colorado

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

summary: CBX7, a chromatin remodeler, typically functions as a gene repressor. We, unexpectedly, found that CBX7 robustly formed methylation-dependent transcriptional and signaling complexes, which induced gene transcription directly by binding to cytokine gene promoters. CBX7 translocated to the cytosol, and formed a methylation-dependent signaling complex with c-Raf, MEK1/2, and CK2- to generate, and sustain ERK1/2 signaling. CBX7 is an allergen-inducible gene.  Genetic and pharmacologic interventions established an essential role for CBX7 for production of cytokines by mouse and asthmatic patient T cells and ILC2s, and for induction of allergic inflammation in multiple mouse models of asthma.  RNA-sequencing demonstrated a large-scale loss and gain in gene transcription in CBX7-/- T cells.  The top downregulated pathways included cytokine-cytokine receptor interaction, asthma and T helper cell differentiation.  CBX7 induction of the transcriptional activation complex and methylation of the ERK1/2 signalosome was specific for lymphoid cells as they were absent in epithelial cells.  Our studies established a new paradigm of CBX7-generated methylation-dependent signaling complexes regulating inflammation.

overall_design: anti-CD3/28 antibody-stimulated splenic CD4 T cells from CBX7+/+ and CBX7-/- mice. Cell samples were collected from a total of 8 mice (four mice per group) following stimulation for 6h.

first: Sirohi

last: Kapil


title: 3D genome landscaping of in vitro totipotent cellular models [ATAC-Seq]

overall_design: ATAC-seq libraries were prepared from the ESC and the two mouse 2C-like cell lines generated from it, the ciTotiSCs and the TBLCs.


title: Transcriptome profiling of peripheral blood mononuclear cells from highly susceptible adult cattle infected with a virulent strain of Babesia bovis

city: Pullman

first: Massaro

middle: Wilson

last: Ueti

state: Washington

address: 3003 ADBF Washington State Univ, 3003 ADBF, Grimes Way

institute: USDA ARS Animal Disease Research Unit

summary: Bovine babesiosis is a tick-borne disease that poses a significant economic threat to cattle industries in tropical and subtropical areas, and Babesia bovis is the most virulent causative agent of bovine babesiosis. This apicomplexan parasite infects erythrocytes of cattle causing severe hemolytic disease, and animals that survive acute infections become persistently infected for life. Young cattle (< 6 months of age) are resistant to infection while adult cattle (>1 year of age) are highly susceptible and succumb to acute infection; however, the immunological mechanisms associated with the age-resistance remain unclear. Protective host immunity involves peripheral blood mononuclear cells (PBMCs) including natural killer (NK) and T cells, and activated macrophages that act to control the pathogen. In this study, we examined the transcriptional signatures of PBMCs from adult cattle (>1.5 years old) experimentally infected with the B. bovis virulent strain S74-T3Bo. Transcriptional signatures evident during the acute phase of babesiosis were categorized into immune-related and non-immune genes. We identified both upregulated and downregulated genes, with fold changes ranging from 2 to 263-fold. We discuss our findings in the context of immune responses to acute disease as a mechanism for adult host survival, with a focus on the molecular functions and biological processes involved in the response to B. bovis infection. In this RNA-Seq analysis, we identified genes related to the immune system, including cytokines and chemokines, complement, cell signaling pathways and surface molecules that may play a role in the recognition of pathogen-associated molecular patterns. In addition, non-immune genes potentially involved in cell proliferation, cell migration, development, energy production, protein-protein interactions, molecular transport, and flagella assembly were also identified.

overall_design: In this study, we examined the transcriptional signatures of peripheral blood mononuclear cells (PBMCs) from adult cattle (>1.5 years old) experimentally infected with the B. bovis virulent strain S74-T3Bo.

first: Janaina

last: Capelli-Peixoto

first: Reginaldo

last: Bastos

first: Anna

last: McDonald

first: Jacob

last: Laughery

first: Sascha

last: Duttke

first: Carlos

last: Suarez

first: Chungwon

last: Chung


title: ATAC-seq of E9.5 Neural Tube defects mouse brain and E9.5 normal mouse brains

city: Taiyuan

first: Yuan

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

institute: Shanxi Medical University

summary: To study the chromatin accessibility  in E9.5d mouse brains with neural tube defects or control, we performed ATAC-seq  in mouse brains. NTDs mouse model: CD-1 mice (7–8 weeks old) were provided by Beijing Vital River laboratory Animal Technology Co., Ltd, China (no: 110011200105514958, 16-25g). Female CD-1 mice were fed on low folate diet for more than 8 weeks. Sexually matured individuals were mated overnight; vaginal plug was detected at 8:00 am in the following morning and was designated as E0.5 day. NTDs mouse models were induced by intraperitoneal injection with 1.5 mg/kg of MTX (Sigma-Aldrich, USA) on E7.5. On E9.5, pregnant mice were euthanized by cervical dislocation, and the phenotypes of the fetuses were observed under a microscope. All samples with NTDs clinical manifestations were collected for experiments.

overall_design: Two biological replicates are set for each group, controlA  and control B were control groups from control. And NTDsA and NTDsB were from NTDs groups.

first: Jianting

last: Li

first: Zhihua

last: Cao


title: 3D genome landscaping of in vitro totipotent cellular models [CUT&Tag]

first: Zheting

last: Zhang

overall_design: CUT&Tag libraries targeting CTCF, H3K27ac, H3K4me3, H3K27me3 and H3K9me3 were prepared from the ESC and the two mouse 2C-like cell lines generated from it, the ciTotiSCs and the TBLCs.

