title: Chronic Cerebral Hypoperfusion Induces Pathological Venous Remodeling via EPAS1 Regulation

first: Vanessa

last: Wazny

address: 59 Nanyang Dr

institute: Nanyang Technological University

summary: Chronic cerebral hypoperfusion, induced by bilateral common carotid artery stenosis (BCAS), models the underlying cause of vascular dementia. We used single-cell transcriptomics to identify endothelial subtype-specific responses to BCAS in the mouse prefrontal cortex. The most dynamic molecular changes were observed in venous endothelial cells, with upregulated pathways linked to vascular remodeling and angiogenesis. Cerebral hypoperfusion upregulated expression of the endothelial PAS domain protein 1 (Epas1 ) gene in venous endothelial cells, while exposure of human venous endothelial cells to 1% oxygen in vitro caused sustained nuclear translocation of EPAS1. Pharmacological inhibition of EPAS1 reduced abnormal venous sprouting and concomitantly dampened microglia activation. Among human subjects with mild cerebrovascular disease, there was a negative correlation observed between their circulating damaged endothelial cells (CECs) and cerebral blood flow levels. In addition, elevated levels of venous-origin CECs were detected in subjects with white matter lesions and were notably linked to poorer overall cognitive function. We conclude that venous endothelial cells are potential therapeutic targets for vessel normalization to mitigate vascular cognitive impairment caused by chronic cerebral hypoperfusion.

overall_design: 10-week old mice underwent BCAS and sham surgery. Prefrontal cortex tissue was dissected and dissociated 10 days post-surgery, and single cells were captured using the 10X Chromium platform. After cDNA synthesis, library preparation, and high-throughput sequencing, a total of 4 sham mice and 4 BCAS mice (2 males and 2 females in each group) were sequenced and analyzed.

first: Nhi

last: Nguyen

first: Hannah

last: Wee

first: Ashwati

last: Vipin

first: Tammy

last: Lam

first: Aparna

last: Mahadevan

first: Martin

last: Graf

first: Kai

middle: Y

last: Tay

first: Gurveen

last: Sandhu

first: Leow

last: Jin

first: James

last: Chen

first: Jia-Xiang

last: See

first: Giuseppe

last: D'Agostino

first: Lay

middle: T

last: Ang

first: Sarah

middle: R

last: Langley

first: Kyle

last: Loh

first: Nagaendran

last: Kandiah

first: George

last: Augustine

first: Christine

last: Cheung


title: TICRR/TRESLIN and MTBP Cut&Run in HCT116 cells with inhibited origin licensing

status: Public on May 27 2025

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

country: USA

institute: Oklahoma Medical Research Foundation

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The selection of replication origins plays a crucial role in eukaryotic DNA replication. However, the mechanisms of origin selection in humans still need to be defined. Recent work in yeast has shown that the recruitment of Sld3-Sld7 to origins during G1 is involved in origin selection. In humans, TICRR/TRESLIN and MTBP are the orthologs of Sld3 and Sld7, respectively. In this study, we have mapped the genomic binding locations of TICRR/TRESLIN and MTBP in cells where loading of MCM2-7 complex has been inhibited by dox-inducible expression of a degradation-resistant Geminin(T25D).

overall_design: We utilized HCT 116 cell lines, where all TICRR/TRESLIN or MTBP alleles were tagged with mClover, to perform Cut&Run experiments with an anti-GFP antibody that specifically binds to the tag. Dox-inducible Geminin cell lines were generated from mClover-TICRR and mClover-MTBP lines by transfecting XLone-GemininT25D and pCMV-hyPBase. To obtain background signal measurements, we simultaneously conducted Cut&Run experiments on the untagged cell lines. Subsequently, the generated Cut&Run reads were aligned to the genome and used to call peaks.

first: Tyler

middle: D

last: Noble

first: Courtney

middle: G

first: Kimberlie

middle: A

last: Wittig

first: Blanka

last: Majchrzycka

middle: L


title: Species-specific gene regulatory network rewiring mediated by the GATA-type regulator NsdD in Aspergillus

status: Public on May 29 2025

city: Madison

first: Heungyun

middle: Harrison

last: Moon

state: WI

address: 1550 Linden drive

department: Bacteriology

institute: University of Wisconsin-Madison

type: Expression profiling by high throughput sequencing

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

sample_organism:
Aspergillus flavus
Aspergillus nidulans

platform_organism:
Aspergillus flavus
Aspergillus nidulans

overall_design: Refer to individual Series

first: Mi-Kyung

last: Lee

first: Junha

last: Shin

first: Sung Chul

last: Park

first: Julio

last: Vazquez

first: Daniel

last: Amador-Noquez

first: Nancy

last: Keller

first: Hee-Soo

first: Kap-Hoon

last: Han

first: Jae-Hyuk

last: Yu


title: Mitochondrial origins of the pressure to sleep

city: Oxford

first: Raffaele

last: Sarnataro

address: 13 Mansfield Road

department: Centre for neural circuits and behaviour

country: United Kingdom

institute: University of Oxford

summary: To gain a comprehensive, unbiased perspective on molecular changes in the brain that may underlie the need for sleep, we have characterized the transcriptomes of single cells isolated from rested and sleep-deprived flies. Here we report that transcripts upregulated after sleep deprivation, in sleep-control neurons projecting to the dorsal fan-shaped body (dFBNs) but not ubiquitously in the brain, encode almost exclusively proteins with roles in mitochondrial respiration and ATP synthesis. These gene expression changes are accompanied by mitochondrial fragmentation, enhanced mitophagy and an increase in the number of contacts between mitochondria and the endoplasmic reticulum, creating conduits for the replenishment of peroxidized lipids. The morphological changes are reversible after recovery sleep and blunted by the installation of an electron overflow in the respiratory chain. Inducing or preventing mitochondrial fission or fusion in dFBNs alters sleep and the electrical properties of sleep-control cells in opposite directions: hyperfused mitochondria increase, whereas fragmented mitochondria decrease, neuronal excitability and sleep. ATP concentrations in dFBNs rise after enforced waking because of diminished ATP consumption during the arousal-mediated inhibition of these neurons, which augments their mitochondrial electron leak. Consistent with this view, uncoupling electron flux from ATP synthesis relieves the pressure to sleep, while exacerbating mismatches between electron supply and ATP demand (by powering ATP synthesis with a light-driven proton pump) precipitates sleep. Sleep, like ageing, may be an inescapable consequence of aerobic metabolism.

overall_design: Brains of flies dissected and dissociated after 12h of sleep deprivation or ad libitum sleep included EGFP+ sleep-control neurons. Via flow cytometry, EGFP+ (sleep-control neurons) and EGFP- (rest of the brain) were sorted separately for both sleep-history conditions, and submitted for single-cell RNA-sequencing. The experiment was repeated in 3 replicates.

first: Gero

last: Miesenböck


title: Interleukin-35 impairs human NK cell effector functions and induces their ILC1-like conversion with tissue residency features

city: LYON cedex 08

first: Nathalie

last: Bendriss-Vermare

address: 28 rue Laennec

department: TERI

country: France

institute: CRCL

summary: While Natural Killer (NK) cells are key players in immune defenses against pathogens and cancers, by directly killing dangerous cells and supporting antitumor functions of other immune cells, they progressively get dysfunctional in chronic inflammatory diseases through mechanisms that remain insufficiently understood. NK cell development, survival, activation, and functions are highly regulated by cytokines. Among them, Interleukin 35 (IL-35), a new member of the IL-12 family released during chronic inflammations, plays a role in immune suppression. However, the direct effect of IL-35 on NK cells is still unknown. In this study, we observed that IL-35-exposed human primary NK cells display dampened proliferation and effector functions associated with differential expressions of activating and inhibitory NK receptors. Brief exposure to IL-35 inhibited NK cell activation and ability to secrete pro-inflammatory cytokines and chemokines, while promoting their production of pro-angiogenic factors and TGF-β. Furthermore, prolonged exposure to IL-35 placed NK cells in a functionally hyporesponsive state associated with a TGF-β-dependent conversion into CD9+ CD103+ CD49a+ ILC1-like cells. Single cell RNAseq further confirmed these observations and revealed an ILC1-like heterogeneity associated to the initial NK subpopulation undergoing the conversion. Thus, our findings identify a new role of IL-35 as a driver of NK cell plasticity leading to the acquisition of tissue residency features and weakened effector functions that might play a role in physiopathological contexts and represent an attractive target for future immunotherapies.

overall_design: Circulating primary NK cells were purified from heatlhy donors' blood and exposed to recombinant IL-35 cytokine in order to evaluate the effect of the cytokine on NK cell identity, phenotype, activation and functions

first: Valentin

last: Picant

first: Lara

last: Revol-Bauz

first: Laurie

last: Tonon

first: Dominique

last: Poujol

first: Emilie

last: Picard

first: Céline

last: Rodriguez

first: Cyril

last: Degletagne

first: Christophe

last: Caux


title: Different mutants impact on the transcriptome response to nutrients depletion

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: Quebec

address: 3201, rue Jean-Mignault

country: Canada

institute: University of Sherbrooke

summary: Mutating genes either from the U1 snRNP or U2 snRNP modified the expression of a common set of genes in the stationary phase of growth.

overall_design: RNA extracted from wild type cells (WT) of Saccharomyces cerevisiae and tor1 delta, nam8 delta, mud1 delta and hsh49::Q24P mutants was sequenced and their expression pattern compared in different phases of growth.

first: Sherif

last: Elela

first: Julie

last: Parenteau

first: Sonia

last: Couture


title: Refined DNA Repair Manipulation Enables a Universal Knock-in Strategy in Mouse Embryos

status: Public on May 26 2025

city: Xuhui, Shanghai

first: Jie

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai

country: China

institute: Center for Excellence in Brain Science and Intelligence Technology (Institute of Neuroscience), Chinese Academy of Sciences

summary: The design and screening of sgRNA in CRISPR-dependent gene knock-in is always laborious. Therefore, a universal and highly efficient knock-in strategy suitable for different sgRNA target sites is necessary. In our mouse embryo study, we find that the knock-in efficiency guided by adjacent sgRNAs varies greatly, although similar editing efficiency. MMEJ-biased sgRNAs usually lead to high knock-in efficiency, whereas NHEJ-biased sgRNAs result in low knock-in efficiency. Blocking MMEJ repair by knocking down Polq can enhance knock-in efficiency, but inhibiting NHEJ repair shows variable effects. We identify a compound, AZD7648, that re-orients NHEJ repair toward MMEJ. Finally, by combining AZD7648 treatment with Polq knockdown, we develop a universal and highly efficient knock-in strategy in mouse embryos. This approach is validated at more than ten genomic loci, achieving up to 90% knock-in efficiency, marking a significant advancement toward predictable and highly efficient CRISPR-mediated gene integration.

overall_design: We constructed an RNA-Seq dataset to investigate the transcriptome-wide effects of Polq knockdown using CasRX in mouse embryos. One-cell stage embryos were microinjected at 20 hours post-hCG administration, and total RNA was extracted 10 hours later when the embryos had reached the 2-cell stage. Each sample consisted of five embryos, and four biological replicates were included for both the Polq knockdown (CasRX/KD-Polq) and control (CasRX) groups.

