title: LOESS-Corrected UMI Counts Enable Absolute RNA Quantification in Single-Cell Transcriptomics

city: Dalian

first: Rulin

last: Hua

state: Liaoning

address: 9 Western Section, Lvshun South Street, Lvshunkou District

institute: Dalian Medical University

summary: The parathyroid gland is one of the endocrine glands in the body and plays a key role in regulating calcium and phosphate homeostasis through the production and release of parathyroid hormone (PTH). Despite its physiological importance, research on the parathyroid gland remains limited due to its small size and concealed anatomical location. Previous studies have suggested that the parathyroid gland consists of principal cells, acidophilic cells, and other cell types. While recent studies have applied single-cell sequencing to investigate the rat parathyroid gland, a comprehensive analysis of cell subpopulations, gene expression differences, and rare cell types is still needed. Therefore, this study aims to further utilize single-cell sequencing technology to analyze the transcriptional profiles of different cell types in the normal rat parathyroid gland, refine the characterization of cellular diversity, and provide additional insights into the molecular landscape of the rat parathyroid gland.

overall_design: Parathyroid glands of twelve-week-old male wild-type Sprague-Dawley rats were promptly excised and preserved in ice-cold tissue preservation solution (Miltenyi Biotec, USA) for immediate transport and processing.

first: Xiaoyan

last: Liu

first: Feng

last: Zheng


title: PCV2 Infection Represses the  Differentiation of Light Zone Germinal Center B Cells by Inhibiting Their  Interaction with Helper Cells

status: Public on Jun 20 2025

city: xianyang

first: Tengfei

last: Shi

address: No.22 Xinong Road. Yangling

country: China

institute: Northwest A&F University

type: Expression profiling by high throughput sequencing

summary: Ten 4-week-old BALB/c mice were randomly divided into two groups, with five mice in each group. PCV2 infected mice were constructed by intraperitoneal injection of PCV2, while the control group was injected with an equal volume of PBS in the same manner. On the 28th day after infection, one PCV2 infected mouse and one control mouse were taken, and their spleens were removed for scRNA-seq.

overall_design: Ten 4-week-old BALB/c mice were randomly divided into two groups. The mice in the PCV2 group were injected intraperitoneally with 500 mL of 105 TCID50 PCV2 suspension for the construction PCV2 infected mouse model, while the mice in the control group were injected with 500 mL of phosphate buffer saline in the same manner. On the 7th, 14th, and 21st day after infection, tail vein blood samples were collected from mice, serum was isolated for the detection of PCV2 load. On the 28th day after infection, mice were euthanized, and their blood, hearts, livers, spleens, lungs, and kidneys were harvested for virus load detection and histological observation, among which one spleen was randomly selected in the control group and one spleen in the PCV2 group for scRNA-seq.

first: Qian

last: Du

first: Yang

last: Wang

first: Dewen

last: Tong

first: Yong

last: Huang


title: Histone deacetylase 5 in prelimbic prefrontal cortex limits context-associated cocaine-seeking behavior

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

country: USA

institute: Medical University of South Carolina

summary:
Background
Repeated cocaine use produces neuroadaptations that support drug craving and relapse in substance use disorders (SUDs). Powerful associations formed with drug-use environments can promote a return to active drug use in SUD patients, but the molecular mechanisms that control the formation of these prepotent drug-context associations remain unclear.
Methods
In the rat intravenous cocaine self-administration (SA) model, we examined the role and regulation of histone deacetylase 5 (HDAC5) in the prelimbic (PrL) and infralimbic (IL) cortices in context-associated drug seeking. To this end, we employed viral molecular tools, chemogenetics, RNA-sequencing, electrophysiology, and immunohistochemistry.
Results
In the PrL, reduction of endogenous HDAC5 enhanced context-associated, but not cue- or drug prime-reinstated cocaine seeking; whereas, overexpression of HDAC5 in PrL, but not IL, reduced context-associated cocaine seeking, but it had no effects on sucrose seeking. In contrast, PrL HDAC5 overexpression following acquisition of cocaine SA had no effects on future cocaine seeking. We found that HDAC5 and cocaine SA altered the expression of hundreds of PrL genes, including many synapse-associated genes. HDAC5 significantly increased inhibitory synaptic transmission onto PrL deep-layer pyramidal neurons, and it reduced the induction of FOS-positive neurons in the cocaine SA environment.
Conclusions
Our findings reveal an essential and selective role for PrL HDAC5 to limit associations formed in cocaine, but not sucrose, SA environments, and that it alters the PrL excitatory/inhibitory balance, possibly through epigenetic regulation of synaptic genes. These results further position HDAC5 as a key factor regulating reward-circuit neuroadaptations that underlie common relapse triggers in SUD.

overall_design: We investigated the role of HDAC5 in the Prelimbic Cortex, a subdivsion of the medial Prefrontal Cortex that is involved in prolonged drug seeking behaviors. We tested the role of the epigenetic enzyme HDAC5 in a variety of relapse tests following cocaine i.v. self-administration. We also examined changes in gene expression following re-exposure to the the self-administration context (in drug experienced and drug naive rats), and the changes in electrophysiological properties of PrL neurons as a result of HDAC5 expression.

first: Sarah

last: Barry

first: Christopher

last: Cowan


title: Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer (ATAC-Seq)

status: Public on Jun 26 2025

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Prostate cancer (PCa) is driven by oncogenic transcription factor enhanceosomes comprising chromatin and epigenetic regulators. The lysine acetyltransferases p300 and CBP are key cofactors that activate enhancers through histone acetylation. Here, we identify p300/CBP-mediated multisite acetylation of the histone H2B N-terminus (H2BNTac) as a defining feature of oncogenic enhanceosomes in androgen receptor (AR)-positive prostate cancerPCa. p300/CBP are essential for AR and ERG transcriptional activity, and their dual degradation eliminates H2BNTac and H3K27ac marks at hyperactive enhancers, leading to stronger suppression of oncogenic transcription more effectively than targeting either paralog or bromodomains alone. Cytotoxicity profiling across >900 cell lines revealed that tumors with high H2BNTac, including AR-positive prostate cancerPCa, are selectively dependent on p300/CBP. In preclinical models, systemic p300/CBP degradation inhibited tumor growth, synergized with AR antagonists, and showed no evident toxicity. These findings position H2BNTac as an  key epigenetic marker of enhancer addiction and establish support dual p300/CBP degradation as a promising therapeutic strategypy for enhancer-driven cancers.

overall_design: Distinct prostate cancer cells were treated in vitro with the 100nM p300/CBP degrader CBPD-409 (abbreviated as CBPD), 1uM p300/CBP inhibitor,  CCS1477 (abbreviated as CCS), 1uM  p300/CBP inhibitor,  GNE-049 (abbreviated as GNE) or 1uM SAMARCA2/4 degrader AU15330 (abbreviated as AU) for indicated durations, and processed for multi-omic characterization.

first: Jie

last: Luo

first: Eleanor

last: Young

first: Abhijit

last: Parolia

middle: M


title: Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users

status: Public on Jun 19 2025

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

summary: The injectable contraceptive, depot medroxyprogesterone acetate (DMPA), is associated with compromised cervical mucosal barriers. High-resolution spatial transcriptomics is applied here to reveal the spatial localization of these altered molecular markers. Ectocervical tissue samples from Kenyan sex workers using DMPA, or non-hormonal contraceptives, underwent spatial transcriptomics and gene set enrichment analyses. Integrated systemic estradiol levels and bulk tissue gene expression data from a larger cohort enhanced the study’s scope. Unsupervised clustering unveiled four epithelial and seven submucosal layers, showcasing spatially restricted and diverse functional epithelial responses, and a less structured submucosal spatial ordering. DMPA associated with mucosal-wide immunoglobulin gene upregulation, verified by CD20+ B-cell immunostaining, and upregulated immune markers adjacent to the basal membrane. Downregulated genes represented spatially restricted disrupted epithelial barrier integrity and submucosal extracellular matrix dysfunction. The transcriptional profile was associated with markers of estrogen regulation. Collectively, our findings reveal estrogen-modulated distinct ectocervical transcriptional profiles associated with DMPA usage. While upregulation of immunoglobulin genes occurs throughout the mucosa, activation of innate immune responses and dysregulation of barrier integrity markers are spatially restricted. These results extend previous analyses using bulk transcriptomics and provide insights into the molecular landscape influenced by DMPA, shedding light on contraceptive effects and health implications.

overall_design:
In this study we compared gene expression between samples from women who had been using DMPA for more than 6 months (DMPA group; n=4), and non-hormonal contraceptives who were in the follicular menstrual stage (control group; n=4). Ectocervical tissue were obtained as part of our broader longitudinal investigation within the Sex Worker Outreach Program in Pumwani, Nairobi, Kenya

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


title: Epigenetic coordination of transcriptional and translational programs in hypoxia. [RNA-Seq, 2]

status: Public on Jun 17 2025

city: Solna

first: Kathleen

middle: Diane

last: Watt

address: Tomtebodevägen 23

department: Oncology-Pathology

summary: Stress adaptation entails perturbations in transcriptional and post-transcriptional mechanisms of regulation of gene expression, but how these programs are coordinated remains largely unknown. To address this, we systematically interrogated the effects of hypoxia on transcriptomes, epigenomes and translatomes of T47D breast cancer cells and H9 human embryonic stem cells. This revealed that hypoxia-induced alterations in H3K4me3 exert unexpectedly minimal effects on transcript abundances. Instead, they were associated with pervasive changes in the transcription start site (TSS) selection, subsequent 5’UTR remodeling, and reshaping of translational landscapes. Importantly, this epigenetically-driven reprograming of translation is distinct from HIF1-dependent transcriptional mechanisms or integrated stress response- or mTOR-guided translational reprogramming. Indeed, comparable effects on TSS selection and 5'UTR remodeling were observed when H3K4me3 was pharmacologically stimulated in the absence of induction of HIF, ISR or modulation of mTOR signaling. These results demonstrate a previously unappreciated physiologically relevant mechanism of translational regulation driven by epigenetic reprograming of the 5’UTRome which is orchestrated with other hypoxia-triggered adaptive mechanisms.

overall_design: Four replicates of RNA-seq in compound 48 (C48) and DMSO-treated T47D breast cancer cells.

first: Bianca

last: Dauber

first: Krzysztof

middle: J

last: Szkop

first: Laura

last: Lee

first: Predrag

last: Jovanovic

first: Shan

last: Chen

first: Ranveer

last: Palia

first: Julia

middle: A

last: Vassalakis

first: Tyler

middle: T

last: Cooper

first: David

last: Papadopoli

first: Laia

last: Masvidal

first: Michael

last: Jewer

first: Kristofersson

last: Tandoc

first: Hannah

last: Plummer Doherty

first: Gilles

last: Lajoie

first: Ivan

last: Topisirovic

first: Ola

last: Larsson

first: Lynne-Marie

last: Postovit


title: Epigenetic coordination of transcriptional and translational programs in hypoxia. [ChIP-Seq, 2]

first: Kathleen

last: Watt

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K4me3 compound 48 (C48) and DMSO-treated T47D breast cancer cells.