first: Yu


title: Analyzing the impact of antibiotics treatment on lung inflammation in Mtb infected mouse lungs using bulk RNA transcriptomics

city: Cambridge

first: Amy

middle: K.

last: Barczak

address: The Ragon Institute, 400 Technology Square

department: Medicine/Infectious Diseases

institute: Massachusetts General Hospital

summary: C3HeB/FeJ mice were infected with Erdman strain of Mycobacterium tuberculosis (Mtb) for 12 weeks. Mice were then treated with RIPE (rifampin, isoniazid, pyrazinamide, and ethambutol) or carrier (water). Lungs were harvested after 2, 4, and 8 weeks of treatment (times 14, 16, and 20 weeks post0infection) for RNA preparation and bulk RNA sequencing.

overall_design: Uninfected, infected/carrier-treated and infected/RIPE-treated mouse lungs were soaked in RNAlater and frozen at -80; RNA was then isolated using Trizol (Invitrogen) according to the manufacturer’s protocols. RNAseq libraries were generated, sequenced, and analyzed


title: Single cell RNA sequencing of placenta in patients with preeclampsia

city: Changchun

first: Shu

last: Zheng

state: 吉林Jilin

address: Xinmin Road

institute: Jilin University

summary: We performed single-cell RNA sequencing in placental tissues from normotensive and preeclamptic term pregnancies after cesarean section to explore placental transcriptomic alterations and pathological mechanisms associated with preeclampsia. Our research aims to elucidate placental dysfunction in PE and its impact on maternal-fetal outcomes, providing new insights into the pathogenesis of preeclampsia and identifying potential biomarkers for early detection and intervention.

overall_design: Following collection of placental biopsies from both normotensive controls and preeclamptic cases, tissues were immediately dissociated into single-cell suspensions. The standardized protocol included gentle enzymatic digestion optimized for placental villous tissue (Collagenase IV/DNase I), followed by sequential processing through mechanical disruption, 70-μm filtration, erythrocyte lysis (ACK buffer), dead cell removal (MACS LD columns), and viability assessment (>85% via Trypan Blue exclusion). After quality control verification, cells were resuspended in PBS with 0.04% BSA and loaded onto the 10x Genomics Chromium Controller (v3.1 chemistry) to generate single-cell GEMs. Libraries were prepared according to manufacturer's protocol and sequenced on Illumina NovaSeq 6000 (PE150, sequencing depth >50,000 reads/cell) with 30% PhiX spike-in for low-diversity libraries.

first: Chang

last: Shu

first: Peng

last: Xu

first: Huimin

last: Shen


title: Transcriptome analysis of circulating microRNAs associated with Chagas disease susceptibility and chronic Chagas cardiomyopathy severity

city: Rio de Janeiro

first: Eric

middle: Henrique

last: Roma

state: Rio de Janeiro

address: Av. Brasil, 4365

department: Instituto Nacional de Infectologia

country: Brazil

institute: Fundação Oswaldo Cruz

summary: Chagas disease (CD), caused by infection with the protozoan parasite Trypanosoma cruzi, is a major public health concern in Latin America. Understanding the molecular mechanisms driving disease progression and identifying biomarkers are crucial. We investigated the association of circulating microRNAs (miRNAs) with CD susceptibility and heart disease progression. A multicentric prospective observational study was conducted with 150 CD patients (46 indeterminate, 104 CCC [chronic chagasic cardiomyopathy] staged A-D) and 42 healthy controls from CD endemic areas. Sequencing of circulating miRNAs was performed, and differential expression analyses were conducted. We identified 40 differentially expressed miRNAs between CD patients and healthy controls, highlighting miR-199b-5p, miR-153-3p, miR-143-3p, and miR-223-3p upregulated, and miR-150-3p, miR-4508, miR-486-5p, and miR-3960, downregulated in CD patients. Moreover, functional analysis using Ingenuity Pathway Analysis software revealed that these miRNAs were involved in immune response and cardiovascular signaling pathways. Several miRNAs (miR-6734-5p, miR-1285-5p, miR-10527-5p, miR-31-5p, miR-5187-5p, miR-6515-5p) tended to present a higher expression in patients with severe compared to those with mild CCC, while miR-30c-2-3p presented lower expression in these groups. This study provides evidence for the dysregulation of specific miRNAs in CD, highlighting their potential role in disease pathophysiology and possible use as biomarkers for CD susceptibility and CCC severity.

overall_design: miRNA-seq profiling total RNA extracted from human serum of samples from patients of Chagas Disease in indeterminate and chronic Chagas cardiomyopathy

first: Fabielle

last: Marques-Santos

first: Alinne

last: Rezentti

first: Luciana

middle: F

last: Portela

first: Filipe

last: da Costa

first: Alejandro

middle: M

last: Hasslocher-Moreno

first: Marcelo

middle: T

last: de Holanda

first: Luiz

last: Sangenis

first: Andréa

first: Joseli

last: Lannes-Vieira

first: Tania

last: Araujo-Jorge

first: Roberto

last: Ferreira

last: Saraiva

first: Maria

last: Bonecini-Almeida


title: CUT&Tag of H3K27me3,  E9.5 Neural Tube defects mouse brain

first: Yuan

last: Fu

summary: To study the histone H3K27me3 enrichment in E9.5d mouse brains with neural tube defects or control, we performed H3K27m3 in mouse brains.NTDs mouse model: CD-1 mice (7–8 weeks old) were provided by Beijing Vital River laboratory Animal Technology Co., Ltd, China (no: 110011200105514958, 16-25g). Female CD-1 mice were fed on low folate diet for more than 8 weeks. Sexually matured individuals were mated overnight; vaginal plug was detected at 8:00 am in the following morning and was designated as E0.5 day. NTDs mouse models were induced by intraperitoneal injection with 1.5 mg/kg of MTX (Sigma-Aldrich, USA) on E7.5. On E9.5, pregnant mice were euthanized by cervical dislocation, and the phenotypes of the fetuses were observed under a microscope. All samples with NTDs clinical manifestations were collected for experiments.