first: Hongyu

last: Chen

first: Zhen

last: Liu


title: Endothelial Sensitivity to Pro-Fibrotic Signals Links Systemic exposure to Pulmonary Fibrosis

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Pulmonary fibrosis (PF) is a life-threatening condition characterised by excessive extracellular matrix deposition and tissue scarring. While much of PF research has focused on alveolar epithelial cells and fibroblasts, endothelial cells have emerged as active contributors to the disease initiation, especially in the context of systemic exposure to pro-fibrotic substances. Here, we investigate early transcriptomic and secretory responses of human umbilical vein endothelial cells (HUVEC) to subtoxic doses of bleomycin, a known pro-fibrotic agent, and TGF-beta, a key cytokine in fibrosis. Bleomycin exposure induced a rapid and extensive shift in the endothelial transcriptional programme, including signatures of endothelial to mesenchymal transition, cellular senescence, and immune cell recruitment. These findings suggest endothelial cells as early initiators of pro-fibrotic signals, independent of contributions from other cell types. In contrast, TGF-beta effects were limited and transient, indicating its pro-fibrotic action may require another initial stimulus and interplay with other cells like fibroblasts. This study highlights the sensitivity of endothelial cells to systemic pro-fibrotic exposure and provides a blueprint of early pro-fibrotic mechanisms, emphasising their pivotal role in PF pathogenesis.

overall_design: RNA-Seq profiling of HUVEC cells grown in a monolayer and exposed to multiple concentrations of bleomycin (0, 7, 14, and 21 µg/ml) and TGF-beta (0, 5, 10, and 20 ng/ml), respectively. RNA-Seq profiling was conducted at three consecutive timepoints by taking samples at 24, 48 and 72 hours of exposure in replicates of four for each experimental condition.

first: Lena

last: Möbus

first: Laura

last: Ylä-Outinen


title: Cells resist starvation through nutrients dependent splice switch

city: Ithaca

first: Jeffrey

last: Pleiss

state: NY

address: 215 Tower Rd. Room 453

department: Molecular Biology and Genetics

institute: Cornell University

summary: Removing introns from coding genes through the process of splicing is a ubiquitous feature of all eukaryotes. Here we show that global remodeling of splicing program through changing the stoichiometry of spliceosomal components is a key mediator of cell resistance to starvation. Transcriptomic and genetic analyses indicate that nutrients depletion reconfigures the splicing program to favor the splicing of meiotic genes and repress ribosomal protein genes by asymmetrically increasing the abundance of U1 small nuclear protein complex. Impairing U1 binding to splice site alters the nutrients dependent changes in the splicing program leading to increased sensitivity to starvation. This work reveals a new mechanism by which cells resist starvation through changes in the stoichiometry of the spliceosomal components and reprograming of the spliceosome splicing preference.

overall_design: To compare splicing genome wide using WT, nam8 deletion, and mud1 mutant strains in both log phase growth and nutrient depeletion/starvation conditions. This was done using Multiplexed Primer Extension Sequencing

first: Sara

last: Downs

last: Abou Elela


title: Serine synthesis pathway regulates cardiac differentiation from human pluripotent stem cells [scRNA-seq]

status: Public on May 24 2025

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

summary: Human induced pluripotent stem cells (hiPSCs) hold significant potential for advancing our understanding of heart development. Differentiating hiPSCs into cardiac cells allows for modeling early cardiac developmental processes and exploring key signaling pathways. However, variations in differentiation efficiency and poor reproducibility of hiPSC-derived cardiomyocytes (hiPSC-CMs) production have remained a challenge. Here, we report a unique metabolic method to promote hiPSC-CM differentiation that involves marked suppression of the mitochondrial oxidative phosphorylation from the mesendoderm to the cardiac mesoderm, which is regulated by PHGDH, a rate-limiting enzyme in the serine synthesis pathway (SSP). Mechanistically, the analysis of scRNA-seq revealed that SSP inhibition promotes CM lineage differentiation by disrupting the cardiopharyngeal mesoderm lineage differentiation. Our findings show that SSP can regulate cardiac differentiation and have implications in elucidating the potential mechanisms of heart development and pathogenesis of heart disease.

overall_design: hiPSCs were differentiated into CMs. Cells were treated with DMSO or NCT-503 from Day 1 to Day 3 and collected on Days 1, 3, 5, and 9 for scRNA-seq.

first: Tomohiko

last: Umei

first: Shugo

last: Tohyama


title: Altered Metabolomics and Inflammatory Transcriptomics in Human Bone Marrow Adipocytes After Acute High Calorie Diet and Acute Fasting

city: Burlinton

first: Arti

last: Sukla

state: VT

address: 89 Beaumont Avenue

department: Pathology and Laboratory Medicine

institute: University of Vermont

summary: Expansion of bone marrow adipocytes has been linked to nutritional pressures, suggesting that bone marrow is a dynamic compartment that responds to fluctuations in systemic nutritional availability to regulate osteogenesis and hematopoiesis. Here we investigated bone marrow metabolism in response to acute overnutrition (high calorie diet) and calorie deprivation (fasting). Participants underwent a 10-day high calorie diet followed by a two-week interval of an ad libitum diet and then underwent 10 days of fasting. Bone marrow adipocytes were collected before and after each dietary intervention. Using RNA-sequencing, we characterized nutritional influences on bone marrow adiposity. Bone marrow adipocytes after high calorie diet showed an upregulation of FOXP3 (p < 0.0001), the transcription factor that controls the development of Tregs, which are critical in reducing inflammatory immune responses. In contrast, bone marrow adipocytes after acute fasting had an upregulation of inflammatory genes (CP, CFH, and IGFBP3) (p < 0.0001). Overall, our results demonstrate key differences in inflammatory responses between high calorie diet and fasting, despite a nearly identical phenotype of bone marrow adipose tissue expansion. Further analyses are needed to understand the effects nutritional pressures have on bone marrow adipogenesis and immune responses.

overall_design: RNA-sequencing of bone marrow adipocytes before (pre) and after (post) acute high calorie diet and acute fasting. P-values were determined based on the comparison of the post to pre groups; high calorie post:pre (high nutritional effect) and fasting post:pre (low nutritional effect).

first: Samantha

middle: N

last: Costa

first: Gisela

last: Pachón-Peña

last: Dragon

first: Scott

last: Tighe

first: Calvin

last: Vary

first: Pouneh

middle: K

last: Fazeli

first: Miriam

last: Bredella

first: Clifford

middle: J

last: Rosen


title: Serine synthesis pathway regulates cardiac differentiation from human pluripotent stem cells [RNA-seq]

city: Shinjuku

address: 35 Shinanomachi

department: Department of Cardiology

institute: Keio University School of Medicine

summary: Differences of metabolism-related gene expression profiles in human pluripotent stem cells (hPSCs) and hPSC-derived cardiomyocytes (hPSC-CMs) were analyzed and successfully identified.

overall_design: 253G4, 201B7, H9, NKX2-5eGFP/w cell lines were used for this experiments. hPSC-CM induction protocol was based on the modulation of the WNT signaling pathway. From Day 13 to Day 17, the cells were incubated with glucose- and glutamine-free medium supplemented with lactate for metabolic selection. hPSC-CMs obtained on Day 30 were used in the experiments.


title: Macrophage-derived Spp1 promotes an adipogenic stromal cell population that contributes to intramuscular fat in dystrophic muscle

status: Public on May 23 2025

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: In this study we used macrophage-specific ablation combined with single cell transcriptional profiling to uncover the impact of macrophage derived Spp1 on cell-cell interactions in mdx muscles. Ablation of macrophage-specific Spp1 (cKO) correlated with reduction of two novel PDGFR+ stromal cell populations, expressing Lifr+ and Procr+ in cKO muscles. Sorting and transcriptional profiling of Lifr+ and Procr+ stromal cells confirmed that they are enriched in adipogenesis genes and are highly related to fibroadipogenic precursors (FAPS). These adipogenic stromal cells (ASC) were sorted and cultured and shown to be more adipogenic than FAPS, likely due to a more differentiated state. Reduction of ASCs correlated with reduced intramuscular diaphragmatic fat and improved diaphragm function in cKO compared to mdx controls. These data suggest a role for myeloid-derived Spp1 in the differentiation of stromal cells towards an adipogenic fate, leading to accumulation of intramuscular fat in dystrophic muscles.

overall_design: scRNAseq on mononucleated cells isolated from murine skeletal muscles in Spp1 cKO and WT mice.

first: Melissa

last: Spencer


title: B cell-extrinsic and intrinsic factors linked to early immune repletion after anti-CD20 therapy in patients with Multiple Sclerosis of African Ancestry

city: New York

first: Abhimanyu

last: Amarnani

address: 435 E 30th Street. 4th floor

institute: New York University

summary: We explored the potential of Illumina Infinium whole-genome genotyping (WGG) arrays to delineate SNPs that may influence treatment response or prognosis in multiple sclerosis (MS). Utilizing the Illumina Infinium ImmunoArray 24v2, our investigation centered on patients of African ancestry with MS. We sought to identify differences in genetic polymorphisms between individuals exhibiting accelerated B cell repopulation after anti-CD20 therapy and those with the expected six-month repopulation kinetics.

overall_design: To investigate and identify genetic polymorphisms of interest that may contribute to more rapid B-cell repopulation after semi-annual infusions of anti-CD20 monoclonal antibody therapies.

first: Gregg

last: Silverman


title: Intercellular communication between hepatic stellate cells and myofibroblasts mediated by osteopontin and FGF18

city: Tokyo

first: Takao

last: Seki

state: Ota-ku

address: 5-21-16 Omori-Nishi

department: Department of Biochemistry

institute: Toho University School of Medicine

summary: Purpose: To further explore FGF18's role in liver fibrosis beyond its known effects on HSC proliferation and TGFβ signaling, we performed RNA sequencing on primary HSCs treated with FGF18 or TGF-b. Methods: Fresh isolated HSCs were starved with DMEM containing 0.2% FBS for 24 hours and then left untreated or stimulated with FGF18 (100 ng/mL), TGFb1 (1 ng/mL). Total RNA was extracted from HSCs using RNeasy Micro Kit (74004, QIAGEN). RNA libraries were prepared using the SMART-Seq HT PLUS Kit (R400748, Takara Bio) according to the manufacturer's protocol.Paired-end sequencing (2 × 150 bp) was performed on a NovaSeq 6000 system (Illumina) to generate approximately 40M reads (20M pairs) per sample, with a target of 6G bases per sample. Results: RNA-seq analysis revealed that FGF18 induced Ccnd1 while suppressing profibrotic genes such as Col1a2, Col3a1, and Acta2, whereas TGFβ showed opposite effects. Among 62 genes upregulated by both factors, we focused on Spp1, encoding osteopontin, given its known role in tissue fibrosis.

