title: Rnf20 links the DNA damage response and metabolic rewiring in lung cancer through HIF1α [H3K4me3_ChIP]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Defective DNA repair and metabolic rewiring are highly intertwined in promoting the development and progression of cancer. However, the molecular players at the interface of these processes remain largely unexplored. Here we show that the Rnf20-HIF1α axis links the DNA damage response and metabolic reprogramming in lung cancer. Haploinsufficiency of Rnf20 which catalyzes monoubiquitylation of histone H2B (H2Bub1), dramatically increased the incidence of spontaneous lung adenocarcinoma and small cell lung cancer (SCLC) in mice. Mechanistically, ablation of a single Rnf20 allele resulted in inadequate tumor suppression via the Rnf20-H2Bub1-p53 axis and induced DNA damage, increased cell growth, epithelial-mesenchymal transition (EMT), and metabolic rewiring through HIF1α-mediated RNA polymerase II promoter-proximal pause release, that was independent of H2Bub1. Importantly, RNF20 levels are reduced in lung adenocarcinoma and SCLC patients, and this reduction negatively correlates with the expression of HIF1α target genes, suggesting HIF1α inhibition as a promising therapeutic approach for lung cancer patients with reduced RNF20 activity

overall_design: MLE-12 cells were transfected with shHIF1a or PLKO. Followed ChiP-seq protocol was performed to obtain DNA associated with the Histone H3K4me3

first: Julio

last: Cordero

first: Hao

last: Liu


title: Pulsed electromagnetic field therapy alters the genomic profile of bladder cancer cell line HT-1197

status: Public on Mar 20 2025

city: Winston Salem

first: Stephen

last: Walker

state: North Carolina

address: 391 Technology Way NE

department: Urology

country: USA

institute: Wake Forest Institute for Regenerative Medicine

summary: Bladder cancer cell lines were subjected to either pulsed electromagnetic field therapy (PEMF) or control (no PEMF) 1 hour/day for a total of 5 days to assess changes in genomic analysis.

overall_design: Results showed that post electromagnetic field therapy resulted in significant changes to genome expression of bladder cancer cells subjected to PEMF.

first: Maxwell

last: Sandberg


title: Rnf20 links the DNA damage response and metabolic rewiring in lung cancer through HIF1α [H2Bub_ChIP-Seq]

country: Germany

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Defective DNA repair and metabolic rewiring are highly intertwined in promoting the development and progression of cancer. However, the molecular players at the interface of these processes remain largely unexplored. Here we show that the Rnf20-HIF1α axis links the DNA damage response and metabolic reprogramming in lung cancer. Haploinsufficiency of Rnf20, catalyzing histone H2B monoubiquitylation (H2Bub1), dramatically increases the occurrence of spontaneous lung adenocarcinoma and small cell lung carcinoma (SCLC) in mice. Mechanistically, ablation of a single Rnf20 allele resulted in insufficient Rnf20-H2Bub1-p53-mediated control and induced pronounced defects in DNA repair, increased cell growth, epithelial-to-mesenchymal transition (EMT), and metabolic rewiring via HIF1α-mediated RNA polymerase II promoter-proximal pause release, which was independent of H2Bub1. Importantly, RNF20 levels are decreased in lung adenocarcinoma and SCLC patients, and this decrease negatively correlates with the expression of HIF1α target genes, suggesting HIF1α inhibition as a promising therapeutic approach for lung cancer patients with decreased RNF20 activity.

overall_design: MLE12 ctrl, Rnf20+/- cells were harvested for H2Bub chipseq.

first: Rui

last: Gao

first: Yongqin

last: Tang


title: Rnf20 links the DNA damage response and metabolic rewiring in lung cancer through HIF1α [tPol2_MLE12_ChIP-Seq]

overall_design: MLE12 ctrl and Rnf20+/- cells were harvested for Pol II chipseq.


title: Rnf20 links the DNA damage response and metabolic rewiring in lung cancer through HIF1α [bulk_polyA_RNA-Seq]

type: Expression profiling by high throughput sequencing

overall_design: MLE12 ctrl and Rnf20+/- after CRISPR-Cas9 deletion cells were harvested for totalRNA extraction and polyARNA-seq.


title: Rnf20 links the DNA damage response and metabolic rewiring in lung cancer through HIF1α

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

overall_design: Refer to individual Series


title: Rnf20 links the DNA damage response and metabolic rewiring in lung cancer through HIF1α [ChIP-Seq_P2t_Rnf20_Het_shHIF1A]

overall_design: MLE12 ctrl, Rnf20+/- , ctrl+shHif1a and Rnf20+/-+shHif1a cells were harvested for Pol II chipseq.


title: DDX54 downregulation enhances anti-PD1 therapy in immune-desert lung tumors with high tumor mutational burden

status: Public on Mar 19 2025

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

type: Non-coding RNA profiling by high throughput sequencing

summary: High tumor mutational burden (TMB) is a predictive biomarker for the responsiveness of cancer to immune checkpoint inhibitor therapy that indicates whether immune cells can sufficiently recognize cancer cells as non-self. However, about 30% of all cancers from The Cancer Genome Atlas are classified as immune-desert tumors lacking T cell infiltration despite high TMB. Since the underlying mechanism of these immune-desert tumors has yet to be unraveled, there is a pressing need to transform such immune-desert tumors into immune-inflamed tumors and thereby enhance their responsiveness to anti-PD1 therapy. Here, we present a systems framework for identifying immuno-oncotargets, based on analysis of gene regulatory networks, and validating the effect of these targets in transforming immune-desert into immune-inflamed tumors. In particular, we identify DEAD-box helicases 54 (DDX54) as a master regulator of immune escape in immune-desert lung cancer with high TMB, and show that knockdown of DDX54 can increase immune cell infiltration and lead to improved sensitivity to anti-PD1 therapy.

overall_design: After euthanizing the LLC1 xenograft mouse model, single cells were obtained from the mouse cancer tissues. From this population, CD45-positive immune cells were separated using Aria Fusion (Becton Dickinson) flow cytometry. A library for single-cell RNA sequencing was constructed using the 10x Genomics 5' single cell RNA-seq kit. This library was then sequenced using next-generation sequencing (NGS) on the Illumina HiSeq 2500 platform. Raw reads were mapped to the Mus musculus mm10 reference genome utilizing the CellRanger pipeline (20) v6.1.0 from 10X genomics.

first: Jungeun

last: Lee

first: Kwang-Hyun

last: Cho


title: Cancer-Associated Fibroblasts Shape a High-Lactate Microenvironment to Drive Perineural Invasion in Pancreatic Cancer via Histone Lactylation

city: 广州

first: li

last: xiaobai

address: 381 Wushan Road, Tianhe District, Guangzhou

country: China

institute: south china university of technology

summary: Perineural invasion (PNI) is a pivotal prognostic factor in pancreatic cancer, associated with aggressive tumor behavior and adverse patient outcomes. Despite its recognized clinical impact, the molecular mechanisms underlying PNI are not well understood. In this study, we isolated perineural invasion-associated cancer-associated fibroblasts (pCAFs), which demonstrated a markedly enhanced capacity to promote neural invasion in pancreatic cancer compared to non-perineural invasion-associated CAFs (npCAFs). Utilizing single-cell, high-throughput sequencing, and metabolomics, we identified a significant upregulation of glycolysis in pCAFs, fostering a high-lactate tumor microenvironment conducive to cancer progression. pCAFs-derived lactate is absorbed by tumor cells, facilitating histone H3K18 lactylation. This epigenetic modification activates the transcription of neural invasion-associated genes such as L1CAM and SLIT1, thereby driving PNI in pancreatic cancer. Further exploration of metabolic reprogramming in pCAFs revealed enhanced acetylation of the glycolytic enzyme GAPDH, correlated with increased enzymatic activity and glycolytic flux. Targeting of GAPDH and lactylation modifications significantly inhibits neural invasion in a KPC mouse model. Clinical data suggested that high levels of H3K18 lactylation correlate with severe PNI and poorer patient prognosis. Our findings provide critical insights into the role of pCAFs in the PNI of pancreatic cancer, highlighting glycolytic reprogramming and lactate-driven histone modifications as potential therapeutic targets for PDAC.

overall_design: Using anti- H3K18la antibodies to delineate the regulatory role of H3K18la in gene expression in PANC-1 cells treated with lactic acid.

first: Tingting

last: Li

first: Chonghui

last: Hu

first: Tianhao

last: Huang

first: Yu

last: Zhou


title: Hematological phenotypes in GATA2 deficiency syndrome arise from aging, maladaptation to proliferation and somatic events

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: The GATA2 transcription factor is a pivotal regulator of hematopoiesis. Disruptions in the GATA2 gene drive severe hematologic abnormalities and are associated with an increased risk of myelodysplastic syndromes and acute myeloid leukemia; however, the mechanisms underlying the pathophysiology of GATA2 deficiency remain still unclear. We developed two different mouse models that are based on serial and limiting donor cell transplantation of (aged) GATA2 haploinsufficient cells and mirror the symptoms of GATA2 deficiency. Similar to what has been observed in patients, our models show that GATA2 haploinsufficiency leads to B lymphopenia, monocytopenia, lethal bone marrow failure (BMF), myelodysplasia and lymphoblastic leukemia. Leukemia arises exclusively as a result of BMF, driven by somatic aberrations and accompanied by increased Myc target expression and genomic instability. These findings were confirmed in human GATA2+/- K562 cell lines showing defects in cytokinesis and are in line with the fact that monosomy 7 and trisomy 8 are frequent events in patients with MDS.

overall_design: The haploinsufficient GATA2 hematopoietic system was challenged by transplanting low numbers (i.e. 2x104) of sorted LSK cells into lethally irradiated WT recipients.

first: Melanie

last: Boerries


title: High fat diet feeding impairs neutrophil phagocytosis, bacterial killing, and neutrophil induced hematopoietic regeneration.

city: Ann Arbor

first: Kanakadurga

last: Singer

state: MI

address: D1205 MPB 1500 E Medical Center Drive

institute: University of Michigan

summary: The prevalence of obesity and metabolic diseases have risen significantly over the past decades. Chronic inflammation in obesity is a link between obesity and secondary disease. While macrophages and monocytes are known to contribute to metabolic disease risk during diet exposure, little is known about the contribution of neutrophils. We assessed the impact of obesity on neutrophils using a 16-week model of diet-induced obesity. Bone marrow (BM) neutrophils significantly expanded with chronic high-fat diet (HFD), significantly decreased TNFɑ protein release, and impaired neutrophil regenerative function compared to normal diet (ND) neutrophils. scRNAseq and flow cytometry demonstrated HFD neutrophil heterogeneity and validated that these cells do not have elevated expression of pro-inflammatory genes without secondary stimulation. HFD neutrophils showed elevated expression of genes associated with lipid metabolism - Acot1, Cpt1a, and Plin2. Consistent with the importance of lipid metabolism in driving dysfunction, neutrophils from HFD fed animals and neutrophils treated with palmitate had impaired bacterial phagocytosis and killing responses. This data sheds light on the complex regulation of intracellular lipids and the role of metabolism on neutrophil function during homeostasis and disease.