overall_design: We compared the h3K27me3 of control and neural tube defects mouse brains of E9.5d. Three biological replicates are set for each group, con1, con2, con3 were control groups from control. And M1, M2 and M3 were from NTDs groups.

first: Jianting

last: li

first: Qie

last: xie


title: Comparative Transcriptome Analysis of Peripheral Blood in High-Risk Preeclampsia versus Normotensive Pregnancies

first: Shu

last: Zheng

summary: This study identifies peripheral blood transcriptomic signatures associated with high-risk preeclampsia (PE). RNA sequencing of 10 PE patients (clinically diagnosed with hypertension and proteinuria) and 10 matched normotensive controls revealed differentially expressed genes (DEGs) enriched in angiogenesis, immune regulation, and endothelial dysfunction pathways, suggesting their potential as early biomarkers for PE.

overall_design: Peripheral blood samples from PE high-risk and control groups were collected in EDTA anticoagulant tubes, immediately mixed with TRIzol Reagent by vigorous vortexing to ensure complete cell lysis and RNA stabilization. Transcriptome profiling was performed using the Illumina NovaSeq 6000 platform with paired-end 150 bp sequencing, generating ~40 million reads per sample to achieve high coverage depth. Differential gene expression analysis focused on PE-associated pathways (angiogenesis, immune dysregulation) using DESeq2 with thresholds of |log2FC| ≥1 and adjusted p <0.05.

first: Chang

last: Shu

first: Huimin

last: Shen

first: Peng

last: Xu


title: 3D genome landscaping of in vitro totipotent cellular models [Hi-C]

first: Zheting

last: Zhang

overall_design: Hi-C libraries were prepared from the ESC and the two mouse 2C-like cell lines generated from it, the ciTotiSCs and the TBLCs.

first: Yu


title: In vitro analysis of gene expression changed caused by induced ablation of Roquin1/2 in cultured  peritoneal and bone marrow derived mast cells

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

summary: The gene expression of in vitro cultured peritoneal mast cells and bone marrow derived mast cells made  deficient for Roquin 1 and Roquin 2 was compared to control mast cells.

overall_design: Cultured CkitCreERT2 Roquin1FF Roquin2FF mouse peritoneal mast cells (cPMC) and bone marrow derived mast cells (BMMC) were made Roquin1/2 deficient  in vitro through exposure to 4-hydroxytamoxifen and their gene expression was compared to control mast cells treated the same way but retaining normal expression of both proteins.

first: Klaus

last: Heger

first: Marc

last: Schmidt-Supprian


title: Comparative TSS-seq analysis among Arabidopsis natural variations revealed genetic stability of genic and non-genic promoters

city: Gifu

first: Kazuki

last: Sugekawa

state: Gifu

institute: Gifu University

summary: In our previous study, more than 300K promoters were identified in the Arabidopsis genome, including many non-genic promoters that do not transcribe gene bodies. Although some functional non-genic promoters have been reported, the biological importance of many others remains unclear. In this study, we evaluated their genetic stability by analysis of promoter sequence and peak positions of TSS clusters using Arabidopsis natural variations. Canonical genic promoters showed high conservation of sequence and TSS peak positions. Moreover, they were well structured in terms of the presence of core elements, promoter context, and epigenetic features. These data revealed that the genic promoters are genetically stable and well-structured, which is consistent with their biological significance for the expression of genes. On the other hand, non-genic promoters showed low stability of TSS peak position and low structured features. Therefore, We concluded that most non-genic promoters are biologically insignificant with some exceptions. Interestingly, the genetic stability of promoters has a positive relation with the expression level. This suggests weak promoters like most non-genic promoters are results of leaky transcription, which supports the concept of “transcriptional noise”.

overall_design: CAGE-seq profiling of two-weeks Arabidopsis 4 accessions(Altenb-2, Kly-1, Shigu-2, and Vash-1) under high light + cold stress condition and control condition

first: Samson

middle: O

last: Ezeh

first: Yoshiharu

middle: Y

last: Yamamoto


title: Spatial transcriptomics reveal lineage complexity of gastric incomplete intestinal metaplasia and its association with gastric cancers [scRNA-Seq]

city: Jejusi

first: Hyesung

last: Kim

address: Aran 13 gil, 15

department: Convergence Biomedical Science

institute: Jeju National University College of medicine

summary: This research underscores the unique molecular phenotype and lineage complexity of Inc IM, emphasizing its significance as a precancerous lesion in gastric tissues. Our findings lay the groundwork for future investigations into the epigenetic and transcriptional dynamics governing metaplastic changes, highlighting the importance of Inc IM in GC progression.

overall_design: scRNA sequencing for 10 types ( Antrum, Antrum+BMP, Incom, Incom+BMP, Com, Com+BMP, SI, SI+BMP, LI, LI +BMP) of Human gastric or Intestinal Organoid


title: Transcriptomic analysis of chemotherapy-associated oropharyngeal candidiasis reveals a novel role of indigenous mucosal bacteria in pathogenesis

city: Farmington

first: Roberto

last: Vazquez-Munoz

state: Connecticut

address: 263 Farmington Avenue, Main building, room L6008

department: General Dentistry

institute: UConn Health

summary: This work reports a new mechanism of pathogenic synergy between C. albicans and E. faecalis, which may be responsible for increased epithelial barrier damage and mucosal invasion by C. albicans hyphae in cancer chemotherapy.