first: Yuichi

last: Tsuchiya

first: Takashi

last: Nishina

first: Hiroyasu

last: Nakano


title: Preclinical and first-in-human of Purinostat Mesylate, a novel selective HDAC I/IIb inhibitor, in relapsed or refractory multiple myeloma and lymphoma [scRNA-seq]

city: Chengdu

first: Qiang

last: Qiu

state: Sichuan

address: No. 17, the Third Part of Renmin South Road

institute: SKLB

summary: Purinostat Mesylate (PM), a highly selective HDAC I/IIb inhibitor, exhibits excellent antitumor activity in multiple MM and lymphoma cell lines and multiple mouse models, outperforming the pan-HDAC inhibitor panobinostat or first-line/second-line multi-drug combinations. Different from panobinostat, bulk RNA-seq analysis results revealed that PM targeted essential tumor survival factors, and triggered inflammation and interferon responses. ScRNA-seq of 5TMM models further indicated that PM enhanced antitumor immunity by boosting monocyte- and T cell-mediated immune responses.

overall_design: To investigate the effect of the I/IIb HDAC inhibitor Purostatin Mesylate (PM) on Multiple Myeloma (MM) gene expression and  its immune microenvironment, we treated 5TGM MM model mice with Vehicle or PM (10 mg/kg) for 24 hours and collected total bone marrow cells for scRNA-seq.

first: Linyu

last: Yang

first: Yi

last: Wen

first: Yunyu

last: Feng

first: Ting

last: Niu

first: Lijuan

last: Chen


title: Single cell and spatial alternative splicing analysis with Nanopore long read sequencing

city: PHILADELPHIA

first: YUNTIAN

last: FU

state: PA

address: 265 S. 37th Street

institute: University of Pennsylvania

summary: Long-read sequencing has become a powerful tool for alternative splicing analysis. However, technical and computational challenges have limited our ability to couple long-read sequencing with single cell and spatial barcoding to explore alternative splicing in the single cell and spatial setting. Though Nanopore-based long reads sequencing are widelyhave been adopted applied to explore single cell alternative and spatially barcoded librariessplicing in recent research, there still exist technical issues have problems which could bias the hindered accurate single cell isoform-level  quantification, which are not well addressed in such settings. First,   Tthe relatively higher sequencing error of Nanopore long reads, despite the recent improvements, has limited the accuracy ofhinder cell barcode and unique molecular identifier (UMI) recovery, a necessary first step in the analysis of single cell/spatial sequencing data.  Then Rread truncation and mapping errors, the latter exacerbated by the higher sequencing error rates, further leads to the false detection of spurious new isoformsdegrade quantification accuracy.  We show that these technical issues persist despite the recent improvements in long read sequencing accuracy.  Beyond the initial data pre-processing, in downstream analysis we are lacking a statistical framework to quantify splicing variation within and between cells/spots.  In light of these multiple challenges, we developed Longcell, a statistical framework and computational pipeline for isoform quantification using single cell and spatial spot barcoded Nanopore long read sequencing data.  Longcell performs computationally efficient cell/spot barcode extraction, UMI recovery, and UMI-based truncation- and mapping-error correction.  Through a statistical model that accounts for varying read coverage across cells/spots, Longcell rigorously quantifies the level of inter-cell/spot versus intra-cell/ spot diversity in exon-usage and detects changes in splicing distributions between cell populations.  Applying Longcell to single cell long-read data from multiple contexts, we found that intra-cell splicing heterogeneity, where multiple isoforms co-exist within the same cell, is ubiquitous for highly expressed genes. On matched single cell and Visium long read sequencing for a tissue of colorectal cancer metastasis to the liver, Longcell found concordant signals between the single cell and spatial data modalities.  On Visium long read sequencing data for multiple tissues, Longcell allows accurate identification of spatial isoform switching.  Finally, on a perturbation experiment for 9 splicing factors, Longcell identified regulatory targets that are validated by targeted sequencing.

overall_design: 9 valid splicing factors are knocoked out by CRISPR in a Jurkat cell sample to assesses how genetic variants at splicing sites and splicing factors contribute to alternative mRNA isoforms

first: Heonseok

last: Kim

first: Sharmili

last: Roy

first: Billy

last: Lau


title: Hepatic NMNAT1 is required to defend against alcohol-associated fatty liver disease

status: Public on May 25 2025

city: hangzhou

first: Qinchao

last: Ding

state: zhejiang

address: 548 Binwen Road, Binjiang District

institute: Zhejiang Chinese Medical University

summary: Nicotinamide mononucleotide adenylyltransferase 1 (NMNAT1), an NAD+ synthetase in Preiss-Handler and salvage pathways, governs nuclear NAD+ homeostasis. This study investigated the role of NMNAT1 on alcohol-associated liver disease (ALD). Decreased NMNAT1 expression and activity were observed in the liver of alcohol-associated hepatitis patients and either liver or primary hepatocytes from ALD mice. F-box and WD repeat domain containing 7 (FBXW7)-regulated interferon regulatory factor 1 (IRF1) ubiquitination degradation contributed to alcohol-inhibited NMNAT1 transcriptional level. Hepatic NMNAT1 knockout aggravated alcohol-induced hepatic NAD+ decline and further hepatic steatosis and liver injury. Metabolomics and transcriptomics interaction revealed that cysteine sulfinic acid decarboxylase (CSAD)-regulated taurine pathway was involved in NMNAT1-disrupted hepatic lipid metabolism in ALD. Hepatic CSAD overexpression or taurine supply attenuated hepatic NMNAT1 knockout-aggravated ALD, respectively. Hepatic NMNAT1 loss inhibited NMN-protected ALD. Replenishing hepatic NMNAT1 reversed liver lipid accumulation in ALD mice. These findings identified NMNAT1 as a promising therapeutic target for ALD.

overall_design: To investigate the function of Nicotinamide mononucleotide adenylyltransferase 1 (NMNAT1) in the development of alcohol-associated liver disease, we generated liver-specific Nmnat1 KO mice using Alb-Cre/loxP system. These mice were subjected to the Lieber-DeCarli ALD model. We then performed RNA sequencing analysis using the liver tissue.

first: Feiwei

last: Cao

first: Songtao

last: Li


title: Cut&Tag data analysis of TgSNF2L on the whole genome of Toxoplasma gondii tachyzoites [SNF2L Cut&Tag]

city: wuhan

first: yuchao

last: zhu

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

summary: Transcriptomic analyses revealed the gene expression changes after SNF2L depletion. To see which of these differentially expressed genes are directly targeted by SNF2L, we used Cut&tag to assess the binding positions of SNF2L in the parasite’s genome.

overall_design: Cut&tag(Cleavage Under Targets and Tagmentation)  for TgSNF2L in Toxoplasma tachyzoites.

first: Yuchao

last: Zhu

first: Bolin

last: Fan

first: Bang

last: Shen


title: MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (ChIP-Seq)

city: Austin

first: Blerta

last: Xhemalçe

state: Texas

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: MePCE is a multifunctional protein that regulates the Positive Transcription Elongation Factor b (P-TEFb) partitioning between the nucleosol and chromatin. While the role of MePCE in sequestering P-TEFb in the nucleoplasm through the 7SK ribonuclear protein complex (RNPc) is well understood, its functions on chromatin remain obscure. In order to address this gap in our knowledge, we performed mass spectrometry of MePCE interactors on chromatin. Our analysis revealed that chromatin-associated-MePCE mainly interacts with factors involved in R-loop processing and DNA repair factors. Consistent with this initial finding, MePCE is rapidly recruited to laser-mediated DNA damage and AsiSI-mediated DNA double stranded breaks (DSBs). Moreover, MePCE depletion specifically impairs DSB repair by homologous recombination (HR). To explore the molecular mechanism behind the observed HR defect, we took advantage of an inducible AsiSI system to analyze the effect of MePCE depletion in DSB repair factor recruitment and R-loop levels at over 100 genomic site-specific DSBs. Consistent with impaired HR, MePCE depletion decreases RAD51 loading and enhances R-loop levels specifically at DSBs. Analysis of R-loop protein complexes by mass spectrometry revealed that in addition to decreasing specific R-loop processing factors and chromatin remodelers, MePCE depletion increased the interaction with R-loops of the other constitutive member of the 7SK RNPc, LARP7, which is degraded by BRCA1/BARD1 upon DSB. Overall, our results uncover dynamic regulation of the 7SK RNPc at DSBs during the repair process and explain the recently observed synthetic lethality of MePCE and BRCA1 deficiency.

overall_design: Chromatin Immunoprecipitation of GFP (control), MePCE in U2OS-Flp-In-TREx siNC or siMePCE cells.

first: Sravan

last: Devanathan

first: Samantha

middle: B

last: Shelton

first: Joshuah

last: Nguyen

first: Wei

middle: C

last: Tseng

first: Nakul

middle: M

last: Shah

first: Marvin

last: Mercado

first: Kyle

last: Miller


title: Cut&Tag data analysis of TgSNF2L-mAID on the whole genome of Toxoplasma gondii tachyzoites [SNF2L Cut&Tag]

overall_design:
Cut&tag(Cleavage Under Targets and Tagmentation) for TgSNF2L-mAID in Toxoplasma tachyzoites.
HA tag was expressed in fusion with SNF2L protein. The antibody used was Anti-HA tag (abcam,[12CA5] (ab1424)), lot number: 1054528-1.


title: RNA-seq data analysis of TgSNF2L on Toxoplasma gondii development [ME49 SNF2L RNAseq]

summary: To investigate transcriptional role of TgSNF2L on type II Toxoplasma gondii (ME49 Tir1), an auxin inducible degron system was introduced to control the protein expression of TgSNF2L after adding IAA.

overall_design: Transgenic parasite ME49 iKD SNF2L-3HA-mAID was treated with IAA for 0h, 12h or 24h then total RNA were extracted for deep sequencing.


title: MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (RNA-Seq)

overall_design: RNA-seq data of siNC or siMePCE in U2OS-Flp-In-TREx or U2OS- AiD DiV A- AsiSI -ER cells.

first: Yi


title: CDK12 tumor suppressor function and therapeutic targeting in newly developed mouse models of serous ovarian cancer

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

summary: Adenocarcinoma of the ovary is the fifth leading cause of cancer death among American women. Most mortality results from high-grade serous ovarian carcinoma (HGS-OvCa)—a disease type resistant to conventional chemotherapy, and therein requiring urgent preclinical modeling for pharmaceutical testing. We generated a novel serous ovarian carcinoma model by employing Ovgp1-driven Cre recombinase to catalyze CRISPR-Cas9-medicated ablation of the Trp53, Rb1 and Nf1 tumor suppressor genes in the mouse ovary (m-sgPRN mice). The gene encoding cyclin dependent kinase 12 (CDK12) is among the most frequently inactivated in HGS-OvCa. Its loss corresponds with increased mortality, DNA damage (including tandem duplications) and tumor immunogenicity. Co-ablation of Cdk12 in the m-sgPRN model (m-sgPRN; Cdk12KO mice) accelerated tumor progression leading to bona fide HGS-OvCa, and early mortality. In a conventional (Cre-lox-medicated) Trp53/ Nf1/ Rb1 triple knockout model, Cdk12 ablation (PRN; Cdk12KO mice) effected immune infiltration characterized by CD3, CD8, CD4, and Granzyme B positivity like that seen in clinical HGS-OvCa. We observed recapitulation of this immunogenic phenotype—with corresponding sensitivity to immune checkpoint blockade—in a novel syngeneic allograft model derived from these animals. To screen for synthetic lethal interactions with Cdk12 loss, we conducted a CRISPR-Cas9 screen in PRN; Cdk12KO cell lines. The gene encoding CDK12 paralog CDK13 emerged as the most depleted, suggesting CDK13 could be targeted to promote paralog-induced synthetic lethality as previously demonstrated in CDK12-mutant prostate cancer. Indeed, m-sgPRN; Cdk12KO and PRN; Cdk12KO -derived cell lines exhibited enhanced sensitivity to the CDK13/12 degrader YJ1206. Our work defines CDK13-targeting as a novel treatment modality for CDK12-inactive HGS-OvCa while establishing biological resources for the in vivo modeling of this disease.