overall_design: Hematopoetic cells from male mice on a normal chow or 60% fat high fat diet were analyzed using the Rhapsody single cell analysis pipeline.

first: Emily

last: Bowers

first: Gabrielle

last: P. Entrup

first: Mohommad

last: Islam

first: Ramkumar

last: Mohan

first: Arianna

last: Lerner

first: Caitlin

last: Ellis

first: Peter

last: Mancuso

first: Bethany

last: B. Moore


title: Steamed Panax Notoginseng Alleviates CA-MRSA USA300-induced Necroptosis in Polymorphonuclear Neutrophils

city: Beijing

first: Lulu

last: Zhang

address: 16 Dongzhimen South St, Dongcheng District, Beijing

institute: Chinese Academy of Traditional Chinese Medicine

summary: Background: Community-associated methicillin-resistant staphylococcus aureus (CA-MRSA) is a drug-resistant bacterium prevalent in community settings, characterized by high pathogenicity and transmission potential. Polymorphonuclear neutrophils (PMNs) represent the first line of defense in innate immunity and are activated to phagocytose MRSA. However, MRSA, once phagocytosed by PMNs, induces necroptosis within the neutrophils, which is a key mechanism contributing to host damage.CA-MRSA releases virulence factors that enhance its pathogenicity by disrupting the host's innate immune response, particularly impairing the phagocytic function of PMNs. Steamed Panax notoginseng (S-PN) has demonstrated immune-regulatory and anti-inflammatory properties, showing promising therapeutic effects in alleviating the severe inflammatory responses induced by pathogenic microbial infections. Objective: This study aims to investigate the pharmacological effects and mechanisms of S-PN in attenuating CA-MRSA-induced necroptosis of PMNs, and to explore the impact of PMN necroptosis on the inflammatory response. Methods: A co-culture model of MRSA USA300 strain and PMNs isolated from healthy human blood was established to observe the changes in necroptosis marker HMGB1, PMNs counts, ROS, chemokine MCP-1 and pro-inflammatory cytokines IL-1β, IL-8, TNF-α. RNA-seq was employed to analyze the effects of S-PN on the transcriptional expression of pathogenesis-related genes of MRSA. RT-PCR was utilized to validate the expression of S-PN on MRSA virulence factors and PMNs necroptosis related genes. Results: S-PN significantly inhibited HMGB1, ROS, MCP-1, IL-1β and IL-8 in MRSA-PMN co-cultures, the PMN count in the S-PN group was higher than that in the model group. S-PN down-regulated MRSA pathogenic-associated Staphylococcus aureus infection and quorum sensing signaling pathways, and significantly reduced the virulence factors PSM and PVL. S-PN suppressed the expression of genes associated with necroptosis ripk1, ripk3, and mlkl in PMNs. Conclusion: S-PN inhibited CA-MRSA-induced necroptosis of PMNs, as well as the excessive inflammatory response and ROS accumulation accompanying this process. The mechanism involves the inhibition of the expression of MRSA virulence factor PSM and necroptosis pathway genes. These findings underscore the significant potential of S-PN in the treatment of CA-MRSA infections.

overall_design: Gene transcriptome profile of MRSA USA300 before and after intervention with 0.5 mg/ml S-PN.

first: Yong

last: Tan

first: Xiaoyu

last: Feng


first: Jeong-Ryeol

last: Gong

overall_design: This study employs a syngeneic mouse model of lung cancer to investigate the role of Ddx54 in tumor biology and its interaction with anti-PD1 immunotherapy. Four formalin-fixed paraffin-embedded (FFPE) tissue blocks were obtained from mice bearing Lewis Lung Carcinoma 1 (LLC1) tumors under distinct experimental conditions:1. Sample #1: Mice injected with wild-type (WT) LLC1 cells and treated with an isotype control antibody. 2. Sample #2: Mice injected with Ddx54 knockdown (KD) LLC1 cells and treated with an isotype control antibody. 3. Sample #3: Mice injected with WT LLC1 cells and treated with an anti-PD1 antibody. 4. Sample #4: Mice injected with Ddx54 KD LLC1 cells and treated with an anti-PD1 antibody.Each treatment group consists of replicates to ensure statistical robustness. Utilizing the Xenium Mouse 5K spatial transcriptomics workflow, spatial gene expression profiles were generated for each FFPE tissue block. This approach allows for the spatial mapping of transcriptomic changes within the tumor microenvironment, facilitating the comparison between WT and Ddx54 KD tumors under both control and immunotherapy conditions. The design enables the assessment of how Ddx54 modulation affects tumor response to anti-PD1 therapy, immune cell infiltration, and overall tumor gene expression landscapes.

first: Jungeun

last: Lee

first: Juhee

last: Kim

first: Kwang-Hyun

last: Cho


title: A Single-cell View of Retina-Specific T cells in a Model of Ocular Immune Privilege Reveals Unique Regulatory and Anergic Signatures

city: Bethesda

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

summary: The healthy eye limits destructive inflammation through the phenomenon known as immune privilege, but despite that, it is subject to autoimmune uveitis driven by retina-specific effector T cells. Using an in vivo immune privilege model based on introducing allotypically marked, TCR-transgenic naive retina-specific T cells into eyes of healthy mice, we found that after one week all the injected cells became primed within the eye. Among them, about 30% had converted to functional Foxp3+ regulatory T cells (Tregs), whereas the remaining ~70% did not convert to Tregs, but nevertheless failed to elicit pathology. It has long been known that ocular fluids in vitro, as well as the ocular environment in vivo, support conversion of T cells to Tregs. However, in-depth investigation of the cell fate of the non-Foxp3-converted T cells, and why they fail to elicit pathology, was hindered by the limited number of cells retrievable from mouse eyes. Therefore, to gain insights into this, we tracked changes in gene expression of retina-specific T cells responding to their cognate antigen in the living eye, at the single-cell level. Our data revealed unique transcriptional signatures not only in the Foxp3+ Tregs, but also in the non-Foxp3-converted T cell populations. Of particular interest, most non-Foxp3-converted T cell populations appeared phenotypically anergic with high levels of inhibitory regulators (Ctla4, Lag3, Pdcd1, Cblb, and Dgkz), and expressed higher levels of some immunosuppressive genes, e.g. Tgfb1, than the converted Foxp3+ Tregs. Moreover, trajectory analyses suggested a branched pattern showing that the Tregs and anergic T cells differentiate simultaneously, rather than in tandem, from a common proliferative precursor. Our findings offer novel insights into ocular immune privilege and its complex underlying network of inhibitory mechanisms and could suggest therapeutic approaches to ocular inflammatory diseases.

overall_design: Fresh naive T cells sorted from donor mice and CD90.2 donor cells retrieved from the recipients’ eyes one week after intravitreal injection were used for scRNA-seq.

first: Zixuan

last: Peng

first: Reiko

last: Horai

first: Yingyos

last: Jittayasothorn

first: Mary

middle: J

last: Mattapallil

first: Rachel

middle: R

last: Caspi


title: Genome-wide CRISPR screen identifies IRF1 and TFAP4 as transcriptional regulators of Galectin-9 in T cell acute lymphoblastic leukemia [HiChIP-seq]

city: Salt Lake City

first: Birgit

last: Knoechel

address: 2000 Circle of Hope

institute: HCI

summary: Galectin-9 is overexpressed in a variety of cancers and associated with worse clinical outcome in some cancers. However, the regulators driving Galectin-9 expression are unknown. Here, we defined the transcriptional regulators and epigenetic circuitry of Galectin-9 in pediatric T cell acute lymphoblastic leukemia (T-ALL), as an example of a disease with strong Galectin-9 expression, in which higher expression was associated with lower overall survival. By performing a genome-wide CRISPR screen, we identified the transcription factors IRF1 and TFAP4 as key regulators for Galectin-9 expression by binding its regulatory elements. While IRF1 was observed exclusively on the promoter, TFAP4 binding was detected at an enhancer solely in T-ALL cells associated with higher Galectin-9 levels. Together, our results show that IRF1 is responsible and indispensable for Galectin-9 expression and TFAP4 further fine-tunes its expression. Our approach, a flow-based genome-wide CRISPR screen complemented by transcription factor binding and enhancer mapping, creates innovative opportunities for understanding and manipulating epigenetic transcriptional regulation in cancer.

overall_design: Hi-Chromatin Immunoprecipitation DNA-sequencing (Hi-ChIP-seq) for histone modification H3K27ac in T-ALL cell lines Jurkat, CCRF-CEM, Loucy and HPB-ALL.

first: Caroline

last: Wiggers

first: Burak

last: Yüzügüldü

first: Jens

middle: G

last: Lohr


title: Transcriptome of HUVECs transfected with CAVIN3-siRNA and TUBB6-siRNA

city: Shanghai

first: Yingji

last: Chen

address: 2005 Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

summary: Pathological ocular angiogenesis are hallmarks of diabetic retinopathy (DR) and wet Age-related macular degeneration (AMD).Cavin3 and Tubb6 was found to upregulated in endothelial cells (ECs) of OIR and CNV mouse models. RNA-Seq analysis was performed in HUVECs with CAVIN3 knockdown and TUBB6 knockdown treatment to explore downstream pathways using standard library construction and Illumina NovaSeq 6000 (Genewiz, South Plainfield, NJ).

overall_design: The study includes endothelial cell (EC) samples derived from HUVECs (Human Umbilical Vein Endothelial Cells) subjected to RNA-Seq analysis. The experimental conditions involve CAVIN3 knockdown and TUBB6 knockdown treatments to investigate downstream pathways related to pathological ocular angiogenesis, specifically in the context of diabetic retinopathy (DR) and wet Age-related Macular Degeneration (AMD). The samples consist of both treated and control groups, with replicates included to ensure statistical robustness and reliability of the data. The controls serve as a baseline to compare the effects of the knockdown treatments, facilitating the identification of gene expression changes directly associated with the loss of CAVIN3 and TUBB6 in endothelial cells.

first: Weiqi

last: Li

first: Yeran

last: Zhang


title: Genome-wide CRISPR screen identifies IRF1 and TFAP4 as transcriptional regulators of Galectin-9 in T cell acute lymphoblastic leukemia [ChIP-seq]

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for transcription factors IRF1 and TFAP4 in T-ALL cell lines Jurkat, CCRF-CEM, Loucy, KOPT-K1, DND-41 and HPB-ALL. In addition, H3K27ac ChIP-sequencing for T-ALL cell line HPB-ALL


title: Targeting Vdac2 enables IFNg-mediated destruction and inflammatory remodeling of tumors to overcome immune evasion [microarray 6]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: Microarray analysis of WT, Vdac2 KO, Bim/Bid dKO and Vdac2/Bim/Bid TKO B16-OVA tumor cells after IFNg treatment for 24 hours.