overall_design: Tongue tissues (stored in RNAlater at -80oC) were thawed on ice for 15 min and RNA isolation was carried out using the RNeasy Kit (Qiagen) with few modifications. Briefly, thawed samples were homogenized in 800µl of RLT buffer containing 1% of βeta-mercaptoethanol (Biorad) using a tissue homogenizer. Subsequently 800µl of Phenol:chloroform:isoamyl-alcohol (Invitrogen) was added to the homogenate in 2ml screw-capped tubes. Following centrifugation, the aqueous phase was collected, and an equal volume of 70% molecular-grade ethanol was added. Kit instructions were followed for subsequent column separation steps. DNAse treatment was performed using the TURBO DNA-free kit (Invitrogen). RNA was analyzed for quality using the Experion automated gel electrophoretic system (Biorad) and only samples with RNA integrity value (RIN) >7 were used for RNA seq. For the RNA sequencing, cDNA libraries were prepared using the TruSeq RNA kit (Illumina) and subjected to poly(A) enrichment according to kit protocol. cDNA fragments (one hundred nucleotides from each end) were sequenced using the Illumina NextSeq platform. To analyze the RNA sequences, we combined the raw reads from each sample and performed a quality check using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Next, we used Sickle to trim the reads and QC them again with FASTQC (https://github.com/najoshi/sickle). Reads were aligned using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) against the Mus musculus (GRCm38) index (Kim et al., 2015). The aligned reads were then converted into binary format using samtools and the duplicates were removed using the tool PICARD (Li et al., 2009). The counts were calculated using HTseq-count program and comparisons were done between the antibiotics and non-antibiotics oropharyngeal candidiasis groups (Anders et al., 2015). False discovery rate adjusted p-values ≤ 0.05 were applied to identify significant differentially expressed (DE) genes using the DESeq2 package. Samples within a group were compared using principal component analysis and sample-to-sample distance matrix. Finally, the R software was used to compare the two groups and DE genes were tabulated and subjected to further downstream analysis.

first: Vazquez-Munoz

last: Roberto

first: Ranjan

last: Amit

first: Bertolini

last: Martinna

first: Thompson

last: Angela

first: Pegah

last: Mosharaf Ghahfarokhy

first: Alannah

last: Harnden

first: Clarissa

last: Nobile

first: Takanori

last: Sobue

first: Paola

last: Vera-Licona

first: Anna

last: Dongari-Bagtzoglou


title: Spatial transcriptomics reveal lineage complexity of gastric incomplete intestinal metaplasia and its association with gastric cancers [Methyl]

overall_design: Methylation chip array for 32 types of Human Gastric and Intestinal Organoids


title: Spatial transcriptomics reveal lineage complexity of gastric incomplete intestinal metaplasia and its association with gastric cancers [ATAC-Seq]

overall_design: Bulk ATACseq profiles of Human gastric organoids ( naGF_ATAC, IncomGF_ATAC and ComGF_ATAC) and Intestinal orgnoids ( SI_ATAC and LI_ATAC)


title: Interleukin-1–mediated inflammation drives long-term cognitive deficits after perinatal asphyxia

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

summary: Perinatal asphyxia remains a leading cause of neonatal mortality, and a major contributor to permanent neurological deficits. Even mild cases can result in long-term neurodevelopmental, cognitive, behavioural, and psychiatric disorders. However, the mechanisms underlying asphyxia-induced hypoxic-ischaemic brain injury remain poorly understood, limiting the development of targeted interventions during the critical early plastic period. To investigate how perinatal asphyxia-induced changes lead to neuropsychiatric deficits and associated histological and molecular alterations that progress into adulthood, we utilised a translationally relevant, non-invasive oxygen deprivation model of asphyxia in postnatal day 7 rats. We conducted comprehensive assessment of asphyxia-induced changes, integrating neurobehavioural profiling (evaluating cognitive, emotional, social, and neuromotor functions), microglial morphology analysis, neuroimaging, stress hormone measurement and whole-transcriptome sequencing techniques to elucidate the acute and long-term functional consequences. Consistent with clinical observations, the extensive functional assessment revealed distinct sex-dependent effects, including increased anxiety and impulsivity, attention deficits, and impaired inhibitory control, which were observed exclusively in males, with no apparent sensorimotor deficits. This phenotype resembling attention deficit hyperactivity disorder in adult rats was associated with a lasting increase in inhibitory bouton densities in the medial prefrontal cortex. The development of an acute inflammatory response after perinatal asphyxia marked by phenotypic transformation of microglia paralleled brain perfusion and stress hormone changes. Notably, microglial changes were mitigated by the blockade of proinflammatory interleukin-1 signalling via systemic IL-1 receptor antagonist (IL-1RA) administration in a therapeutically relevant time window. Importantly, early blockade of proinflammatory responses was able to prevent cognitive deficits in adulthood, and normalised inhibitory bouton densities. RNA sequencing analysis revealed asphyxia-induced dysregulation of molecular pathways targeting GABAergic signalling, potentially contributing to subsequent morphological and neuropsychiatric alterations. IL-1RA treatment appeared to engage distinct regulatory mechanisms, rather than merely reversing these disruptions in the acute post-asphyxia period. Collectively, these findings demonstrate that perinatal asphyxia induces marked behavioural deficits in attention and inhibitory control, paralleled by lasting inhibitory dysregulation, preceded by acute induction of microglia-driven inflammatory processes in the medial prefrontal cortex. Systemic IL-1RA administration may represent a promising therapeutic opportunity to prevent long-term cognitive impairments caused by perinatal asphyxia. Perinatal asphyxia remains a leading cause of neonatal mortality, and a major contributor to permanent neurological deficits. Even mild cases can result in long-term neurodevelopmental, cognitive, behavioural, and psychiatric disorders. However, the mechanisms underlying asphyxia-induced hypoxic-ischaemic brain injury remain poorly understood, limiting the development of targeted interventions during the critical early plastic period. To investigate how perinatal asphyxia-induced changes lead to neuropsychiatric deficits and associated histological and molecular alterations that progress into adulthood, we utilised a translationally relevant, non-invasive oxygen deprivation model of asphyxia in postnatal day 7 rats. We conducted comprehensive assessment of asphyxia-induced changes, integrating neurobehavioural profiling (evaluating cognitive, emotional, social, and neuromotor functions), microglial morphology analysis, neuroimaging, stress hormone measurement and whole-transcriptome sequencing techniques to elucidate the acute and long-term functional consequences. Consistent with clinical observations, the extensive functional assessment revealed distinct sex-dependent effects, including increased anxiety and impulsivity, attention deficits, and impaired inhibitory control, which were observed exclusively in males, with no apparent sensorimotor deficits. This phenotype resembling attention deficit hyperactivity disorder in adult rats was associated with a lasting increase in inhibitory bouton densities in the medial prefrontal cortex. The development of an acute inflammatory response after perinatal asphyxia marked by phenotypic transformation of microglia paralleled brain perfusion and stress hormone changes. Notably, microglial changes were mitigated by the blockade of proinflammatory interleukin-1 signalling via systemic IL-1 receptor antagonist (IL-1RA) administration in a therapeutically relevant time window. Importantly, early blockade of proinflammatory responses was able to prevent cognitive deficits in adulthood, and normalised inhibitory bouton densities. RNA sequencing analysis revealed asphyxia-induced dysregulation of molecular pathways targeting GABAergic signalling, potentially contributing to subsequent morphological and neuropsychiatric alterations. IL-1RA treatment appeared to engage distinct regulatory mechanisms, rather than merely reversing these disruptions in the acute post-asphyxia period. Collectively, these findings demonstrate that perinatal asphyxia induces marked behavioural deficits in attention and inhibitory control, paralleled by lasting inhibitory dysregulation, preceded by acute induction of microglia-driven inflammatory processes in the medial prefrontal cortex. Systemic IL-1RA administration may represent a promising therapeutic opportunity to prevent long-term cognitive impairments caused by perinatal asphyxia.

