title: Rewiring the fusion oncoprotein EWSR1::FLI1 in Ewing scarcoma with bivalent small molecules  [ATAC-seq]

status: Public on Mar 17 2025

city: Boston

first: Kimberly

last: Stegmaier

address: 450 Brookline Ave

institute: Dana Farber Cancer Institue

summary: Dysregulated transcription is a defining hallmark of cancer. Recently, novel chemically induced proximity approaches have enabled the rewiring of transcriptional machinery to drive expression of pro-apoptotic genes using bivalent small molecules.  In this work, we demonstrate that this strategy is amenable to relocalizing DNA bound transcriptional machinery, such as fusion transcription factors that commonly drive pediatric malignancies. Targeting fusion transcription factors, such as EWSR1::FLI1 in Ewing sarcoma, with these bivalent compounds may open new therapeutic avenues. Here, we develop a small molecule, EB-TCIP, that recruits FKBP12F36V-tagged EWSR1::FLI1 to DNA sites bound by the transcriptional regulator BCL6, leading to rapid chromatin remodeling and expression of BCL6 target genes. This proof-of-concept study demonstrates that DNA binding proteins with pioneering transcription factor activity, such as EWSR1::FLI1, can be relocalized on chromatin to induce expression of repressed genes. Insights herein will guide the development of future bivalent molecules that rewire DNA binding transcriptional machinery.

overall_design: Investigate changes in chromatin accessibility after 4 hour treatment with EB-TCIP compared to DMSO, NEG-1 and NEG-2 controls (two replicates).  Under GEO GSE290893 (ATAC-Seq) 24 hour samples EB-TCIP is labelled as BAK212,

first: Michael

last: Bond

first: Giulia

last: DiGiovanni


title: Rewiring the fusion oncoprotein EWSR1::FLI1 in Ewing scarcoma with bivalent small molecules [ChIP-Seq]

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Investigate changes in chromatin binding of FKBP-EWSR1::FLI1 and BCL6 after 4 h treatment with 1 µM EB-TCIP compared to DMSO. FKBP-EWSR1::FLI1 was immunoprecipitated with an HA antibody. Two replicates of each condition were performed. Under GEO GSE290894 (ChIP-Seq) 24 hour samples, BI3812 is labelled as BI, EB-TCIP is labelled as BAK212,


title: Improved split prime editors enable efficient in vivo genome editing.

status: Public on Mar 15 2025

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

summary: Prime editor (PE) is a precise genome-editing tool capable of all possible base conversions, as well as insertions and deletions without DSBs or donor DNA. The efficient delivery of PE in vivo is critical for realizing its full potential in disease modeling and therapeutic correction. Although PE has been divided into two halves and delivered using dual adeno-associated viruses (AAVs), editing efficiency at different gene loci varies among split sites, and efficient split sites within Cas9 nickase are limited. In this study, by screening multiple split sites, we demonstrated a series of efficient split site when delivering PE by dual-AAV. Additionally, we utilized a feature reported by others recently that RNase could be detached from the Cas9n and designed split sites in the first half of Cas9n. To test the editing efficiency in vivo, a novel dual-AAV split-ePE3 was packaged in AAV9 and delivered via tail vein injection in mice, achieving 24.4% precise genome editing 3 weeks post-injection. Our findings establish an alternative split-PE architecture that could achieve robust gene editing efficiency, facilitating the potential utility both in model organisms and as a therapeutic modality.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Split PE from different split sites was cloned into the AAV genome plasmid, and a series of split-PE systems were established by employing different promoters, truncated reverse transcriptase and untethered reverse transcriptase under the size restriction condition of the AAV packaging. Cells transfected with plasmids and mice infected with dual-AAV virus, the desired editing was integrated into the genome of host cells. Cells were harvested 72 hours after plasmid transfection, and mouse livers were collected 3 weeks after the virus injection into the tail vein. To detect the outcome of prime editing, we amplified the gDNA harvested from the edited cells and subjected the amplicons to high-throughput sequencing.

Additional data for this study are in: GSE270813


title: Depletion of ribosome biogenesis factors in NPM1-mutant acute myeloid leukemia: Insights into direct consequences of the mutation and implications for treatment

status: Public on Feb 27 2025

city: Cambridge

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: University of Cambridge

type: Expression profiling by high throughput sequencing

summary: Mutations in the NPM1 gene are found in more than 30% of acute myeloid leukemia (AML) cases. The mutations disrupt a nucleolar localization signal (NoLS) and create a novel nuclear export signal (NES), leading to cytoplasmic displacement of the protein (NPM1c). NPM1c mutations prime hematopoietic progenitors to leukemic transformation, but their precise molecular consequences remain elusive. Here, we first examined the effects of isolated NPM1c mutations on the global proteome of pre-leukemic hematopoietic progenitors using a conditional knock-in Npm1cA/+ mouse model. We discovered a significant depletion of many factors involved in the ribosome biogenesis pathway which, importantly, persists in NPM1-mutant AML patients. Next, we found that pre-leukemic Npm1cA/+ cells display higher sensitivity to Actinomycin D (ActD) and other RNA pol I inhibitors when compared to wild-type Npm1+/+ cells. Combination treatment with ActD and Venetoclax inhibited the growth and colony forming ability of pre-leukemic and leukemic NPM1c+ cells and low-dose ActD treatment was able to re-sensitize resistant NPM1c+ cells to Venetoclax. Finally, by contrasting our findings with data from CRISPR drop-out screens, we identified and validated TSR3, a ribosome maturation factor of the 40S ribosomal subunit whose knock-out preferentially inhibited the proliferation of NPM1c+ AML cells by activating a p53-dependent response.  Similar to low-dose ActD treatment, TSR3 depletion could partially restore sensitivity to Venetoclax in therapy-resistant NPM1c+ AML models.

overall_design: Transcriptomes of lineage negative (HSPC) bone marrow cells 6 weeks post-pIpC

first: Aristi

last: Damaskou

first: Rachael

last: Wilson

first: Malgorzata

last: Gozdecka

first: Maria

last: Eleftheriou

first: Eliza

last: Yankova

first: Justyna

last: Rak

first: George

middle: S

last: Vassiliou


title: Rewiring the fusion oncoprotein EWSR1::FLI1 in Ewing scarcoma with bivalent small molecules [RNA-Seq]

overall_design: Investigate alterations in gene expression in parental EWS502 Ewing sarcoma cells and EWS502 cells expressing FKBP treated for 4 hours with DMSO, BI3812, EB-TCIP, NEG-1, or NEG-2. Three replicates were performed for each conditon. NEG-1 samples were harvested from a latter passage of cells with a separate DMSO control labelled DMSO-2. Under GEO GSE290895 (RNA-Seq),  8 hours and 24 hours samples,  EB-TCIP is labelled as BAK212, BI3812 is labelled as BI, and NEG-1 is labelled as O89.


title: Graft-versus-host disease prophylaxis shapes T cell biology and immune reconstitution after hematopoietic cell transplant

status: Public on Mar 20 2025

first: Leslie

last: Kean

state: MA

address: 300 Longwood Ave

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: Successful hematopoietic cell transplant requires immunosuppression to prevent graft-versus-host disease (GVHD), a lethal, T-cell-mediated post-transplant complication. The phase 3 BMT CTN 1703 trial demonstrated superior GVHD-free/relapse-free survival for post-transplant cyclophosphamide (PT-Cy)-based GVHD prophylaxis versus tacrolimus/methotrexate (Tac/MTX), but did not improve overall survival. To compare T-cell biology between GVHD prophylaxis regimens, 324 patients were co-enrolled onto BMT CTN 1801 (NCT03959241). We quantified T-cell immune reconstitution using multi-modal analysis, including T-cell receptor (TCR) sequencing of 2,359 longitudinal samples (180,432,350 T-cells). Compared to Tac/MTX, PT-Cy was associated with an early, substantial reduction in TCR diversity that was sustained for 2 years. PT-Cy led to a T-cell reconstitution bottleneck, including reduced thymic output and virus-associated TCRs. Decreased D+14 TCR diversity predicted prevention of chronic GVHD, but also correlated with increased moderate-to-severe infections. This study reveals how distinct immunosuppression strategies have significant effects on the global immune repertoire, underpinning post-transplant clinical outcomes.

overall_design:
Examination of single-cell TCR- and RNA-sequencing of T cells in BMT patients receiving post-transplant cyclophosphamide-based GVHD prophylaxis versus tacrolimus/methotrexate.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Edward

last: Chen

first: Nicholas

last: Winn

first: Jim

last: Kaminski

first: Alex

last: Albanese


title: Bulk RNAseq of Caki cells with ectopic expression of YAP1 and HPV E6/E7 oncogenes

status: Public on Feb 25 2025

city: boston

first: Jiyuan

last: Liu

state: Massachusetts

address: 55 fruit st.