overall_design: WT, Vdac2 KO, Bim/Bid dKO and Vdac2/Bim/Bid TKO B16-OVA tumor cells were treated with IFNg treatment (10ng/ml) for 24 hours.

first: Hao

last: Shi


first: Jeong-Ryeol

last: Gong

first: Jungeun

last: Lee


title: Chloroplast precursor protein overaccumulation triggers multilevel reprogramming and a heat shock-like response in plant cells [Ribo-Seq]

city: shanghai

first: zhenghui

last: hong

state: --- Select a state ---

address: dongchuan road NO.800

department: life of science

institute: shanghai jiaotong university

summary: Most of chloroplast proteins are encoded by nucleus ,synthesied in cytosol as precursors. theses precursor contains tranzit peptide and will be cut off after import finished. How plant response to chloroplast precursor overaccumulation stress(cPOS) is still unkown. Here we constructed constutitive and induced overexpression line to lead preClpD accumulation. Proteomic analysis revealed cytosolic ribosome upregulated, which means translation changed upon cPOS. So we conducted RNA-seq and Ribo-seq experiment to find which genes response at transcription level or translation level.Finally, we want to uncover the cellular events upon chloroplast precursor overaccumulation.

overall_design: we conducted costitutive ClpD overexpression line and western blot showed preClpD accumulated in 6-day-old seedlings. polysome profiling showed that polysome increase upon cPOS.So we used this plant materials to conduct RNA-seq and Ribo-seq to find transcription-dependent expressed genes and translation-dependent expressed genes.

first: Zheng-hui

last: Hong


title: Targeting Vdac2 enables IFNg-mediated destruction and inflammatory remodeling of tumors to overcome immune evasion [ATAC-seq2]

summary: ATAC-seq analysis of intratumoral CD8+ T cells in Vdac2-deficient and control B16-OVA tumors.

overall_design: Vdac2-deficient or control B16-OVA tumor cells were inoculated into C57BL/6 mice, CD8+ T cells were collected at day 14 after tumor injection by sorting from tumor tissues, followed by ATAC-seq analysis.


title: Genome-wide CRISPR screen identifies IRF1 and TFAP4 as transcriptional regulators of Galectin-9 in T cell acute lymphoblastic leukemia [CRISPR]

overall_design: Genome-wide CRISPR screen (Brunello library) of Galectin-9 in T-ALL cell line Jurkat


title: Targeting Vdac2 overcomes immunotherapy resistance by inducing tumor cell death and inflammation [microarray 3]

summary: Uncovered IFNg signal and mitochondrial stress shaping tumor immune evasion

overall_design: We treated B16-OVA-Cas9-sgNTC, sgVdac2, sgNTC + sgSting1 or sgVdac2 + sgSting1 tumor cells with IFNg, survived tumor cells were collected for RNA extraction and microarray analysis.

first: Sujing

last: Yuan


title: Targeting Vdac2 overcomes immunotherapy resistance by inducing tumor cell death and inflammation [microarray 2]

overall_design: We treated B16-OVA-Cas9-sgNTC (indicated as WT) or sgVdac2 (indicated as KO) tumor cells with IFNg, survived tumor cells were collected for RNA extraction and microarray analysis.


title: A single-cell atlas of bobtail squid visual and nervous system highlights molecular principles of convergent evolution

city: Onna

first: Daria

last: Gavriouchkina

state: Kunigami District, Okinawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

summary: RNA-seq and scRNA-seq of dissected organs from adult and hatchling-stage cephalopod Euprymna berryi

overall_design: Animals were euthanised using 4% ethanol in natural seawater. Organs were dissected and Total RNA extraction was carried  out using TRIzol reagent (Invitrogen) for lysis followed by on-column purification using PureLink RNA Mini Kit (Invitrogen)  as described in TRIzol Plus RNA Purification instructions from manufacturer.  (https://assets.fishersci.com/TFS-Assets/LSG/manuals/Trizol_Plus_man.pdf). RNA-seq was carried out on a Hiseq4000.  Demultiplexing was carried out using bcl2fastq (v2.19). scRNA-seq was carried out using 10x Genomics protocols for v.2 and v.3.1 kits as per manufacturer's instructions.

first: Ferdinand

last: Marlétaz

first: Daniel

middle: S

last: Rokhsar


title: SIRT6-dependent functional switch via K494 modifications of RE-1 Silencing Transcription factor [REST_experiment_1]

city: Beer Sheva

first: Adam

last: Zaretsky

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben Gutrion University of the Negev

summary: RE-1 Silencing Transcription factor (REST) is a key repressor of neural genesREST functions as a key factor for cell differentiation, repressing neural genes in non-neural somatic tissues. REST is upregulated under stress signals, aging, and neurodegenerative diseases, but loses its function in Alzheimer's Disease. However, why it becomes inactive remains unclear. Here we show that the NAD-dependent deacetylase SIRT6 regulates REST expression, location, and activity. In SIRT6 absence, REST is overexpressed, but mis localized and inactive. SIRT6 deficiency abrogates REST and EZH2 interaction, perturbs its location to heterochromatin Lamin B ring, and leads to REST target gene overexpression. SIRT6 reintroduction or REST methyl-mimic K494M expression rescues this phenotype, while an acetyl-mimic mutant loses its function even in WT cells. Our studies define a novel regulatory switch, where the function of a critical repressor is regulated by post-translational modifications on K494 depending on SIRT6 existence, in turn modulating neuronal gene expression.

overall_design: ChIP-seq against endogenous human RE-1 Silencing transcription factor (REST) was performed on WT (CC) SIRT6 KO (C3) SHSY-5Y cell line. The experiment was conducted 3 times  (N1, N2, N3). For each replicate, ChIP was performed using IgG or Anti-REST antibodies. For each sample, an input sample was allocated before antibody introduction for background signal. Per replicate, 8 samples were sequenced (CC - IgG + Input, CC - REST + Input, C3- IgG+ Input, C3- REST+Input).

first: Alfredo

last: Venzor

first: Dmitrii

last: Smirnov

first: Deboarh

last: Toiber


title: Transcriptomic analysis of RNA Granules and Exosomes: Unmasking the Intra- and Intercellular organelle overlap in Huntington's Disease

city: Siegen

first: Florian

last: Centler

state: NRW

address: Am Eichenhang 50

institute: University of Siegen

summary: Introduction:Repetitive RNA sequences like CAG repeats that trigger aberrant RNA-protein interactions cause several neurodegenerative diseases including Huntington's disease (HD). Importantly, these aberrant RNA-protein complexes also seed the formation of cytoplasmic liquid-like granules, such as the stress granules. Emerging evidence demonstrates that granules formed via liquid-liquid phase separation can mature into gel-like inclusions that persist within the cell and may act as precursor to aggregates that occur in patients’ tissue. Thus, deregulation of RNA granule biology is an important component of neurodegeneration. Interestingly, the formation of intracellular membrane-less organelles like stress granules increases along with the secretion of exosomes. Exosomes are small membrane-bound vesicles that are secreted generally by all cell types. They may participate in the spreading of misfolded proteins and aberrant RNA-protein complexes across the central nervous system in neurodegenerative diseases like HD. Moreover, due to their capability to cross the blood-brain barrier, exosomes hold great potential as sources of biomarkers available from the periphery, e.g., from blood. In this study, we performed a comparative transcriptomic analysis of exosomes and RNA granules in an HD model.Methods: Exosomes and RNA granules were isolated from an HD cell model, stably expressing HTT exon 1 with 83 CAG repeats under an inducible promoter. Both exosomes and RNA granules were isolated from induced (HD) and non-induced (control) cells and analysed by RNA sequencing.Results: Comparative analysis between the transcriptomics data of HD RNA granules and exosomes showed that: (I) intracellular RNA granules and extracellular RNA vesicles share content, (II) several non-coding RNAs translocate to RNA granules, (III) the composition of RNA granules and exosomes is affected by expression of mutant HTT.Discussion: Our data show that intracellular RNA granules and exosomes share content, suggesting that formation of RNA granules and exosome loading may be related. Moreover, our data suggest that both intracellular RNA granules and extracellular RNA vesicles may serve as a source for diagnostic strategies. For example, disease-specific RNA-signatures of exosomes can serve as biomarker of central nervous system diseases. However, the cell-type specific signature of EV-secreted RNAs may make it difficult to detect these biomarkers in blood.

overall_design: To explore and compare the composition of RNA content in exosomes and RNA granules under WT conditions and in Huntington, exosomes and RNA granules were separately extracted from control or HD-induced HEK293 cells and total RNA was sequenced. Five biological replicates were perfomed for both sample types and both conditions.

first: Nabariya

last: Deepti Kailash

first: Knüpfer

last: Lisa Maria

first: Hartwich

last: Patrick

first: Kilian

last: Manuela

first: Centler

last: Florian

first: Krauss

last: Sybille


title: Targeting Vdac2 overcomes immunotherapy resistance by inducing tumor cell death and inflammation [microarray 4]

first: Hongbo

last: Chi

overall_design: We treated B16-OVA-Cas9-sgNTC (indicated as WT), sgVdac2 (indicated as V2-KO), sgBak1 (indicated as Bak1-KO), sgApaf1 (indicated as Apaf1-KO), sgVdac2 + sgBak1 (indicated as Vdac2-Bak1-dKO) or sgVdac2 + sgApaf1 (indicated as Vdac2-Apaf1-dKO) tumor cells with IFNg, survived tumor cells were collected for RNA extraction and microarray analysis.

first: Hao

last: Shi


title: Chloroplast precursor protein overaccumulation triggers multilevel reprogramming and a heat shock-like response in plant cells [RNA-Seq]

first: zhenghui

last: hong

first: Zheng-hui

last: Hong


title: An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying translocation RCC

city: UTRECHT

first: PHILIP

last: LIJNZAAD

state: Utrecht

address: HEIDELBERGLAAN 25

department: Single Cell Facility

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Translocation renal cell carcinoma (tRCC) is a rare, aggressive kidney cancer primarily occurring in children. They are genetically defined by translocations involving MiT/TFE gene family members, TFE3 or, rarely, TFEB. The biology underlying tRCC development remains poorly understood, partly due to the lack of representative experimental models. We utilized human kidney organoids, or tubuloids, to engineer a tRCC model by expressing one of the most common MiT/TFE fusions, SFPQ-TFE3. Fusion expressing tubuloids adopt a tRCC-like phenotype and gene expression signature in vitro and grow as clear cell RCC upon xenotransplantation in mice. Genome-wide binding analysis suggests that SFPQ-TFE3 reprograms gene expression signatures by aberrant genome-wide DNA binding. Combining these analyses with single-cell mRNA readouts reveals a derailed epithelial differentiation trajectory that is at the root of transformation towards tRCC. Our study demonstrates that SFPQ-TFE3 expression is sufficient to transform kidney epithelial cells into tRCC and defines the trajectories underlying malignant transformation.