first: Bianca

last: Dauber


title: Epigenetic coordination of transcriptional and translational programs in hypoxia. [RNA-Seq]

overall_design: Three or four replicates of polysome profiling were performed on hypoxia and normoxia-treated H9 and T47D cells, respectively. Hypoxia treatments were 0.5% oxygen for 24 (H9 cells) or 48 hours (T47D cells). Total cytosolic RNA, and polysome-associated mRNA (mRNA associated with > 3 ribosomes) were isolated and quantified using RNA sequencing.

first: Krzysztof

last: Szkop

first: Laura

last: Lee

last: Masvidal Sanz


title: Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer

first: Arul

last: Chinnaiyan

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

overall_design: Refer to individual Series


title: Epigenetic coordination of transcriptional and translational programs in hypoxia. [nanocage]

overall_design: Nano-cap analysis of gene expression (nanoCAGE) sequencing for profiling transcription start sites and 5'UTRs in hypoxia and normoxia-treated T47D breast cancer and H9 human embryonic stem cells. Three biological replicates were performed for T47D cells, however one normoxia sample failed and was discarded. Four biological replicates were performed for H9 cells. In addition, 4 biological replicates were also performed for T47D cells treated with compound 48 (C48, 10 uM, 24 hrs), and or DMSO.

first: Predrag

last: Jovanovic

first: Shan

last: Chen

first: Ranveer

last: Palia


title: Epigenetic coordination of transcriptional and translational programs in hypoxia.


title: Epigenetic coordination of transcriptional and translational programs in hypoxia. [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K4me3 in hypoxia and normoxia-treated T47D breast cancer and H9 human embryonic stem cells.


title: scRNA-seq reveals persistent aberrant differentiation of nasal epithelium driven by TNFα and TGFβ in post-COVID syndrome

status: Public on Jun 16 2025

city: Lübeck

first: Yamil

middle: Abdala

last: Maluje

state: Schleswig- Holstein

address: Ratzeburger Allee 160

department: Institute of Experimental Dermatology

country: Germany

institute: University of Luebeck

summary: Background: Post-COVID syndrome (PCS) currently affects approximately 3-17% of people following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and has the potential to become a significant global health burden. While PCS exhibits diverse symptoms, improved assessment methods are being developed to guide therapy. Despite this, there is a lack of mechanistic insights and treatment options. Objective: To elucidate molecular mechanisms underlying PCS by employing single-cell RNA transcriptomics on patients’ nasal tissue and in vitro validation. Methods: Single-cell RNA transcriptomic analysis was conducted on nasal biopsies from 25 PCS patients with moderate or severe PCS  symptoms. Identification of cell types, signaling, and cell-cell communication was performed. In vitro, air-liquid interface cultures were employed to validate findings, with a particular focus on the TNFα-TGFβ axis. Results: Severe PCS was associated with reduced numbers of ciliated cells, increased immune cell presence, and inflammatory signaling leading to TGFβ and TNFα upregulation, all without any viral load. This induced an epithelial-mesenchymal transition, increasing basal cell abundance and a mis-stratified nasal epithelium. In vitro experiments validated TGFβ and TNFα as causal cytokines promoting the reduced abundance of ciliated epithelium and expansion of basal epithelial cells. As such, we posit that a sustained severe PCS phenotype was not linked to continued viral load but instead to immune cell presence and persistent cytokine production. Conclusions: Our study reveals a pathway for persistent severe PCS involving immune-mediated nasal tissue damage, suggesting therapeutic potential by targeting the TNFα-TGFβ axis. The restoration of the nasal epithelium may prove to be a possible treatment strategy for PCS, akin to interventions in other chronic inflammatory conditions.

overall_design: Healthy donor nasal epithelial cells (NECs) were subcultured and plated onto collagen IV-coated transwell supports. Cells were differentiated at air-liquid interface for 28 days. Experimental conditions included treatment with TGFβ (1 ng/ml), TNFα (10 ng/ml), or both, added to the basal chamber. PBS was used as control. Media were changed three times weekly, and cells were washed with hanks balanced salt solution (HBSS). Cells across all stimulation conditions were harvested at 28 days post-airlift for single-cell RNA-seq (Singleron).

first: K

middle: D

last: Reddy

first: Y

first: F

last: Ott

first: R

last: Saurabh

first: A

last: Schaaf

last: Bohnhorst

first: S

middle: B

last: Biedermann

first: J

last: Pierstorf

last: Winkelmann

first: B

last: Voß

first: M

last: Laudien

first: T

last: Bahmer

last: Heyckendorf

last: Brinkmann

last: Schreiber

first: W

last: Lieb

first: C

last: Jakwerth

last: Schmidt-Weber

first: G

last: Hansen

first: E

last: von Mutius

middle: F

last: Rabe

last: Dittrich

first: N

last: Maison

last: Schaub

middle: V

last: Kopp

first: H

last: Busch

last: Weckmann

last: Fähnrich


title: Dataset of transcriptional signature of the MAPK ERK5 in leiomyosarcoma

city: Albacete

first: Francisco

middle: J.

last: Cimas

state: Albacete

address: Almansa 14

country: Spain

institute: UCLM

summary: Sarcoma, and more specifically leiomyosarcoma, are pathologies with poor prognosis due to the lack of molecular targets and personalised therapeutic approaches. In this context, understanding the molecular bases of these tumors may enable new therapies. Our study investigates the ERK5 kinase activity mediated signaling by comparing RNASeq analysis for genetic inhibition. To do so, a couple of leiomyosarcoma cells lines were abrogated using specific shRNA for ERK5. Total RNA was extracted and sequenced in the DNBSEQ platform and analysed for differentially expressed genes between the conditions.

overall_design: RNA-seq profiling of leiomyosarcoma SK-UT-1 and AA cell lines abrogated genetically by shRNA

first: Jaime

last: Jiménez-Suarez

first: María José

last: Ruiz-Hidalgo

first: Borja

last: Belandia

first: Cristina

last: Garnés-García

first: Pablo

last: Fernández-Aroca

first: Ricardo

last: Sánchez-Prieto


title: Epigenetic coordination of transcriptional and translational programs in hypoxia. [ATAC-Seq]

first: Kathleen

last: Watt

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATACseq) in hypoxia and normoxia-treated, and compound 48 (C48) and DMSO-treated T47D breast cancer cells.

first: Bianca

last: Dauber

first: Krzysztof

last: Szkop

first: Laura

last: Lee

first: Predrag

last: Jovanovic

first: Shan

last: Chen

first: Ranveer

last: Palia

first: Julia

last: Vassalakis

first: Tyler

last: Cooper

first: David

last: Papadopoli

first: Laia

last: Masvidal

first: Michael

last: Jewer

first: Kristofersson

last: Tandoc

first: Hannah

last: Plummer Doherty

first: Gilles

last: Lajoie

first: Ivan

last: Topisirovic

first: Ola

last: Larsson

first: Lynne-Marie

last: Postovit


title: Age-dependent accumulation of mitochondrial tRNA mutations in mouse kidneys linked to mitochondrial kidney diseases [RNA-Seq]

city: Hangzhou

first: Guo-shi

last: Chai

state: --- Select One ---

address: No. 600 Dunyu Road, Sandun Town, Xihu District, Hangzhou, Zhejiang PR China

institute: Westlake University

summary: Heteroplasmic pathogenic mitochondrial DNA (mtDNA) mutations are known to cause mitochondrial diseases with varied clinical symptoms. The tissue-specific selection of heteroplasmic pathogenic mtDNA mutations and its correlation with clinical and pathological outcomes remains to be elucidated. To date, negative selection of pathogenic mutations has been observed in a limited range of cell types, including female germ cells, blood cells, particularly T cells, and intestinal epithelial cells. However, evidence of positive selection in any tissue or cell type has not been reported. In this study, we utilized the DddA-derived cytosine base editor (DdCBE) technique to generate a heteroplasmic pathogenic mutant mouse model harboring a mutation in the mito-tRNA Glu anticodon arm site. Over a two-year longitudinal investigation, we assessed the mutational selection dynamics in eight solid organs and blood from this model. Our findings reveal a significant positive selection for pathogenic mtDNA in the kidney and liver. Notably, the kidney exhibited mitochondrial kidney disease during aging, reflecting the clinical kidney defects observed in patients with mito-tRNA mutations. Intriguingly, disparate selection patterns emerged within multiple cell types of kidneys, with tubular epithelial cells and podocytes presenting positive selection, whereas immune cells exhibited purifying selection. Leveraging Sc-RNA seq and Stereo-seq, we identified Clu and Spp1 as molecular markers of the high mutant kidney tubular epithelial cells and suggest that up-regulation of these markers may activate the p-AKT pathway, thereby increasing the proliferation of high mutant tubular epithelial cells, hence leads to the positive selection on this site in mutant kidneys during aging. Our comprehensive analysis provides compelling evidence for the significance of tissue-specific selection of pathogenic mtDNA mutations. This study enhances our understanding of the mechanistic links between tissue-specific selection and mitochondrial disease pathogenesis, paving the way for the development of targeted therapeutic strategies in the future.

overall_design: Kidneys from 100-week-old female mice, including both the TrnE high mutation groups and the control groups, were freshly collected and analyzed using RNA-seq.

first: Min

last: Jiang

first: Leping

last: Zhang

first: Guoshi


title: A Stat1 gain-of-function mutant disrupts normal Stat4 innate lymphocyte programs during viral infection [RNA-seq]

status: Public on Jun 13 2025

city: Bethesda

first: Kan

state: MD

address: 9000 Rockville Pike

institute: NIAMS/NIH

summary: Interferonopathies drive autoimmunity but can also impair host responses to pathogens including viral infection. To better understand viral susceptibility of patients with STAT1 gain-of-function (GOF) mutations, we generated conditional-knockin mouse models to elucidate disease mechanisms and relevance of different immune subsets. Virally infected Stat1-GOF mice exhibited impaired early IFN-γ production from innate lymphocytes, and lethality due to excess prolonged multi-cytokine production. The presence of the Stat1-GOF allele resulted in premature usage of interferon-stimulated gene factor 3 (ISGF3) over the normal Stat4/AP-1 dependent transcriptomic program in activated innate lymphocytes. Administration of anti-IFN-γantibodies in wild-type (WT) mice after infection phenocopied Stat1-GOF mice presenting exaggerated inflammation despite viral control. Conversely, early administration of exogenous IFN-γ to infected Stat1-GOF mice prevented lethality and exaggerated cytokine response.Although Stat1-GOF mutations facilitate IFN-γ-mediated autoimmunity, early IFN-γ response to viral infection via a normal Stat4 program was impaired, leading to overcompensated inflammatory responses in Stat1-GOF mice.

overall_design: To investigate how a Stat1 gain-of-function variant alters gene expression in NK cells, splenic NK cells from WT and STAT1-T385M/+ mice were FACS sorted and RNA-seq was performed after in vitro stimulation with or without IFN-a.

first: Rachael

middle: L

last: Philips

first: John

last: O'Shea


title: Age-dependent accumulation of mitochondrial tRNA mutations in mouse kidneys linked to mitochondrial kidney diseases [scRNA-Seq]

overall_design: Kidneys were harvested from mitochondrial TrnE point mutation and WT C57BL/6J mice and analyzed using scRNA-seq


title: Age-dependent accumulation of mitochondrial tRNA mutations in mouse kidneys linked to mitochondrial kidney diseases [mtscATAC-Seq]

overall_design: Kidneys were harvested from 3-week-old and 75-week-old mitochondrial TrnE point mutation mice and analyzed using mtscATAC-seq


title: A Stat1 gain-of-function mutant disrupts normal Stat4 innate lymphocyte programs during viral infection [CUT&Tag]

overall_design: Cut&Tag for Stat4 and Stat1 in WT and Stat1-T385M NK cells after IFNa+IL-18 stimulation.