overall_design: To investigate role of CDK12 in ovarian cancer development, we established cell lines from mouse model of ovarian cancer and performed RNA-seq

first: Tien

last: Jean

first: Zhai

last: Yali

first: Wu

last: Rong

first: Zhang

last: Yuping

first: Chang

last: Yu

first: Cheng

last: Yunhui

first: Todd

last: Abbey

first: Wheeler

last: Christina

first: Li

last: Shquin

first: Ekanayake

last: Derrick

first: Mannan

last: Rahul

last: Caleb

first: Magnuson

last: Brian

first: Cao

last: Michael

first: Mahapatra

last: Somnath

last: Xuhong

first: Su

last: Fengyun

first: Wang

last: Rui

first: Qiao

last: Yuanyuan

first: Xiao

last: Lanbo

first: Chou

last: Jonathan

first: Cieslik

last: Marcin

first: Ding

last: Ke

first: Cho

last: Kathleen

first: Chinnaiyan

last: Arul


title: γδ+ T cell-derived IL-17A stimulates airway epithelial/stromal cells to secrete G-CSF, promoting lung-specific pathogenic Siglec-F+ neutrophil development in PPE-induced emphysema

city: Suwon

first: JungHyub

last: Hong

address: 2066 Seobu-ro

country: South Korea

institute: University of SungKyunKwan

summary: Neutrophils play a pivotal role in the progression of IL-17-mediated airway inflammation, but the mechanisms underlying their pathological differentiation remain poorly understood. In this study, we identified a distinct population of lung-specific pathogenic Siglec-F+ neutrophils in a porcine pancreatic elastase (PPE)-induced mouse model of emphysema. These Siglec-F+ neutrophils exhibited enhanced phagocytic activity, increased extracellular trap formation, and elevated production of pro-inflammatory cytokines, alongside reduced IL-10 levels, compared to conventional neutrophils. During the early phase of acute inflammation following PPE instillation, IL-17A levels in the lung increased, primarily driven by γδ+ T cells. IL-17A stimulated lung epithelial/stromal cells to secrete granulocyte colony-stimulating factor (G-CSF), which promoted the differentiation of Siglec-F+ neutrophils via the JAK2/STAT3 pathway, PI3K-independent mTOR, and p38 MAPK signaling pathways. Neutralizing G-CSF or inhibiting JAK2/STAT3, mTOR or p38 MAPK signaling significantly suppressed Siglec-F+ neutrophil development, resulting in alleviation of emphysematous symptoms. Our findings underscore the crucial role of Siglec-F+ neutrophils in the pathogenesis of PPE-induced emphysema and suggest that targeting the IL-17A/G-CSF axis or G-CSF receptor downstream signaling pathways may represent a promising therapeutic strategy for treating emphysema.

overall_design: RNA-seq profiling of neutrophils derived from the bone marrow of C57BL/6J wild-type mice after 6 hours of stimulation with Medium or G-CSF.

first: Yong-Soo

last: Bae


title: RNA-seq data analysis of TGME49_217480 on Toxoplasma gondii development [TGME49_217480 RNAseq]

first: yuchao

last: zhu

summary: To investigate transcriptional role of TGME49_217480 on type II Toxoplasma gondii (ME49 Tir1), an auxin inducible degron system was introduced to control the protein expression of TGME49_217480 after adding IAA.

overall_design: Transgenic parasite ME49 iKD TGME49_217480-3HA-mAID was treated with IAA for 0h or 12h then total RNA were extracted for deep sequencing.

first: Yuchao

last: Zhu

first: Bolin

last: Fan

first: Bang

last: Shen


title: MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (ChIP-Seq & DRIP-seq)

first: Blerta

last: Xhemalçe

overall_design:
ChIP-seq: Chromatin Immunoprecipitation of GFP (control), RAD51, XRCC4, MePCE in U2OS- AiD DiV A- AsiSI -ER cells.
DRIP-seq: DNA/RNA hybrid Immunoprecipitation of siNC, siNC + RNase H, siMePCE, siMePCE +RNase H samples in U2OS- AiD DiV A- AsiSI -ER cells.

first: Sravan

last: Devanathan

first: Yi

last: Li

first: Samantha

last: Shelton

first: Joshuah

last: Nguyen

first: Wei

last: Tseng

first: Nakul

last: Shah

first: Marvin

last: Mercado

first: Kyle

last: Miller


title: Effect of KSHV lytic reactivation on host mRNA m5C modification landscape in lymphoma B cell

city: Columbus

first: Zhenyu

last: wu

state: Ohio

address: 281 W Lane Ave

department: Pathology

institute: The ohio state university

type: Methylation profiling by high throughput sequencing

summary: Herpesviruses are a group of double-stranded DNA viruses known to develop versatile viral strategies to escape host immune surveillance for promoting their replication and propagation. This is illustrated by Kaposi’s sarcoma-associated herpesvirus (KSHV), an oncogenic gamma-herpesvirus that overcomes host immune suppression by multiple mechanisms. In this study, we reported that KSHV dysregulates 5-methylcytosine (m5C) modification and mRNA stability of host antiviral factors to benefit its lytic replication. KSHV lytic reactivation or de novo challenge led to downregulation of m5C RNA methyltransferases, NSUN2 and NSUN1 (NSUN2/1), while NSUN2/1 depletion promoted KSHV lytic replication. We further performed the RNA bisulfite sequencing (RNA-BS-seq) to identify KSHV-dependent m5C modification of host mRNAs. Overall, our results highlighted a new strategy for human gamma-herpesviruses to counteract host antiviral factors and promote their lytic replication by manipulating host m5C RNA methylation.

overall_design: To study the impact of KSHV lytic reactivation on host mRNA modifications, we utilize TREx.BCBL1.Rta cell, a cell line with Doxcycline induced RTA expression system.  TREx.BCBL1.Rta cells were treated with Doxcycline (2 ug/ml) for 48 hours to induce RTA expression and Lytic reactivation. We then perform RNA-BS-seq on the samples (with or without Dox treatment) with two biological repeats. Differential m5c sites were identified using meRanTk package between samples.

last: Wu

first: Jian


title: Cysteine deficiency triggers adipose tissue thermogenesis and weight-loss [single-cell RNA-seq]

status: Public on May 22 2025

city: New Haven

first: Lucie

last: Orliaguet

state: CT

address: 310 Cedar Street

institute: Yale University

summary: Caloric restriction (CR) and methionine restriction driven enhanced lifespan and healthspan induces ‘browning’ of white adipose tissue (WAT), a metabolic response that increases heat production to defend core-body temperature. However, how specific dietary amino acids control adipose thermogenesis is unknown.  Here, we identified that weight-loss induced by CR in humans reduces thiol-containing sulfur amino acid cysteine in WAT. Systemic cysteine-depletion in mice causes lethal weight-loss with increased fat utilization and browning of adipocytes that is rescued upon restoration of cysteine in diet. Mechanistically, cysteine restriction induced adipose browning and weight-loss requires sympathetic nervous system derived noradrenaline signaling via β3-adrenergic-receptors that is independent of FGF21 and UCP1. In obese mice, cysteine deprivation induced rapid adipose browning, increased energy expenditure leading to 30% weight-loss and reversed metabolic inflammation. These findings establish that cysteine is essential for organismal metabolism as removal of cysteine in the host triggers adipose browning and rapid weight loss.

overall_design: single cell RNA-seq of stromal vascular cells from subcutaneous (SFAT)adipose depots of Cth+/+ (WT) and Cth-/- (KO) mice fed with control or cystine deficient diet fro 4 days.

first: Aileen

middle: H

last: Lee

first: Vishwa Deep

last: Dixit


title: Lactate facilitates pancreatic repair following acute pancreatitis by promoting reparative macrophage polarization

city: SHANGHAI

first: jing

last: jiang

state: China

address: CHINA SHANGHAI

institute: SHANGHAI GENERAL HOSPITAL

summary: Based on the role of lactate in mitigating inflammation during acute pancreatitis (AP) repair, we focused on macrophages, as previous studies have highlighted their essential role in pancreatic tissue repair following AP. To investigate the relationship between lactate and the phenotype and function of macrophages during the recovery phase after AP, we performed high-throughput mRNA sequencing on macrophages isolated from the pancreatic tissues of C57BL/6J wild-type mice, which were administered lactate or PBS following induction of a recovery AP model.

overall_design: Macrophages were isolated from the pancreas of caerulein-treated C57BL/6J wild-type mice on days 0, 1, and 3 following the induction of a recovery AP model, using fluorescence-activated cell sorting. Total RNA was extracted from these macrophages and prepared for RNA sequencing.

first: Jing

last: Jiang

first: Ruiyan

last: Wang

first: Pengli

last: Song

first: Qi

last: Peng

first: Xuerui

last: Jin


title: RNA-seq data analysis of TGME49_203980 on Toxoplasma gondii development [TGME49_203980 RNAseq]

first: yuchao

last: zhu

summary: To investigate transcriptional role of TGME49_203980 on type II Toxoplasma gondii (ME49 Tir1), an auxin inducible degron system was introduced to control the protein expression of TGME49_203980 after adding IAA.

overall_design: Transgenic parasite ME49 iKD TGME49_203980-3HA-mAID was treated with IAA for 0h or 12h then total RNA were extracted for deep sequencing.

first: Yuchao

last: Zhu

first: Bolin

last: Fan

first: Bang

last: Shen


title: Cysteine deficiency triggers adipose tissue thermogenesis and weight-loss

overall_design: RNA-seq profiling of brown (BAT), visceral (EFAT) and subcutaneous (SFAT)adipose depots of Cth+/+ and Cth-/- mice fed with control or cystine deficient diet.


title: ATAC-seq data analysis of TgSNF2L on the whole genome of Toxoplasma gondii tachyzoites [SNF2L ATAC-seq]

summary: To understand the changes in chromatin structure following SNF2L deletion, we used the Assay for Transporse-Accessible Chromatin with High-throughput Sequencing (ATAC-seq) to assess changes in chromatin accessibility following SNF2L deletion.

overall_design: ATAC-seq for SNF2L-mAID in Toxoplasma tachyzoites with or without IAA treatment.