overall_design: This experiment assessed the differentially expressed genes of the medial prefrontal cortex in the acute period (24h) following perinatal asphyxia (PA) in male rat pups and the possible effects of interleukin-1 receptor antagonist (IL-1RA) treatment. Treatment groups were control vehicle, control IL-1RA, PA vehicle and PA IL-1RA. N= 8-10/ experimental group. No replicates were included.

first: Hanga

last: Kelemen

first: Gyula

last: Balla

first: Kornél

last: Demeter

first: Eszter

last: Sipos

first: András

last: Buzás-Kaizler

first: László

last: Biró

first: Manó

last: Aliczki

first: Barbara

last: Orsolits

first: Áron

last: Kerényi

first: Zoltán

last: Balogh

first: Benedek

last: Pászthy Szabó

first: Diána

last: Pejtsik

first: Lajos

last: Hegyi

first: Krisztián

last: Szigeti

first: Domokos

last: Máthé

first: Parasuraman

last: Padmanabhan

first: Csaba

last: Bödör

first: Andrea

last: Fekete

first: Miklós

last: Szabó

first: Kai

last: Kaila

first: Ádám

last: Dénes*

first: Éva

last: Mikics*


title: Bulk RNA-Seq of male and female lumbosacral dorsal root ganglia after VEGFA-instillation

city: Aurora

first: SATHISH KUMAR

last: YESUPATHAM

state: CO

address: Rm 6440 D, 12700 E 19th Ave., Mail Stop 317

institute: Univerity Of Colorado

summary: This study examined transcriptomics in lumbosacral dorsal root ganglia that carries bladder afferent signals in a bladder-origin visceral pain animal model. C57BL6/J male and female mice underwent intravesical instillations of VEGF165, a mouse recombinant of VEGFA to induce visceral hypersensitivity. Saline-instilled male and female mice were used as controls. Across the four experimental groups, we found significant sex differences in the transcriptome profile in both saline-instilled animals and VEGF-induced signaling pathway changes in the lumbosacral sensory ganglia. These findings provide insight into potential molecular targets for alleviating visceral pain symptoms when considering sex as a biological variable.

overall_design: Total of 16 C57BL6/J mice were used in this study.  Four experimental groups are Saline-instilled male mice (n=4) Saline-instilled female mice (n=4),VEGFA -instilled male mice (n=4) and VEGFA -instilled female mice (n=4). Intravesical instillations of VEGF165 (6.41 nM in 100 μL saline) or saline (100μL) were instilled  on Day 1,Day 5 and Day 9.  Manual Von Frey testing (VFT) was used to assess visceral mechanical sensitivity on Day 16. Four animals from each group were euthanized and their lumbosacral L1, L2, L6, S1, and S2 DRGs were harvested immediately. Total RNA was extracted using a RNAeasy miniprep kit (Qiagen, CA, USA). Extracted RNA was resuspended in 15 μL of RNase-free water and stored at −80°C. QC passed 300 ng of RNA per sample was used for library preparation using  universal mRNA Poly-A tail prep kit.Samples were sequenced on  Illumina NovaSEQ 6000 platform  (Paired End 2x150bp) at a depth of 40 million reads per sample.