title: Age-dependent accumulation of mitochondrial tRNA mutations in mouse kidneys linked to mitochondrial kidney diseases


title: Lithium Deficiency and the Onset of Alzheimer’s Disease [3xTG_LiO]

status: Public on Jun 12 2025

city: Boston

first: Jae Joon

last: Choi

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: The earliest molecular changes in Alzheimer’s disease (AD) are poorly understood.  Here we show that endogenous lithium (Li) is dynamically regulated in the brain and contributes to cognitive preservation during aging.  We demonstrate that cortical uptake of Li is the most significantly impaired of all metals analyzed in mild cognitive impairment (MCI) and AD, and that Li bioavailability is further reduced by amyloid sequestration.  Li deficiency was recapitulated by feeding AD model and wild-type mice a lithium-deficient diet.  Reducing endogenous cortical Li by ~50% markedly elevated Aβ deposition and phospho-tau accumulation, and led to proinflammatory microglial activation, synapse loss, and accelerated cognitive decline. These effects were mediated, at least in part, through activation of the kinase GSK3β in neurons, microglia, and oligodendrocytes.  Single nucleus RNA-seq showed that Li deficiency gives rise to significant transcriptome changes in all major brain cell types that overlap with transcriptome changes in AD. Replacement therapy with lithium orotate (LiO), a Li salt with reduced amyloid sequestration, prevents pathological changes and memory loss in AD mouse models and aging wild-type mice at a physiological concentration. Thus, Li deficiency may be among the earliest molecular events that link amyloid deposition to protean multisystem effects on the brain. Li replacement with amyloid-evading salts is a potentially novel therapeutic approach to AD and brain aging.

overall_design: To investigate the transcriptomic changes caused by lithium orotate treatment, hippocampus are isolated from 12-month-old 3xTg mice that were treated with 4.3 µM Li orotate (n=9 females) or vehicle (water; n=9 females) from 6 to 12 months. Comparitive gene expression profiling analysis was performed between control and LiO treatment.

first: Zhen Kai

last: Ngian

first: Jaejoon

first: Liviu

last: Aron

first: Bruce

last: Yankner


title: High-density cultures (3D-cultures) associated therapy resistance in AML THP-1 cells

status: Public on Jun 09 2025

city: Puschino

first: Kirill

middle: S

last: Krasnov

state: Moscow region

address: institutskay 3

country: Russia

institute: ITEB RAS

summary: Acute myeloid leukemia (AML) is an aggressive hematologic malignancy characterized by the rapid proliferation of immature myeloid cells in the bone marrow, leading to impaired hematopoiesis and life-threatening complications. Despite advances in chemotherapy, targeted therapy, and stem cell transplantation, treatment resistance remains a major clinical challenge, contributing to high relapse rates and poor survival outcomes. Understanding the mechanisms of resistance — including genetic mutations, epigenetic alterations, and microenvironmental interactions — is crucial for developing more effective therapies. Investigating how AML cells develop treatment resistance, particularly under pro-inflammatory conditions, may reveal novel therapeutic targets and improve patient prognosis. Our study focuses on resistance mechanisms in AML cells under density-induced sterile pro-inflammatory conditions (modelled via high-density culture, HDC). This approach aims to identify key molecular pathways associated with therapy resistance in AML.

overall_design: Comparison of RNA-seq profiles between: (1) AML THP-1 cells under high-density culture (HDC; reversible therapy resistance via sterile pro-inflammatory signaling), (2) AML THP-1 cells under low-density culture (LDC; non-inflammatory condition), and (3) mutant macrophage-like AML THP-1 (THP-1ad) cells derived from HDC (exhibiting fully resistant, differentiated phenotype)

first: Fadeev

last: Roman

first: Kobyakova

middle: I

last: Margarita

first: Lomovskaya

last: Yana

first: Krasnov

last: Kirill

first: Meshcheriakova

last: Elena


title: A Stat1 gain-of-function mutant disrupts normal Stat4 innate lymphocyte programs during viral infection [scMulti-omics-seq]

overall_design:
Multiome-seq: WT and Stat1-T385M/+ mice were infected with MCMV. 1.5 days post infection, immune cells from the liver were FACS sorted (Live, Ter119-, CD45+, Ly6G-) and single nuclei were isolated. Joint snRNA- and scATAC libraries were prepared using the 10x Genomics platform.
CITE-seq: The following mice were infected with MCMV (WT, Stat1-T385M/+, WT given anti-IFN-g antibodies, and Stat1-T385M/+ given rec-IFN-g). Four days post infection, immune cells from the liver were FACS sorted (Live, CD45+, Ter119-) and stained with CITE-seq antibodies (ADTs and HTOs). CITE-seq libraries were prepared using the 10x Genomics platform.


title: RNA-seq Analysis Reveals the Anti-inflammatory Role of hnRNPF in Diabetic kidney disease

status: Public on Jun 07 2025

city: Wu Han

first: LAN

last: WANG

state: Hubei

address: 湖北省武汉市武昌区湖北中医药大学昙华林校区昙华林188号

institute: Hubei University of Chinese Medicin

summary: In this study, a hyperosmotic environment was simulated using 30 mM mannitol. Human renal proximal tubular epithelial (HK-2) cells were transfected to overexpress hnRNP-F, with empty vector-transfected cells serving as the negative control (NC). RNA sequencing (RNA-seq) was performed to profile transcriptomic changes, enabling comprehensive analysis of hnRNP-F overexpression-induced alterations in differentially expressed genes (DEGs) and alternative splicing events (ASEs) under hyperosmotic stress. These data were integrated with our previously acquired dataset profiling hnRNP-F-driven DEG and ASE regulation in HK-2 cells under hyperglycemic conditions.

overall_design: 6 samples, 3 controls, 3 HNRNPF overexpression inHK-2 cells

first: Lan

last: Wang

first: Huimeng

last: Li

first: Xiaoqin

first: Xinyuan

last: Guo


title: Lithium Deficiency and the Onset of Alzheimer’s Disease

first: Chenxi

last: Qiu

address: NRB 858, 77 Avenue Louis Pasteur

summary: The non-genetic causes of Alzheimer’s disease (AD) are poorly understood1-4. Here, we show that endogenous lithium (Li) is a dynamically regulated metal in the brain.  Li uptake is the most significantly impaired of all metals analyzed in aged individuals with mild cognitive impairment (MCI) and AD, but not in aging individuals with normal cognitive function.  In addition, lithium is sequestered by aggregated amyloid β-protein (Aβ) in human AD and AD mouse models, significantly reducing Li bioavailability. The loss of Li observed in human AD was recapitulated in AD mouse models by feeding a lithium-deficient diet.  Loss of only 50% of endogenous brain Li resulted in markedly elevated Aβ deposition through a predominant effect on Aβ42, as well as elevated tau phosphorylation in neurofibrillary tangle-like structures.  Li deficiency also resulted in synapse loss, oligodendrocyte and myelin loss, and microglia with impaired Aβ degradative capacity and a proinflammatory phenotype, as well as significantly accelerated memory loss.  Diet-induced Li deficiency in aging wild-type mice also gave rise to elevated Aβ42 generation, synapse loss, proinflammatory astroglial and microglial responses, and accelerated memory loss.   A major consequence of endogenous Li deficiency is activation of the tau kinase GSK3β. At the systems level, Li deficiency induced a state of neural hyperexcitation.  To explore a new therapeutic approach to AD, we screened lithium salts and identified lithium orotate as a salt with low amyloid binding and high brain uptake. LiO prevents and reverses AD pathology and memory loss in AD mouse models and wild-type mice, and is approximately 100-fold more potent than the clinical standard Li carbonate.  LiO did not show evidence of toxicity after treatment with a therapeutic dose for most of the adult mouse lifespan. Thus, Li deficiency may be an early molecular event in the ontogeny of AD with protean multisystem effects in the brain.

overall_design: We performed snRNA-seq on the hippocampus of n=4 3xTg mice with regular diet and n=5 3xTg mice after 1 month of lithium deficient diet.

first: Jason


title: Distinct BMP-Smad Signaling Outputs Confer Diverse Functions in Dental Mesenchyme

status: Public on Jun 05 2025

city: New Orleans

first: Qinghuang

last: Tang

state: LA

address: 2000 Percival Stern Hall

department: Cell and Molecular Biology

institute: Tulane University


title: Distinct BMP-Smad Signaling Outputs Confer Diverse Functions in Dental Mesenchyme [ChIP-seq]

summary: The canonical bone morphogenetic protein (BMP) signaling pathway plays a crucial regulatory role in tooth development by activating Smad proteins to regulate gene expression. We previously identified an atypical canonical BMP signaling in dental mesenchyme that is Smad4-independent but Smad1/5-dependent. This study demonstrates that phosphorylated Smad1/5 (pSmad1/5) and Smad4 regulate distinct gene sets in dental mesenchyme. Real-time monitoring of BMP-Smad transcriptional activity revealed that Smad4-dependent canonical BMP signaling is restricted to neurovascular cells surrounding the condensed dental mesenchymal cells where pSmad1/5 is present. Notably, pSmad1/5 in dental mesenchymal cells form complexes with pSmad3 to prevent canonical BMP signaling. CUT&RUN assays revealed genome-wide co-occupancy of pSmad1/5 and pSmad3, indicating their function as transcriptional regulation units. Integrative analyses demonstrated that this atypical canonical BMP signaling regulates tooth sensory innervation and maintains odontogenic inductive potential in dental mesenchyme, enabling the identification of critical genes for maintaining tooth inductive capability. Our findings elucidate the operating mechanism of atypical canonical BMP signaling in dental mesenchymal cells and clarify how BMP-Smad signaling exerts diverse functions across different cell types, informing future tooth bioengineering strategies.

overall_design: ChIP-seq of pSmad1/5 and Smad4 was performed on E13.5 mouse molar tooth germs, as well the embryonic limb tissues at the same developmental stage. Both molar and limb tissues were harvested from wild-type CD1 mice.

first: Liwen

first: YiPing

last: Chen


title: Distinct BMP-Smad Signaling Outputs Confer Diverse Functions in Dental Mesenchyme [CUT&Run]

overall_design: Cut&Run of pSmad1/5 and pSmad3 was performed in duplicate on E13.5 mouse molar tooth germs collected from wild-type CD1 mice.