title: Normothermic human kidney preservation drives iron accumulation and ferroptosis

city: Leiden

first: Roan

middle: Hugo

last: van Scheppingen

address: Albinusdreef 2

country: Netherlands

institute: LUMC

summary: Ex vivo normothermic machine perfusion has been proposed to protect deceased donor kidneys. However, its benefits remain ambiguous. We postulate that the use of red blood cells (RBCs) and associated secondary hemolysis may in fact cause renal injury, offsetting potential advantages. During 48-hour normothermic perfusion of seven human donor kidneys, we observed progressive hemolysis, leading to iron accumulation in perfusate, tissue, and urine. Untargeted lipidomic profiling  revealed significant increases in oxidized phospholipid species in perfused kidneys, pointing towards iron-dependent cell death known as ferroptosis. Next, in twelve additional perfusions, we assessed strategies to mitigate hemolysis-driven injury. Dialysis-based free hemoglobin removal reduced lipid peroxidation, but a ferroptosis gene signature persisted. In contrast, cell-free perfusion at subnormothermia negated iron accumulation, the ferroptosis gene signature, phospholipid peroxidation, and acute kidney injury. Our findings highlight the pathological role of hemolysis and iron on the kidney, urging restraint in the clinical application of RBC-based kidney perfusion.

overall_design: Human kidney biopsies were taken prior to, during, or at the end of warm preservation.

first: Marlon

last: de Haan

first: Marleen

middle: E

last: Jacobs

first: Annemarie

last: de Graaf

first: Rico

last: Derks

first: Dorottya

last: de Vries

first: Jesper

last: Kers

first: Ian

middle: P

last: Alwayn

first: Cees

last: van Kooten

first: Elena

last: Sánchez-López

first: Martin

last: Giera

first: Marten

last: Engelse

first: Ton

last: Rabelink


title: Replication stress responses in human lymphocytes change sex-specifically during aging

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: The varying incidence of aging-related diseases and the gender gap in life expectancy suggest differences in the aging process between the sexes. Yet, little is known about sexspecific differences in genomic instability, a key factor in aging. Here we analyzed DNA damage responses (DDRs) in cycling human peripheral blood lymphocytes (PBL) from female and male donors of different age focusing on replication stress. Transcriptomics revealed striking sex-dependent expression changes in DDR pathways during aging. Particularly, various DDR components, involved in DNA repair and replication fork remodeling were upregulated with age in men. In contrast, functional analysis indicated reduced activity of the Fanconi Anemia pathway in PBL from older women. In line, DNA fiber spreading and PCNA ubiquitination analyses revealed a shift from fork remodeling to faster DNA damage tolerance (DDT) mechanisms in older women, accompanied by an increase in replication stress. While replication dynamics were unaltered and replication stress rather reduced, PBL from older men were highly dependent on PARP activity. In conclusion, our findings revealed sex-specific strategies to cope with replication stress in PBL from older individuals, namely through DDT pathway switching in women and PARP activation in men, differentially contributing to the decline of genomic stability with age.

overall_design:
The experiment is an analysis to compare gene expression in peripheral blood lymphocytes (PBLs) based on age (young [18-25 yrs]/ old [>60 yrs]) and sex (male / female).

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

first: Melanie

last: Rall-Scharpf

first: Marco

last: Groth

first: Helmut

last: Pospiech

first: Lisa

last: Wiesmüller


title: Loss of genome maintenance is linked to mTORC1 signaling and accelerates podocyte damage

city: Cologne

first: Björn

last: Schumacher

address: Joseph-Stelzmann-Str. 26

institute: CECAD Research Center

summary: DNA repair is essential for preserving genome integrity. Podocytes, post-mitotic epithelial cells of the kidney filtration unit, bear limited regenerative capacity, yet their survival is indispensable for kidney health. Podocyte loss is a hallmark of the aging process and of many diseases, but the underlying factors remain unclear. We investigated the consequences of DNA damage in a podocyte-specific knockout mouse model for Ercc1 and in cultured podocytes under genomic stress. Furthermore, we characterized DNA damage-related alterations in mouse and human renal tissue of different ages and patients suffering from minimal change disease and focal segmental glomerulosclerosis. Ercc1 knockout resulted in accumulation of DNA damage ensuing albuminuria and kidney disease. Podocytes reacted to genomic stress by activating mTORC1 signaling in vitro and in vivo. Perturbed DNA repair gene expression and genomic stress in podocytes was also detected in focal segmental glomerulosclerosis. Beyond that, DNA damage signaling occurred in podocytes of healthy aging mice and humans. We provide evidence that genome maintenance in podocytes is linked to the mTORC1 pathway, involved in the aging process and the development of glomerulosclerosis.

overall_design: Bulk total RNA-seq of isolated glomeruli from podocyte-specific ERCC1 fl/fl mice and control mice at 9w of age.

first: Fabian

last: Braun

first: David

last: Meyer

first: He

last: Chen

first: Christine

last: Kurschat


title: Targeting microglial Cx43 in Alzheimer's disease

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

summary: Alzheimer's disease (AD) remainsis a prevalent major cause of senile dementia without effective therapeutic strategiesy. Although Recent studies highlight the critical role of microglia has been well accepted to play a critical role in AD pathology, particularly in the early stages, this study is the first breakthrough to show, suggesting that modulation of pathological microglial states represents a therapeutic opportunity. Here we provide evidence that microglial connexin 43 (Cx43) hemichannel is the main switch ofs regulate microglial reactivity in the context of AD, as well as a promising  hence presenting a potential therapeutic target. We demonstrated a marked increase in Cx43 protein level in the periplaque microglia in the post-mortem tissue from AD patients. In APPswe/PS1dE9 mouse model, we discoveredfound that microglial Cx43 operates as a hemichannel to influence microglial function, which in turn affects in  β-amyloid pathology. Ablation of microglial Cx43 hemichannels by genetic knockout screwed microglia to neuroprotective phenotype by promotinges the microglia-plaque interaction while suppressing the neurotoxic microglial signature, and thereby mitigating the progression of AD. Following this lead, wWe developed a novel formulation of small molecule peptide, treatment strategy employing lipid nanoparticle-delivered molecule TAT-Cx43266-283 (TAT-CX43@LNPs), which selectivespecifically targets blocks Cx43 hemichannels, and conducted a. Our preclinical trialstudy that demonstrated its efficacyeffectiveness in delaying and rescuing β-amyloid-related neuropathology and cognitive impairment in AD mice. This study provides strong evidence to progress our novel drug into clinical trials and translate it not only into a therapeutic agent during disease progression but also offer strong preventive benefits when administered early.

overall_design: To investigate the role of Microglial Cx43 in Alzheimer's disease, we used Cx3cr1-CreER:Cx43-flox/flox:APP/PS1 mice to specifically knockout Cx43 in microglial. At 9-month-old, microglial was isolated from the mouse cortex and hippocampus by immunopanning using rat-anti mouse CD45 antibody. Age matched wild type and APP/PS1 mice were setup as controls. All mice are in C57BL6/j background.

first: Jianqin

last: Niu

first: Chenju

last: Yi


title: Early NK-cell and T-cell dysfunction marks progression to severe dengue in patients with obesity and healthy weight

city: Oxford

first: Lucy

last: Garner

address: Experimental Medicine, Level 5, John Radcliffe Hospital

department: Nuffield Department of Medicine

institute: University of Oxford

summary: Dengue is a mosquito-borne virus infection affecting half of the world’s population for which therapies are lacking. The role of T and NK-cells in protection/immunopathogenesis remains unclear for dengue. We performed a longitudinal phenotypic, functional and transcriptional analyses of T and NK-cells in 124 dengue patients using flow cytometry and single-cell RNA-sequencing. We show that T/NK-cell signatures early in infection discriminate patients who will progress to severe dengue (SD) from those who do not. In patients with overweight/obesity these signatures are exacerbated compared to healthy weight patients, supporting their increased susceptibility to SD. In SD, CD4+/CD8+ T-cells and NK-cells display increased co-inhibitory receptor expression and decreased cytotoxic capacity compared to non-SD. Furthermore, type-I Interferon signalling is downregulated in SD, suggesting defective virus-sensing mechanisms may underlie NK/T-cell dysfunction. We propose that dysfunctional “professional killer” T/NK-cells underpin dengue pathogenesis. Our findings pave the way for the evaluation of immunomodulatory therapies for dengue.

overall_design: BD Rhapsody single-cell RNA-sequencing (Targeted mRNA) of PBMCs from 24 dengue patients at T1 (≤ five days from fever onset). N=12 severe dengue and N=12 non-severe dengue patients, with each group including six healthy weight and six overweight/obesity patients matched by sex and age.

first: Paul

last: Klenerman

first: Laura

last: Rivino


title: A PIF-SAUR module safeguards hypocotyl elongation from ABA inhibition in the dark

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Driven by cell elongation, hypocotyl growth is tightly controlled by light and responds to both external stimuli and endogenous hormonal pathways. Hypocotyls are responsive to the stress signalling hormone abscisic acid (ABA), which effectively inhibits cell elongation. However, how this regulation is connected to light signalling has been a subject of limited studies. Here, we show that, contrary to light-grown seedlings, hypocotyl elongation of dark-grown seedlings is ABA-insensitive. In the dark, hypocotyl sensitivity to ABA is restored in the constitutive photomorphogenic pifq and cop1-4 mutants, suggesting that an active light signalling pathway is necessary for hypocotyl responsiveness to ABA. Surprisingly, etiolated hypocotyls retain an intact ABA signalling pathway, as could be detected by the induction of ABI1 and RD29B transcripts in response to exogenous ABA, suggesting that inhibition of hypocotyl elongation occurs through a divergent path that can be inhibited by PIFs. Here, using RNA-seq analysis we identified a number of ABA differentially expressed genes (DEGs) that correlate with ABA inhibition of hypocotyl elongation. Among these DEGs a number of SMALL AUXIN-UP RNA (SAUR) genes that are known to directly repress D-CLADE TYPE 2C PROTEIN PHOSPHATASES (PP2C.D) were found. The abrogation of PP2CD.D2-SAUR interaction in the pp2c.d2/PP2C.D2M331K -GFP line, restored ABA sensitivity in the dark, suggesting that SAUR proteins, upregulated by PIFs, are sufficient to render hypocotyls insensitive to ABA. This hypocotyl-specific mechanism enables to promote growth towards the light at all costs, overriding ABA inhibition of cell elongation, to ensure subsequent seedling establishment and survival.

overall_design: RNA-Seq profiling of wild type and pifq mutant arabidopsis seedlings with or without ABA and in presence or absence of light. Three biological replicates per sample type.

first: Esther

last: Cañibano

first: Natalia

last: Rodríguez-Sánchez

first: Daniela

last: Gómez-Soto

first: Fátima

middle: Z

last: El-Kendi

first: Jorge

last: Lozano-Juste

first: Toshinori

last: Kinoshita

first: Clara

last: Bourbousse

first: Sandra

last: Fonseca


title: The RNA-binding protein PCBP2 is a regulator of microRNAs partition between cell and extracellular vesicles.