institute: Mass Gen Hospital

summary: The most notable progress in renal clear cell carcinoma (ccRCC) in the past decades is the introduction of drugs targeting the VHL-HIF signaling pathway-associated angiogenesis. However, mechanisms underlying the development of VHL mutation-independent ccRCC are unclear. Here we provide evidence that the disrupted Hippo-YAP signaling contributes to the development of ccRCC independent of VHL alteration. We found that YAP1 and its primary target genes are frequently upregulated in ccRCC and the upregulation of these genes is associated with unfavorable patient outcomes. Research results derived from our in vitro and in vivo experimental models demonstrated that, under normoxic conditions, hyperactivated YAP1 drives the expression of FGFs to stimulate the proliferation of tumor and tumor-associated endothelial cells in an autocrine/paracrine manner. When rapidly growing cancer cells create a hypoxic environment, hyperactivated YAP1 in cancer cells induces the production of VEGF, which promotes the angiogenesis of tumor-associated endothelial cells, leading to improved tumor microenvironment and continuous tumor growth. Our study indicates that hyperactivated YAP1 is essential for maintaining a sustainable ccRCC progression, and targeting the dual role of hyperactivated YAP1 represents a novel strategy to improve renal carcinoma therapy.

overall_design: Ectopic expressions of YAP1 or YAPS127A in CAKI cells were confirmed by Western blot. RNA was extracted from these cells. High-quality libraries were prepared and sequenced using Illumina HiSeq 4000 next-generation sequencer in the Next-Generation Core at the Mass General Hospital.

first: Xiangmin

last: Lv

first: Cheng

last: Wang


title: Skeletal Muscle Resident Macrophages Undergo Expansion and Pathogenic Activation in mdx5cv/Ccr2-/- mice

status: Public on Feb 24 2025

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

summary: Infiltrating macrophages contribute to muscle dystrophic changes in Duchenne muscular dystrophy (DMD). In a DMD mouse model, mdx5cv mice, CC chemokine receptor type 2 (CCR2) deficiency diminishes Ly6Chi macrophage infiltration by blocking blood Ly6Chi inflammatory monocyte recruitment. This is accompanied by transient improvement of muscle damage, fibrosis, and regeneration. The benefit is lost, however, after expansion of intramuscular Ly6Clo macrophages. To address mechanisms underlying the Ly6Clo macrophages expansion, we compared mdx5cv/Nur77-/- and mdx5cv/Ccr2-/-/Nur7-/- mice with mdx5cv and mdx5cv/Ccr2-/- mice, respectively, and found no evidence to suggest Ly6Clo monocyte recruitment by dystrophic muscles. Single-cell RNA sequencing analysis and Flt3cre/Rosa26LSL-YFP-based lineage tracing of macrophage origins demonstrated expansion and pathogenic activation of muscle resident macrophages in CCR2-deficient mdx5cv mice. The expansion was associated with increased cell proliferation, which appeared induced by colony stimulating factor 1 derived from fibro/adipogenic progenitors. Our study establishes a pathogenic role for skeletal muscle resident macrophages in muscular dystrophy.

overall_design: Single cell suspension were prepared from quadriceps and diaphragm of mdx5cv and mdx5cv/Ccr2-/- mice at 14 weeks of age, and then used for single cell based RNA sequencing.

first: Yinhang

first: Xingyu

first: Salam

last: Alabdullatif

first: Sachiko

middle: T

last: Homma

first: Yuriy

last: Alekseyev

first: Lan

last: Zhou


title: Joint single-cell profiling of Cas9 edits and transcriptomes reveals on- and off-target effects on gene expression (Superb-seq)

city: La Jolla

first: Graham

last: McVicker

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: A longstanding barrier in genome engineering with CRISPR-Cas9 has been the inability to measure Cas9 edit outcomes at single-cell resolution. Here we present Superb-seq, a new technology for joint measurement of on-target and off-target Cas9 edits and transcriptomes by single-cell RNA sequencing. In contrast to Perturb-seq methods that read each cell’s guide RNA, Superb-seq directly reads Cas9 edits by leveraging T7 in situ transcription. We performed Superb-seq on 9,500 K562 cells, targeting four chromatin remodeler genes with seven guide RNAs. Superb-seq identified 11,891 edit events in 6,230 edited cells at all seven on-target sites and at 36 off-target sites. One notable off-target edit fell within the first intron of the deubiquitinase gene USP9X, which decreased its expression and perturbed the expression of downstream genes. Superb-seq uses off-the-shelf kits, standard equipment, and requires no virus, which will enable CRISPR screens in virus-intolerant cell types and functional characterization of off-target events.

overall_design:
To demonstrate that Cas9 genome edits can be identified through T7 RNA, we performed T7 in situ transcription and bulk RNA-seq on human nuclei containing T7 promoter-labeled edits.
To demonstrate single-cell edit capture and gene expression association, we performed Superb-seq on K562 cells edited at four chromatin remodeler genes (ARID1A, SMARCA4, CHD3, CHD4) with seven guide RNAs, and analyzed two single-cell libraries of 500 and 10,000 cells.

first: Michael

middle: H

last: Lorenzini

first: Brad

last: Balderson


title: Distinguish response of low-dose radiation with different dose-rate on gene expression of human coronary artery endothelial cells: A bioinformatic study based on transcriptomic sequencing

status: Public on Mar 08 2025

city: Seoul

first: Yeonghoon

last: Son

address: 75, Nowon-ro

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences (KIRAMS)

summary: The biological effects of radiation below 100 mGy are still unproven. In this study, we observed the effects of low-dose radiation (100 mGy) on gene expression in human coronary artery endothelial cells (HCAECs) and its effect on molecular signaling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCAEC cells according to dose rate of 100 mGy low-dose radiation

first: Soo-Ho

last: Lee

first: Kyu-Jin

last: Choi

first: Chang-Geun

first: Hae-June


title: Improved Prediction of Venetoclax and Azacitidine Efficacy in Acute Myeloid Leukemia through Machine Learning

status: Public on Feb 18 2025

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Despite the transformative impact of venetoclax-azacitidine in treating acute myeloid leukemia (AML), reliable markers for accurately predicting patient responses remain urgently needed. To address this challenge, we employed a multidisciplinary approach that combined transcriptomic profiling, ex vivo drug sensitivity testing, functional assays, and clinical data to identify robust predictors of venetoclax-azacitidine response. We pinpointed a set of core genes linked to both ex vivo and in vivo drug responsiveness, validated through CRISPR-Cas9 screens in the setting of both venetoclax and azacitidine therapies. In particular, silencing BCL2L1 and PINK1 preferentially enhanced response to the venetoclax-azacitidine treatment. Building on these insights, we further developed and validated an 8-gene random forest model (RF8) that demonstrated high specificity and sensitivity in four independent cohorts comprising 498 patients. This model was capable of distilling downstream effects of genetic alterations to assist in predicting treatment response and outperformed existing genetic mutation-based signatures. Furthermore, the RF8 score demonstrated a nearly monotonic relationship with venetoclax-azacitidine response probabilities and patient outcomes, enabling precise stratification of patients. These findings illustrated the feasibility of translating integrated transcriptomic and drug-response profiling data into more refined risk stratification approaches, offering a new avenue for optimizing clinical decision-making in AML.

overall_design: RNA-seq profiling of MOLM13 and OA3 cells transduced with scrambled control shRNA and PINK1 knockdown.

first: Dan

first: Kankan


title: RNA sequencing of HCC cells after endoplasmic reticulum stress induced by tunicamycin

status: Public on Feb 12 2025

city: Hefei

first: Yue

last: Zhu

address: The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China

summary: In order to explore the role of ER stress in the development and progression of HCC, RNA sequencing was performed to detect the differential RNA levels before and after ER stress, thus providing strong evidence for the search of ER stress-related genes.

overall_design: We treated HepG2 cells with tunicamycin for 24 h and then extracted total RNA for detection.

first: Guoping

last: Sun

first: Jiatao


title: Promoter-centric gene regulation in drug-resistant cancer

city: South San Francisco

first: Bence

last: Daniel

address: 1 DNA Way

department: Department Proteomic and Genomic Technologies

institute: Genentech Inc.

summary: In eukaryotic cells, gene-distal regulatory elements (REs) facilitate long-range gene regulation, ensuring cell type-specific transcriptional programs. This mechanism is frequently disrupted in cancer, often driven by transcription factors (TFs) that serve as targets for cancer therapy. However, targeting these TFs can lead to acquired resistance mechanisms that are not fully understood. We show that mesothelioma cancer cells, dependent on the oncogenic driver TF TEAD, develop resistance to a pan-TEAD inhibitor and revert to an evolutionarily ancient, promoter-centric gene regulatory mechanism to recover gene expression. Base-pair-resolution 3D chromatin conformation mapping reveals that RE-promoter interactions are disrupted in resistant cells, despite epigenetic and transcriptomic recovery. Mechanistically, in resistant cells, TF complexes, including resistance-specific FOSL1 and KLF4, preferentially bind and enhance promoter activity to recover gene expression, rendering distal REs dispensable. Our findings highlight promoter elements and promoter-specific TFs as potential therapeutic targets using a model of drug-resistant cancer.

overall_design:
Micro-Capture C: Examination of local chromatin folding in parental and drug resistant mesothelioma cancer cells (NCI-H226).