title: Two microbiome metabolites compete for tRNA modification and mammalian cell proliferation

status: Public on Jun 02 2025

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: Microbiome interacts with the eukaryotic host through many metabolites to affect cell physiology. A direct molecular pathway of microbial-host interaction is the incorporation of the microbial metabolite queuine at the wobble anticodon nucleotide of host tRNAs by a host enzyme that regulates host cell translation. Microbes also produce the intermediary metabolite pre-queuosine1 (preQ1) in the queuine pathway, and how preQ1 affects the host cell biology has not been explored. Here we show that preQ1 strongly represses human and mouse cell proliferation, but this effect is suppressed or reversible with queuine and depends on the same host enzyme that installs queuosine tRNA modification. PreQ1 and queuine are present in plasma and mouse tissues and incorporated into tRNA in cells and in mice, and preQ1 reduces mouse xenograft tumor growth. Mechanistically, preQ1 reduces cognate tRNA levels specifically and translation of house-keeping genes in a highly codon dependent manner. Genomic-wide CRISPR screen and validation identify pathways in sterol biosynthesis regulation, lipid metabolism, and Golgi-ER transport that mitigate the preQ1 proliferation effects through alleviation of cognate tRNA levels. Our results show an inter-dependent relationship of two microbial metabolites from the same biosynthesis pathway that compete and regulate host cell proliferation through multiple pathways.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Study the effect of preQ1 and queuine on tRNA levels in HEK293T cells using control, preQ1, and/or queuine treated total RNA . Study the effect of preQ1 on protein translation in HEK293T cells using control or preQ1 treated input and polysome associated mRNA. Study the queuosine modification in different bacterial classes using human stool RNA samples. Study the effect of preQ1 and queuine on tRNA levels in BMDC cells using control, preQ1, and/or queuine treated total RNA. Study the effect of IRE1 inhibitor on preQ1 effect on tRNA levels. Study the effect of +/- PNK treatment on tRNA fragments levels in sequencing. Study the effect of preQ1 on translation using ribo-seq with input mRNA and ribosome protected fragments (RPF) RNA.

first: Wen

last: Zhang

first: Kuldeep

last: Lahry

first: Denis

last: Cipurko

first: Sihao

last: Huang

first: Olivia

last: Zhibley

first: Dominika

last: Rudzka

first: Luke

middle: R

last: Frietze

first: Mahdi

last: Assari

first: Christopher

last: Katanski

first: Marisha

last: Singh

first: Aurore

last: Attina

first: Hélène

last: Guillorit

middle: P

last: Watkins

first: Delphine

last: Gourlain

first: Didier

last: Varlet

first: Hankui

first: Françoise

last: Macari

first: Kate

last: Johnson

first: Nicolas

last: Chevrier

first: Alexandre

last: David


title: Distinct BMP-Smad Signaling Outputs Confer Diverse Functions in Dental Mesenchyme [RNA-seq]

first: Qinghuang

last: Tang

overall_design: RNA-seq profiling of in vitro cultured E12.5 BRE-GFP mouse molar tooth germs treated with SIS3, SB431542, or DMSO for 1 day, and E13.5 tooth germs treated with DMSO as developmental stage controls.

first: Liwen

last: Li

first: YiPing

last: Chen


title: Inherited Variant in MRC2 Causes Cardiac Fibroblast Dysfunction and Increases Atrial Fibrillation Susceptibility [fibroblast]

status: Public on Jun 01 2025

city: Houston

first: Xander

middle: H T

last: Wehrens

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

summary: Background. A recent study identified a rare variant in the MRC2 gene in individuals with familial reentrant supraventricular tachycardia, a Wolff-Parkinson-White (WPW) ECG pattern, and structurally normal hearts. WPW syndrome is associated with atrial fibrillation (AF), and MRC2 was recently proposed as a protective gene for AF. Objective. We aimed to determine whether the E990G-heterozygous (het) loss-of-function variant in MRC2 increases AF susceptibility and aberrant atrial cardiofibroblast (ACF) function in mice. Methods. Programmed electrical stimulation (PES) was performed to determine AF susceptibility in E990G-het mice and wild-type (WT) controls. ACFs were isolated from these mice and cultured, and their migration, and collagen deposition were quantified. Finally, transcriptomic profiling by RNA sequencing and secretomic/proteomic profiling by mass spectrometry were performed on ACFs and whole atrial tissue. Results. E990G-het mice exhibited increased susceptibility to pacing-induced AF and had decreased atrioventricular effective refractory periods compared to WT controls. ACFs isolated from E990G-het mice deposited greater amounts of acid-soluble collagen in 2D cultures as quantified by Sirius red staining compared with WT controls. Transcriptomic, secretomic, and proteomic profiling of cultured ACFs and whole-atrial tissue suggest that some fibrotic regulators are differentially expressed or secreted, including decreased ACF expression of matrix metalloproteinase 13 (MMP-13), which degrades collagen types I, II, and III; decreased ACF expression, ACF secretion, and atrial tissue levels of matrix metalloproteinase 12 (MMP-12), which degrades collagen types I, III, IV, elastin, and fibronectin; and increased tissue levels of cellular communication network factor 2/connective tissue growth factor (CCN2/CTGF), a profibrotic regulator. Conclusions. MRC2 E990G-het mice exhibit increased AF susceptibility, altered collagen deposition by ACFs, and differentially regulated fibrotic genes and proteins. Together, these findings suggest that excessive collagen deposition and reduced MMP-mediated collagen removal generate a substrate for the development of AF in the presence of a loss-of-function variant in MRC2.

overall_design: 5 WT and 5 MRC2 E990G-het mouse hearts between 14 and 19 weeks old were harvested for ACF insolation and culture.

first: Kevin

last: Ho

first: Hassan

last: Samee


title: Inherited Variant in MRC2 Causes Cardiac Fibroblast Dysfunction and Increases Atrial Fibrillation Susceptibility [atrial tissue]

overall_design: 6 WT and 4 MRC2 E990G-het mouse cardiac atria between 4 and 10 months old were harvested and immediately snap-frozen in liquid nitrogen.


title: Klf5 functions as a multi-lineage reprogramming transcription factor

city: Shen Zhen

first: Xinyu

last: Wu

address: BGI Space-Time Research Center

institute: BGI

summary: The transcription factor Klf5 is indispensable for both embryonic (redundantly with Klf4) and extra-embryonic development during pre-implantation, yet its role in re-establishing these different fates in vitro remains largely unexplored. Here, we demonstrate that in the absence of WNT signaling activation at the beginning, ectopic expression of Klf5 in post-implantation epiblast stem cells (EpiSCs) not only induces naïve pluripotency, but also exclusively drives reprogramming into trophoblast stem cells (TSCs) and primordial germ cells (PGCs) by directly reactivating key lineage-specific determinants. Single-cell transcriptome analysis reveals distinct reprogramming trajectories toward these three fates, alongside a non-reprogramming trajectory that driven by Klf5-mediated BMP signaling activation. Moreover, endogenous Klf5 is crucial for establishing TSC and PGC fates from embryonic stem cells driven by other inducers. Our findings highlight Klf5’s multipotent reprogramming capacity and its pivotal role in early TSC and PGC fate specification, offering new insights into its versatile functions during embryonic development.

overall_design: To study Klf5 drived primed to naive transition, we performed Klf5 CUT&Tag and RNA-seq in LIF or CHIR/L condition.We use RNA-seq to compare the transcriptome between Klf5 induced iTSC and TSCs.

first: Yinhua

last: Huang

first: Hai

last: Zhou

first: Shihao

last: Zhang


title: Enhanced gliogenesis and delayed maturation underpin the neurodevelopmental defects in Lowe syndrome

status: Public on Jun 03 2025

city: Bangalore

first: Raghu

last: Padinjat

state: Karnataka

address: Kodigehalli

country: India

institute: National Centre for Biological Sciences (NCBS)

summary: The activity of signaling pathways is required for coordinated cellular and physiological processes that lead to the normal development of brain structure and function. Mutations in OCRL, a phosphatidylinositol 4,5-bisphosphate (PIP₂) 5-phosphatase, lead to the neurodevelopmental disorder Lowe Syndrome (LS). However, the mechanism by which mutations in OCRL lead to the brain phenotypes observed in LS remains unclear.We found that LS patient-derived induced pluripotent stem cells (iPSCs), when differentiated into neural cultures, exhibited significantly reduced neuronal excitability along with increased expression of the astrocytic marker GFAP. Multiomic single-nucleus RNA and ATAC sequencing revealed an early fate switch of LS patient-derived neural stem cells (LSP-NSCs) toward gliogenesis. Pseudobulk analysis of snRNA-seq data showed increased levels of DLK1, a non-canonical Notch ligand, in LS patient NSCs. This was associated with elevated levels of cleaved Notch protein and increased expression of its transcriptional target HES5, indicating upregulated Notch signaling. Treatment of iPSC-derived brain organoids with an inhibitor of PIP5K1C, the lipid kinase responsible for synthesizing PIP₂, restored neuronal excitability and rescued Notch signaling defects in LS patient-derived organoid cultures. Overall, our results demonstrate a role for PIP₂-dependent regulation of Notch signaling, cell fate specification, and the development of neuronal excitability mediated by OCRL activity.

overall_design:
Multiomics (GEX+ATAC): Nuclei from WT1, LSP2 and LSP3 iPSC-derived neural stem cells (NSCs) were isolated using 10x Genomics protocol. Joint snRNA seq and snATAC libraries were prepared using the 10x genomics platform.

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

first: Yojet

last: Sharma

first: Priyanka

last: Bhatia

first: Gagana

last: Rangappa

first: Sankhanil

last: Saha

first: Padinjat

last: Raghu


title: Targeted Apoptosis of the Angiotensin AT1R (Agtr1a)-Expressing Subtype of Agouti-Related Peptide Neurons in Adult Mice Increases Food Intake and Resting Metabolism, and Alters Blood Pressure Control

city: Milwaukee

first: Justin

last: Grobe

state: WI

address: 8701 W Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

summary: Background: Neurons of the hypothalamic arcuate nucleus that express Agouti-related peptide (AgRP) have been implicated in control of energy intake and expenditure. Recently we discovered that subtypes of AgRP neurons can be distinguished based upon expression of angiotensin II receptors. The Type 1 subtype is inhibited via the angiotensin type 1 receptor (AT1R / Agtr1a). We hypothesized that ablation of Type 1 AgRP neurons would have long-term consequences on energy balance. Methods: Young adult mice expressing Cre-recombinase via the Agtr1a locus received bilateral microinjection of an AAV vector encoding Cre-dependent expression of caspase-3 into the arcuate nucleus. An array of cardiometabolic phenotypes were then serially evaluated in mice housed at 22°C or 30°C. Results: Ablation of Type 1 AgRP neurons caused increased food intake, adiposity, resting metabolic rate via a mechanism involving hepatic function and nutrient partitioning, increased preferred ambient temperature, progressive loss of core temperature defense, and changes in the relationship between blood pressure and heart rate. Many phenotypes were ameliorated by housing animals at thermoneutrality. Conclusions: The Type 1 AgRP neuron influences cardiometabolic control through modulation of thermoregulatory responses to cold. Some functions of Type 1 AgRP neurons appear to oppose canonical roles of other AgRP neuron subtypes.

overall_design: Cell-specific ablation of Type 1 AgRP neurons was achieved by injecting an Adeno-associated virus (AAV) encoding Cre-activatable Caspase3 into the ARC of adult AT1RCRE mice that express Cre-recombinase via the AT1R locus. Male and female ablated and control mice were housed at either 22°C or 30°C from time of surgery. Two weeks after surgery, liver samples were snap frozen for future processing.