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: "Sapienza" University of Rome

type: Non-coding RNA profiling by high throughput sequencing

summary: While it is accepted that Extracellular Vesicles (EVs)-mediated transfer of microRNAs contributes to intercellular communication, the knowledge about molecular mechanisms controlling the selective and dynamic partition of miRNAs between intracellular and EV compartments is still largely limited. As yet, the interactions between specific RNA-binding proteins (RBPs) and short RNA sequences, have been proved causal for the loading of multiple miRNAs in EVs. Conversely, although in silico and mutagenesis analysis demonstrated the presence/function of specific sequence determinants causal to miRNAs intracellular retention, the interacting protein/s remained unknown. Here, the RBP Poly-C-binding protein 2 (PCBP2, also known as hnRNPE2 or αCP2), was identified as a direct interactor of the CELL-motif: RNA immunoprecipitation (RIP) after UV cross-linking, coupled to RNA pull down, demonstrated that this protein directly binds to miRNAs embedding this sequence and mutagenesis of the motif proved the specificity of its binding. Functionally, PCBP2 knock-down allows the EV-loading of specific intracellular microRNAs. Furthermore, a second requirement for PCBP2 specific binding was identified in SYNCRIP, a previously characterized miRNA EV-loader. SYNCRIP and PCBP2 may contemporarily bind to miRNAs endowed of both hEXO and CELL motifs, as demonstrated by RIP and EMSA assays. Mechanistically, SYNCRIP knock-down appears to limit PCBP2 recruitment. Overall, this body of evidence i) extends PCBP2 known pleiotropic functions to the role of intracellular determinant of miRNAs retention acting as a dominant inhibitor of SYNCRIP function and ii) highlights that multiple proteins/miRNA interactions govern miRNA compartmentalization.

overall_design: To investigate PCBP2 functional role in miRNA partition bewteen cell and extrecellular vesicles, we established a 3A cell line in which PCBP2 has been knocked down by shRNA. Then we performed small RNA squencing of shPCBP2 and shCTR cells and their extracellular vesicles.

first: Francesco

last: Marocco

first: Sabrina

last: Garbo

first: Claudia

last: Montaldo

first: Gioele

last: Gaboardi

first: Carla

last: Cicchini

first: Gian

middle: G

last: Tartaglia

first: Andres

last: Ramos

first: Cecilia

last: Battistelli

first: Marco

last: Tripodi


title: Transcriptional repatterning in early liver regeneration is driven by regeneration-specific and developmental enhancers

city: Barcelona

first: Marina

last: Ruiz-Romero

state: Catalonia

address: Dr. Aiguader 88

institute: CRG

summary: Tissue regeneration is characterised by a series of coordinated molecular and physiological events. Central to this process is the precise modulation of gene expression, triggered by changes in chromatin structure and temporal activation of distant regulatory elements. The mammalian liver is a unique organ with remarkable regenerative capabilities after injury or resection. Through the integration of chromatin accessibility and transcriptomic data following partial hepatectomy in mice, we show the highly dynamic nature of the early regenerative response at the chromatin level. Our findings suggest a model in which the expression of crucial regeneration genes is orchestrated by a plethora of cis-regulatory elements, each under the control of specific transcription factors. We have discovered enhancers exclusive to the regenerating tissue that collaborate with enhancers co-opted from various developmental stages. These, along with liver enhancers that exhibit increased activity post-injury, contribute to activating the transcriptional programs required for hepatocyte priming and proliferation. Altogether, these enhancers are likely under the control of the AP-1 complex together with other transcription factors such as ATF3 and NRF2. Furthermore, we show that a pivotal aspect of hepatic regeneration involves downregulation of genes associated with liver-specific functions in lipid metabolism through the inactivation of their enhancers, and we propose the potential role of regeneration-specific silencer elements governed by YY1.

overall_design: To identify the regulatory elements involved in the early stages of liver regeneration, we conducted genome-wide chromatin accessibility profiling (ATAC-Seq) analysis in mouse livers during the first two days after partial hepatectomy (PHx). We collected the tissue at 6, 24, and 48 hours after SHAM-surgery (CTRL) or after 2/3 PHx (REG)

first: Palmira

last: Llorens-Giralt

first: Ramil

last: Nurtdinov

first: Macarena

last: Herranz-Itúrbide

first: Guillermo

last: Vicent

first: Florenci

last: Serras

first: Isabel

last: Fabregat

first: Montserrat

last: Corominas


title: MADS-Box Transcription Factors Regulate Dimorphic Transition and Temperature Adaptation in the Pathogenic Fungus  Talaromyces marneffei [RNA-Seq]

status: Public on May 21 2025

city: Beijing

first: Xueyan

last: Hu

state: Beijing

address: 38 Xueyuan Rd, Haidian District

institute: Peking University Health Science Center

summary: The dynamic transition between yeast and hyphal forms is a crucial adaptive mechanism for many human pathogenic fungi, including Talaromyces marneffei, a thermodimorphic fungus responsible for causing fatal talaromycosis globally. This study aimed to uncover the genetic mechanisms underlying the dimorphic transition in T. marneffei, focusing on the MADS-box transcription factor family. Using adaptive laboratory evolution, we identified MADS-box genes enriched in dimorphism-defective mutants, revealing a notable expansion of this gene family in T. marneffei. Phylogenetic analysis and functional genetic manipulations confirmed the involvement of mads9, mads10, and mads13 in regulating the yeast-hypha transition. Integrating RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq), we demonstrated that these transcription factors target genes involved in transmembrane transport, redox processes, and cellulose binding. Our findings not only clarify the role and regulatory mechanisms of the MADS-box family in dimorphic transitions but also present a valuable strategy for identifying regulatory genes based on morphological variations and high-throughput sequencing, paving the way for further systematic genetic studies of fungal temperature adaptation.

overall_design: ChIP-seq and paried RNA-seq were performed on wild type PM1 strain, madsA overexpression, mads9 overexpression, and madsA knockout, and mads9 knockout strains under both mycelia and yeast conditions.

first: Yun

last: Zhang

first: Minghao

last: Du

first: Juan

last: Wang

first: Yang

last: Yang

first: James

last: Cai

first: Ence


title: scRNA-seq of human cerebral organoids derived from healthy and FOXG1 syndrome patients iPSCs at d105

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

institute: University of Freiburg

summary: Disruptions in gene expression programs during nervous system development?affecting both transcriptional and post-transcriptional regulation?are implicated in a range of neurodevelopmental disorders. Among these, FOXG1 syndrome remains poorly understood, particularly with respect to the mechanistic role of its namesake gene, FOXG1. In this study, we performed single-cell RNA sequencing (scRNA-seq) on day 105 (d105) cerebral organoids derived from healthy controls as well as from iPSCs carrying FOXG1^del and FOXG1^c.460dupG mutations, to investigate cell type?specific gene expression changes.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on day 105 (d105) human cerebral organoids derived from healthy controls (2 replicates) and FOXG1-syndrome patient-derived iPSCs representing two genotypes (2 replicates each). The patient-specific mutations include the FOXG1^del and FOXG1^c.460dupG frameshift mutations.

first: Fabian

last: Gather

first: Camila

last: Fullio

first: Ipek

last: Akol


title: A next-generation inhaled aerosol COVID-19 vaccine boosts lung immunity in human

city: Hamilton

first: Zhou

last: Xing

state: Ontario

address: MDCL building, 1280 Main St W

department: Division of Respirology

institute: McMaster University

summary: A new inhaled aerosol vaccine using chimpanzee adenoviral vectors induces robust mucosal immunity in the lungs, including T cell, innate, and antibody responses, providing broader protection against SARS-CoV-2 variants. This strategy is superior to intramuscular mRNA vaccines and prior SARS-CoV-2 infection.

overall_design: Bronchoalveolar lavages were collected from individuals before and 4 weeks after receiving an inhaled aerosol next-generation COVID-19 vaccine. Cells from bronchoalveolar lavage fluid (BALF) were cryopreserved and later revived for analysis. Alveolar macrophages (AMs) were enriched and cultured in vitro with or without stimulation using Mycobacterium tuberculosis whole cell lysate (WCL), a bacterial pathogen-associated molecular pattern cocktail. After stimulation, RNA was extracted from the AMs and subjected to RNA sequencing (RNA-Seq) to assess transcriptional changes associated with vaccination and innate immune training.

first: Mangalakumari

last: Jeyanathan

first: Sam

last: Afkhami

first: Michael

middle: R

last: D’Agostino

first: Imran

last: Satia

first: Dominik

last: Fritz

first: Kate

last: Miyasaki

first: Jann

last: Ang

first: Anna

last: Zganiacz

first: Karen

last: Howie

first: Marilyn

last: Swinton

first: Emilio

last: Aguirre

last: Zheng

first: Natallia

last: Kazhdan

last: Dvorkin-Gheva

first: Lawrence

last: Mbuagbaw

first: Maria Fe

last: Medina

first: Nermin

last: Diab

first: Danica

middle: L

last: Brister

first: Gail

last: Gauvreau

first: Brian

middle: D

last: Lichty

first: Matthew

last: Miller

first: Fiona

last: Smaill


title: Binding sites of FOXG1 in human iPSC derived neural stem cells and 105 day old cerebral organoids

first: Tanja

last: Vogel

summary: Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and posttranscriptional processes, are implicated in diverse neurodevelopmental diseases. One of those debilitating diseases, the FOXG1-syndrome, lacks full understanding of the mechanistic role of its eponymous gene product, FOXG1. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions in the mouse, it is unclear which parts of the human chromatin associate with FOXG1. Here, we analyzed FOXG1 binding at the chromatin in  human iPSC derived neural stem cells and 105 day old cortical organoids.

overall_design: FOXG1-ChIPseq in human neural stem cell and cerebral organoids

first: Fabian

last: Gather

first: Ipek

last: Akol


title: Cellular Defense Mechanisms Show Stronger Response to Linear DNA Compared to Circular Plasmid [RNA-seq]

city: Hong Kong

first: yicen

last: zhou

address: Block 2, To Yuen Building, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Low transfection efficiency poses a significant challenge to experimental success, making the improvement of gene-carrying plasmid delivery and expression essential across various research fields. The stability of transfected vector DNA or mRNA significantly impacts transgene expression, as the innate immune system may recognize plasmid DNA as foreign and initiate a degradation response. Currently, it is unclear whether RNA transcribed from plasmids can activate RNA sensors, affecting transfection efficiency. This study employed RNA sequencing to analyze cellular responses to various circular and linear DNAs across five cell lines—HEK293T, HCT116, HeLa, L02, and NCM460—revealing that the innate immune response is a primary contributor to low transfection efficiency. Additionally, we used ChIP-seq to detect H3K27ac histone marks to explore whether the immune response triggered by plasmid transfection is regulated by epigenetic mechanisms. Finally, we performed ChIP assays for IRF7 and p-IRF3 in HeLa cells transfected with the linear pcDNA3.1-neo plasmid to demonstrate that these two transcription factors can indeed bind to the RTV genes.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of HEK293T, HCT116, HeLa, L02, and NCM460 cells transfected with an empty vector, pcDNA3.1-neo plasmid, linear pcDNA3.1-neo plasmid, pre-gRNA plasmid, or linear pre-gRNA plasmid. Additionally, we incorporated RNA sequencing data from  L02 and HCT116 cells transfected with linear pcDNA3.1-neo plasmid and linear pre-gRNA plasmid treated with PNK or AP.

first: Xiaoyu

last: Li

first: Yicen

last: Zhou

first: Jie

last: Wei

first: Wei

last: Sun

first: Ligang

last: Fan

first: Jian

last: Yan


title: Comparative bulk RNAseq analysis of Control and Ctnnb1-deficient CXCL12+ apical papilla cells.