ATACseq: For each sample, ~100k viable cells were processed with the Active Motif ATAC-seq kit according to the manufacturer?s instructions. Nuclei were isolated, tagmentation was performed with Tn5 transposase for 30-minutes at 37C, and libraries were PCR-amplified (12 cycles) using indexing primers. Libraries were size-selected, quality-checked by Tapestation, quantified by Qubit, and sequenced as paired-end (2 × 50 bp).

CUT&Run: Epigenetic mapping in parental and drug resistant mesothelioma cancer cells.

ChIPseq: NF2-null H226 and MSTO-211H cells were generated by long-term, stepwise dose adaptation to the pan-TEAD inhibitor GNE-7883. H226 cells were gradually exposed from 0.25 µM to 2.5 µM over ~55 days, and MSTO-211H cells from 0.25 µM to 3.0 µM, with incremental increases every 1?2 weeks while maintaining at least 25% cell confluence. During escalation, transient cytostasis was followed by the emergence of proliferating persister populations under sustained drug pressure. Resistant pools were expanded from these outgrowths and maintained in medium containing 5 µM GNE-7883. Characterization of these resistant models followed previously described procedures. For acute treatment conditions, H226 and MSTO cells were treated with 2.5 µM GNE-7883 for 48-hours before collection.

RNAseq: NF2-null H226 and MSTO-211H cells were generated by long-term, stepwise dose adaptation to the pan-TEAD inhibitor GNE-7883. H226 cells were gradually exposed from 0.25 µM to 2.5 µM over ~55 days, and MSTO-211H cells from 0.25 µM to 3.0 µM, with incremental increases every 1?2 weeks while maintaining at least 25% cell confluence. During escalation, transient cytostasis was followed by the emergence of proliferating persister populations under sustained drug pressure. Resistant pools were expanded from these outgrowths and maintained in medium containing 5 µM GNE-7883. Characterization of these resistant models followed previously described procedures. For acute treatment conditions, H226 and MSTO cells were treated with 2.5 µM GNE-7883 for 48-hours before collection.

first: Daniel

last: Bence

first: Kameswaran

last: Vasumathi


title: Leveraging RNA-seq Deconvolution to Improve Complex In Vitro Model Characterization

status: Public on Feb 15 2025

city: Seattle

first: Edward

last: Kelly

state: Washington

address: 1959 NE Pacific St

institute: University of Washington

summary: Accelerating development of complex in vitro models (CIVMs) drives a need for additional methods to characterize these systems for use in toxicology and drug development. Relative to traditional cell culture, CIVMs may use a lower number of cells, are cultured for longer periods of time, and typically involve engineered 3-D cell organization. Standard single-cell assessment tools are not conducive to these types of complex models due to cell isolation stress, cell loss, and high cost. In this report, we benchmark RNA-seq deconvolution, which utilizes publicly available scRNA-seq datasets to predict cell proportions from bulk RNA-seq data derived from two CIVMs: a stem-cell-based human intestine epithelia model and a neonatal rodent testis model. We consider the impact of multiple imputation methods for scRNA-seq to restore the gene distribution of the original tissue to generate a better cell type signature and multiple deconvolution methods. The accuracy of deconvolution methods varied significantly in our analyses but provided valuable information on the emergence of an enterocyte cell population from the LGR5+ crypt stem cells following differentiation. In the testis model, deconvolution indicated that a small population of germ cells were retained over time, and that cell type estimates remained stable with physiologically relevant hormone stimulation. In our analysis, using imputed single cell references improved deconvolution accuracy. Deconvolution can be a useful tool for novel CIVM characterization, especially with rapidly growing libraries of single-cell data across tissues and developmental time.

overall_design: All samples are from a complex in vitro model of neonatal rodent testis. All models are seeded with cells isolated from post-natal day five Sprague Dawleys rats, a complete testis cell mixture was used, without enrichment or depletion of specific cells types. Samples are included for two experiments. The "baseline" experiment, where models seeded from one litter of rats were sampled in technical replicate across 3 days (days 3, 5, and 7). Primary tissue isolates were also sequenced in triplicate for this baseline. The "induction" experiment, where models are maintain in vitro for 10 days, then 50 mIU/mL LH and 20 mIU/mL FSH are added and samples are collected after 2 hours, 6 hours, 12 hours and 48 hours. Samples were also collected on day 10 (time 0) before hormone addition. These are three biological replicates, where three replicates cultures are combined at each timepoint to form one biological replicate (one litter). This is repeated across three litters.

middle: C

last: Hansen

first: Christopher

middle: M

last: Arian

first: Yuting

last: Zeng

first: Meg

middle: G

last: Takezawa

first: Ashleigh

middle: B

last: Theberge

first: Elaine

last: Faustman

first: Kenneth

middle: E

last: Thummel

middle: J


title: Single-cell RNA sequencing revealed the transcriptional landscape and heterogeneity of macrophages in the intestinal tissues of WT and LncRNA17Rik knockout mice.

status: Public on Feb 02 2025

city: Tianjin

first: Yun Huan

last: Gao

address: 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

summary: CD11b+ cell populations, especially macrophages, are highly heterogeneous tissue-resident immune cells in mice and humans. The exact subpopulation and its phenotype remain unknown. Here, we analyzed intestinal CD11b+ cell populations from normal and  LncRNA17Rik knockout mice using scRNA-seq.

overall_design: 10X Genomics scRNA-seq was performed to better assess immune cell heterogeneity in gut lamina propria (LP).

first: yunhuan

last: gao

first: yi

last: shi


title: Mapping the Temporal Impact of Perturbations on Lineage Plasticity and Gene Regulation

status: Public on Feb 03 2025

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

institute: EMBL-EBI

summary: This study characterizes gene and enhancer knockout phenotypes of 30 genes in a human pluripotent stem cell (hPSC)-directed islet differentiation system. Samples were collected at five differentiation stages from hPSCs to SC-islet cells for scRNA-seq to examine transcriptional impact of the knockouts over time.

overall_design:
30 genes were edited using CRISPR-Cas9, including HHEX, GATA6, PDX1, GATA4, FOXA1, FOXA2, MNX1, NEUROD1, NKX2-2, RFX6, GSC, HNF4A, PAX6, PBX1, GLIS3, NEUROG3, ARX, OTUD5, BMPR1A, TLE3, BCOR, QSER1 , TET1, TET2, TET3, TADA2B, KDM2B, PROSER1 gene knockouts, and HHEX, ONECUT1 and NANOG enhancer deletions. The CRISPR-Cas9 edited lines were generated in two hPSC backgrounds (HUES8 and H1 human embryonic stem cells), with each genotype represented by multiple clones. The clonal lines were individually barcoded (using the expressed LARRY barcodes) and pooled for differentiation. Samples were collected at five differentiation stages as follows, ESC, definitive endoderm (DE, Day 3), Posterior foregut (PFG or PP1, Day 7), pancreatic progenitor (PP, Day 11), islet-like (SC-islet, Day 18) for scRNA-seq. In addition, WT cells in H1 and HUES8 backgrounds were differentiated and sequenced in parallel at 17 time points: day -1 (ESC), 3, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 21, 25, 26, 35.
Please note that processed .h5ad data was generated from both *transcriptome and *larry samples, and is linked to the corresponding *transcriptome records.

first: Danwei

last: Huangfu

first: Dingyu

last: Liu

first: Dapeng

last: Yang

first: Renhe

last: Luo


title: Longitudinal ovarian cancer (BOB)

status: Public on Feb 08 2025

city: Basel

first: Francis

last: Jacob

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel and University of Basel

summary: High-grade serous ovarian cancer presents significant challenges due to its poor prognosis and high heterogeneity, both of which complicate treatment responses. This project aims to understand intra-patient tumor evolution by investigating different sampling sites (primary and metastatic) at the time of diagnosis and during disease recurrence. A total of 183 biopsies from 50 patients were collected for this purpose, and bulk mRNA sequencing was performed. The majority of samples originated from following tissue types: omentum, ovary, and ascites.

overall_design:
The samples included in this cohort are derived from clinical biopsies of patients diagnosed with high-grade serous ovarian cancer.