first: Jhonatan

last: Cortes

first: Valerie

last: Wagner

first: Samuel

last: Lawton

first: Alyssa

last: Madison

first: Kush

last: Nandani

first: Natalia

last: Mathieu

first: Connie

first: John

last: Reho

first: Bonnie

last: Freudinger

first: Alexander

last: Sherman

first: Daniel

last: Brozoski

first: Lisa

last: Morselli

first: Colin

last: Burnett

first: Jeffery

last: Segar

first: Curt

last: Sigmund

first: Pablo

last: Nakagawa


title: EMG1 cooperates with GRHL3 in β-catenin–mediated  surface ectoderm differentiation to regulate neural tube closure

status: Public on Jul 02 2025

city: Izumi

first: Isao

last: Matsuo

state: Osaka

address: 840 Murodo-cho

department: Department of Molecular Embryology

country: Japan

institute: Research Institute, Osaka Women's and Children's Hospital,  Osaka Prefectural Hospital Organization

summary: Grainyhead-like transcription factor 3 (GRHL3) directs surface ectoderm differentiation under the control of the canonical Wnt/β-catenin pathway. However, the molecular mechanisms that control nuclear GRHL3 expression through β-catenin are not fully understood. Here, we show that the essential for mitotic growth 1 (EMG1) protein constitutes a protein complex with GRHL3, and that EMG1 is required for correct nuclear localization of GRHL3, and for activation of the canonical Wnt signaling pathway. Conditional knockout mutation of Emg1 in the GRHL3-positive surface ectoderm causes neural tube defects at the level of the spinal cord, i.e. spina bifida. Additionally, the severity of compound mutant phenotypes of the Emg1 and Grhl3 genes indicates that they interact genetically in neurulation and palate development. These lines of evidence demonstrate that EMG1 cooperates with GRHL3 in β-catenin–mediated surface ectoderm differentiation. Since the EMG1 mutation causes Bowen-Conradi syndrome and the GRHL3 mutation causes Van der Woude syndrome 2, both of which are associated with neural tube dysplasia and cleft palate, our study will help to better understand the pathogenic mechanisms of these two human genetic diseases.

overall_design: To characterize the molecular basis underlying impaired neural tube closure caused by conditional KO of beta-catenin, conditional KO of Emg1 and Van Gogh-like 2 Lp, (Vangl2 Lp) mutations, gene expression profiles were performed using RNA sequencing of each caudal spinal cord region of three kinds of mutant and wild type embryos at E10.5. To minimize variability between samples, we extracted mRNA from pools of 4 to 7 embryos.

first: Chiharu

last: Kimura-Yoshida


title: Effects of TCF-1 de-repression on heterogeneity of chromatin states in memory and effector cells following acute infecton [scATAC-seq]

status: Public on May 31 2025

city: Stanford

first: Andy

last: Chen

address: 240 Pasteur Dr.

institute: Stanford

summary: The transcription factor TCF-1 is downregulated during effector differentiation of CD8+ T cells. However, how its downregulation impacts epigenetic regulation of different effector- and memory-biased populations remains unclear. Here, we generate mice in which TCF-1 fails to become downregulated in differentiated effector cells and probe the epigenetic impact of TCF-1 retention on gene accessibiltiy patterns and moif enrichment patterns in CD8+ T cells on 8 dpi with LCMV-13 using scATAC-seq.

overall_design: CD8+ T cells specific to the LCMV-gp3 antigen were sorted from the spleens of two WT control and two Tcf7+22kb mice on 8 dpi with LCMV-Armstrong. Samples were subjected to scATAC-sequencing.

first: Maegan

last: Murphy

first: Takeshi

last: Egawa


title: Loss of ALK3 Ameliorates Acute but Aggravates Chronic Lung Inflammation In Vivo

status: Public on May 29 2025

city: shenzhen

first: Jiang

last: Yamei

address: longfei

institute: The Chinese University of Hong Kong-Shenzhen

summary: ALK3 (BMPR1a) is a type-1-receptor of the TGF-β-receptor superfamily, which translates mostly bone morphogenetic proteins, but also TGF-β1. Previously, we could show that specific deletion of ALK3 in APCs leads to increased inflammation in the skin. Whether this effect is specific to the skin or found in other tissues as well has been unknown so far.Here, we used ALK3ΔCD11c-mice as well as pharmacological blockade of ALK3-signaling with DMH-1 to investigate the role of ALK3 in Bleomycin- and LPS-induced lung inflammations. We analysed lung inflammation via histology and studied the immune reaction via flow cytometry and single-cell-RNA-sequencing. Fitting to our results from the skin, we found that deletion or blockade of ALK3 aggravates long-lasting lung inflammations by reducing the number of TREG. Thus, ALK3 in APCs is important for dampening chronic lung inflammations. Surprisingly, we observed the opposite effect in acute inflammations: here, blockade of ALK3 ameliorated the inflammation. We found that ALK3 acts on APCs, reducing their state of activation and changing the secretion of chemokines. This in turn reduces activity of neutrophils, leading to reduced lung inflammation.Thus, ALK3 has a dual role in lung inflammations. It contributes to initiation of acute inflammation, but dampens longer-lasting inflammations.

overall_design: To understand the underlying mechanisms of how DMH1 partially rescue lung inflammation cased by LPS, we performed scRNA-seq to analyze gene expression in different lung cell types under 3 different conditions.

first: Mathias

last: Hochgerner

first: Yamei

last: Jiang

first: Shenfei

last: Sun

first: Fujing

last: Huang

first: Leigh

last: Marsh

first: Xinhua

last: Lin

first: Xiaofang

last: Tang


title: Effects of TCF-1 de-repression on heterogeneity of effector and memory progenitor T cell transcriptomes in acute infection [scRNA-seq]

summary: The transcription factor TCF-1 is downregulated during effector differentiation of CD8+ T cells. However, how its downregulation impacts gene expression in different effector- and memory-biased populations remains unclear. Here, we generate mice in which TCF-1 fails to become downregulated in differentiated effector cells and probe the transcriptional impact of TCF-1 retention in different T cell differentiation states by scRNA-sequencing.

overall_design: CD8+ T cells specific to the LCMV-gp3 antigen were sorted from the spleens of two WT control and two Tcf7∆+22kb mice on 8 dpi with LCMV-Armstrong. Samples were subjected to scRNA-sequencing.


title: Spatiotemporal molecular and cellular dynamics of intratelencephalic neurons in mouse prefrontal cortex during postnatal development

status: Public on May 28 2025

city: Wuhan

first: Hu

last: Zheng

address: shizishan street No.1

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

summary: In early postnatal brain, the prefrontal cortex (PFC) remains immature and highly plastic, particularly for the intratelencephalic (IT) neurons. However, the spatiotemporal molecular and cellular dynamics of PFC during this period remain poorly characterized. Here, we performed spatiotemporal single-cell RNA analysis on mouse PFC during different postnatal time points and systematically delineated the molecular and cellular dynamics of mouse PFC during early postnatal development, among which IT neurons exhibit most dramatic alterations. Based on these comprehensive spatiotemporal atlases of PFC, we deciphered the time-specific molecular and cellular characteristics during the maturation process of IT neurons in PFC, particularly the dynamic expression programs of genes regulating axon development and synaptic formation, and the risk genes of neurological developmental diseases. Furthermore, we revealed the dynamic neuron-glia interaction patterns and the underlying signaling pathways during early postnatal period. Our study provided a comprehensive resource and important insights for PFC development and PFC-associated neurological diseases.

overall_design: To delineate the molecular trajectories underlying postnatal development of prefrontal cortex (PFC) neurons and investigate the mechanisms governing early neural circuit assembly, we performed high-throughput single-cell RNA sequencing (scRNA-seq) on PFC tissues from mice across key developmental timepoints (postnatal day: P1, P4, P10 and adulthood: P84). Our comprehensive transcriptomic atlas captured dynamic gene expression patterns during critical stages of neuronal maturation.


title: Epigenetic array data of saliva samples in individiduals with esophageal cancer (with controls)

city: London

first: Laurence

middle: Bruce

last: Lovat

address: 43-45 Foley Street

department: Division of Surgery & Interventional Science

country: United Kingdom

institute: University College London

summary: We previously deposited a similar batch of data to the Gene Expression Omnibus (GEO) database under the accession code GSE232332. This dataset was to be a further validation of that study. Unlike the previous dataset, this has not, however, been submitted for publication. This dataset includes epigenetic data form 23 patients with invasive oesophageal adenocarcinoma, 25 with intramucosal oesophageal adenocarcinoma, 35 patients with non-dysplastic Barrett's esophagus and 32 controls who did not have Barrett's esophagus or cancer at endoscopy, performed within 2 weeks of the saliva sample which was obtained after fasting for at least 1  hour.

overall_design: The principle design was a two group case-control study of Cancer (intramucosal + invasive adenocarcinoma) vs Controls (Non-dysplastic Barrett's and Controls)

first: Timothy

middle: C

last: Stone

first: Laurece


title: Genetic variants affecting RNA stability influence complex traits and disease risk II

status: Public on May 27 2025

city: Los Angeles

first: Xinshu

middle: Grace

last: Xiao

state: CA

address: 610 Charles E. Young Drive South

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

summary: Gene expression is jointly modulated by transcriptional regulation and mRNA stability, yet the latter is often overlooked in studies on genetic variants. Leveraging metabolic labeling data (Bru/BruChase-seq) and a new computational pipeline, RNAtracker, we distinguished allele-specific RNA stability (asRS) from allele-specific RNA transcription (asRT) events. Our analysis identified >5,000 asRS variants, revealing comparable impact of stability on allelic imbalance as transcriptional regulation. This study highlights RNA stability as a critical, yet understudied mechanism linking genetic variation and disease.

overall_design: Synthetic DNA oligos containing the variants of interest and their flanking sequences (164 nucleotides total) were cloned into the 3’UTR of the eGFP gene. The expression of this reporter gene was driven by the CMV early enhancer/chicken beta actin (CAG) promoter. These oligos were then electroporated into HeLa cells. Following electroporation (24 h), total RNA was extracted for sequencing targeting the tested variant regions. Specifically, the test sequences were amplified from both the plasmid library and mRNA to generate DNA-seq and RNA-seq libraries. Three biological replicates were collected for each experiment and a high correlation was observed between replicates (R=0.84). Sequencing data of the plasmid DNA and mRNA were compared to identify sites associated with significant expression differences between the two alleles using MPRAnalyze. FDR ≤ 0.1 and |ln(Fold Change)|  ≥ 0.1 were required to call significance.


title: PD-1high memory-phenotype CD4 T cells mediate type 2 bystander immunity and promote pulmonary fibrosis via BATF/amphiregulin axis

city: Seoul

first: Jaehyun

last: Choi

address: 50, Yonsei-ro, Seodaemun-gu

department: systembiology

country: South Korea

institute: Yonsei university

summary:
Single-cell RNA sequencing(scRNA-seq) was performed to investigate the differentiation process of steady-state CD4 T cells following treatmernt with IL-25 and IL-33, after initial isolation via FACS. This analysis revealed that steady-state PD-1high CD4 T cell  differentiate into patogenic Th2 cells, characterized by the expression of IL-13, IL-5 and amphireguling. These findings suggest that steady-state PD-1high CD4 T cells may contribute to pulmonary fibrosis through its differntiation into pathogenic Th2 cells. This dataset includes previously published scRNA-seq data from [Min-Ji Cho et al., 2023]
To investigate the tissue-specific roles of Pdcd1 in CD4⁺ T cells, bulk RNA sequencing was performed on Pdcd1^high and Pdcd1^low CD4⁺ T cells isolated from the spleen and lungs of mice. Differential gene expression analysis revealed that Pdcd1^high CD4⁺ T cells in both tissues were enriched for Th2- and fibrosis-related gene signatures. Notably, chemokine receptor expression profiles differed between spleen and lung, suggesting tissue-specific transcriptional programs associated with Pdcd1 expression.