first: Sathish Kumar

last: Yesupatham

first: Alison Xiaoqiao

last: Xie


title: Ex vivo analysis of gene expression in Roquin1/2 deficient peritoneal mast cells

first: Assa

last: Yeroslaviz

summary: To evaluate the impact of Roquin1/2 deficiency on mast cells, peritoneal mast cells were FACS-purified directly ex vivo. As controls mast cells were FACS-purified from peritoneal cavity lavages of cKitCreERT2, Mcpt5Cre and wild-type mice.

overall_design: The gene expression of Roquin1/2 deficient directly ex vivo isolated peritoneal mast cells was compared to different controls: ex vivo isolated peritoneal mast cells from cKitCreERT2 mice, which have lower peritoneal mast cell numbers and reduced cKit expression, as to Roquin1/2 deficient mast cells, Mcpt5Cre mice as Cre controls and wild-type mice.

first: Klaus

last: Heger

first: Marc

last: Schmidt-Supprian


title: Whole transcriptome comparison between two groups of PKU patients: Non-carriers vs. Carriers of rs113883650

city: Krakow

first: Miroslaw

last: Bik-Multanowski

address: ul. Wielicka 265

department: Dept. of Medical Genetics

institute: Jagiellonian University

summary: We demonstrated a decrease of expression of proteasome pathway (KEGG) incells treated with high Phe concentrations.

overall_design: Comparison of two groups of cells treated with various concentrations of Phe


title: The effects of the combination of arachidonic acid and ethanol on H9c2 cardiomyoblasts

city: Omaha

first: Weilun

last: Ai

state: NE

address: 42nd and Emile

institute: University of Nebraska Medical Center

summary: Arachidonic acid (AA) is an omega-6 polyunsaturated fatty acid, is abundant in the food. Recent studies showed that AA and AA-derived metabolites play an important role in alcohol-associated cardiomyopathy. To determine the role of AA in mediating ethanol-induced cardiomyocyte injury, we used an in vitro model, in which H9c2 cells were exposed to AA and ethanol (ET), and we performed bulk RNA-seq to identify genes altered due to ET+AA exposure.

overall_design: H9c2 cells are treated with/ without ET+AA for 24 hours.

first: Ai

last: Weilun

first: Viswanathan

last: Saraswathi


title: alpha tocopherol ameliorates allergic airway inflammation by regulating ilc2 ferroptosis in an lkb1-dependent manner_Aalter vs VE

city: guangzhou

first: xiaogang

last: zhang

address: Sha Tai nan Lu 1023hao, Baiyun District

department: School of Basic Medical Sciences

institute: Southern Medical University

summary: Dietary immunization is vital in regulating allergic airway inflammation mediated by group 2 innate lymphoid cells (ilc2s).

overall_design: this study identifies alpha tocopherol, a vitamin e component, as a significant modulator of allergic airway inflammation.


title: Systems Pharmacology Screening Reveals Targetable Kinases in Supratentorial Ependymoma Kinases in Supratentorial Ependymomas

city: Seattle

first: Mehlam

last: Saifudeen

state: WA

address: 1100 Fairview Ave North

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Ependymomas (EPN) are central nervous system tumors arising from ependymal cells, primarily affecting young children and accounting for 10% of intracranial tumors in children and 4% in adults. Current treatments are limited to surgery and radiotherapy, with chemotherapy providing minimal benefit. Over 70% of supratentorial ependymomas (ST-EPNs) are driven by ZFTARELA fusions (ZFTA-RELAfus), which are associated with poor prognosis. Recent molecular classifications have identified two distinct ST-EPN clusters, E1 and E2, with the E1 cluster predominantly composed of ZFTA-RELAfus tumors. However, effective targeted therapies for these tumors remain lacking. Here, we show that the ZFTA-RELAfus mouse model closely mirrors the human E1 cluster, validating its use for therapeutic discovery. Using this model and a systems polypharmacology approach called Kinome Regularization, we identified mer tyrosine kinase (Mertk) as a key regulator of ZFTA-RELAfus cell viability and proliferation. Genetic depletion or pharmacological inhibition of Mertk reduced cell growth ex vivo and treatment with the clinical-grade Mertk inhibitor significantly suppressed tumor proliferation in vivo. Mechanistically, both human E1 tumors and mouse ZFTA-RELAfus tumors showed elevated Mertk expression, with Mertk inhibition leading to decreased activity of pro-survival pathways. Further, substantial overlap (>80%) between genes upregulated in ZFTA-RELAfus tumors and those downregulated following Mertk inhibition treatment suggest a dependency on Mertkmediated signaling for tumor growth. These findings highlight Mertk as a promising therapeutic target and support the clinical development of Mertk inhibitors for treating human E1 subtype and ZFTA-RELAfus -driven ependymomas.

overall_design: Mice with confirmed tumors by MRI were randomly assigned to receive either a vehicle or 50 mg/kg of MRX-2843. Treatment was administered once daily via oral gavage for 5 consecutive days. Mice were euthanized one hour after the final treatment, and the whole brains were harvested. Total RNA was extracted from naïve brain tissue and tumors.


title: Transcriptomic Profiling of Kinase Inhibitor Treated Cancer Cell Lines Reveals Insights into Drug Response Mechanisms

summary: Protein kinases regulate essential cellular processes, including growth, differentiation, and apoptosis, and their dysregulation is implicated in cancer progression. Kinase inhibitors have emerged as critical therapeutic agents; however, challenges such as drug resistance and selectivity gaps necessitate further investigation. To address these challenges, we performed RNA sequencing-based transcriptomic profiling to assess the impact of targeted kinase inhibitors on cancer cells. Specifically, we analyzed the gene expression changes induced by Tepotinib (1 μM) in GSC923 glioblastoma cells, Gilteritinib (1 μM) in MDA-MB-231 triple-negative breast cancer cells, and Brigatinib (1 μM) in PANC-1 pancreatic cancer cells. Wild-type (WT) untreated controls were included for comparative analysis. RNA sequencing was conducted using a paired-end strategy, and differential gene expression analysis was performed to uncover treatment-induced transcriptional alterations. This dataset provides insights into the molecular mechanisms of kinase inhibitor response, highlighting potential repurposing opportunities and informing future therapeutic strategies in glioblastoma, breast cancer, and pancreatic cancer.