overall_design:
Single-cell mRNA expression profiles of translocated renal cell carcinoma organoid models (both control and with engineered SFPQ-TFE3 gene fusion) were determined to study processes leading to oncogenic transformation.
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Authors state "Raw data are unavailable due to patient privacy concerns."

first: Maroussia

middle: P

last: Ganpat

first: Francisco

last: Morales-Rodriguez

first: Nhung

last: Pham

first: Philip

last: Lijnzaad

first: Terezinha

last: de Souza

first: Sepide

last: Derakshan

first: Arianna

last: Fumagalli

first: Peter

last: Zeller

first: Aleksandra

last: Balwierz

first: Dilara

last: Ayyildiz

first: Marry

middle: M

last: van den Heuvel-Eibrink

first: Ronald

last: de Krijger

first: Alexander

last: van Oudenaarden

first: Thanasis

last: Margaritis

first: Susana

last: Chuva de Sousa Lopes

first: Jarno

last: Drost


title: Targeting VDAC2 enables IFNg-mediated destruction and inflammatory remodeling of tumors to overcome immune evasion [microarray 5]

first: Hongbo

last: Chi

summary: Microarray analysis of WT and VDAC2 KO LOVO tumor cells without or with IFNg treatment for 48 hours.

overall_design: WT and VDAC2 KO LOVO tumor cells were left untreated or treated with IFNg treatment (10ng/ml) for 48 hours.

first: Hao

last: Shi


title: Loss of LATS1 and LATS2 promotes ovarian tumor formation by enhancing AKT activity and PD-L1 expression

status: Public on Mar 18 2025

city: Ottawa

first: Yalun

last: Zhu

address: 501 Smyth Road

country: Canada

institute: University of Ottawa

summary: High-grade serous ovarian cancer (HGSOC) is the deadliest and most common subtype of ovarian cancer. Unfortunately, most patients develop recurrence and ultimately resistance to standard platinum chemotherapy. Large tumor suppressors LATS1 and LATS2, the core Hippo signaling kinases, have been implicated in various cancer types, including ovarian cancer. The mechanism by which LATS1/2 suppresses ovarian cancer progression is currently elusive, but the expression of LATS1/2 is frequently reduced or lost in these cancers. In this study, we demonstrate that the inactivation of LATS1/2 is sufficient to transform normal mouse ovarian epithelium into tumorigenic cells associated with increased cell proliferation, invasion and stemness and epithelial–mesenchymal transition (EMT) characteristics. Knockout of Lats1/2 in the epithelial cells also leads to higher expression levels of the immune checkpoint molecule PD-L1, suggesting a regulatory role of LATS1/2 in modulating immune responses and immune evasion. In addition to the loss of LATS1/2 activating the downstream transcriptional coactivators YAP and TAZ, PI3K-AKT activity was also increased, likely contributing to enhanced tumor proliferation and survival. The stimulatory effect of Lats1/2 knockout on cell proliferation can be partially reversed by treatment with the AKT inhibitor MK2206. Treatment with verteporfin, a potent inhibitor of YAP/TAZ, decreases ovarian tumor progression and reduces the activated AKT in the tumors. In summary, this study uncovers several biological mechanisms for the initiation of HGSOC and identifies LATS1/2 as potential prognostic indicators and therapeutic targets.

overall_design: We report the analysis of RNA sequencing aimed at understanding the effects of Lats1/2 knockout in ovarian surface epithelial (OSE) cells. LATS1/2 are the core kinases of the Hippo signaling pathway, which plays a critical role in regulating cell proliferation and differentiation. Specifically, we performed RNA-seq seven days after OSE cells were transduced with Ad-Cre-GFP or Ad-GFP to investigate the transcriptional consequences of Lats1/2 deletion. The study aims to elucidate the impact of Lats1/2 loss on gene expression profiles, providing insights into its role in ovarian cancer initiation and progression.

first: Atefeh

last: Abedini

first: Barbara

middle: C

last: Vanderhyden


title: Acidic pH Reduces Fluconazole Susceptibility in Cryptococcus neoformans by Altering Iron Uptake and Enhancing Ergosterol Biosynthesis

city: Chuncheon-si

first: Jiwon

last: Bang

address: 1, Kangwondaehak-gil

institute: Kangwon National University

summary: The opportunistic fungal pathogen Cryptococcus neoformans faces a wide range of environmental pH within the host, and adaptation to different pH conditions plays a critical role in their survival and pathogenesis. In the current study, how environmental pH influences antifungal susceptibility and iron uptake in C. neoformans was investigated. We found that acidic pH conditions significantly reduced antifungal susceptibility of C. neoformans to fluconazole. Moreover, our study revealed that iron acquisition in C. neoformans at acidic pH is independent of the high-affinity iron uptake system, and leads to increase of intracellular iron accumulation, increased ergosterol and heme levels, which may contribute to reduced fluconazole susceptibility of the fungus. Transcriptome analysis further elucidated the molecular mechanisms underlying the pH-dependent shift of iron uptake and antifungal susceptibility of C. neoformans. Our findings highlight the importance of environmental pH in physiology and pathogenesis of C. neoformans and provide insights into developing novel treatment for cryptococcosis.

overall_design: RNA-seq was performed to analyze differentially expressed genes in the C. neoformans cells grown at pH 5.0 compared to that in the cells grown at pH 7.0. The cells were grown in YPD for overnight, harvested and reinoculated into YNB LIM pH 6.8 for overnight, and the cells were harvested and incubated to YNB LIM pH 6.8 or pH 5.0 at 1×107 cells/mL for 6 hr. The cells were harvested by centrifugation and the total RNA was extracted by the RNeasy Mini Kit following the manufacturer's instructions. Contaminating DNA was eliminated by RNase-free DNase (Invitrogen, Waltham, MA, USA). Libraries for RNA sequencing were prepared using high-quality RNA with the value of RNA integrity greater than 7.0, and TruSeq Stranded mRNA Sample Prep Kit (Illumina, US) following the manufacturer’s protocol. The libraries were submitted to an Illumina HiSeq2500 platform, and the 100-bp paired-end reads were generated and sequenced. Quality-filtered reads were mapped to the reference genome sequence (http://www.broadinstitute.org/annotation/genome/cryptococcus_neoformans/MultiHome.html) using CLC Genomics Workbench 4.0 (CLC bio). Mapped reads were counted by featureCounts in Subread package v1.4.3 and the relative transcript abundance was TPM-normalized.

first: Donghyeun

last: Kim

first: Yong-Joon

last: Cho

first: James

middle: W

last: Kronstad

first: Won Hee

last: Jung


title: Glioma-neuronal circuit remodeling induces regional immunosuppression [RNA-Seq]

city: San Francisco

first: Hideho

last: Okada

state: CA

department: Neurological Surgery

institute: University of California, San Francisco

summary: Neuronal activity-driven mechanisms impact glioblastoma cell proliferation and invasion (1–7), and glioblastoma remodels neuronal circuits (8,9). Distinct intratumoral regions maintain functional connectivity via a subpopulation of malignant cells that mediate tumor-intrinsic neuronal connectivity and synaptogenesis through their transcriptional programs (8). However, the effects of tumor-intrinsic neuronal activity on other cells, such as immune cells, remain unknown. Here we show that regions within glioblastomas displaying elevated connectivity are characterized by regional immunosuppression. This is accompanied by different cell compositions and inflammatory status of tumor-associated macrophages (TAMs) in the tumor microenvironment. In preclinical models, genetic knockout of Thrombospondin-1 (TSP1/Thbs1), a synaptogenic factor critical for glioma-induced neuronal circuit remodeling, in glioblastoma cells suppressed synaptogenesis and glutamatergic neuronal hyperexcitability. Moreover, this restored antigen-presentation and pro-inflammatory responses, promoted the infiltration of pro-inflammatory TAMs and CD8+ T-cells, and mitigated the immunosuppressive effect of TAMs on T-cell proliferation. Furthermore, pharmacological inhibition of glutamatergic excitatory neuronal signaling redirected TAMs toward a less immunosuppressive phenotype, resulting in prolonged mouse survival. Lastly, pharmacological inhibition of glutamatergic signaling showed potential to enhance the efficacy of immune cell-based therapy. Altogether, our results demonstrate previously unrecognized immunosuppression mechanisms resulting from glioma-neuronal circuit remodeling and suggest that targeting glioma-neuron-immune crosstalk could provide new avenues for immunotherapy.

overall_design: Bulk RNAseq: RNA-seq profiling of in vivo mouse brain tumors of SB28-TSP1-WT (n = 4) and KO (n = 4) at day 20-22 after tumor cell inoculation.

first: Takahide

last: Nejo


title: Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated  gene editing in hematopoietic stem cells [BAR-seq]

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Gene editing (GE) using homology-directed repair (HDR) in hematopoietic stem and progenitor cells (HSPCs) offers promise for long-range gene correction of inherited genetic disorders. However, adverse cellular responses induced by CRISPR-Cas9/AAV6 engineering impair the long-term repopulating potential of HDR-edited HSPCs, limiting clinical translation. Our study uncovers a senescence-like response in genetically-engineered HSPCs triggered by p53 and IL-1/NF-κB activation, which restricts graft size and clonal diversity in long-term transplantation assays. We show that transient p53 inhibition or blocking inflammatory pathways can mitigate senescence-associated responses, enhancing the repopulating capacity of edited HSPCs. Importantly, we identify Anakinra, an IL-1 signaling antagonist, as a safer and effective strategy to enhance polyclonal output in HDR-edited cells while minimizing genotoxicity risks associated with the gene-editing procedure. These findings present strategies to overcome key hurdles in HDR-based HSPC therapies, providing a framework for enhancing the efficacy and safety of these approaches in future clinical applications.

overall_design: Clonal tracking by using an AAV6 repair template pool with a heritable “barcode” sequence (BAR) downstream of the GFP reporter cassette. Enhanced long-term polyclonal reconstitution of HDR-edited cells in the BM was observed for GSE56 and Anakinra treatments.

first: Anastasia

last: Conti

first: Kety

last: Giannetti

first: Federico

last: Midena

first: Stefano

last: Beretta

first: Ivan

last: Merelli

first: Luigi

last: Naldini


title: Glioma-neuronal circuit remodeling induces regional immunosuppression [visium]

overall_design: Visium Spatial Transcriptomics: Mice (n = 2) intracranially inoculated with the SB28 glioma cell line were euthanized at day 20–22. Brain tissue was harvested, FFPE-embedded, and analyzed using Visium spatial transcriptomic analysis.


title: Gene expression profile at single cell level of ferret peripheral blood mononuclear cell (PBMC) and splenocyte samples

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the PBMC and Splenocyte cell diversity.

overall_design: PMBC and Splenocyte cells from ferret were unsorted and analyzed using scRNAseq.