overall_design:
CD44 high CD4 T cells from the spleen of C57BL/6J mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.
RNA seq profilling of PD-1 high and PD-1 low CD4 T cells sorted from mouse spleen and lung tissues

first: Min-Ji

last: Cho

first: Je-Min

first: Hyobin

last: Jeong


title: Genetic variants affecting RNA stability influence complex traits and disease risk I

overall_design: We performed prime editing in HEK293T cells to evaluate the effect of asRS variants. After introducing the edits, total RNA was harvested from cells 0h (pre-treatment), 2h, 8h, and 24h after treatment with 10 ug/ml of ActD (3 replicates per timepoint). After reverse transcription using the SuperScript™ IV Reverse Transcriptase (Thermo Fisher Scientific, Cat# 18090010), the cDNA was amplified using gene-specific primers  to generate amplicons containing the variant of interest. Amplicons containing different variants from the same timepoint were pooled together before a second round of PCR to add Illumina adaptors for sequencing. The PCR reactions were stopped before the plateau of the amplification curves.  The libraries were purified using 2% agarose gel and sequenced with NovaSeq X Plus 150 PE.


title: A network of intra and extra-tumoural cytotoxic T cells with precursor and residency features constrained by TGF-b

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: Anti-tumour immunity is limited by loss of T cell function and sustained expression of inhibitory receptors or immune checkpoints, including PD-1, a state known as T cell exhaustion. Exhausted T cells are maintained by precursors of exhausted T (TPEX) cells, that self-renew and generate effector cells, particularly in response to therapeutic immune checkpoint blockade (ICB). Similarly, tissue-resident memory T (TRM)-like cells have been implicated in tumour control and ICB response. However, the factors governing TPEX and TRM-like cell differentiation and function within the tumour environment, their relationship, and their response to ICB, remain insufficiently understood. Using single cell RNA sequencing and innovative mouse models that enable the identification and targeting of both TPEX and TRM-like cells within and outside the tumour microenvironment, we systemically dissect the developmental and functional relationship between tumour-responsive TPEX cells in the tumour microenvironment and in lymph nodes. We show that within the tumour microenvironment, TPEX cells and their progeny could acquire a tissue residency program that limits their contribution to tumour control and response to checkpoint inhibition. In contrast, stem-like TPEX cells, dependent on the transcription factor MYB and located within the tumour-draining lymph nodes (tdLN), were essential for fueling CD8+ T cell tumour infiltration and response to ICB. We identify TGF-β as the common factor enforcing residency of TPEX cells in the tumour and limiting the abundance of stem-like TPEX cells in tdLN. Finally, we provide evidence for the presence of a similar network of intra- and extratumoural CD8+ T cells in human cancer, exhibiting precursor and residency characteristics that is constrained by TGF-β.

overall_design: Analysis of tumor infiltrating CD8 T cells revealed the presence of four distinct populations of CD8 T cells that could be identified on the basis of Hobit and Id3 expression, namely ID3 single positive (termed TPEX cells), Hobit single positive (termed TRM-like cells), ID3/Hobit double positive (termed tissue-resident TPEX cells) and ID3/Hobit double negative (termed TEX cells).

first: Sarah

last: Gabriel

first: Yang

last: Liao

first: David

last: Chisanga

first: Axel

last: Kallies


title: Effects of Acetylcholine and Porphyromonas gingivalis on Oral Epithelial Cells

status: Public on May 21 2025

city: Guangdong

first: Shihan

last: Xu

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Road/Street, Yuexiu District, Guangzhou City

institute: Sun Yat-sen University

summary: Periodontitis patients exhibit significant upregulation of the cholinergic signaling pathway in gingival epithelial cells, accompanied by elevated acetylcholine (ACh) levels in saliva. However, the role of ACh in the pathogenesis of periodontitis remains unclear.  P. gingivalis, a keystone pathogen in periodontitis, triggers host inflammatory responses and compromises the epithelial barrier function. As the first line of defense against pathogens, the reparative capacity of the oral epithelium critically influences the progression of periodontitis. This study investigates whether ACh modulates P. gingivalis-induced inflammatory responses and epithelial repair in human oral keratinocytes (HOKs), aiming to elucidate the mechanistic role of cholinergic signaling in periodontitis.

overall_design: The HOK cells were treated differently for 2 hours after starvation: ACh group: Treated with ACh (100 nM) Pg group: Stimulated with Pg (MOI = 50) PA group: Treated with Pg + ACh NC group: Control

first: Jiaxin

last: Guo

first: Shiwen

last: Yang

first: Bin

last: Cheng

first: Juan

last: Xia


title: AMPK-beta1 Activation Induces Fetal Hemoglobin

city: Cambridge

first: Samuel

last: Lessard

state: Massachusetts

address: 350 Water street

institute: Sanofi

summary: Previous studies report that metformin triggers fetal hemoglobin (HbF) induction in human erythroid cells through indirect activation of the AMPK/FOXO3 pathway. Here we investigated the underlying mechanism of HbF induction by direct activation of AMPKβ1 in erythroid cells to understand their potential as safe medication for sickle cell disease (SCD). Single-cell RNA sequencing of human bone marrow cells determined that AMPKβ1 predominates in the erythroid lineage compared to AMPKβ2 and expression of AMPKβ1 is mostly restricted to this lineage. Novel selective AMPKβ1 activators greatly increased expression of HbF, activated markers of the noncanonical Nrf2 pathway (phosphorylated ULK1 and SQSTM1), and ultimately decreased sickling of SCD donor CD34+ cells under hypoxia. Confirmation of the noncanonical Nrf2 pathway in AMPKβ1 driven HbF induction was achieved by abolishing increased HbF using a potent and selective inhibitor for SQSTM1/Keap1 complex formation. Preclinical studies in Townes SCD mice treated with PF-06409577, a clinical candidate AMPKβ1 activator, confirmed increased HbF induction and non-canonical Nrf2 pathway activation in erythroid cells, associated with decreased reactive oxidative species in bone marrow and decreased chronic inflammation markers. Based on the narrow tissue expression of AMPKβ1, our study strongly supports AMPKβ1 activators as safe activators of Nrf2 driven HbF induction compared to direct inhibitors of ubiquitous Keap1. Activation of the AMPKβ1/Nrf2 noncanonical pathway may be a promising therapeutic approach for SCD patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD34+ cells treated with compound B, oxindole (N=3) or DMSO (N=3). RNA-seq was conducted after 14 days of erythroid differentiation for each condition.

first: Hara

last: Yannis

first: Viktor

last: Lemgart

first: Courtney

last: Mercadante

first: Mithilesh

last: Jha

first: Kiana

last: Mahdaviani

first: Jean-Antoine

last: Ribeil

first: Pauline

last: Rimmele

first: Alexandra

last: Hicks

last: Light


title: Missense variants in human forkhead transcription factors reveal determinants of forkhead DNA bispecificity

city: Boston

first: Stephen

last: Gisselbrecht

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

type: Genome binding/occupancy profiling by array

summary: Recognition of specific DNA sequences by transcription factors (TFs) is a key step in transcriptional control of gene expression. While most forkhead (FH) TFs bind either an FKH (RYAAAYA) or an FHL (GACGC) recognition motif, some FHs can bind both motifs. Mechanisms that control whether a FH is monospecific versus bispecific have remained unknown. Screening a library of 12 reference FH proteins, 61 naturally occurring missense variants including clinical variants, and 22 designed mutant FHs for DNA binding activity using universal (“all 10-mer”) protein binding microarrays (PBMs) revealed non-DNA-contacting residues that control mono- versus bispecificity. Variation in non-DNA-contacting amino acid residues of TFs is associated with human traits and may play a role in the evolution of TF DNA binding activities and gene regulatory networks.

overall_design: Variants of human forkhead gene DNA-binding domains were generated by site-directed mutagenesis of synthesized reference alleles and Gateway cloned into pDEST15. The resulting GST fusion proteins were expressed by in vitro transcription and translation. Agilent microarrays (AMADID #030236) containing all 10-nt sequences were made double-stranded by primer annealing and on-array extension with Cy3-labelled nucleotides to monitor double-stranding efficiency, then WT and variant GST-tagged proteins were applied and detected with Alexa488-labelled anti-GST antibody. Alexa488 signal was scanned at multiple intensities; scans were combined with Masliner and the resulting file was normalized to Cy3 signal and analyzed with the Universal PBM Analysis Suite (Berger et al., Nature Biotechnology 2006) to report Enrichment scores for each 8-mer.

first: Jessica

last: King

first: Julia-Alexia

last: Dias

first: Raehoon

last: Jeong

first: Elisabeth

last: Rothman

first: Martha

last: Bulyk


title: Single-nucleus transcriptomics of inducible Ngly1-/- cerebellum

status: Public on May 08 2025

city: DALLAS

last: YAN

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: To explore the cell type-specific effects of NGLY1 deficiency and the STING pathway in the cerebellum, we performed single-nucleus RNA sequencing (snRNA-seq) of cerebella from Ngly1fl/fl, iNgly1-/- and iNgly1-/-Sting1-/- mice

overall_design: Eight-week-old Ngly1fl/fl, iNgly1-/- and iNgly1-/-Sting1-/- male mice (2 mice/genotype) were sacrificed and cerebella were collected and frozen in liquid nitrogen. Nuclei were isolated from frozen cerebella and droplet-based snRNA-sequencing was performed using 10x Genomics.

last: Yan

first: Kun

last: Yang


title: Genetic variants affecting RNA stability influence complex traits and disease risk

first: Xinshu

last: Xiao

overall_design: To validate asRS genes identified by RNAtracker, we performed RNA-seq for GM12878, MCF-7, and HCT116 cells before treatment with 10 ug/ml (GM12878, HCT116) or 5 ug/ml (MCF-7) of the transcriptional inhibitor Actionomycin D, as well as 2h, 8h, and 24h post-treatment (3 replicates per timepoint).


title: Transcriptional Regulation of human NMNAT2: Insights from 3D Genome Sequencing and Bioinformatics [4C-seq]

status: Public on May 07 2025

city: Bloomington

first: Hui-Chen

last: Lu

state: Indiana

address: 702 N Walnut Grove Ave, Multidisciplinary Science Building II

department: Psychological and Brain Sciences

institute: Indiana University Bloomington

summary: Nicotinamide mononucleotide adenylyl transferases 2 (NMNAT2) is a crucial nicotinamide adenine dinucleotide (NAD)-synthesizing enzyme essential for neuronal health. In the Religious Orders Study/Memory and Aging Project (ROSMAP), human brain levels of NMNAT2 mRNA positively correlated with cognitive capabilities in older adults. NMNAT2 mRNA abundance is significantly reduced following various insults or proteinopathies. To elucidate the transcriptional regulation of NMNAT2, we employed circular chromosome conformation capture followed by high-throughput sequencing (4C-seq) to identify potential NMNAT2 enhancer and silencer regions by determining genomic regions interacting with the NMNAT2 promoter in human SH-SY5Y cells. We discovered distinct NMNAT2 promoter interactomes in undifferentiated versus neuron-like SH-SY5Y cells. Utilizing bioinformatics analyses, we identified putative transcriptional factors and NMNAT2-associated genes. Notably, the mRNA levels of many of these genes showed a significant correlation with NMNAT2 mRNA levels in ~400 single-nuclei RNA-seq datasets from ROSMAP. Additionally, using CRISPR-Cas9 strategies, we confirmed the requirement of two specific genomic regions within the interactomes and four transcription factors in regulating NMNAT2 transcription. In summary, our study identifies genomic loci containing NMNAT2 regulatory elements and predicts associated genes and transcription factors through computational analyses.