***************************************************************
Raw sequencing data from human patient samples were not submitted to GEO due to data-protection considerations. Controlled access to the raw files is provided through the European Genome-phenome Archive (EGA; accession EGAD50000002064) via the MF-DAC.
***************************************************************

first: Natalie

last: Rimmer

first: Anne

last: Bertolini

first: Franziska

last: Singer

first: Michael

last: Prummer

first: Flavio

last: Lombardo

first: Viola

last: Heinzelmann-Schwarz

first: Monica

last: Nunez


title: The G-Quadruplex experimental drug QN-302 effectively impairs liposarcoma cell viability by inhibiting MDM2 expression and restoring p53 levels [RNA-seq]

status: Public on Jan 31 2025

city: Padova

first: Beatrice

last: Tosoni

state: Padova

address: via Aristide Gabelli 63

country: Italy

institute: University ofPadova

summary: Well-differentiated (WD) and dedifferentiated (DD) liposarcomas (LPS) account for ~60% of all liposarcomas, characterized by 12q13–q15 region amplification and aberrant MDM2 expression. Current therapies are limited, particularly for advanced stages, leading to poor outcomes. G-quadruplexes (G4s), secondary structures in G-rich nucleic acid sequences, were identified in the MDM2 P2 promoter. We investigated MDM2 inhibition via small molecule G4 ligands. Laboratory and patient-derived LPS cell lines, and normal pre-adipocytes were analyzed using CUT&Tag, RNA-seq, cell viability, qRT-PCR, Western blot, siRNA, and nascent transcript assays. QN-302, a naphthalene diimide (NDI)-derivative, emerged as the most effective G4 ligand, significantly impairing WD/DDLPS cell growth in a dose-dependent manner by stabilizing MDM2 G4 at the P2 promoter, inhibiting polymerase progression, and reducing full-length MDM2 transcripts, leading to p53 accumulation and apoptotic cell death. In vivo, QN-302 reduced tumor volume and was well-tolerated in xenograft models. This novel therapeutic strategy to inhibit MDM2 and reactivate p53 in WD/DDLPS could extend to all tumors with wild-type TP53 and enhance anticancer efficacy when combined with other drugs.

overall_design: Differential gene expression analysis after QN-302 treatment in human well-differentiated liposarcoma cell line (WD), two patient-derived de-differentiated liposarcoma cell lines (DD-1 and DD-2) and normal human subcutaneous pre-adipocytes cell line (PA) through RNAseq.

first: Eisa

last: Naghshineh

first: Irene

last: Zanin

last: Gallina

first: Lorenzo

last: Di Pietro

first: Loredana

last: Cleris

first: Matteo

last: Nadai

first: Mara

last: Lecchi

first: Paolo

last: Verderio

first: Pietro

last: Pratesi

first: Sandro

last: Pasquali

first: Nadia

last: Zaffaroni

first: Stephen

last: Neidle

first: Marco

last: Folini

first: Sara

middle: N

last: Richter


title: The G-Quadruplex experimental drug QN-302 effectively impairs liposarcoma cell viability by inhibiting MDM2 expression and restoring p53 levels [CUT&Tag]

overall_design: G-quadruplex analysis in human well-differentiated liposarcoma cell line (WD), two patient-derived de-differentiated liposarcoma cell lines (DD-1 and DD-2) and normal human subcutaneous pre-adipocytes cell line (PA) through CUT&Tag method.


title: Control, MGO-treated, and Paclitaxel-treated RNAseq data with matched ribosome profiling

city: Madison

first: Zachary

last: Campbell

state: WI

address: 1111 Highland Avenue

department: Anesthesiology

institute: University of Wisconsin - Madison

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

overall_design: Refer to individual Series


title: Effects of exposure to the trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine (DCVC) and percholorethylene metoblite S-(1,1,2-trichlorovinyl)-L-cysteine (TCVC) on term placental villous explants differential gene expression

status: Public on Jan 25 2025

city: San Diego

first: Elana

middle: R

last: Elkin

address: 5500 Campanile Drive

department: School of Public Health

institute: San Diego State University

summary: Volatile organic chemicals Trichloroethylene (TCE) and perchloroethylene (PCE) are liquid solvents used for dry cleaning, industrial degreasing operations, and more. The multiple industrial uses of TCE and PCE have led to large volumes of TCE and PCE being released into the air, surface water, groundwater, and soil worldwide. Maternal exposure to TCE and/or PCE are associated with increased risk of restricted fetal growth (TCE), preterm birth (PCE), placental abruption (PCE) and stillbirth (PCE), suggesting that the placenta may be a key target of TCE and PCE due to its critical role in maintaining maternal and fetal health in pregnancy and mediating fetal growth. We previously showed that TCE and PCE metabolites activate stress response and cell death pathways in placental cell and tissue models. However, there are still key gaps in our knowledge on TCE and PCE metabolites impact the placenta, particularly across fetal sex. We aimed to identify transcriptomic responses to the TCE metabolite S-(1,2-dichlorovinyl)-L-cysteine (DCVC) and PCE metabolite S-(1,2,2-trichlorovinyl)-L-cysteine (TCVC) using a placental explant model and to determine the extent to which fetal sex modifies DCVC and TCVC impacts on the transcriptome. We isolated both male- and female-associated villous placental tissue (n=8, four male and four female), followed by treatment with DCVC or TCVC at the following concentrations: 0 μM (control), 10 μM, and 20 μM. Following treatment, we isolated RNA from explants and generated whole transcriptome profiles using RNA sequencing. We conducted differential gene expression analysis to identify significant gene expression changes across treatment groups, stratified by fetal sex (adjusted p-value < 0.05 and |log2 fold change| > 1). We performed Gene Set Enrichment Analysis (GSEA) to evaluate differences in biological pathway enrichment across treatment groups. Finally, we performed placental cell type deconvolution using CIBERSORTx and used beta regression to compare proportions of cell types between VOC-metabolite exposed tissue and unexposed tissue in both fetal sexes. Significant gene expression changes for both fetal sexes were observed across all treatment groups compared to controls.

overall_design: Differential gene expression: DCVC: 0 (control) vs 10 µM  DCVC,   0 (control) vs 20 µM  DCVC; TCVC: 0 (control) vs 10 µM  TCVC,   0 (control) vs 20 µM  TCVC'  Subset by male vs female. Eight term placental donors (4 boys and 4 girls)

first: Tiffany

last: Russell

first: John

middle: F

last: Dou

first: Kelly

last: Bakulski

first: Justin

middle: A

last: Colacino

first: Vasantha

last: Padmanabhan

first: Sean

last: Harris


title: Gene expression profling of BAL cells in people living with HIV and healthy controls in response to Mtb infection at single cell resolution

status: Public on Jan 28 2025

city: Atlanta

first: Jyothi

last: Rengarajan

state: GA

address: 954 Gatewood Road NE

department: Emory Primate Center

institute: Emory University

summary: Understanding why PLWH remain highly susceptible to TB despite anti-retroviral therapy (ART) is critical for improving treatment and prevention strategies. We aimed to determine how HIV impacts the transcriptional responses of AMs and other immune cells in response to Mtb infection at the single cell level using ScRNAseq. Our analyses revealed that transcriptional responses of AMs from PLWH following Mtb infection show significant deficits in costimulatory capacity and TNF/IL-6 signaling networks.

overall_design: Bronchoalveolar lavage (BAL) samples were collected from HC and PLWH on ART in Atlanta, GA. Single cell transcriptional profiling was assessed by scRNAseq (10x Genomics), both at baseline and after 4 hours of infection with Mtb ex vivo.

first: Sushma

middle: K

last: Cribbs


title: Effects of exposure to the trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine on HTR-8/SVneo differential gene expression under hypoxic vs. normoxic  conditions (O2 < 2%)

status: Public on Jan 24 2025

summary: Trichloroethylene (TCE) is an industrial solvent and widespread environmental contaminant. Human TCE exposure is prevalent, though epidemiological studies testing TCE exposure and adverse birth outcomes are inconclusive. The TCE metabolite S-(1,2-dichlorovinyl)-L-cysteine (DCVC) exhibits toxicity at human-relevant concentrations in a placental cell line. To date, DCVC cytotoxicity mechanistic studies have only been performed under normoxic  conditions. In the current study, two parallel experiments under hypoxic or normoxic conditions were conducted. Genome-wide gene expression and gene set enrichment analyses (GSEA) were used to identify novel genes and pathways altered by human exposure-relevant DCVC concentrations in the human placental cell line HTR-8/SVneo.

overall_design: Differential gene expression in hypoxic vs. normoxic condition and treated vs. control within each condition were explored.