first: Walsh

last: Evan

first: Tollison

last: Tammy

first: Peng

last: Xinxia


title: Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated  gene editing in hematopoietic stem cells [NHEJ]

overall_design: Targeted deep sequencing on Bone Marrow HSPC donors, treated with different editing conditions (i.e., standard editing, + ANAK, +GSE56, adn +SC514).


title: Identifying genes directly regulated by Gal1 through its DNA promoter binding in pancreatic stellate cells (PSCs)

city: Barcelona

first: Neus

last: Martínez

address: Dr.Aiguader 88

department: Cancer

country: Spain

institute: Hospital del Mar Medical Research Institute

summary: Galectin-1 (Gal1) is highly expressed in activated PSCs nuclei, a cell type which plays a key role in PDA progression. In order to identify whether Gal-1 is able to recognize regulatory gene elements and regulate their expressión we performed a chromatin immunorecipitation assay followed by sequencing (ChIP-seq). Its analysis revealed that 16% of Gal-1 targets correspond to gene promoters, Indeed, most of these candicates are cancer-associated genes. Among them we found KRAS, which plays an important role in PSC activation. ChIP-seq results were validated by ChIP-qPCR using two independent Gal1 antibodies. These results identify a novel role for nuclear Gal1 by controlling transcriptional gene expression of cancer-associated genes in PSC in the PDA TME.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Galectin-1 in activated pancreatic stellate cells

first: Judith

last: Vinaixa

first: Joan

last: Gibert

first: Luciana

middle: L

last: Almada

first: Martin

middle: E

last: Fernández-Zapico

first: Pilar

last: Navarro


title: Targeting Vdac2 overcomes immunotherapy resistance by inducing tumor cell death and inflammation [microarray 1]

first: Hongbo

last: Chi

overall_design: We treated B16-OVA-Cas9-sgNTC/Vdac2 tumor cells with activated OT-I CD8+ T cells for 24h, survived tumor cells were collected for RNA extraction and microassay analysis.

first: Hao

last: Shi

first: Sujing

last: Yuan


title: Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling [VisiumHD]

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

summary: Colorectal cancer (CRC) is the second-deadliest cancer in the world, yet a deeper understanding of spatial patterns of gene expression in the tumor microenvironment (TME) remains elusive. Here, we introduce the Visium HD platform (10x Genomics) and use it to investigate human CRC and normal adjacent mucosal tissues from formalin fixed paraffin embedded (FFPE) samples. The first assay available on Visium HD is a probe-based spatial transcriptomics workflow that was developed to enable whole transcriptome single cell scale analysis. We demonstrate highly refined unsupervised spatial clustering in Visium HD data that aligns with the hallmarks of colon tissue morphology and is notably improved over earlier Visium assays. Using serial sections from the same FFPE blocks we generate a single cell atlas of our samples, then we integrate the data to comprehensively characterize the immune cell types present in the TME, specifically at the tumor periphery. We observed enrichment of two pro-tumor macrophage subpopulations with differential gene expression profiles that were localized within distinct tumor regions. Further characterization of the T cells present in one of the samples revealed a clonal expansion that we were able to localize in the tissue using in situ gene expression analysis. In situ analysis also allowed us to perform in-depth characterization of the microenvironment of the clonally expanded T cell population and we identified a third macrophage subpopulation with gene expression profiles consistent with an anti-tumor response. Our study provides a comprehensive map of the cellular composition of the CRC TME and identifies phenotypically and spatially distinct immune cell populations within it. We show that the single cell-scale resolution afforded by Visium HD and the whole transcriptome nature of the assay allows investigations into cellular function and interaction at the tumor periphery in FFPE tissues, which has not been previously possible.

overall_design: 5 µm sections were taken from the FFPE tissue blocks with a microtome (Epredia HM355S). Sections were adjacent or near-adjacent (within 5-10 µm of each other). Sectioning followed the Visium CytAssist Spatial Gene Expression for FFPE – Tissue Preparation Guide (CG000518, Rev C). We placed FFPE tissue sections on plain glass slides for deparaffinization, H&E staining and imaging following the Visium HD FFPE Tissue Preparation Handbook (CG000684). Probe hybridization, probe ligation, slide preparation, probe release, extension, library construction, and sequencing followed the Visium HD Spatial Gene Expression Reagent Kits User Guide (CG000685). Sequencing was performed on an Illumina NovaSeq 6000 with paired-end reads (43 cycles Read 1, 10 cycles i7, 10 cycles i5, 50 cycles Read 2).

first: Michelli

middle: F

last: Oliveira

first: Meii

last: Chung

first: Stephen

last: Williams

first: Andrew

middle: D

last: Gottscho

first: Anushka

last: Gupta

first: Susan

last: Pilipauskas

first: Syrus

last: Mohabbat

first: Nandhini

last: Raman

first: David

last: Sukovich

last: Patterson

first: Sarah

last: Taylor


title: Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling [Xenium]

overall_design: 5 µm sections were taken from the FFPE tissue blocks with a microtome (Epredia HM355S). Sections were adjacent or near-adjacent (within 5-10 µm of each other). Sectioning followed the Xenium In Situ for FFPE - Tissue Preparation Guide (CG000578, Rev C). The 10x Genomics Xenium Human Colon Gene Expression Panel (322 genes) was supplemented with an additional 100 genes chosen to characterize the TME. Three genes, each with unique probesets, were designed for the two alpha and one beta chains of the TCR clonotype identified from the Single Cell Immune Profiling data in sample P5 CRC. The other 97 genes included markers that were enriched in different subsets of tumor cells from the single cell reference atlas and from the Visium HD data. They include marker genes for macrophages, neutrophils, cancer-associated fibroblasts, granulocytes, chemokines, and other TME markers. The panel was designed using Xenium Panel Designer following the guidance in the Xenium Add-on Panel Design Technical Note (CG000643, RevB).


title: Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling [VDJ]

overall_design: Sorted cells were directly loaded onto the 10x chip for generation of 5′ gene expression and TCR libraries following the Chromium Next GEM Single Cell 5′ Reagent Kits v2 (Dual Index) User Guide (CG000331) on the Chromium X instrument. Libraries were sequenced on an Illumina NovaSeq 6000 with paired-end dual-indexing (28 cycles Read 1, 10 cycles i7, 10 cycles i5, 90 cycles Read 2).


title: Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling [Flex]

overall_design: We collected Chromium Single Cell Gene Expression Flex data (10x Genomics) to create a sample-specific annotated reference atlas. Cells were dissociated from 50 µm FFPE curls from CRC tissue samples (n=5 patients) and a subset of paired normal adjacent tissues (n = 3 patients) using the Demonstrated Protocol for Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling (CG000632). The FFPE curls used for this analysis were serial to the sections used for the Visium HD assay, to ensure that the single cell reference atlas would closely represent the tissue analyzed with the spatial analysis.


title: Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling [VisiumV2]

overall_design: 5 µm FFPE serial sections were placed on standard glass slides and H&E-stained following the Demonstrated Protocol Visium CytAssist Spatial Gene Expression for FFPE – Deparaffinization, H&E Staining, Imaging & Decrosslinking (CG000520).The CytAssist instrument was used to facilitate the transfer of transcriptomic probes from the standard glass slide to the Visium CytAssist Spatial Gene Expression Slide. Space Ranger v3.0 (10x Genomics) was used to map FASTQ files to the human reference, detect the tissue section, align the sequencing data to the microscope image and the CytAssist image, and output gene-barcode matrices for further analysis.


title: Single embryo RNA-seq analysis in RIF1 depleted preimplantation mouse embryos

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: RNAseq datasets from control and RIF1-depleted mouse embryos to address whether RIF1 depletion results in changes in gene expression. siRNA was microinjected at the zygote stage and controls (embryos injected with siRNA control) and RIF1-depleted embryos (embryos injected with siRNA against Rif1) were collected either at the 4-cell or at the 8-cell stage. RNAseq was performed using SMART-Seq2 in single embryos.

overall_design: siRNA for Rif1 or control siRNA in 4-cell and 8-cell stage embryo.

first: Tsunetoshi

last: Nakatani

last: schauer

first: Maria-Elena

last: Torres-Padilla


title: Gene expression changes between term pregnant (TNIL) and labouring (LAB) human myometrium.

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

summary: We have generated transcriptomic datasets of the human uterine smooth muscle (myometrium) tissue. RNA-seq experiments were conducted to evaluate gene expression changes that occur as the uterus transitions from pregnancy to labour using human myometrium tissue.

overall_design: To investigate the transcriptional changes between  term pregnant (TNIL) and labouring (LAB) human myometrium tissues obtained from consenting patients.

first: Nawrah

last: Khader

middle: A


title: Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated  gene editing in hematopoietic stem cells [RNA-seq]

first: Raffaella

last: Di Micco

overall_design: Cord-blood (CB) hematopoietic stem and progenitor cells (HSPCs) were cultured for three days in early active and stem-preserving medium and at day 3 we performed the following treatments: the electroporation with an RNP with no predictive activity in the human genome in presence (RNP NEG + ANAK) or absence  (RNP NEG) of Anakinra and the standard gene editing procedure with HS RNP and transduction with an AAV6 carrying the DNA donor template for HDR in presence (HS/AAV6 + ANAK) or absence (HS/AAV6) of Anakinra. After 96 hours post treatments, HSPCs were collected for RNA-seq analysis.

first: Anastasia

last: Conti

first: Stefano

last: Beretta

first: Kety

last: Giannetti

first: Teresa

last: Tavella

first: Ivan

last: Merelli


title: Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos

summary: Repli-seq datasets were generated using single cell Repli-seq as described in Nakatani et al. (2024). Embryos were microinjected with an siRNA control or an siRNA against Rif1 at the zygote stage. Individual cells were collected for scRepli-seq at the 4-cell, 8-cell and Morula stage embryos.

overall_design: siRNA for Rif1 or control siRNA in 4-cell, 8-cell and morula stage embryo.


title: LaminB1 DamID, RNA-seq and Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos

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

overall_design: Refer to individual Series


overall_design: Cord-blood (CB) hematopoietic stem and progenitor cells (HSPCs) were cultured for three days in early active and stem-preserving medium and at day 3 we performed the following treatments: the electroporation with an RNP with no predictive activity in the human genome in presence (RNP NEG + ANAK) or absence  (RNP NEG) of Anakinra and the standard gene editing procedure with HS RNP and transduction with an AAV6 carrying the DNA donor template for HDR in presence (HS/AAV6 + ANAK) or absence (HS/AAV6) of Anakinra. After 24 hours post treatments, HSPCs were collected for RNA-seq analysis.


title: LaminB1 DamID analysis in RIF1 depleted preimplantation mouse embryos

summary: We investigated how RIF1 depletion affects the nuclear organization in mouse preimplantation embryos by performing DamID-seq to map lamina-associated domains (LADs).

overall_design:
LaminB1 DamID in control or RIF1 depleted 4-cell and 8-cell stage embryos.
Please note that the processed data files generated from all replicates are linked to the corresponding *rep1 sample records.