overall_design: To examine the 4C interactomes of NMNAT2 promoter in SH-SY5Y and differentiated SH-SY5Y cells.

first: Yu Chen

last: Chang

first: Sen

first: Hu-Chen


title: INTEGRATED ATAC-SEQ AND RNA-SEQ ANALYSIS IDENTIFIES KEY REGULATORY ELEMENTS IN FEEDER CELL-ACTIVATED NK CELLS [RNA-seq]

status: Public on May 22 2025

city: Minneapolis

first: Pedram

last: Motallebnejad

state: MN

address: 421 Washington Ave SE

institute: University of Minnesota

summary: NK cells can potentially be used in allogeneic immunotherapy; however, for such use as off-the-shelf medicines, NK cells need to undergo ex vivo expansion, typically through activation with feeder cells, to generate enough cells for clinical applications. Upon stimulation with feeder cells, NK cells undergo profound changes in gene expression, altering their metabolic activity, cell cycle progression, and growth behavior. After examining the transcriptome and chromatin accessibility of NK cells before and 7 days after feeder cell activation, significant alterations were seen. These changes are even more pronounced in genome regions closer to enhancers. Several transcription factors, including AP-1, IRF4, STATs, T-bet, Eomes, and bHLHE40, which play key roles in NK cell development and immune response, exhibited differential binding activity between unstimulated and day 7 NK cells. Gene sets composed of target genes downstream of these transcription factors were also enriched at day 7, implying their involvement in NK cell activation. Moreover, we compared potential super-enhancer regions in NK cells before and after coculture, combined with the transcriptional activity of nearby genes. We identified stable and transcriptionally active super-enhancers in unstimulated and day 7 NK cells, as well as those that form or disappear after coculture initiation. The transcriptomic and epigenetic characterization of NK cells presented in this study could facilitate the ex vivo expansion and engineering of functionally superior NK cells.

overall_design: To investigate the transcriptional changes in NK cells that are activated with K562 feeder cells engineered to express membrane-bound IL-21 and 4-1BB-L, we carried out RNA-seq on NK cells before stimulation (unstimulated samples) and 7 days after coculture with NK cells. We utilized 3 different donors for the analysis. We then performed differential gene expression analysis between day 7 and unstimulated samples.

first: Zion

last: Lee

first: Jen

last: One

first: Samira

last: Azarin

first: Wei-Shou

last: Hu


title: A multiomic analysis of Waldenström macroglobulinemia defines distinct disease subtypes

status: Public on May 02 2025

city: New York

first: Gareth

last: Morgan

address: 550 1st Avenue

institute: NYU Langone Health

summary: We carried out a single-cell (sc) multiomic analysis on a series of MYD88 mutated Waldenström macroglobulinemia (WM) cases and identified two distinct subtypes of disease, memory B-cell-like (MBC-like) and plasma cell-like (PC-like), based on their expression of key lineage defining genes. Biologically, the subtypes are characterized by their variable capacity to differentiate fully towards a plasma cell (PC) and exhibit unique transcriptomic, chromatin accessibility, and genomic profiles. The MBC-like subtype is unable to differentiate beyond the memory B-cell (MBC) stage, upregulates key MBC genes, and is characterized by upregulated BCR and AKT/mTOR signaling. In contrast, the PC-like subtype can partially differentiate towards a PC, upregulates key PC genes, has enhanced NF-kB signaling, and has an upregulated unfolded protein response. Pseudotime trajectory analysis of combined scRNA-sequencing and scATAC-sequencing supports the variable differentiation capacity of each subtype and implicate key transcription factors SPI1, SPIB, BCL11A, and XBP1 in these features. The existence and generalizability of the two disease subtypes were validated further using hierarchical clustering of bulk RNA-seq data from a secondary set of cases. The biological significance of the subtypes was further established using whole genome sequencing, where it was shown that CXCR4, NIK, and ARID1A mutations occur predominantly in the MBC-like subtype and 6q deletions in the PC-like subtype. We conclude that the variable differentiation blockade seen in WM manifests itself clinically as two disease subtypes with distinct epigenetic, mutational, transcriptional, and clinical features with potential implications for WM treatment strategies.

overall_design: B-cells from 13 MYD88 mutated Waldenstrom macroglobulinemia (WM) patients were flow sorted from bone marrow (BM) using CD3-/CD19+. Sorted cells were pooled and libraries prepared for single-cell RNA-seq and single-cell ATAC-seq using 10x Genomics protocol and sequenced on an Illumina NovaSeq 6000.

first: Dylan

last: Gagler

first: Hussein

last: Ghamlouch

first: Di

last: Zhang

first: Patrick

last: Blaney

first: Avital

last: Tenenbaum

first: James

last: Langton

first: Marine

last: Armand

first: Alexandre

last: Eeckhoutte

first: Amina

last: Joudat

first: Michael

last: Degaud

first: Michela

last: Esposito

first: Gaurav

last: Varma

first: Yubao

last: Wang

first: Sanghoon

first: Sanxiong

last: Liu

first: Oscar

last: Lahoud

first: David

last: Kaminetzky

first: Marc

last: Braunstein

first: Louis

last: Williams

first: Florence

last: Nguyen-Khac

first: Brian

last: Walker

first: Damien

last: Roos-Weil

first: Faith

middle: E

last: Davies

first: Olivier

middle: A

last: Bernard

middle: J


title: Gene expression profile at single cell level of CD44+CD8+ from tumors and PD-1+CD8+ T cells from draining LNs of untreated and aPDL-1 and CTLA-4 treated  AT3-OVA-bearing mice.

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

institute: University of Melbourne

summary: Tumor-infiltrating CD8+ (TILs) exhibit heterogeneity, encompassing precursors of exhausted T (TPEX) cells and terminally exhausted T cells. We employed single cell RNA sequencing to analyze the diversity of TILs and explore the developmental and functional relationship between TPEX cells within the tumor and in those in tumor-draining lymph nodes.

overall_design: Lymphocytes were isolated from AT3-OVA tumors and tumor-draining lymph nodes that were either left untreated or treated 3x with aPDL-1 and aCTLA4, and single-cell suspensions were prepared. CD44+ T cells from tumors or CD44+PD-1+ CD8+ T cells from lymph nodes were sorted using Fluorescence-Activated Cell Sorting (FACS) and analyzed through single-cell RNA sequencing (scRNAseq)

first: Sharanya

last: Wijesinghe

first: Lisa

last: Rausch

first: Lifen

last: Wen

first: Lei

last: Qin

first: Axel

last: Kallies


title: Transcriptional Regulation of human NMNAT2: Insights from 3D Genome Sequencing and Bioinformatics [RNA-seq]

first: Hui-Chen

last: Lu

overall_design: To examine the differentially expressed genes between SH-SY5Y and differentiated SH-SY5Y cells.

first: Yu Chen

last: Chang

first: Sen

last: Yang

first: Hu-Chen


title: Bacillus subtilis root biofilm social interactions influence on potato transcriptome

status: Public on Apr 24 2025

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: To investigate bacteria-plant social interactions and their influence on plant growth and immunity on transcriptional level, we performed RNA-seq analysis in plants inoculated with B. subtilis monocultures and their combinations. The results show differences in regulation in various social interactions both at the level of processes and at the level of individual genes.

overall_design: potato shoots and roots, non-inoculated control (incubated in MS30 medium without bacteria) and Bacillus subtilis inoculated samples. B. subtilis inoculations. Two experiments were performed: Exp 1 - 'Monocultures', with individual strains (PS-216 YFP and PS-218 YFP), and control; and Exp 2 - 'Interactions', with individual strains (PS-216 YFP, PS-218 YFP, PS-218 mKate2), an isogenic mixture of two strains (PS-218 mKate2 + PS-218 YFP), a non-kin mixture of strains (PS-218 mKate2 + PS-216 YFP), and control. Sampling was performed in 4 biological replicates per treatment group.

first: Tim

last: Godec

first: Katja

last: Stare

first: Tjaša

last: Lukan

first: Kristina

last: Gruden


title: Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples

status: Public on May 16 2025

city: Chicago

first: Cheng-Wei

last: Ju

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

type: Genome variation profiling by high throughput sequencing

summary: Circulating cell-free RNA (cfRNA) in plasma represents a promising avenue for cancer detection. We report low-input multiple methylation sequencing, a method for profiling modification patterns in cfRNA, enabling the detection of diverse transfer RNAs and small noncoding RNAs derived from both the human genome and the microbiome. RNA modification patterns in microbiome-derived cfRNA accurately reflect host microbiota activity and hold potential for the early detection of colorectal cancer.

sample_organism:
Homo sapiens
Stenotrophomonas maltophilia

overall_design:
A total of 27 patients with colorectal cancer and a total of 36 sex, age matched non-cancer individuals were recruited from the Lutheran General Hospital and the University of Chicago Medical Center. Blood from patients with CRC was collected before surgical resection (CRC). Peripheral blood samples from all participants were collected using standardized venipuncture protocols in antecubital venipuncture regions, with skin surfaces disinfected with 70% ethanol prior to phlebotomy to ensure aseptic conditions. All specimens were visually inspected to confirm absence of hemolysis. Blood from non-cancer individuals was collected from those undergoing screening colonoscopies at the University of Chicago Medical Center, with strict adherence to the same pre-analytical quality control measures, and only included subjects with no tumor upon post-colonoscopy pathological analyses.

We included two validation cohorts in this study. Validation cohort 1 consisted of 8 non-cancer individuals and 30 patients with CRC. These samples were obtained from stored specimens, which were collected and processed by a separate research group at the same institute. To ensure comparability, CRC patients at different disease stages were age- and sex-matched with the non-cancer individuals. Validation cohort 2 included samples from additional individuals, with 8 non-cancer individuals and 7 patients with CRC, who were recruited in a different phase of this study. These samples were collected using the same procedures as the training cohort and processed by the same research group.