overall_design: 1. GSC923 Cells - Tepotinib Treatment: RNA-seq profiling of human glioblastoma GSC923 cells cultured in Neurobasal-A medium supplemented with N2 and B27 supplements, recombinant human basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF), L-glutamine, penicillin, and streptomycin. Cells were treated with 1 μM Tepotinib for 1 day, and total RNA was extracted for sequencing. DMSO controls were included for comparison.  2. MDA-MB-231 Cells - Gilteritinib Treatment: RNA-seq profiling of human triple-negative breast cancer MDA-MB-231 cells (ATCC) cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS), penicillin, and streptomycin. Cells were treated with 1 μM Gilteritinib for 3 days, and total RNA was extracted for sequencing. DMSO controls were included for comparison.  3. PANC-1 Cells - Brigatinib Treatment: RNA-seq profiling of human pancreatic cancer PANC-1 cells (ATCC) cultured in DMEM medium supplemented with 10% FBS, penicillin, and streptomycin. Cells were treated with 1 μM Brigatinib for 1 day, and total RNA was extracted for sequencing.DMSO control controls were included for comparison.

first: [contributor]  Gujral Lab


title: Rbfox2-dependent alternative splicing of Numb regulates Notch signaling during muscle stem cell activation II

city: Hong Kong

first: Tom

last: Cheung

state: Please Select...

address: Clear Water Bay

country: Hong Kong

institute: HKUST

summary: Satellite cells (SCs), or muscle stem cells, are the resident somatic stem cells responsible for skeletal muscle regeneration. Most SCs remain quiescent in resting adult muscles but can activate rapidly upon receiving a stimulus. While alternative splicing has been reported to play important role in stem cells , its role in the activation process of SCs remains elusive. We identified Numb as one of the genes that display rapid splicing change during SC activation. To investigate the role of Numb splicing during satellite cell activation, we use morpholino to inhibit the inculstion of Numb exon 6 on early activated SCs and performed RNA-seq to profile the transcriptome changes upon Numb splicing change.

overall_design: To investigate the role of Numb splicing during SC activation, we design a vivo morpholino, which enable morpholino to enter the cell without transfection and inhibit the inclusion of Numb exon 6 . We treated the minced muscle with vivo morpholino during the first digestion. Satellite cells were then isoalted to extract the RNA and perform RNA-seq. Analysis is performed to identify differentially expressed genes.

first: Kangning

last: Lin

first: Jing

last: Liu

first: Tsz Ching

last: Chan


title: Neonatal bone marrow interstitial fluid supports expansion and osteogenic ability of human bone marrow mesenchymal stromal cells

city: Houston

first: Junfeng

last: Zhang

state: TX

address: 2130 W. Holcombe Blvd

department: Department of Cancer Biology

institute: The University of Texas MD Anderson Cancer Center

summary: The bone marrow microenvironment is critical for the maintenance and functionality of stem/progenitor cells, which is essential for bone development and regeneration. However, the composition and potential use of bone marrow interstitial fluid have not been extensively explored. In this study, we report a role of neonatal bovine bone marrow interstitial fluid (NBIF) in enhancing bone regeneration capacity of human bone marrow mesenchymal stem cells (hBMSCs). Unlike adult bovine bone marrow interstitial fluid (ABIF), NBIF-fed hBMSCs exhibit enhanced self-renewal and osteogenic potential and bone marrow homing ability with transcriptome changes as against hBMSCs cultured in standard fetal bovine serum (FBS) supplemented medium. Mass spectrometry analysis reveals that multiple secreted factors associated with tissue repair and bone development are enriched in NBIF compared to FBS and ABIF. The combined use of NBIF-enriched Nerve Growth Factor (NGF), Lactoferrin (LTF) and High Mobility Group Protein B1 (HMGB1) with Insulin-Like Growth Factor 1(IGF1) for culturing hBMSCs in the presence of FBS can enhance osteogenic potential and bone marrow homing ability, mimicking NBIF’s effects. These findings highlight the role of interstitial fluid in the bone marrow microenvironment and its potential to optimize stem cell based therapies.

overall_design: To understand molecular changes after culture in hBMSCs, we performed transcriptome analysis of hBMSCs after 7-day culture in NBIF or FBS in three replicates.