city: Houston

first: Wenbo

last: Chen

address: 7000 Fannin Street

institute: The University of Texas Health Science Center at Houston

summary: Lack of Ctnnb1 in CXCL12+ apical papilla cells causes a cell fate shift and fail to differentiate into root forming cells such as odontoblasts or cementoblasts. Here, we set out to reveal the transcriptome change induced by Ctnnb1 deficiency in CXCL12+ apical papilla cells

overall_design: tdTomato+ cells were FACS-isoalted from postnatal day 10 (P10) apical papilla of Ctnnb1 conditional Het and conditional KO mandibular molars (tamoxifen pulse at P3). mRNA were amplifed by SMART-Seq V4 PLUS Kit (R400752, Takara Bio) before deep-sequenced by Illumina NextSeq550.

first: Noriaki

last: Ono

first: Wanida


title: The lincRNA Pantr1 mediates site-specific chromatin binding of FOXG1 in hippocampal neurons

summary: Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and posttranscriptional processes, are implicated in diverse neurodevelopmental diseases. One of those debilitating diseases, the FOXG1-syndrome, lacks full understanding of the mechanistic role of its eponymous gene product, FOXG1. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions, it is unclear what factors control its presence at specific sites. Long non-coding RNAs (lncRNAs) can mediate site-directed transcription factor binding, but their potential role in FOXG1-syndrome has not been described. Here, we show that the lncRNA Pantr1 mediates site specific binding of FOXG1 using FOXG1 ChIP sequencing upon Pantr1 knockdown.

overall_design: FOXG1 ChIP-seq was performed on samples collected from DIV7 primary hippocampal neurons treated with shPantr1 or shLuciferase.


title: The role of the lincRNA Pantr1 during the development of the neurons in the FOXG1 syndrome mouse model

summary: This study instigates the role of the long non-coding RNA Pantr1 (or Brn1a) in the context of nervous system development and in the neurodevelopmental disorder Foxg1-related syndrome. We report a high-throughput single-end RNA sequencing experiment in hippocampal neurons cultured in vitro in mouse. We performed the knockdown of Purb, Pantr1 and Foxg1 in hippocampal neurons cultured in vitro to 7 days and performed RNA-seq analysis.

overall_design: Loss of function: three knock down conditions (sh_Pantr1, Sh_Foxg1, Sh_Purb ) and one control (Sh_luciferase(CTL), all having 5 replicates.

first: Tudor

last: Rauleac

first: Teresa

last: Müller


title: Deconvoluting clonal and cellular architecture in IDH-mutant Acute Myeloid Leukemia

city: New York

first: Maria

last: Sirenko

state: NY

address: 550 1st Avenue

institute: NYU Langone

summary: Isocitrate dehydrogenase 1/2 (IDH) mutations are early initiating events in acute myeloid leukemia (AML). The complex clonal architecture and cellular heterogeneity in IDH-mutant AML underlies the heterogeneous clinical presentation and outcomes. Integrating single-cell genotyping and transcriptomics, we demonstrate a stem-like and inflammatory phenotype of IDH-mutant AML and identify clone-specific programs associated with NPM1, NRAS, and SRSF2 co-mutations. Furthermore, these clones had distinct responses to treatment with combination IDH inhibitors and chemotherapy, including elimination, reconstitution of myeloid differentiation, or retention within progenitor populations. At relapse after IDH inhibitor monotherapy, we identify upregulated stemness, inflammation, mitochondrial metabolism, and anti-apoptotic factors, as well as downregulated major histocompatibility complex (MHC) class II antigen presentation. At the pre-leukemic stage, we observe upregulation of IDH2-associated pathways, including inflammation. We deliver a detailed phenotyping of IDH-mutant AML and a framework for dissecting contributions of recurrently mutated genes in AML at diagnosis and following therapy, with implications for precision medicine.

overall_design:
To study the role of co-mutations in shaping disease presentation and treatment response in IDH1/2-mutant AML to either conventional cytotoxic chemotherapy and/or IDH-directed inhibitors +/- hypomethylating agents, we screened the OSU biobank for samples from patients receiving targeted IDH1/2 inhibitors and prioritized samples on the basis of availability of sequential samples, including matched diagnostic and post-treatment samples. In total, we obtained 30 cryopreserved bone marrow aspirate or peripheral blood samples from 9 patients at longitudinal timepoints beginning at diagnosis. We profiled 9 newly diagnosed patients (AML07-11) receiving IDH1/2 inhibitor monotherapy or in combination with Azacytidine (AML12-13) or chemotherapy alone (AML14-15). Serial samples were collected at remission (n= 9 patients, median time after diagnosis (41 days) and relapse timepoints (n=4 patients; median time 985 days). Frozen bone marrow samples were thawed and transferred into 50ml conical tubes containing 1x PBS +2% fetal bovine serum (FBS). Cell suspensions were centrifuged at 300 x g for 5 minutes at 4℃, and supernatant was removed. Samples were then enriched for >90% alive cells by using a dead cell removal kit, or stained with DAPI before sorted for alive cells using SY3200 Cell Sorter (SONY). For cell sorting, DAPI low cells are collected into 15ml conical tubes containing 3ml FBS on ice. Samples were then centrifuged at 300 x g for 5 mins at 4℃. For CITE-seq, enriched alive cells were first stained with cell-hashing oligo-tagged antibodies (Biolegend) according to manufacturer’s instructions. Then samples were counted and pooled together and stained with a CITE-seq antibody cocktail (Biolegend) according to the manufacturer’s instructions. After staining, samples were processed using 10X Genomics Chromium controller with the Single Cell Gene Expression 3’ Reagent Kits (v3 and v3.1). Libraries were sequenced on an Illumina NovaSeq 6000. The detailed information of antibody panels, antibody barcodes, hashtag assignment for each sequencing library is provided in the “CITEseq_panels.xlsx” file.
To study the role of co-mutations in shaping disease presentation and treatment response in IDH-mutant AML to either conventional cytotoxic chemotherapy and/or IDH-directed inhibitors +/- hypomethylating agents, we screened the MSKCC and OSU biobank sfor samples from patients receiving targeted IDH inhibitors and chemotherapy and prioritized samples on the basis of availability of sequential samples, including matched diagnostic and post-treatment samples. We obtained cryopreserved bone marrow aspirate or peripheral blood samples from 20 patients. Two peripheral blood samples from IDH-mutant clonal hematopoiesis were also profiled. All samples were profiled by 10X RNA-seq. Please see manuscript methods for more details.
We ascertained 20 IDH-mutated AML patients with representative co-mutations by clinical sequencing (Figure 1D, STAR Methods, and Table S1). Six had IDH1 mutations, 13 had IDH2 mutations, and 1 had both IDH1 and IDH2 (IDH1 25% VAF and IDH2 12% VAF). IDH mutations had clonal VAFs, indicating early acquisition. The co-occurring mutations in DNMT3A (n = 15 patients), NPM1 (n = 7), and SRSF2 (n = 7) reflect the genomic landscape of IDH-mutant AML (Figure 1A). Five patients had copy-number aberrations reported by clinical cytogenetics. In total, 57 longitudinal bone marrow or peripheral blood samples (median 3 samples per patient) were profiled under treatment with IDHi monotherapy (n = 6), IDHi in combination with intensive chemotherapy (NCT02632708, n = 6) or in combination with hypomethylating agent (n = 3), or chemotherapy alone (n = 4). Finally, to study how IDH2 mutations affect hematopoiesis at a pre-leukemic state, we profiled two individuals with IDH2-mutant CH (VAF 17%). The single-cell RNA sequencing (scRNA-seq) dataset comprises 386,794 cells from 20 AML patients (n = 317,317 cells), 2 CH individuals (n = 16,705), and 12 unaffected age-matched donors (n = 52,772 cells; n = 8 donors previously published24) (Figure 1E).

first: Soobeom

last: Lee

first: Zhengxi

first: Elli

last: Papaemmanuil

first: Iannis

last: Aifantis

first: Ann-Kathrin

last: Eisfeld

first: Dan

last: Landau


title: FOXG1 associates with RNA

first: Tanja

last: Vogel

summary: Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and posttranscriptional processes, are a frequent cause of diverse neurodevelopmental diseases. One of those debilitating diseases, the FOXG1-syndrome, lacks full understanding of the mechanistic role of its eponymous gene product, FOXG1. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions, it is unclear what factors control its presence at specific sites. Long non-coding RNAs (lncRNAs) are implicated in site-directed transcription factor binding, but their potential role in FOXG1-syndrome has not been described. This data set is based on sequencing of co-immunoprecipitated RNA and it shows that FOXG1 associates with different RNAs.

overall_design: FOXG-RIPseq of P0 mouse brain

first: Fabian

last: Gather


title: Hippocampal epitranscriptomic (m6A) in human model of Temporal Lobe Epilepsy

status: Public on May 20 2025

city: Dublin

first: Gary

last: Brennan

state: Dublin

address: UCD Conway Institute, Stillorgan Road

department: School of Biomolecular and Biomedical Sciences

country: Ireland

institute: UCD

type:
Methylation profiling by array
Other

summary: Analogous to DNA methylation and protein phosphorylation it is now well understood that RNA is also subject to extensive processing and modification. N6-methyladenosine (m6A) is the most abundant internal RNA modification and regulates RNA fate in several ways including stability and translational efficiency. The role of m6A in both experimental and human epilepsy remains unknown. Here we use transcriptome-wide m6A arrays to obtain a detailed analysis of the hippocampal m6A-ome from human temporal lobe epilepsy samples. We show that epileptic tissue displays disrupted metabolic and autophagic pathways which may be directly linked to m6A-processing. Together our findings indicate that m6A represents a novel layer of gene regulation complexity in epilepsy and may contribute to the pathomechanisms which drive the development and maintenance of hyperexcitable brain networks.

overall_design:
The study investigates the m6A methylation differences between epilepsy and non-epilepsy controls. The epilepsy group is further stratified into two subtypes, based on clinical characterisation of either temporal lobe epilepsy with hippocampal sclerosis (sclerotic TLE) or temporal lobe epilepsy without hippocampal sclerosis (non-sclerotic TLE.  Sclerotic TLE (n = 7) vs Non-sclerotic TLE (n = 7) vs Non-epilepsy autopsy control (n = 10). Arraystar Human m6A Single Nucleotide Resolution Microarray was used to identify differential methylation patterns across groups
Please note that experiments are carried out as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed as single channel (Cy3 and Cy5 signals are calculated). Each raw file contains both Cy5 (MazF-Digested) and Cy3 (MazF-UnDigested) data, and is linked to the corresponding MazF-Digested sample record.

first: Marc-Michel

last: Wilson


title: RNA-Seq analysis of high-fiber diets and caloric restriction in mouse liver

city: Shanghai

first: Ziyun

last: Wu

state: Shanghai

address: 800 Dongchuan RD

department: Food Science and Engineering

institute: Shanghai Jiao Tong University

summary: mRNA expression profiling of genes regulated by high-fiber diets and caloric restriction in 3-month-old mouse liver.

overall_design: Three months male mice fed with CR, RD, IF30, IF30m, CF30 and CF30m diets for 4 hours were evaluated.