first: Mrinmoy

last: Pal


city: STANFORD

first: Yuki

last: Miura

state: California

address: 318 Campus Drive, W200

department: Department of Psychiatry and Behavioral Sciences

institute: Stanford University

summary:
Single cell RNA-seq characterization of human induced pluripotent stem cells-derived human cortical organoids (hCO) cultured in control and XG-supplemented conditions

Reference:
Narazaki, Genta; Miura, Yuki;  Pavlov, Sergey D.; Thete, Mayuri Vijay; Roth, Julien G.; Avar, Merve; Kim, Ji-il; Hudacova, Zuzana; Heilshorn, Sarah C.; Pașca, Sergiu P. Scalable production of human cortical organoids using a biocompatible polymer. GSE232581. DOI: (2025).

overall_design: Single-cell RNA sequencing of human induced pluripotent stem cell-derived cortical organoids cultured in control and XG-supplemented medium

first: Sergiu

last: Pașca


title: Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated  gene editing in hematopoietic stem cells

first: Federico

last: Midena

first: Luigi

last: Naldini


title: Collagen V regulates renal function after kidney injury and can be pharmacologically targeted  to enhance kidney repair in mice [scRNAseq]

status: Public on Mar 17 2025

city: Los Angeles

first: Lianjiu

last: Su

address: 500 Landfair Ave.

institute: University of California, Los Angeles

summary: Kidney fibrosis an important determinant of clinical outcomes in individuals with chronic kidney disease (CKD). The stoichiometric ratio of collagens in renal scar tissue differs from that of ECM  of healthy kidneys but the functional importance of altered collagen types injured kidneys remains unclear. Using population studies and multiple independent clinical datasets, we show that circulating protein and renal mRNA amounts of Col5a1   exhibited associations with kidney disease and incident CKD risk. Using murine models of tubulo-interstitial kidney injury, we show that Col V  regulates the degree of post injury fibrosis and renal function. We demonstrated that mice with conditionally knocked out Col5a1 (Col5a1CKO ) exhibited  decreased renal function and greater renal fibrosis after kidney injury .  Renal fibroblasts in Col5a1CKO animals upregulated 𝛼vβ3 integrin. Inhibition of 𝛼vβ3 signaling with a small molecule, cilengitide, rescued post-injury renal function in Col5a1 CKO  animals. Using the hybrid mouse diversity panel (HMDP) that comprises 100 diverse inbred strains of mice, we observed that the ratio  of expression of Col5a1 after injury compared to healthy animals exhibited genetic variation . Strains with low Col5a1 ratios exhibited worse renal function compared to animals that had higher ratios . Col5a1 expression in peripheral blood mononuclear cells after injury compared to uninjured animals to identify Col5a1-non responder strains, we demonstrate that cilengitide can significan tly rescue kidney function in non-responder strains . Overall we found that Col V  regulates renal function and fibrosis after kidney injury. These data suggest the feasibility of precision medicine approaches for targeting pathways downstream of Col5a1 to promote kidney repair.

overall_design: Generation of Col5a1CKO Mice:Col1a2CreERT mice were crossed with Col5a1 floxed mice. Tamoxifen was administered to Cre(-) or Cre+Col5a1fl/fl animals with 7days (0.5mg/kg) from starting model. To induce kidney fibrosis, Cre(-) (Col1a2 cre(-) Col5a1 fl/fl) and Col5a1 CKO (Col1a2 cre(+) Col5a1 fl/fl) mice were fed a 0.2% adenine diet for 14 days.  For experiments involving cilengitide, 20 mg/kg of cilengitide, diluted in PBS, was administered via  IP injection every other day.


title: Acid-dependent beta-lactam resistance in Klebsiella pneumoniae is mediated by paralogous class B PBPs and the class A PBP, PBP1b

city: St. Louis

first: Petra

middle: Anne

last: Levin

state: MISSOURI

address: 1 Brookings Drive, Rebstock Hall, Room 323

department: Biology

institute: Washington University in St. Louis

summary: Klebsiella pneumoniae is a leading cause of global deaths due to antibiotic resistance. Of particular concern, is the rapid expansion within K. pneumoniae lineages of resistance to beta-lactams, the most prescribed class of antibiotics. Additionally, the environmental factors that influence pathogen physiology and, subsequently, antibiotic resistance remain poorly understood. Here we demonstrate that physiologically-relevant drops in culture medium pH result in increased antibiotic resistance particularly towards beta-lactams that inhibit cell division. We identified two genes that contribute to acid-dependent beta-lactam resistance, the class A PBP, PBP1b, and the paralogous class B PBP, PBP3PARA. Loss of either gene increases K. pneumoniae  susceptibility to beta-lactams at low pH. Our data suggests that functional redundancy among cell wall synthesis enzymes allows for specialization and ensures that cell wall synthesis occurs robustly across a range of pH conditions.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Comparison of gene expression during growth at low pH (4.8) versus at neutral pH (6.8) in Klebsiella pneumoniae and Escherichia coli.

first: Sarah

last: Beagle


title: Xenium data for a comparison of spatial transcriptomics technologies for medulloblastoma cryosections

city: Heidelberg

first: Michele

last: Bortolomeazzi

address: TP3 B4.105.5, Im Neuenheimer Feld 580

institute: DKFZ

summary: 10X Genomics Xenium data from human Medulloblastoma samples. The data was acuired in the course of a study performing a comparison of four imaging-based ST methods – RNAscope HiPlex, Molecular Cartography, MERFISH/Merscope, and Xenium – together with sequencing-based ST (Visium). These technologies were used to study cryosections of medulloblastoma with extensive nodularity (MBEN), a tumor chosen for its distinct microanatomical features. Our analysis reveals that automated imaging-based ST methods are well suited to delineating the intricate MBEN microanatomy, capturing cell-type-specific transcriptome profiles. We devise approaches to compare the sensitivity and specificity of the different methods together with their unique attributes to guide method selection based on the research aim. Furthermore, we demonstrate how reimaging of slides after the ST analysis can markedly improve cell segmentation accuracy and integrate additional transcript and protein readouts to expand the analytical possibilities and depth of insights. This study highlights key distinctions between various ST technologies and provides a set of parameters for evaluating their performance. Our findings aid in the informed choice of ST methods and delineate approaches for enhancing the resolution and breadth of spatial transcriptomic analyses, thereby contributing to advancing ST applications in solid tumor research.

overall_design: Cryosections from brain tissue of human patients with medullonlastoma with extensive nodularity of 10 µm thickness were obtained using a Cryostar NX50 (Epredia) cryostat at a cutting temperature of -15 °C. Tissues were sectioned into 10 µm slices, and four samples were placed on a single Xenium slide. After sectioning, the slides were stored at -80°C for less than two weeks. On the day of the experiment, the tissue was fixed with PFA according to the manufacturer's protocol. Tissues were permeabilized with SDS, incubated in 70% ice-cold methanol, and washed with PBS. Hybridization of the human generic brain panel with 70 add-on genes (Supplementary Dataset 1) was performed at 50°C in a Bio-Rad C1000 touch cycler for 20 hours. The washing, ligation, and amplification steps were carried out according to the manufacturer’s instructions. ROIs were selected based on the tissue area, excluding non-tissue-covered tiles. Each transcript was imaged in a bright state five times across 60 cycle-channels (15 cycles x 4 channels). After the run on the Xenium analyzer, slides were removed, and buffer was exchanged with PBS-T for further storage at 4°C.

first: Anne

last: Rademacher

first: Alik

last: Huseynov

first: Sina

last: Wille

first: Sabrina

last: Schumacher

first: Pooja

last: Sant

first: Denise

last: Keitel

first: Konstantin

last: Okonechnikov

first: David

last: Ghasemi

first: Kristian

last: Pajtler

first: Jan-Philipp

last: Mallm

first: Karsten

last: Rippe


title: RNA sequencing of normal and unilateral ureteral obstruction (UUO) operated mouse kidneys

first: Andrew

last: Advani

address: 6-151 61 Queen Street East

department: Medicine

institute: St. Michael's Hospital

summary: RNA-sequencing of mouse left kidneys for which the left ureter was obstructed (UUO) or not obstructed (sham) animals, isolated 14 days after the surgery

overall_design: Whole left kidneys were collected from either sham or UUO kidneys of C57BL/6 mice and bulk kidney tissue RNA was isolated for sequencing

first: Harmandeep

last: Kaur


title: IFN-gamma and donor leukocyte infusions for relapsed myeloblastic malignancies after allogeneic hematopoietic stem cell transplantation

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

institute: University of Pittsburgh

summary: We conducted a phase I trial (NCT04628338) of IFN-γ combined with donor leukocyte infusions (DLI) in myeloblastic malignancies that relapsed post-HLA-matched allogeneic stem cell transplantation (alloSCT). Patients self-administered IFN-γ for 1-4 weeks, followed by DLI and concurrent IFN-γ for 12 weeks. IFN-γ monotherapy was well tolerated by all subjects (n=7). Four of 6 DLI recipients achieved minimal residual disease-negative complete remissions and full donor hematopoietic recovery. Median overall survival was 579 days (range, 97-906) in responders. Single cell RNA sequencing (scRNAseq) was performed on bone marrow (BM) samples collected before IFN-γ treatment and 48-60 hours after the 1st or 2nd dose of IFN-γ from three patients: one responder (Patient 1) and two non-responders (Patients 5 and 7). Recipient-derived cells were distinguished from donor-derived cells based on single nucleotide polymorphisms (SNP) in expressed genes. As expected, most immature pluripotent and myeloid lineage cells (HSC, myeloid progenitor cells, early erythroid cells) at relapse were of recipient genotypic origin, while lymphoid progenitors were mainly donor derived. Genomic copy number in single cells showed that most HSCs or myeloid progenitor cells harbored recurrent chromosome abnormalities known to each patient. To investigate the effects of in vivo IFN-γ within the major lineage clusters, we performed single-cell pathway analyses (SCPA). Transcription changes in the post-IFN-γ specimens were predominantly found in the non-lymphoid subsets (HSC-like cells, myeloid progenitors, CD14 or CD16 monocytes, and erythroid cells). IFN-γ response pathway was activated in HSC-like cells (Patients 1 and 7) and myeloid progenitor cells (Patients 1, 5, 7) in the post-IFN-γ samples. Post-IFN-γ samples also had evidence of activation of “TNF-alpha signaling via NFkb” in HSC-like and myeloid progenitor cell populations. “IL2 STAT5 signaling” and “inflammatory response” pathways were also engaged in post-IFN-γ myeloid populations. These scRNAseq analysis confirmed in vivo IFN-γ action on the dominant malignant myeloid population.