first: Franny

last: Stein


title: SETD2 loss-of-function uniquely sensitizes cells to epigenetic targeting of NSD1-directed H3K36 methylation [RNA-seq]

status: Public on Jan 17 2025

city: Rochester

first: Keith

middle: Darrell

last: Robertson

state: MN

address: 200 First Street SW, Stabile 12-70

department: Pharmacology

institute: Mayo Clinic

summary: SETD2 is the sole epigenetic factor responsible for catalyzing histone 3, lysine 36, tri-methylation (H3K36me3) in mammals. Its role in regulating diverse cellular processes such as RNA splicing, DNA repair, and spurious transcription underlie its broader tumor suppressor function, which has been detailed in a multitude of cancer types. SETD2 mutation, and by extension loss of H3K36me3, promotes the epithelial-mesenchymal transition (EMT) and is clinically associated with adverse outcomes highlighting a therapeutic need to develop targeted therapies against this dangerous mutation. To this end we employed an unbiased genome-wide synthetic lethal screen, which identified another H3K36me writer, NSD1, as a synthetic lethal modifier in SETD2-mutant cells. Confirmation of this synthetic lethal interaction was performed via modeling in isogenic clear cell renal cell carcinoma (ccRCC ) cell lines. Depletion of NSD1 using a CRISPRi targeting approach promoted the loss of SETD2-mutant cells coincident with elevated DNA damage and apoptosis. Surprisingly, only suppression of NSD1, and not the related H3K36-methyltransferases NSD2 or NSD3, promoted synthetic lethality (SL) in these models. Further investigation of H3K36me2 targeting by NSD1 and NSD2 respectively highlight the independent functions of these epigenetic writers. Furthermore, as a proof-of-principle we demonstrate the therapeutic feasibility of targeting this synthetic lethal interaction by recapitulating the phenotype using a first-of-its kind pharmacologic inhibitor against NSD1 (BT5). Notably, these findings unify unbiased genome-wide screening approaches with the latest genetic and pharmacologic modeling methodologies to reveal an entirely novel epigenetic approach in the advancement of individualized therapies for the treatment of SETD2-mutant cancer.

overall_design: RNA-seq on SETD2 wild-type and mutant cell lines with genetic or phamacologic inhibition of NSD1

first: Ryan

last: Wagner

last: Hlady


title: SETD2 loss-of-function uniquely sensitizes cells to epigenetic targeting of NSD1-directed H3K36 methylation.

overall_design: ChIP-seq on SETD2 wild-type and mutant cell lines with genetic or phamacologic inhibition of NSD1


title: SETD2 loss-of-function uniquely sensitizes cells to epigenetic targeting of NSD1-directed H3K36 methylation

overall_design: HAP1 synthetic lethal screen in parental and SETD2 mutant cells


title: Gene expression profile at single cell level of kidney cells of papillary renal cell carcinoma from mice at different stages

status: Public on Jan 27 2025

first: Jiyuan

last: Liu

summary: The role of the Hippo/YAP signaling pathway in renal cell carcinoma remains unclear. Large-scale cancer genetic/genomic studies demonstrated that papillary renal cell carcinoma (PRCC) is featured with a frequent shallow deletion of the upstream tumor suppressors of the Hippo/YAP signaling pathway, suggesting that this signaling pathway may play a role in PRCC development. We developed a transgenic mouse model with a renal epithelial cell-specific hyperactivation of YAP1 and found that hyperactivation of YAP1 can induce dedifferentiation and transformation of renal tubular epithelial cells leading to the development of PRCC. We analyzed at the single-cell resolution the cellular landscape alterations during PRCC development. Our data indicated that the hyperactivated YAP1, via manipulating multiple signaling pathways, induced epithelial cell transformation, MDSC accumulation, and PRCC development. Blocking YAP1 activity with MGH-CP1, a newly developed TEAD inhibitor, suppressed tumor development and MDSC accumulation. Our results identify the disrupted Hippo/YAP signaling as a major contributor to PRCC and suggest that targeting the disrupted Hippo pathway represents a novel strategy to prevent and treat PRCC.

overall_design: Kidneys from Pax8-rtTA;tet-on-YAPS127A mice (Pax8-YAPS127A) treated with doxycycline (Dox) for 0, 7days and 4 months.

first: Xiangmin

last: Lv

first: Cheng

last: Wang


title: Deciphering the interplay between SETD2 mediated H3K36me3 and RNA N6-methyladenosine in clear cell renal cell carcinoma (ccRCC) [RNA-seq]

summary: RNA N6-methyladenosine (m6A) plays diverse roles in RNA metabolism and its deregulation contributes to tumor initiation and progression. Clear cell renal cell carcinoma (ccRCC) is characterized by near ubiquitous loss of VHL followed by mutations in epigenetic regulators PBRM1, SETD2, and BAP1. Mutations in SETD2, a histone H3 lysine 36 trimethylase (H3K36me3), are associated with reduced survival, greater metastatic propensity, and metabolic reprogramming. While m6A and H3K36me3 deregulation are separately implicated in renal tumorigenesis, H3K36me3 may participate directly in m6A targeting, but the m6A-H3K36me3 interplay has not been investigated in the context of ccRCC. Using RCC-relevant SETD2 isogenic knockout and rescue cell line models, we demonstrate a dynamic redistribution of m6A in the SETD2 depleted transcriptome, with a subset of transcripts involved in metabolic reprogramming demonstrating SETD2 dependent m6A and expression level changes. Using a panel of six histone modifications we show that m6A redistributes to regions enriched in gained active enhancers upon SETD2 inactivation. Finally, we demonstrate a reversal of transcriptomic programs involved in SETD2 loss mediated metabolic reprogramming, and reduced cell viability through pharmacological inhibition or genetic ablation of m6A writer METTL3 specific to SETD2 deficient cells. Thus, targeting m6A may represent a novel therapeutic vulnerability in SETD2 mutant ccRCC.

overall_design: METTL3 was genetically incativated using CRISPR-CAS9 targeting or pharmacologically inhibited using METTL3 small molecule inhibitor STM2457 and RNA-seq was performed comparing METTL3 depletion/inhibiton to sgRNA control or DMSO control

first: Shafiq

last: Shaikh

middle: D


title: Single Alkyl Phosphonate Modification of the siRNA Backbone in the Seed Region Enhances Specificity and Therapeutic Profile

status: Public on Jan 15 2025

city: Carlsbad

first: Sagar

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: We evaluated the effect of alkyl phosphonate linkages in enhancing the specificity and therapeutic profile of siRNA when incorporated into the seed region. Modified siRNAs with a single alkyl phosphonate linkage demonstrated improved specificity, particularly when positioned at the internucleotide linkage between positions 6 and 7 from the 5'-end of the guide strand. These modifications maintained robust on-target activity both in vitro and in vivo while significantly reducing off-target effects, as shown by differential gene expression analysis. Additionally, we observed enhanced safety in mice, as evidenced by reduced ALT/AST elevation and the absence of histopathological changes.

overall_design: To validate the target specificity of siRNAs with a single alkylphosphonate modification in the seed region, we employed differential gene expression (DGE) analysis. This approach was applied to data from both cultured cells and in vivo models, offering a detailed assessment of the modification's impact on gene expression.

first: Mehran

last: Nikan

first: Qingfeng

last: Li

first: Michael

last: Tanowitz

first: Hongda

first: Marie

last: Annoual

first: Rodrigo

last: Galindo-Murillo

first: Audrey

last: Low

first: Stephanie

last: Klein

first: Clare

last: Quirk

first: Guillermo

last: Vasquez

first: W. Brad

last: Wan

first: Andy

last: Watt

last: Migawa

first: Eric

last: Swayze

first: Thazha

middle: P

last: Prakash


title: Deciphering the interplay between SETD2 mediated H3K36me3 and RNA N6-methyladenosine in clear cell renal cell carcinoma (ccRCC) [MeRIP-seq]

first: Keith

last: Robertson

overall_design: SETD2WT and SETD2KO ccRCC (786-O) and surrogate normal (RPTEC) cell lines were profiled for m6A methylome to determine the impact of SETD2 inactivation on m6A methylation patterns


title: Ovarian cancer metastasis to the human omentum disrupts organ homeostasis and induces fundamental tissue reprogramming

status: Public on Jan 08 2025

first: Francis

last: Jacob

summary: The omentum, a visceral adipose tissue critical for metabolic, immunological, and stem cell functions, is a key site for ovarian cancer metastasis. However, its role in homeostasis and response to metastasis is not fully understood. Using single-cell transcriptomics, we profiled different omental regions in patients with benign conditions and ovarian cancer metastasis. We found that the benign omentum maintains stable cell composition and a stem cell niche. Metastasis led to immune landscape diversification and loss of mesothelial and progenitor cells. The lesser omentum, often spared in surgery, emerged as a premetastatic niche with neutrophil infiltration, NETosis, and micrometastases. Cancer cells orchestrated reprogramming of resident cells, inducing regulatory, anti-adipogenic, and immunosuppressive phenotypes across the omentum. This cell atlas illuminates the cellular and molecular determinants of organ homeostasis and reveals a high degree of plasticity and cellular reprogramming promoted by cancer colonization.

overall_design:
Single-cell RNAseq data obtained from human omentum tissue samples of 15 patients at time of diagnosis. Human data raw files wil be available upon request >>Submitter states: Raw data couldn't be included due patient privacy concerns. Requests can be made to the PI for access to the raw data.<<<