first: Zhang

last: Junfeng


title: Alpha tocopherol ameliorates allergic airway inflammation by regulating ilc2 ferroptosis in an lkb1-dependent manner_Aa-cko VS Aa-flox


title: Transcriptional profiling of bulk liver tissue from male and female PPARa knockout mice and mice expressing a human PPARa transgene following treatment with PFOA or vehicle drinking water in conjunction with an American diet

city: Boston

first: Jennifer

last: Schlezinger

state: MA

address: 715 Albany St

department: Environmental Health

institute: Boston University

summary: Per- and polyfluoroalkyl substances (PFAS) are a family of persistent chemicals that have been released pervasively in the environment leading to widespread human exposure. Emerging epidemiological evidence shows adverse effects on liver lipids, however the extent of this impact and the mechanisms through which PFAS disrupt hepatic lipid homeostasis in humans are not well understood. Here, we examine the effects of perfluorooctanoic acid (PFOA) on liver lipid profiles and probe transcriptional mechanisms contributing to liver lipid dysregulation in mice expressing human peroxisome proliferator activated receptor a (PPARa) in comparison to PPARa null mice. Male and female mice were fed a What We Eat In America diet and exposed to PFOA via drinking water for 6 weeks. Serum PFOA concentrations averaged 48 ± 9 μg/mL. Across male and female hPPARa mice, PFOA increased liver total lipids and total triacylglycerides, which was stronger in males than females and largely dependent on hPPARa. Additional lipid class strongly altered by PFOA exposure predominantly belong to phosphatidylcholine and sphingolipid classes. PFOA significantly decreased sphingomyelin abundance and increased ceramide abundance regardless of genotype, which coincided with an increase in expression of SMase, the enzyme that converts sphingomyelin to ceramide. PFOA changed the expression of ~2,000 hepatic genes with a larger impact in hPPARa versus PPARa null mice. In this human-relevant PFOA exposure scenario, less than 60% of transcriptional changes induced by PFOA depended on PPARa expression. CAR appears to be another major molecular initiating event, with other transcription factors pathways more likely to be modulated downstream, including PPARg, pregnane X receptor, estrogen receptor a, farnesoid X receptor, and pregnane X receptor. These results highlight the ability of PFOA to modulate liver lipids beyond triacylglycerides and the need to further refine our understanding of the molecular initiating and downstream transcriptional regulators in PFAS-induced mechanisms of action.

overall_design: Male and female PPARa knockout mice and male and female mice expressing human PPARa were used in this study. Beginning at weaning, mice in each sex and genotype were provided ad libitum access to vehicle drinking water (NERL water containing 0.5% sucrose) or PFOA water (8 µm PFOA in NERL water containing 0.5% sucrose) for 6-7 weeks. All mice in both vehicle and PFOA drinking water exposure groups consumed a custom diet containing 51.8% carbohydrate, 33.5% fat, and 14.7% protein, as a % energy intake based on "What we eat in America." Total RNA was extracted from bulk liver tissue samples. Comparative expression analyses were performed between sex, genotype, and exposure groups.

first: Greylin

last: Nielsen

first: Eric

last: Reed

first: T

last: Webster

first: W

last: Heiger-Bernays

first: B

last: Lara

first: D

last: Sherr

last: Hyötyläinen

first: J


title: Transcriptional regulation of temporal dynamics in human neurogenesis and neuronal maturation [scRNA-seq]

city: Hefei

first: lingling

last: zhu

address: JinZhai Road

institute: University of Science and Technology of China

summary: Human pluripotent stem cells (hPSCs) provide a valuable platform for studies of human neuronal differentiation, but the mechanisms regulating the timing of this process remain poorly understood. This study compares two differentiation systems with distinct timing of differentiation, transcription factor (TF)-induced forward programming and stepwise cellular differentiation. Our analyses reveal that divergent cellular trajectories drive distinct neurogenesis timing. Multi-omic analysis identifies crucial gene regulatory networks (GRNs) that govern cell fate determination and timing control. Modulation of these GRNs modulates neurogenesis and timing of neuronal maturation. Specifically, OLIG family TFs, enriched in the TF-induced system, promoted cell cycle exit through NOTCH signaling regulation; conversely, ablation of these TFs delayed neurogenesis. In contrast, NEUROD2 overexpression accelerated neuronal maturation through precocious activation of maturation gene modules. Collectively, these findings illuminate characteristics of the cell-intrinsic mechanisms that govern timing of differentiation; the studies also offer a framework for investigation into, and the rational design of, timing-controlled in vitro differentiation strategies.

overall_design: We performed scRNA-seq on cells over the time course of TF-induced forward programming (hPSCs female and male cell lines, with mRNA or dox inducbile NEUROG1, NEUROG2, NEUROD1 overexpression induced neurogenesis) and stepwise cellular differentiation (dual-SMAD inhibition).Taken together, these data indicate that TF-induced forward programming represents a distinct differentiation shortcut from hPSCs to neuronal fate. In order to further decipher the regulatory landscape underlying the drastic cell fate changes, several experiments were performed including high-resolution time-course RNA expression profiling, chromatin accessibility analysis, and TF binding profiling by CUT-TAG (NEUROG1, NEUROG2, and NEUROD1). We next aimed to infer GRNs that may play a crucial role in facilitating rapid neurogenesis (OLIG1, OLIG2, OLIG3) and subsequent neuronal maturation (NEUROD2, MSC). To gain mechanistic insights, scRNA seq of cells induced from OLIG KO cell line, TF binding profiling by ChIP (OLIG2) and CUT-TAG (NEUROD2, MSC) were performed.


title: Small intestinal crypt cell subsets and gene expression in sleep-deprived mice

city: Beijing

first: Mingxin

address: 2 West Yuanmingyuan Road

institute: China Agricuture University

summary: The level of 5-HT in the intestine of sleep-deprived mice is increased, which induces oxidative stress of intestinal stem cells by acting on HTR4 receptor. Single-cell RNA sequencing was used to analyze the changes in intestinal cell subsets and HTR4 expression after sleep deprivation

overall_design: Intestinal epithelial cells of mice before and after sleep deprivation were isolated  and analyzed using scRNA-seq

first: Xi

last: Wu

first: Di

first: Wuqi

last: Yang


title: Transcriptional regulation of temporal dynamics in human neurogenesis and neuronal maturation [RNA-seq]


title: Transcriptional regulation of temporal dynamics in human neurogenesis and neuronal maturation [ATAC-seq]