overall_design: scRNAseq was performed on BM from Patients 1, 5 and 7 collected before and 48-72 hours after the 1st or 2nd dose of IFN-γ. For Patient 1, we prepared bulk, unenriched bone marrow (BM) as well as BM enriched in CD34+ BM myeloblasts by immunomagnetic selection; for Patients 5 and 7, only bulk BM cells were analyzed. Samples were captured with Chromium Controller (10x Genomics) and libraries were generated using the Chromium Next GEM Single Cell 5′ v2 (Dual Index) kit (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced using a NextSeq 2000 in 1 run (Illumina P3 kit), with a target of 20,000 reads per cell for gene expression.

first: Sawa

last: Ito

first: Shruti

last: Bhise

first: Scott

last: Furlan


title: JunD cistrome of the human myometrium at during term pregnancy and labour

first: Jennifer

last: Mitchell

summary: We have generated JunD ChIPseq datasets of the human uterine smooth muscle (myometrium) tissue. ChIP-seq experiments were conducted to evaluate changes in the regions bound by JUND that occur as the smooth muscle cells transition from pregnancy to labour using human myometrium tissue.

overall_design: JunD ChIPseq of human myometrium at term-not-in-labour (TNIL),  term labour (LAB) stages (n=2).

first: Nawrah

last: Khader


title: Single Cell RNA-sequencing analysis of the juvenile and postnatal mouse enteric nervous system of the small intestine

city: Stockholm

first: Ulrika

last: Marklund

state: - If in U.S, Select a State -

address: Tomtebodavägen 16

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: The study aimed to achieve a molecular definition of submucosal neuron classes in the mouse small intestine and describe their differentiation from enteric stem cells during postnatal stages. Method: We performed single cell RNA-sequencing of enteric neurons from small intestine at the postnatal day (P)24; (Baf53b-CrexR26RtdTom mice) and ENS cells from the small intestine at P7 (Wnt1-CrexR26RtdTom).  Results: 3 unique cardinal submucosal enteric neuron classes (smENC1-3) were identified and confirmed in native tissue by histochemical methods and class-specific Cre mice mated with reporter mice. Analysis of postnatal transcriptomes revealed that enteric stem cells differentiate into two neuronal branches, that successively diversify into smENC3 (Branch A) or smENC1 and smENC2 (Branch B). Conclusion: Utilizing single cell RNA-sequencing we conclude that murine small intestine consists of 3 cardinal submucosal classes that arise from binary neurogenic branching and postmitotic identity conversions.

overall_design: We isolated single submucosal neurons from pan-neuronal Baf53bCre;R26R-Tomato mice (P24) and single ENS cells (including enteric stem cells, glia and neurons) from Wnt1-Cre;R26RtdTom postnatal animals (P7) using flow cytometry and obtained transcriptomes by single cell RNA-sequencing (10xGenomics).


title: Toward identification of all modulators of erythropoiesis

city: Ann Arbor

first: Rami

last: Khoriaty

state: Michigan

address: 109 Zina Pitcher Pl

department: Internal Medicine

institute: University of Michigan

summary: The complete array of genes required for terminal erythroid differentiation remains unknown. To address this knowledge gap, we performed a genome-scale CRISPR knock-out screen in the human erythroid progenitor cell line HUDEP-2. We validated candidate regulators of erythroid differentiation in a custom secondary screen. Comparison of sgRNA abundance in the CRISPR library, proerythroblasts, and orthochromatic erythroblasts, resulted in the identification of genes that are essential for proerythroblast survival and genes that are required for terminal erythroid differentiation. Among the top genes identified were known regulators of erythropoiesis, underscoring the validity of this screen. Notably, using a Log2 fold change of <-1 and false discovery rate of <0.01, the screen identified 277 genes that are required for terminal erythroid differentiation, including multiple novel genes not previously nominated through GWAS. NHLRC2, which was previously implicated in hemolytic anemia, was a highly ranked gene. We suggest that anemia due to NHLRC2 mutation results at least in part from a defect in erythroid differentiation. Another highly ranked novel gene in the screen was VAC14, which was validated for its requirement in erythropoiesis in vitro and in vivo. Thus, data from this CRISPR screen may help classify the underlying mechanisms that contribute to erythroid disorders.

overall_design: DNA sequencing of sgRNA amplicons isolated from populations of HUDEP2 cells

first: Greggory

last: Myers

first: Ann

last: Friedman

first: Lei

last: Yu

first: Claire

last: Kerpet

first: Masaki

first: Rilie

last: Saba

first: Vi

last: Tang

first: Ayse Bilge

last: Ozel

first: Ingrid

last: Bergin

first: Craig

middle: N

last: Johnson

first: Chia-Jui

last: Ku

first: Yu

last: Wang

first: Ginette

last: Balbin-Cuesta

first: Kim-Chew

last: Lim

first: Zesen

last: Lin

last: Drysdale

first: Beth

last: McGee

first: Ryo

last: Kurita

first: Yukio

last: Nakamura

first: Xiofang

last: Liu

last: Siemieniak

first: Sharon

last: Singh

first: Ivan

last: Maillard

first: Lois

last: Weisman

first: James

last: Engel


title: Cholinergic regulation of thymocyte negative selection

first: Shaofeng

state: <None>

address: 8th floor, Dr. Tak Mak lab, Princess Margaret Cancer Centre

institute: UHN

summary: Acetylcholine (ACh) and its receptors (AChRs) are widely produced by various kinds of immune cells and fine-tune both innate and adaptive immune responses. However, whether cholinergic signaling regulates immune cell development is unclear. Here, we show that mouse CD4+CD8+ double-positive (DP) thymocytes express high levels of a9 nicotinic (n) AChR, and that this receptor controls the negative selection of thymocytes. Knock-out mice lacking a9 nAChR show an altered TCR repertoire and reduced CD4+ and CD8+ T cells in a mixed bone marrow chimera setting. Although thymic tuft cells, B cells, and a portion of T cells were all found to express choline acetyltransferase (ChAT) and so are sources of ACh in mouse thymus, T cell-derived ACh plays a more important regulatory role. Our results thus reveal a new mechanism of immune cell development control that involves lymphocyte-mediated cholinergic signaling.

overall_design: CD4 SP thymocytes (1x106 cells/sample) and CD8 SP thymocytes (3.3x105 cells/sample) from WT or Chrna9-/- mice (two pairs of males and one pair of females) were FACS-sorted. RNA was extracted using an RNeasy microkit from Qiagen. TCR libraries were prepared using a SMARTer Mouse TCR a/b Profiling Kit and sequenced using the MiSeq platform (Illumina). Data were analyzed using MiXCR and VDJtools. Statistical analyses were performed using Prism 5.0 (GraphPad), with the two-tailed paired t-test employed for comparison of repertoire properties.

first: Ping

last: Luo

first: Tak

last: Mak


title: microRNA-218-5p Coordinates Scaling of Excitatory and Inhibitory Synapses during Homeostatic Synaptic Plasticity

city: Zurich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190 Building 17

department: D-HEST

country: Switzerland

institute: ETH Zürich

summary: Homeostatic synaptic plasticity (HSP) is a fundamental neuronal mechanism that allows networks to compensate for prolonged changes in activity by adjusting synaptic strength. This process is crucial for maintaining stable brain function and has been implicated in memory consolidation during sleep. While scaling of both excitatory and inhibitory synapses plays an important role during homeostatic synaptic plasticity, molecules coordinating both of these processes are unknown.  In this study, we investigate the role of miR-218-5p as a regulator of inhibitory and excitatory synapses in the context of picrotoxin (PTX)-induced homeostatic synaptic downscaling (HSD) in rat hippocampal neurons. Using enrichment analysis of miRNA-binding sites in differentially expressed genes changing upon PTX-induced HSD, we bioinformatically predicted and experimentally validated increased miR-218-5p activity upon PTX-treatment in the process compartment. By monitoring synapse structure in vitro with confocal microscopy, we demonstrate that miR-218-5p exerts a dual effect in HSD: it prevents the downscaling of excitatory synapses and dendritic spines, while at the same time blocking inhibitory synapse upscaling. Furthermore, we identify the Neuroligin2 interacting molecule Mdga1 as a crucial target of miR-218-5p in the context of homeostatic upscaling of inhibitory synapses. By performing long-term electroencephalographic (EEG) recordings, we further revealed that local inhibition of miR-218-5p in the somatosensory cortex reduced local slow-wave activity (SWA) during non-rapid-eye-movement (NREM) sleep. In summary, this study uncovers miR-218-5p as a key player in coordinating inhibitory and excitatory synapses during homeostatic plasticity and sleep. Our findings contribute to a deeper understanding of how neural circuits maintain stability in the face of activity-induced perturbations, with potential implications for both physiological and pathological conditions.

overall_design: microRNA-inhibitors called LNAs against miR-218-5p were injected into one hemisphere of the somatosensory cortex I of mice, while the other hemisphere was injected with a scrambled negative control. 4 independent biological replicates (number of animals) were used in the study and denoted as Mxx were xx is a animal identifier. Per mouse (or animal identifier) we have two conditions: LNA218 (or hemisphere injected with miR-218-5p inhibitor) and NC (negative control, injected in the contralateral hemisphere). RH or LH denote whether the right or left hemisphere was injected. RNA was then extracted from the injected site 10 days after stereotactic injections, polyA-enriched and sequenced using an Illumina Novaseq 6000).

first: David

last: Colameo


title: An antisense oligonucleotide-based strategy to ameliorate cognitive dysfunction in the 22q11.2 Deletion Syndrome [miRNA-seq]

city: New York

first: Joseph

middle: A.

last: Gogos

state: NY

address: 3227 Broadway

department: Zuckerman Institute

institute: Columbia University

summary: Adults and children with the 22q11.2 Deletion Syndrome demonstrate cognitive, social and emotional impairments and high risk for schizophrenia. Work in mouse model of the 22q11.2 deletion provided compelling evidence for abnormal expression and processing of microRNAs. A major transcriptional effect of the microRNA dysregulation is up-regulation of Emc10, a component of the ER membrane complex, which promotes membrane insertion of a subset of polytopic and tail-anchored membrane proteins. We previously uncovered a key contribution of EMC10 in mediating the behavioral phenotypes observed in 22q11.2 deletion mouse models. Here we show that expression and processing of miRNAs is abnormal and EMC10 expression is elevated in neurons derived from 22q11.2 deletion carriers. Reduction of EMC10 levels restores defects in neurite outgrowth and calcium signaling in patient neurons. Furthermore, antisense oligonucleotide administration and normalization of Emc10 in the adult mouse brain not only alleviates cognitive deficits in social and spatial memory but remarkably sustains these improvements for over two months post injection, indicating its therapeutic potential. Broadly, our study integrates findings from both animal models and human neurons to elucidate the translational potential of modulating EMC10 levels and downstream targets as a specific venue to ameliorate disease progression in 22q11.2 Deletion Syndrome.

overall_design: We performed miRNA expression profiling from human iPSC-derived cortical neurons. The cortical neurons were derived from hiPSC lines from one female patient with 22q11.2DS diagnosed with SCZ as well as one unaffected twin control. Three independet samples (batches) were sequenced per condition.