***************************************************************
Raw sequencing data from human patient samples were not submitted to GEO due to data-protection considerations. Controlled access to the raw files is provided through the European Genome-phenome Archive (EGA; accession EGAD50000002110) via the MF-DAC.
***************************************************************

first: Ulrike

last: Lischetti

first: Ching-Yeu

last: Liang

first: Matteo

last: Carrara

first: Ricardo

last: Coelho

first: Flavio

last: Lombardo

first: Arthur

last: Dondi

first: Sandra

last: Goetze

first: Christian

last: Kurzeder

first: Céline

last: Montavon

first: Jitka

last: Fucikova

first: Franziska

last: Singer

first: Niko

last: Beerenwinkel

last: Beisel

first: Viola

last: Heinzelmann-Schwarz


title: Cellular cartography reveals mouse prostate organization and determinants of castration resistance [Spatial Transcriptomics]

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

institute: University of Michigan

summary: Inadequate response to Androgen Deprivation Therapy (ADT) frequently arises in Prostate Cancer (PCa) via unclear cellular mechanisms and drives aggressive forms of the disease. Here, we integrated single-cell RNA sequencing, single-cell multiomics and spatial transcriptomics to reveal the transcriptional, epigenetic and spatial basis of cell identity and cell-specific castration response in mouse prostates, and used this reference along with meta-analysis to identify determinants of ADT-response and castration resistance in human PCa. We found that that the mouse prostate contains lobe-specific luminal epithelial cell types (LEs), as driven by unique gene regulatory modules, and anatomically-defined androgen responsive transcriptional programs, which together indicate developmental divergence. Androgen recalcitrant stem-like epithelia that bear semblance to Club and Hillock cells of the human prostate were enriched in the urethra and Ventral Prostate (VP), but rarely present in other lobes. Strikingly, the VP contained two additional LEs, Pbsn-positive and Spink1-positive (enriched in SPOP mutant PCa) androgen responsive cells, which effectively mapped to human LEs and potentially denote cell types that drive distinct PCa subtypes. Castration reorganized LE transcriptomes, with castration resistant LEs activating stress responsive (e.g. Nfe2l2) and stemness (e.g. Klf6) programs. Tumor cells of ADT-treated and Castration Resistant PCa patients were enriched for these castration programs, suggesting their role in driving the emergence and sustenance of castration resistance. Overall, our cellular cartography effort culminates in a comprehensive atlas of the mouse prostate, highlights the potential for lobe-specific PCa modeling in mice and identifies potential therapeutic targets that inhibit castration resistance.

overall_design: Four serial sections of prostates from sham operated or castrated mice were sequenced by 10x Visium to test for differential spatial gene expression after castration.

first: Hanbyul

last: Cho

first: Yuping

last: Zhang

first: Jean

last: Tien

first: Jie

last: Luo

first: Rahul

last: Mannan

first: Sathiya

last: Narayanan

first: Somnath

last: Mahapatra

first: Greg

last: Shelly

first: Gabriel

last: Cruz

first: Lisha

last: Wang

first: Fengyun

last: Su

first: Rui

first: Saravana

last: Dhanasekaran

first: Xuhong

last: Cao

first: Evan

last: Keller

first: Sethuramasundaram

last: Pitchiaya


title: Circadian transcriptional profile of tissues with and without neutrophil depletion

status: Public on Jan 09 2025

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

summary: We previously reported that neutrophils infiltrate most tissues in a circadian fashion, as they clear out from the circulation (Casanova‑Acebes et al., 2018). In our current study we hypothesized that neutrophils are relevant contributors to the matrix of barrier tissues and that then their elimination should leave a temporal footprint in the circadian pattern of expression of matrix-associated genes. To answer this question, we generated a circadian transcriptional dataset from the bone marrow, lung, liver, intestine and skin in wild type and neutrophil-depleted animals. The anlysis of the circadian patern of matrix related genes obtained from this datasets indicates that their temporal expression patterns in the analysed tissues is disrupted following neutrophil depletion. This results directly implicate neutrophils in the circadian biology of the matrix organization in various tissues.

overall_design: For the circadian transcriptional analysis of lung, bone marrow, liver and intestine (Neutropenia model: Antibody depletion) we used an anti-Ly6G (characteristics: depleted) or an anti- IgG isotype control (characteristics: WT) antibodies. Tissues were harvested at ZT1-5-9-13-17-21 (characteristics: ZT) from 3 mice per group. For the circadian transcriptional analysis of the skin we used the Mrp8CRE; iDTR mouse model (neutropenia model: DT depletion) in which administration of diphtheria toxin induces neutropenia in CRE+ mice (genotype: Mrp8CRE; iDTR ) but not in wild type mice (C57BL/6 WT). In addition, a mouse model in which the intrinsic circadian clock is disrupted specifically in neutrophils by floxing out the Anrtl gene (genotype: Mrp8CRE; Bmal1-flox) was included in the Skin dataset. Skin was harvested at ZT1-3-4-5-7-9-10-12-13-15-16-18-19-21-22-24 (characteristics: ZT) from one mouse per group.

first: Iván

last: Ballesteros

first: Georgiana

last: Crainiciuc

first: Andrea

last: Rubio-Ponce

first: Tommaso

last: Vicanolo


title: Af-CUT&Tag: A Sensitive and Antibody-Free Chromatin Profiling Method Using Genetically Encoded Tags and High-Affinity Binders Fused to Tn5

status: Public on Dec 15 2024

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

summary:
Conventional chromatin profiling techniques are often limited by antibody availability and performance. Here, we introduce Af-CUT&Tag, a target antibody-free method that overcomes these limitations by using CRISPR-integrated peptide tags (HiBiT/ALFA-tag) recognized by engineered binders (LgBiT/NbALFA) fused to a Tn5 transposase. Af-CUT&Tag eliminates dependence on traditional target antibodies, achieving robust specificity and sensitivity with as few as 500 cells. It provides high-quality chromatin profiles, with improved signal-to-noise ratios and library quality compared with conventional antibody-based counterparts, while also enabling single-cell resolution (scAf-CUT&Tag). Applying Af-CUT&Tag to Hippo effectors (YAP1/TAZ) during liver regeneration revealed dynamic chromatin remodeling, including YAP1/TAZ-mediated control of lipid metabolism (e.g., Lpin1, Fasn) and heme clearance (Hpx, Trf). We further identify miR-122 as a critical regulator of these processes, impacting liver regeneration. The versatility of Af-CUT&Tag in cell lines, bulk tissues, and single nuclei establishes it as a powerful tool for studying gene regulation in development, disease, and regeneration.
Keywords:
Antibody-Free CUT&Tag; Chromatin Binding; Epigenetic Profiling; Peptide-binder; Single-cell analysis

overall_design: Af-CUT&Tag, an antibody-free and sensitive tool for epigenetic analysis, utilizes C-terminal peptide tagging of proteins of interest (POIs) and a Tn5 transposase fused to a peptide binder for precise chromatin profiling.

first: Yongyou

last: Zhang

first: Xindong

first: Xusheng

last: Deng


title: Regulated resource re-allocation is transcriptionally hard wired into the yeast stress response

status: Public on Jan 03 2025

first: Audrey

last: Gasch

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

summary: Many organisms maintain generalized stress responses activated by adverse conditions. Although details vary, a common theme is the redirection of transcriptional and translational capacity away from growth-promoting genes and toward defense genes. Yet the precise roles of these coupled programs are difficult to dissect. Here we investigated Saccharomyces cerevisiae responding to salt as a model stressor. We used molecular, genomic, and single-cell microfluidic methods to examine the interplay between transcription factors Msn2 and Msn4 that induce stress-defense genes and Dot6 and Tod6 that transiently repress growth-promoting genes during stress. Surprisingly, loss of Dot6/Tod6 led to slower acclimation to salt, whereas loss of Msn2/4 produced faster growth during stress. This supports a model where transient repression of growth-promoting genes accelerates the Msn2/4 response, which is essential for acquisition of subsequent peroxide tolerance. Remarkably, we find that Msn2/4 regulate DOT6 transcription, influence Dot6 activation dynamics, and are required for full repression of growth-promoting genes.  Thus, Msn2/4 directly regulate the resource re-allocation needed to mount their own response. We discuss broader implications for common stress responses across organisms.

overall_design: RNA-seq profiling of Saccharomyces cerevisiae BY4741 strains (wild-type, msn2∆msn4∆, and dot6∆tod6∆) before and 10, 20, 30, 40, 50, 60, and 90 minutes after salt stress. Samples were grown in low fluorescent media and harvested at log-phase (proliferative growth). Each strain and timepoint was measured in biological duplicate.