first: Fangchao

last: Hu

first: Yu

last: Lu

first: Xingyu

last: Tu

first: Rong

last: Huang

first: Xinyue

first: Xinlin

last: Wei


title: Simulating Neonatal Microglial Pan-Programmed Cell Death to Unlock Regenerative Potential in Adult Mice Spinal Cord Injury [RNA-seq]

city: Xi'an

first: Beibei

last: Yu

address: No. 157, Xiwu Road, Xincheng District, Xi'an City, Shaanxi Province

institute: The Second Affiliated Hospital, Xi’an Jiaotong University

summary: In adult mammals, dysregulated programmed cell death (PCD) following spinal cord injury (SCI) impairs regeneration by causing neuronal loss, exacerbating inflammation, and disrupting tissue repair. However, the complex interplay of PCD pathways necessitates the establishment of an SCI-specific diverse cell-death (pan-PCD) framework to quantify PCD dynamics and identify therapeutic targets. Here, we found that, unlike adults, neonatal mammals exhibit superior regenerative capacity due to a balanced PCD response, making them a valuable model for mimicking pan-PCD levels to promote regeneration. To address this, we introduce "Thanatoset," a pan-PCD gene panel, to comprehensively profile cell death dynamics in SCI. Among various cell types, microglia were identified as key mediators of pan-PCD, exhibiting heightened susceptibility in adult mice. Through computational drug screening, we identified Withaferin A (WFA), a compound capable of reprogramming microglial PCD to a neonatal-like regenerative state. In vitro and in vivo experiments demonstrated that WFA modulates NF-κB signaling, reducing inflammation, improving motor function, decreasing scar formation, and facilitating neuronal recovery. These findings underscore the therapeutic potential of modulating pan-PCD to restore regeneration and improve SCI outcomes in adults.

overall_design: Neonatal C57BL/6 mice (P2) were anesthetized using isoflurane, while adult female C57BL/6 mice (weighing 18–20 g) were anesthetized via intraperitoneal injection of 3% sodium pentobarbital solution (40 mg/kg). Spinal cord crush injury was performed as previously described. Briefly, a laminectomy was performed at the thoracic level (T9-10) to fully expose the spinal cord laterally. The spinal cord was then crushed using No. 5 Dumont forceps (Fine Science Tools) at the final 5 mm portion of the forceps, with a tip width of 0.1 mm. In the sham-operated group, only the laminectomy was performed without subsequent spinal cord injury. Postoperative care included the application of diclofenac sodium ointment for analgesia and the use of a heating pad to maintain the animals' body temperature overnight. Neonatal mice were returned to the maternal cage after being covered with maternal mouse feces. Manual bladder expression was performed daily until the mice were euthanized.      Neonatal C57BL/6 mice (P2) were anesthetized using isoflurane, while adult female C57BL/6 mice (weighing 18–20 g) were anesthetized via intraperitoneal injection of 3% sodium pentobarbital solution (40 mg/kg). Spinal cord crush injury was performed as previously described. Briefly, a laminectomy was performed at the thoracic level (T9-10) to fully expose the spinal cord laterally. The spinal cord was then crushed using No. 5 Dumont forceps (Fine Science Tools) at the final 5 mm portion of the forceps, with a tip width of 0.1 mm. In the sham-operated group, only the laminectomy was performed without subsequent spinal cord injury. Postoperative care included the application of diclofenac sodium ointment for analgesia and the use of a heating pad to maintain the animals' body temperature overnight. Neonatal mice were returned to the maternal cage after being covered with maternal mouse feces. Manual bladder expression was performed daily until the mice were euthanized.After injury, take 1cm of the injury area for transcriptome sequencing on 1, 3, and 7 days.

first: Yongfeng

last: Zhang

first: Jinghui


title: Cellular and Molecular Characteristics of Drug Resistance in AML cells Unveiled by Multi-Omics Analysis

city: Zhengzhou

first: Yanfang

address: Weiwu road 7th

institute: Zhengzhou University

summary: Acute myeloid leukemia (AML) exhibits a spectrum of responses to chemotherapy, with drug resistance being a significant clinical challenge. This study employs a multi-omics approach, particularly multiplexed single-cell RNA sequencing (scRNA-seq), to characterize the molecular mechanisms underlying drug resistance in AML cells. We identified significant cellular heterogeneity and a dynamic transcriptomic trajectory in AML cells with specific drug treatment, and discovered a reprogramming towards a more stem-like state. Interestingly, Ara-C-resistant KG-1a cells predominantly originated from G2/M subpopulations, indicating a cell cycle-specific resistance mechanism. Our analysis also revealed that epigenetic changes of DNA methylation and chromatin architechture, and altered transcription factor activities were implicated in rapid Ara-C resistance, whereas exomic mutations did not significantly contribute to it. We suggest both intrinsic and acquired resistance mechanisms act together and build a resultant force that aids AML cells in evading therapeutic interventions. The multidimensional changes observed post-treatment showed a complex interplay in the development of drug resistance. This study provides a cellular and molecular portrait of drug response and resistance in AML, offering potential therapeutic targets and a foundation for future research aimed at overcoming chemoresistance.

overall_design: Cell lines in a different conditions were labeled with specific sample barcodes, and then were subjected to multiplexed scRNA-seq on 10x Genomics or BD Rhapsody platform.

first: Yulong


title: scRNAseq analysis of WT and tfeb-tfe3s triple knock-out zebrafish embryos at 4 days post fertilization

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

institute: nih

summary: The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions, they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however, the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock-out (KO) alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple-KO (tfeb-tfe3a-tfe3b) animals are lethal, and these transcription factors are involved in pancreas and liver development.

overall_design: Wild-type (WT) and tfeb-tfe3a-tfe3b triple knock-out (TKO) embryos were collected at 4 days post fertilization (dpf), and GFP+ (neurons and pancreatic acinar cells) or dsRED+ (hepatocytes and pancreatic endocrine beta-cells) cells from dissociated embryos were isolated by Fluorescence-activated cell sorting (FACS) and analyzed by scRNA-seq.

first: Alberto

last: Rissone

first: Martina

last: La Spina

first: Erica

last: Bresciani

first: Syed

last: Zulfeqhar

first: Chris

last: Combs

first: Martha

last: Kirby

first: Abdel

last: Elkahloun

first: Vicky

last: Chen

first: Raman

last: Sood

first: Shawn

last: Burgess

first: Rosa

last: Puertollano


title: TGFβ inhibition during radiation therapy enhances immune cell infiltration and decreases metastases in a novel humanized mouse model Ewing sarcoma.

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

summary: Ewing sarcoma is an aggressive cancer most commonly diagnosed in adolescents and young adults. Various mechanisms of TGFβ inhibition are being tested in clinical trials for patients with relapsed Ewing sarcoma. However, the functional impact of TGFβ inhibition on the Ewing tumor microenvironment remains largely unstudied given the historical lack of immunocompetent preclinical models of Ewing sarcoma. Here, we use single cell RNAseq analysis of human Ewing tumors to demonstrate that immune cells are the largest source of TGFβ production in the human Ewing tumor microenvironment. We develop and utilize a humanized mouse model of Ewing sarcoma to study the effect of TGFβ inhibition on the Ewing tumor immune microenvironment both at baseline and during radiation therapy, a treatment that enhances TGFβ activation and is often used to treat patients with aggressive Ewing sarcoma.  Finally, we utilize a bivalent ligand TGFβ TRAP and demonstrate that, in combination with radiation, TGFβ inhibition both increases immune cell infiltration in Ewing tumors and decreases lung metastatic burden.

overall_design: In this study, tumor specimens were obtained from two patients with Ewing sarcoma. Dissociated single cell suspensions were subjected to 5'-based single-cell RNA sequencing using 10X Genomics.

first: Jessica

last: Daley

first: Kelly

last: Bailey


title: Direct genetic transformation bypasses tumor-associated DNA methylation alterations

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

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

overall_design: Refer to individual Series


title: Identification of the Notch ligand DLK1 as an immunotherapeutic target and regulator of tumor cell plasticity and chemoresistance in adrenocortical carcinoma

status: Public on May 19 2025

city: Bethesda

first: Nitin

last: Roper

address: 37 Convent Drive

department: Developmental Therapeutics Branch

institute: National Cancer Institute

summary: While immunotherapeutic targeting of cell surface proteins is an increasingly effective cancer therapy, identification of new surface proteins, particularly those with biological importance, is critical. Here, we uncover delta-like non-canonical Notch ligand 1 (DLK1) as a cell surface protein with limited normal tissue expression and high expression in multiple refractory adult metastatic cancers including small cell lung cancer (SCLC) and adrenocortical carcinoma (ACC), a rare cancer with few effective therapies. In ACC, ADCT-701, a DLK1 targeting antibody-drug conjugate (ADC), shows in vitro and in vivo activity but is overall limited due to high expression and activity of the drug efflux protein ABCB1 (MDR1, P-glycoprotein). In contrast, ADCT-701 induces complete responses in DLK1+ ACC and SCLC in vivo models with low or no ABCB1 expression. Genetic deletion of DLK1 in ACC dramatically downregulates ABCB1 and increases ADC payload and chemotherapy sensitivity through NOTCH1-mediated transdifferentiation. This work identifies DLK1 as an immunotherapeutic target that regulates tumor cell plasticity and chemoresistance in ACC and supports an active phase I clinical trial targeting DLK1 with an ADC in ACC and neuroendocrine neoplasms (NCT06041516).

overall_design: We assesssed for gene expression changes among ACC PDX tumors relapsed after ADCT-701 treatment.

first: Nai-Yun

last: Sun


title: MADS-Box Transcription Factors Regulate Dimorphic Transition and Temperature Adaptation in the Pathogenic Fungus  Talaromyces marneffei [ChIP-Seq]

first: Xueyan

last: Hu

summary: The dynamic transition between yeast and hyphal forms is a crucial adaptive mechanism for many human pathogenic fungi, including Talaromyces marneffei, a thermodimorphic fungus responsible for causing fatal talaromycosis globally. This study aimed to uncover the genetic mechanisms underlying the dimorphic transition in T. marneffei, focusing on the MADS-box transcription factor family. Using adaptive laboratory evolution, we identified MADS-box genes enriched in dimorphism-defective mutants, revealing a notable expansion of this gene family in T. marneffei. Phylogenetic analysis and functional genetic manipulations confirmed the involvement of mads9, mads10, and mads13 in regulating the yeast-hypha transition. Integrating RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq), we demonstrated that these transcription factors target genes involved in transmembrane transport, redox processes, and cellulose binding. Our findings not only clarify the role and regulatory mechanisms of the MADS-box family in dimorphic transitions but also present a valuable strategy for identifying regulatory genes based on morphological variations and high-throughput sequencing, paving the way for further systematic genetic studies of fungal temperature adaptation.

overall_design: ChIP-seq and paried RNA-seq were performed on wild type PM1 strain, madsA overexpression, mads9 overexpression, and madsA knockout, and mads9 knockout strains under both mycelia and yeast conditions.

first: Yun

last: Zhang

first: Minghao

last: Du

first: Juan

last: Wang

first: Yang

last: Yang

first: James

last: Cai

first: Ence