Plasma cell-free RNA (cfRNA) or small RNA (<200 nt) were used to build libraries with LIME-seq following the protocol.

first: Li-Sheng

last: Zhang

first: Chuan

last: He


title: Post-Radiotherapy GSCs EGR1-Induced GAL3 Upregulation and T Cell Exhaustion in GBM

status: Public on Apr 20 2025

city: Nanjing

first: Hui

last: Huang

address: Longmian Avenue No.101

institute: Nanjing Medical University

summary: Background: Glioblastoma (GBM), a highly aggressive brain cancer, inevitably recurs due to therapy-resistant glioblastoma stem cells (GSCs). Lymphocyte activation gene 3 (LAG3) contributes to T cell exhaustion, a key immune escape mechanism. Here, we investigate that the more exhausted state of GBM-infiltrating T cells after recurrence is associated with the LAG3 and its ligand galectin 3 (GAL3).  Methods: The analysis of Single-cell RNA sequencing to characterize the landscape of immune cells in newly diagnosed GBMs and recurrent GBMs respectively. Post-radiotherapy GAL3 in GSCs upregulation was validated via cell biology experiments. In vitro/in vivo loss-of-function assays assessed GAL3's impact on CD4+/CD8+ T cell cytotoxicity against GSCs. Chromatin immunoprecipitation quantitative real-time PCR was leveraged to map the regulation of GAL3 after radiotherapy in GSCs.  Results: The phenomenon that recurrent glioma patients had their T cells in a more exhausted state compared to primary glioma patients, is associated with the expression of LAG3. Elevated EGR1 in post-radiotherapy GSCs upregulates LAG3 ligand GAL3 expression in GSCs, impairing CD4+/CD8+ T-cell cytotoxicity. Small molecule inhibitors targeting EGR1 in combination with anti-LAG3 monoclonal antibody suppressed GBM tumor growth and prolonged survival of orthotopic xenograft-bearing mice.  Conclusions: GAL3 in GSCs plays critical roles in maintaining the exhaustion stage of T cells and inhibits cytotoxic capacity of CD4+/CD8+ T cells, highlighting an interplay between GSCs and GBM-infiltrating T cells. Small molecule inhibitors in combination with anti-LAG3 monoclonal antibody may effectively improve GBM treatment.

overall_design: GSCs were preconditioned with 5 Gy irradiation followed by a 72-hour culture period to assess the effects of radiotherapy on cellular responses and gene expression.

first: Chenhua

last: Li

first: Zhen

first: Qiankun

last: Lin

first: Junlei

first: Hang

last: Yu

first: Hao

last: You

first: Zhiting

first: Gaoyuan

last: Cui

first: Kefan

last: Song

first: Qian

first: Junxia

first: Yun

last: Chen

first: Xiuxing

last: Wang

first: Danling

last: Gu

first: Chao

last: Cheng

first: Junfei

last: Shao


title: Leucegene: AML sequencing (part 1-6, GRCh38 reference)

status: Public on Apr 23 2025

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: RNA sequencing of human leukemia

overall_design:
The goals of this project are to obtain a comprehensive study of mutations and gene expression in human acute myeloid leukemia (AML). Methods: AML cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an illumina HiSeq 2000 sequencer.
**Re-analysis/re-quantification with new methods and updated reference genome of samples already found in the following Series: GSE49642, GSE52656, GSE62190, GSE66917, GSE67039 and GSE106272**

first: Camille

last: Simon

first: Jalila

last: Chagraoui

first: Jana

last: Krosl

first: Patrick

last: Gendron

first: Geneviève

last: Boucher

first: Pierre

last: Chagnon

first: Simon

last: Drouin

first: Raphaëlle

last: Lambert

first: Claude

last: Rondeau

first: Annie

last: Bilodeau

first: Sylvie

last: Lavallée

first: Martin

first: Caroline

last: Pabst

first: Anne

last: Bergeron

first: Vincent

first: Jonathan

last: Yeh

first: Eric

last: Deneault

first: Jessica

last: Simard

first: Giovanni

last: D'Angelo

first: Bernhard

last: Lehnertz

first: Radia

last: Johnson

first: Clarisse

last: Thiollier

first: Tara

last: McRae

first: Miriem

last: Marquis

first: Frédéric

last: Barabé

first: Brian

last: Wilhelm

last: Marinier

first: Sébastien

last: Lemieux

first: Josée

last: Hébert


title: Leucegene: AML sequencing (GRCh38 reference)

first: Guy

last: Sauvageau

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

overall_design: Refer to individual Series


title: Median Raphe Glutamatergic and Serotonergic Inputs Support Recruitment of Hippocampal CA1 VIP Interneurons During Novel Experience

status: Public on Apr 18 2025

city: Quebec

first: Lisa

last: Topolnik

state: Quebec

department: Biochemistry, Microbiology and Bio-informatics

institute: Université Laval

summary: We sequenced thirteen vasoactive intestinal peptide (VIP)-expressing interneurons from the mouse CA1 oriens/alveus area using patch-seq technique to determine their molecular identity.

overall_design:
Six neurons were recorded using patch-clamp technique, filled with biocytin for morphological identification and aspirated for next-generation sequencing. We also reanalyzed seven neurons from our previos dataset (GSM2966346-GSN2966352, GSE109755). The new analysis has focussed on the expression levels of the Htr genes. A total of 11 VIP-eGFP mice of either sex were used for these experiments.

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

first: Xiao

last: Luo

first: Dimitry

first: Vandana

last: Dulam

first: Aurelie

first: Louis-David

last: Coulombe

first: Megan

last: Besner

first: Justine

last: Fortin-Houde

first: Judy

last: Davies

first: Felix

last: Michaud

first: Risna

last: Radhakrishnan

first: Benedicte

last: Amilhon


title: A Possible Role for CAF1 in the Incorporation of H3.3 in Arabidopsis [RNA-Seq]

status: Public on Apr 12 2025

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

summary: Eukaryotic organisms organize their genetic material in chromatin rather than unprotected DNA. Efficient chromatin assembly is essential for all DNA-templated processes, including replication, transcription, and DNA repair. Our research focused on two major histone H3 deposition complexes: Chromatin Assembly Factor (CAF1), which deposits canonical H3 on naked DNA immediately after replication during the S-phase in yeast and metazoans, and the Histone Regulator A (HIRA) complex, which is thought to incorporate the H3.3 variant in a transcription-dependent manner. By combining biochemical, genetic, genomic, and proteomic data, we surprisingly discovered that CAF1 incorporates the histone variant H3.3 into Arabidopsis chromatin. Moreover, CAF1's role inH3.3 deposition is particularly pronounced in the transcribed regions of the genome.

overall_design: RNA-Seq profiling of wildtype Columbia-0 and hira-1 and fas2-4 mutants at 12 days after germination (12DAG) seedlings.

first: Israel

last: Ausin

first: Yafei

last: Wang

first: Fan

last: Yang

first: Yingpei

last: Su

first: Weijie

last: Xi


title: Integrative metaprogram analysis reveals transcriptional dysregulation of oxidative stress response in granulosa cells from polycystic ovary syndrome

status: Public on Apr 05 2025

city: Kunming

first: Xi

state: Yunnan Province

address: 157#, Jinbi Street

department: Reproductive Medicine

institute: First People’s Hospital of Yunnan Prov.

summary: Objective: The molecular mechanisms underlying polycystic ovary syndrome (PCOS) pathogenesis were investigated using an integrative metaprogram analysis framework, with specific focus on oxidative stress-related pathways through combined single-cell and bulk RNA sequencing approaches. Methods: Three datasets were integrated: a single-cell RNA-seq dataset (GSE240688), a laboratory-generated bulk RNA-seq dataset, and a validation microarray dataset (GSE34526). Transcriptional programs in granulosa cells were identified by non-negative matrix factorization, while dysregulated genes were characterized by differential expression and weighted gene co-expression network analyses. An integrative multi-omics approach was employed to identify key regulatory genes at the intersection of these complementary analytical methods. Results: Ten distinct transcriptional metaprograms in granulosa cells were identified, with metaprogram 4 (MP4) significantly enriched in PCOS samples and associated with oxidative stress response pathways. 199 consistently dysregulated genes across independent patient cohorts were revealed by differential expression analysis. Through integrative analysis, glutathione peroxidase 3 (GPX3) was identified as the only gene present across all three analytical approaches. GPX3 was significantly upregulated in PCOS samples with robust discriminatory power (AUC>0.8) and was functionally associated with insulin signaling, glucose metabolism, and mitochondrial pathways, suggesting its role in connecting oxidative stress and metabolic dysfunction. Conclusions: Oxidative stress responses were revealed as central to PCOS pathophysiology by our comprehensive multi-omics approach, with GPX3 identified as a key regulatory node connecting metabolic and reproductive dysfunction. A molecular basis for the oxidative stress-mediated pathology in PCOS is established by these findings.

overall_design: RNA was extracted from granulosa cells of 9 PCOS patients and 9 controls. PCOS diagnosis followed Rotterdam 2003 criteria (at least two of: oligo/anovulation, hyperandrogenism, polycystic ovarian morphology). Controls were women undergoing IVF for tubal or male factor infertility. Controls were matched with PCOS patients by age, BMI, and thyroid function. Patients with other endocrinopathies, diabetes, or taking reproductive/metabolic medications within three months were excluded. Granulosa cells were collected during oocyte retrieval. Total RNA was extracted using TRIzol reagent. Libraries were prepared with TruSeq RNA Library Prep Kit v2 and sequenced on Illumina NovaSeq 6000. The study aimed to identify transcriptional differences in granulosa cells between PCOS and control subjects.

first: Yunxiu

last: Li

first: Lei

first: Haishan

last: Zheng

first: Lanping

last: Zhong

first: Weiyuan

last: Ding

first: Manqing

last: Zhang

first: Zhenlin

last: He


status: Public on Apr 07 2025

city: Torrance

first: Michelle

last: Matter

address: 1124 West Carson Street

department: Genomics

institute: The lundquist Institute

summary: We conducted transcriptomic profiling of PPCM patient and normal hearts to examine differential gene expression and identified the peptidyl-tRNA hydrolase 2 (PTRH2, Bit-1; BIT1) gene and protein were significantly downregulated in PPCM patient hearts.

overall_design: Heart mRNA profiles of normal and diseased (PPCM) patients

first: Vanessa

last: Montoya-Uribe


title: Multivalent binding of the tardigrade Dsup protein to chromatin promotes yeast survival and longevity upon exposure to oxidative damage

status: Public on Apr 08 2025

city: Chapel Hill

first: Christopher

middle: K

last: Cummins

state: NC

address: 120 Mason Farm road

department: BCBP

institute: UNC Chapel Hill

summary: Tardigrades are remarkable in their ability to survive extreme environments. The damage suppressor (Dsup) protein is thought to contribute to their extreme resistance to reactive oxygen species (ROS) generated by irradiation. Here we show that expression of Ramazzottius varieornatus Dsup in Saccharomyces cerevisiae reduces oxidative DNA damage and extends lifespan in response to chronic oxidative genotoxicity. Dsup uses multiple modes of engagement with the nucleosomal H2A/H2B acidic patch, H3/H4 histone tails and DNA to bind across the yeast genome without bias. Effective chromatin binding and genome protection requires the Dsup HMGN-like motif and C-terminal sequences. These findings give precedent and mechanistic understanding for engineering an organism by physically shielding its genome to promote survival and longevity in the face of oxidative damage.

overall_design: RNA-seq analysis of yeast containing either a Dsup expressing plasmid or empty vector after treatment with 0mM, 4mM or 8mM H2O2.

first: Rhiannon

last: Aguilar

first: Laiba

last: Khan

first: Nina

last: Arslanovic

first: Thea

last: Grauer

first: Kyla

last: Birmingham

first: Kritika

last: Kasliwal