first: Rachel

last: Kocik


title: Decoding the immune checkpoint signatures in human atherosclerosis: implications of type 2 diabetes and lipid-lowering intervention [human PBMC scRNA-Seq]

status: Public on Dec 18 2024

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

summary: Immune checkpoint inhibitor (ICI) therapies in cancer accelerate atherosclerosis progression. Here, we have charted the landscape of immune checkpoint gene expression and defined the network of disease-relevant interactions with single-cell resolution. We found that signaling through PD-1 and CTLA4 is driven by a population of dendritic cells enriched for FSCN1 that can be derived from peripheral blood cells following anti-PD-1 or -CTLA4 treatment ex vivo. Type 2 diabetes dampened plaque PD-1 and CTLA4 signaling, showing that cardiometabolic comorbidities elicit unique responses to ICIs. Lipid-lowering therapy equalized the intensity and direction of immune checkpoint interactions in human blood, while atherosclerotic mice subjected to a lipid-lowering diet displayed both increased co-inhibitory signaling and a downregulation of inflammatory transcriptional programs in plaques. Our findings underscore the potential of lipid-lowering therapies in stabilizing immune checkpoint interactions and reducing plaque inflammation, offering new insights on atherosclerosis and cardiovascular risks in cancer patients undergoing ICI treatments.

overall_design:
profiling of peripheral blood mononuclear cells from humans before and after lipid loweing treatment via scRNA-seq. The cohort contains patients with and without type 2 diabetes

UPDATE: [Dec-22-2025] The 'condition' attribute of the Samples was updated.

first: Jose

last: Barcia Duran

first: Dayasagar

last: Das

first: Kathryn

last: Moore

first: Chiara

last: Giannarelli


last: Wang


title: Measuring the transcriptional effect of the Caulobacter cckA(ts) mutation and genetic suppression of the cckA(ts) phenotype by loss-of-function mutations in ntrC.

city: East Lansing

first: Sean

last: Crosson

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: We have discovered an unusual two-tiered pattern of suppression in Caulobacter whereby temperature sensitive mutations in the "essential" cell cycle regulatory histidine kinase, CckA, are variably rescued by structurally distinct loss-of-function mutations in ntrC. NtrC regulates nitrogen assimilation and contains structural features that indicate interaction with σ70 RNA polymerase to control transcription. Considering that NtrC is a transcription factor, we hypothesized several mechanisms through which loss-of-function mutations in ntrC could rescue cckA(ts) conditional lethality through its effect on transcription: (a) ntrC mutations in a cckA(ts) background broadly restore Caulobacter gene expression to wild-type levels, (b) ntrC mutations shift gene expression into a state entirely distinct from both wild-type and the primary mutant, or (c) a combination of these two effects. To assess these models, we used RNA sequencing (RNA-seq) to measure the effect of shifting the cckA(ts) strain to the restrictive temperature and the global transcriptional impact of combining loss-of-function ntrC mutations with cckA(ts) at the restrictive temperature.

overall_design: We cultivated the cckA(ts) strain and three additional strains in which we combing ntrC mutations (L242P, A446P, and in-frame deletion of ntrC) with the cckA(ts) mutations. These strains were grown at 37 degrees C to mid-log phase and total RNA was isolated by Trizol extraction followed by alcohol precipitation. RNA-sequencing libraries were prepared utilizing the Illumina TruSeq Stranded RNA Kit and sequenced on the Illumina NextSeq 500 platform at SeqCenter (Pittsburgh, PA).

first: North

last: Hunter

first: Fiebig

last: Aretha

first: Crosson

last: Sean


title: Improved split prime editors enable efficient in vivo genome editing

status: Public on Dec 01 2024

city: Hangzhou

first: Lijia

last: Ma

address: Shilongshan Road No.18, Cloud Town, Xihu District

institute: Westlake university

summary: Prime editor (PE) is a precise genome-editing tool capable of all possible base conversions, as well as insertions and deletions without DSBs or donor DNA. The efficient delivery of PE in vivo is critical for realizing its full potential in disease modeling and therapeutic correction. Although PE has been divided into two halves and delivered using dual adeno-associated viruses (AAVs), editing efficiency at different gene loci varies among split sites, and efficient split sites within Cas9 nickase are limited. In this study, by screening multiple split sites, we demonstrated a series of efficient split site when delivering PE by dual-AAV. Additionally, we utilized a feature reported by others recently that RNase could be detached from the Cas9n and designed split sites in the first half of Cas9n. To test the editing efficiency in vivo, a novel dual-AAV split-ePE3 was packaged in AAV9 and delivered via tail vein injection in mice, achieving 24.4% precise genome editing 3 weeks post-injection. Our findings establish an alternative split-PE architecture that could achieve robust gene editing efficiency, facilitating the potential utility both in model organisms and as a therapeutic modality.

overall_design:
Split PE from different split sites was cloned into the AAV genome plasmid, and a series of split-PE systems were established by employing different promoters, truncated reverse transcriptase and untethered reverse transcriptase under the size restriction condition of the AAV packaging. Cells transfected with plasmids and mice infected with dual-AAV virus, the desired editing was integrated into the genome of host cells. Cells were harvested 72 hours after plasmid transfection, and mouse livers were collected 3 weeks after the virus injection into the tail vein. To detect the outcome of prime editing, we amplified the gDNA harvested from the edited cells and subjected the amplicons to high-throughput sequencing.

Additional data for this study are in: GSE291960

first: Rongwei

last: Wei

first: Zhenxing

last: Yu

first: Zhike

last: Lu


title: Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations

status: Public on Dec 26 2024

city: San Francisco

first: Hani

last: Goodarzi

department: Department of Biochemistry and Biophysics

institute: UCSF

overall_design: Refer to individual Series


title: Single-cell RNA sequencing revealed the transcriptional landscape and heterogeneity of macrophages in the intestinal tissues of WT and RUNX3 macrophage conditional knockout mice.

status: Public on Jan 29 2025

first: Yun Huan

last: Gao

institute: Nankai University

summary: CD11b+ cell populations, especially macrophages, are highly heterogeneous tissue-resident immune cells in mice and humans. The exact subpopulation and its phenotype remain unknown. Here, we analyzed intestinal CD11b+ cell populations from normal and Runx3 macrophage conditionally deficient mice using scRNA-seq. We found that the transcription factor RUNX3 plays a key role in the entry of inflammatory monocytes into resident macrophages. Decreased resident macrophages and elevated ZFP36 in RUNX3flow/flowlyz2-Cre mice, leading to cytokine and chemokine degradation in colon tissue-resident macrophages. RUNX3 promotes the expression of NR4A1, thereby inducing the differentiation of inflammatory monocytes into resident macrophages. Single-cell population analysis revealed that the ERK1/2/MAPK pathway plays a key role in NR4A1-mediated gut-resident macrophage differentiation.

overall_design: 10X Genomics scRNA-seq was performed to better assess immune cell heterogeneity in gut lamina propria (LP).

first: yunhuan

last: gao

first: yi

last: shi


title: Embyoid organizer

status: Public on Dec 09 2024

city: Los Angeles

first: Dario

last: Boffelli

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

summary: Recapitulation of development in vitro relies primarily on treatment of progenitor cells with media-borne morphogens, without the complex spatial instructions normally presented by native developmental niches.  Here we build simple spatially asymmetric developmental niches by engineering synthetic organizer cells that self-assemble around stem cells and provide spatially-defined morphogenic instructions.   Using a toolkit of natural and engineered adhesion molecules we harness differential adhesion to program the formation of specific organizer cell geometries around the stem cells, allowing the generation of morphogen gradients with tunable position, amplitude, and signal types. Synthetic niches presenting the antagonistic morphogens WNT3A and DKK1 were used to guide development of pluripotent stem cells.  These synthetic organizers generated distinct morphological outcomes, including formation of a beating heart-like chamber and embryoids containing a complement of diverse cell lineages derived from mesoderm, endoderm and ectoderm. The resulting morphologies were reproducible in high-throughput format. Spatially programmable synthetic organizer cells, which integrate the principles of differential adhesion and positional information, thus provide a systematic approach to guide, recapitulate, and modify development in a controlled fashion.

overall_design: Embryoids were combined with either a WNT3A-producing node, a DKK1-producing node, or both. WNT3A expression was induced on day 1, DKK1 expression on day 2. Embryoids from 300 mESC were collected on day 8, dissociated, and cells were labelled for MULTIseq then sorted for viability.

first: Toshimichi

last: Yamada

first: Coralie

last: Trentesaux

first: Ophir

last: Klein

first: Wendell

last: Lim


title: Salmonids on Insect Protein – Impact on Performance and Health

status: Public on Nov 30 2024

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

country: Germany

institute: Research Institute for Farm Animal Biology

summary: In order to find out whether insects are suitable as a pure protein source and what potential problems or benefits can be expected, a 10-week feeding experiment was set up. In this experiment, the overall protein content were identical, while the protein content from soy and fishmeal was replaced with 25, 50, 75 and 100% insect meal. In order to evaluate the effect of the insect protein on the fish, fish size and weight were determined at the beginning and end of the experiment, and transcriptomic analyses of proximal intestine were performed. Finally, samples of the liver and intestine were examined histologically.