first: Martin

last: Lackinger


title: An antisense oligonucleotide-based strategy to ameliorate cognitive dysfunction in the 22q11.2 Deletion Syndrome


title: An antisense oligonucleotide-based strategy to ameliorate cognitive dysfunction in the 22q11.2 Deletion Syndrome [RNA-seq]

overall_design: We performed gene expression profiling from human iPSC-derived cortical neurons. The cortical neurons were derived from hiPSC lines from one female patient with 22q11.2DS diagnosed with SCZ as well as one unaffected twin control. Three independet samples (batches) were sequenced per condition.


title: Collagen V regulates renal function after kidney injury and can be pharmacologically targeted  to enhance kidney repair in mice [bulkRNAseq]

first: Lianjiu

last: Su

overall_design: Generation of Col5a1CKO Mice:Col1a2CreERT mice were crossed with Col5a1 floxed mice. Tamoxifen was administered to Cre(-) or Cre+Col5a1fl/fl animals with 7days (0.5mg/kg) from starting model. To induce kidney fibrosis, Cre(-) (Col1a2 cre(-) Col5a1 fl/fl) and Col5a1 CKO (Col1a2 cre(+) Col5a1 fl/fl) mice were fed a 0.2% adenine diet for 28 days.  For experiments involving cilengitide, 20 mg/kg of cilengitide, diluted in PBS, was administered via  IP injection every other day.


title: Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling

first: Juan

last: Romero

overall_design: Refer to individual Series


title: FG repeats drive co-clustering of nuclear pores and P. granules in the C elegans germline [RNA-seq]

status: Public on Mar 16 2025

city: Baltimore

first: Geraldine

last: Seydoux

address: 725 N Wolfe Street

department: HHMI and Department of Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Condensates that accumulate small RNA biogenesis factors (nuage) are common in germ cells and often associate with nuclei. In the C. elegans germline, P granules overlay large clusters of nuclear pores and this organization has been proposed to facilitate surveillance of nascent transcripts by Argonaute proteins enriched in P granules. We report that co-clustering of nuclear pores and P granules depends on FG repeat containing nucleoporins and FG repeats in the Vasa class helicase GLH-1. Mutants that prevent co-clustering are fertile under standard growth conditions and only mis-regulate a minority of genes, including replication-dependent histones. Our observations suggest that association with nuclear pores, while non-essential for genome surveillance, may serve to tune mRNA flow through P granules and other nuage condensates.

overall_design: ribo-depleted total RNA sequencing of adult N2 and npp-214∆ mip∆ mutants

first: Laura

last: Thomas

first: Devavrat

last: Bodas


title: FG repeats drive co-clustering of nuclear pores and P. granules in the C elegans germline [smallRNA-seq]

overall_design: small RNA sequencing of adult N2 and npp-214∆ mip∆ mutants


title: single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex

city: Cold Spring Harbor

first: Lucas

last: Cheadle

address: 1 Bungtown Road

institute: Cold Spring Harbor Lab

summary: Sensory experience drives the refinement and maturation of neural circuits during postnatal brain development through molecular mechanisms that remain to be fully elucidated. One likely mechanism involves the sensory-dependent expression of genes that encode mediators of circuit remodeling within developing cells. However, while studies in adult systems have begun to uncover crucial roles for sensory-induced genes in modifying circuit connectivity, the gene programs induced by brain cells in response to sensory experience during development remain to be fully characterized. Here, we present a single-nucleus RNA-sequencing dataset describing the transcriptional responses of cells in mouse visual cortex to sensory deprivation or acute sensory stimulation during a developmental window when visual input is necessary for circuit refinement. We sequenced 118,529 individual nuclei across sixteen neuronal and non-neuronal cortical cell types isolated from control, sensory deprived, and sensory stimulated mice, identifying over 1268 unique sensory-induced genes within the dataset.  To demonstrate the utility of this resource, we compared the architecture and ontology of sensory-induced gene programs between cell types, annotated transcriptional induction and repression events based upon RNA velocity, and discovered Neurexin and Neuregulin signaling networks that underlie cell-cell interactions in visual cortex. We find that excitatory neurons, especially pyramidal neurons in cortical layers two and three, are highly sensitive to sensory stimulation, and that the sensory-induced genes in these cells are poised to strengthen synapse-to-nucleus crosstalk by heightening protein serine/threonine kinase activity. Altogether, we expect this dataset to significantly broaden our understanding of the molecular mechanisms through which sensory experience shapes neural circuit wiring in the developing brain.

overall_design: we leveraged a sensory deprivation and stimulation paradigm, the late-dark-rearing (LDR) paradigm, to dampen or increase visual experience between P20 and P27, when sensory-dependent synapse remodeling begins and peaks, respectively. We then performed single-nucleus RNA-sequencing (snRNAseq) on V1 tissue across six conditions encompassing normally reared, sensory deprived, and four cohorts of sensory stimulated mice

first: Qianyu

last: Lin

first: Andre

last: Xavier

first: Chris

last: Kang


title: SUMOylated Etv1 establishes tumor-initiating cells during mammary oncogenesis [CUT&RUN]

city: Iowa City

first: Zhijie

last: Li

state: IA

address: 285 Newton Road

institute: University of Iowa

summary: Sumoylation alters the transcriptional activity of many of the transcription factors known to regulate CSCs/TICs and epithelial-mesenchymal transition (EMT). To identify transcription factor involved in the growth effects mediated by SUMO inhibition,  Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) was used to evaluate genomic occupancy by HA-tagged Etv1.

overall_design: To investigate SUMOylation inhibition, we established Ube2iF/F cell line to achieve complete conditional knockout by Adneovirus-Cre. We then performed Adenovirus comparing to control to knockout SUMOylation before ChIP-seq. We can then measure the quantitative occupancy of HA-tagged Etv1 throughout the genome.

first: Jeremy

last: Chang

first: Ronald

middle: J

last: Weigel


title: Characterization and comparative analysis of multifunctional natural killer cell engagers (NKCEs) during antitumor responses

city: South San Francisco

first: Ittai

middle: Ethan

last: Eres

address: 750 Gateway Boulevard

department: CRADI

institute: Amgen

summary: T cell engagers (TCEs) are transformational oncology therapies but limited in use due to the induction of cytokine release syndrome (CRS). In comparison to T cells, natural killer (NK) cells produce less cytokines upon activation, leading to the exploration of NK cell engagers (NKCEs). However, why NK cells secrete less cytokines such as tumor necrosis factor (TNF) and how NKCEs perform directly against TCEs remain unclear. Here we report that relative to T cells, NK cells have reduced trafficking and processing of TNF. Systematic development and benchmarking studies show that NKCEs can be optimized to engage multiple activating receptors and incorporate the interleukin (IL)-2, thereby increasing their potency and durability. Furthermore, comparative studies of NKCE, IL-2, and TCE therapy in animal tumor models reveal both common and different therapeutic benefits. Our results provide a blueprint for development of multifunctional NKCEs that may serve as an alternative to current TCE therapies.

overall_design: CD4+ T, CD8+ T, and natural killer (NK) cells were treated either with PBS (control) or various T-cell engager (TCE) or NK-cell engager (NKCE) molecules, respectively. One molecule was tested on T-cells while several others were tested on NK cells. RNA pellets were collected both at 16H and 64H post-treatment.

first: Hang

first: Ryan

last: Case

first: Kathy

last: Wei

first: Benjamin

last: Alba

first: Joelle

last: Kaner

first: Yen-Chi

last: Wu

first: Tracy

last: Yamawaki

first: Mina

last: Mostafavi

first: Hong

last: Zhou

first: Hayley

last: Ma

first: Paolo

last: Manzanillo

first: Weiwen

last: Deng


title: Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells.

city: Brisbane

first: Lachlan

middle: Ian

last: Harris

state: QLD

address: 300 Herston Road

department: Cancer Research Program

country: Australia

institute: QIMR Berghofer MRI

summary: Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation.

overall_design:
Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4 °C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100.

**Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025**

first: Piero

last: Rigo

first: Sara

last: Ahmed de Prado

first: Rebecca

last: Johnston

first: Chandra

last: Choudhury

first: François

last: Guillemot


title: SUMOylated Etv1 establishes tumor-initiating cells during mammary oncogenesis

first: Zhijie

last: Li

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


title: SUMOylated Etv1 establishes tumor-initiating cells during mammary oncogenesis [RNA-seq]

summary: RNA-seq was used to compare the effect of SUMOylation inhibition, and Etv1 knockdown on Ube2iF/F cell line transcriptiome. 5xKR or 5xKR-S1 was expressed to examine differential phenotypic transcriptiome changes.

overall_design: To investigate SUMOylation inhibition, we established Ube2iF/F cell line to achieve complete conditional knockout by Adneovirus-Cre. We then performed Adenovirus or siEtv1 comparing to control (EV/siNT) to knockout SUMOylation or knockdown Etv1. Stable expression with either 5xKR or 5xKR-S1 was established before adenovirus-Cre to examine different genetic changes.

first: Dakota

middle: T

last: Thompson

first: Christopher

last: Franke

first: Ronald

last: Weigel


title: Fragile X Syndrome Patient–Derived Neurons Developing in the Mouse Brain Show FMR1-Dependent Phenotypes

city: Leeds

first: Marine

last: Krzisch

state: West Yorkshire

address: Woodhouse Lane

department: School of Biomedical Sciences

country: United Kingdom

institute: University of Leeds


title: SUMOylated Etv1 establishes tumor-initiating cells during mammary oncogenesis [ChIP-seq]

summary: Sumoylation alters the transcriptional activity of many of the transcription factors known to regulate CSCs/TICs and epithelial-mesenchymal transition (EMT). To identify transcription factor involved in the growth effects mediated by SUMO inhibition,  Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) was used to evaluate genomic occupancy by SUMO1 and Etv1.

overall_design: To investigate SUMOylation inhibition, we established Ube2iF/F cell line to achieve complete conditional knockout by Adneovirus-Cre. We then performed Adenovirus comparing to control to knockout SUMOylation before ChIP-seq. We can then measure the quantitative occupancy of SUMO1 and Etv1 throughout the genome.

first: Mohammed

middle: O

last: Suraju


title: Fragile X Syndrome Patient-Derived Neurons Developing in the Mouse Brain Show FMR1-Dependent Phenotypes

summary: The gene expression profiles of 1 month-old FXS patient-derived and isogenic control neurons transplanted in the brain of mice were compared by single-cell RNA sequencing

overall_design: FXS patient-derived and isogenic control iPSC were differentiated into neural precursor cells, labeled with fluorescent proteins (tdTomato for FXS and GFP for control) and injected in immune deficient mouse neonates. 1 month after injection, the brains were dissociated, and the human cells isolated by FACS sorting. The viable cells (DAPI-negative) were then sent for single-cell RNA sequencing.

first: Bingbing

last: Yuan

first: Troy

last: Whitfield

first: Rudolf

last: Jaenisch