overall_design: The animal trial was conducted at the Fisheries Research Station of Baden-Württemberg (Langenargen, Germany) for a period of 69 days. The feeds were largely identical in their isocaloric and isonitrogenic composition. The feeds were based on soy and insect meal and optimized for rainbow trout of the age class used (6 months) and formulated with the objective of testing their effects on performance, health and faecal stability. Feed was manufactured by Skretting (Stavanger, Norway), who also provided the black soldier fly meal. Four different levels of insect protein, plus a control feed were produced, meaning that either 0, 25, 50, 75 or 100% of the protein content originating from soy meal was replaced by insect protein. Additionally, each feed was produced without and with 0.3% of the manure-stabilizing binder Guar Gum.

first: Tamara

last: Wind

first: Sara

last: Sousa e Brito

first: Dirk

last: Koczan

first: Mark

last: Schumann

first: Carsten

last: Schulz

last: Brinker


title: Extensive length and homology dependent chimerism in pool-packaged AAV libraries

status: Public on Jan 14 2025

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

country: Canada

institute: University of Montreal

summary: Adeno-associated viruses (AAVs) have emerged as the foremost gene therapy delivery vehicles due to their versatility, durability and safety profile. Here we demonstrate extensive chimerism among complex AAV libraries that are packaged as a pool. The observed chimerism is length- and homology-dependent but capsid-independent, in some cases affecting >60% of packaged AAV genomes. These results have important implications for the design and deployment of functional AAV libraries in research and clinical settings.

overall_design: Barcoded plasmid dictionary generation and barcode swap assessment in long-read data.

first: Jean-Benoît

first: Chau

last: Huynh

first: John

last: Mich

first: Avery

last: Hunker

first: Troy

last: McDiarmid

first: Haedong

last: Kim

first: Boaz

last: Levi

first: Jonathan

last: Ting

first: Jay

last: Shendure


title: The RNA-Seq reveal flight-induced ribosome impairment in the cerebellum of racing pigeons

status: Public on Nov 20 2024

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

summary: The avian cerebellum is known for its relatively large size and high degree of development, functioning as a crucial region for multisensory integration and motor control, particularly important for flight. This study aimed to investigate changes in gene expression in the cerebellum of racing pigeons using RNA-Seq analysis. The researchers analyzed samples from 10 racing homers' cerebellums before and after a 300 km flight back to their loft. The findings revealed that flight induces ribosome impairment in the cerebellum, suggesting potential alterations in the protein synthesis machinery due to prolonged flight activity as response to stress and maintain homeostasis.

overall_design: The profiling of cerebellum transcriptome was performed on 5 samples obtained from racing homers competing in a 300 km flight and 5 birds of the same age form the same loft but which rested in the loft on the day of the competition.  The performing group upon their return and the control group were sedated and deceased using the cervical dislocation method

first: Monika

last: Stefaniuk-Szmukier

first: Anna

last: Steg

first: Grzegorz

last: Smołucha

first: Katarzyna

last: Ropka-Molik


title: Characterization of Pro-Fibrotic Signaling Pathways in Human Hepatic Organoids

status: Public on Nov 22 2024

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

summary: Due to the limitations of available in vitro systems and animal models, we lack a detailed understanding of the pathogenetic mechanisms and have minimal treatment options for liver fibrosis. To overcome this barrier, we engineered a live cell imaging system that identifies collagen producing cells in a human multi-lineage hepatic organoid. This system was adapted for use as a microwell-based platform (i.e., microHOs) where exposure to PDGF or TGFb1 induced the formation of thick collagen fibers. Transcriptomic analysis revealed that TGFb1 converted mesenchymal cells into collagen producing myofibroblasts.

overall_design: To characterize the pro-fibrotic effects of PDGFB and TGFB1 at transcriptome level, scRNA-Seq data was generated from day 9 control hepatoblast cultures and from day 21 control, TGFB1-treated or PDGFB-treated microHOs.

first: Yuan

last: Guan

first: Gray

last: Peltz


title: m6A sites in the coding region trigger translation-dependent mRNA decay (in vitro methylation)

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

institute: Würzburg University

summary: N6-Methyladenosine (m6A) is the predominant internal RNA modification in eukaryotic messenger RNAs (mRNAs) and plays a crucial role in mRNA stability. In this study, we reveal that m6A sites in the coding sequence (CDS) trigger CDS–m6A decay (CMD), a novel mRNA decay pathway that is distinct from previously reported m6A-dependent degradation mechanisms. Importantly, CDS m6A sites act considerably faster and more efficiently than those in the 3' untranslated region, which to date have been considered the main effectors of m6A-mediated RNA decay. Mechanistically, CMD depends on translation whereby m6A deposition in the CDS induces ribosome pausing and transcript destabilization. We found that the target transcripts of CMD are recognized by the m6A reader protein YTHDF2, selectively enriched in processing bodies (P-bodies) and degraded via the decapping factor DCP2. Our findings highlight CMD as a previously unknown pathway for m6A-mediated decay, which is particularly important for controlling the expression of developmental regulators and retrogenes.

overall_design: To investigate if the sequence preference is intrinsic to the METTL3–METTL14 writer complex, we established a high-throughput in vitro methylation assay. In brief, we generated a library of 11,999 in vitro transcripts (IVTs, 183 nucleotides [nt] each), which represent 3,488 human transcript loci. The IVT sequences were chosen around DRACN motifs ("selected DRACN") that represent different DRACN 5-mers with or without m6A modification from different transcript regions. We then used a recombinantly reconstituted METTL3–METTL14 writer complex to methylate the IVT library and analyzed the resulting methylation profile using miCLIP2. Experiments were performed in duplicate.

first: Peter

last: Hoch-Kraft

last: König

first: Anke

last: Busch

first: You

last: Zhou

first: Kathi

last: Zarnack

first: Natalie

last: Meiser

first: Martin

last: Hengesbach


title: Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically-diverse Caenorhabditis nematodes.

status: Public on Oct 22 2024

city: Eugene

first: Patrick

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

institute: University of Oregon

summary: We present a survey of longevity effects for compounds suggested by a previously published computational prediction set using the comprehensive, multi-species approach utilized by the Caenorhabditis Intervention Testing Program (CITP). The compound all-trans retinoic acid extended lifespan in the nematode Caenorhabditis elegans. Given the dependency of lifespan extension under atRA treatment, we used RNA-seq to assess transcriptional changes under atRA treatment in wildtype N2 animals. In order to further dissect transcriptional response in detail, we repeated our transcriptional analysis in hsf-1(sy441) and aak-2(ok524) mutants.

overall_design: We performed differential gene expression analysis comparing atRA-treated and DMSO control samples (4 biological replicates each) in 4 day old adult worms in the wildtype N2, PS3551 [hsf-1(sy411)], and RB754 [aak-2(ok524)] strains.

first: Stephen

last: Banse

first: Christine

last: Sedore

middle: L

last: Coleman-Hulbert

first: Erik

last: Johnson

first: Brian

last: Onken

first: David

last: Hall

last: Segerdell

first: E

last: Jones

first: Yuhua

last: Song

first: Hadley

last: Osman

first: Jian

last: Xue

first: Elena

last: Battistoni

first: Suzhen

last: Guo

last: Foulger

first: Madhuri

last: Achanta

first: Mustafa

last: Sheikh

first: Theresa

last: Fitzgibbon

first: John

last: Willis

first: Gavin

last: Woodruff

first: Monica

last: Driscoll

first: Gordon

last: Lithgow


title: CD137 agonism enhances anti-PD1 induced activation of clonally expanded CD8+ T cells in a neoadjuvant pancreatic cancer clinical trial

status: Public on Dec 16 2024

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: Successful pancreatic ductal adenocarcinoma (PDAC) immunotherapy requires therapeutic combinations that induce quality T cells. Tumor microenvironment (TME) analysis following therapeutic interventions can identify response mechanisms to guide design of more effective combinations. We provide a reference single-cell dataset from PDAC-infiltrating T cell and monocyte subsets from a human neoadjuvant clinical trial comparing the granulocyte-macrophage colony-stimulating factor (GM-CSF)-secreting allogeneic PDAC vaccine GVAX alone, in combination with anti-PD1, or with both anti-PD1 and a CD137 agonist. Tumor infiltrating leukocytes analyzed two weeks post neoadjuvant therapy revealed shifts in CD8+ T cell activation as well as cytoskeletal and extracellular matrix (ECM)-interacting components with Cy/GVAX and anti-PD1. Addition of a CD137 agonist was associated with increased abundance of activated and clonally expanded CD8+ T cells with distinct perturbations in cytoskeletal and ECM components. Furthermore, a new computational method to compare ligand-receptor networks between patients from different treatment arms found that CD137 agonism is associated with immunosuppressive TREM2 signaling in tumor associated macrophages (TAMs) that corresponds to changes in cell metabolism, function, and ECM interactions. Altogether these findings associate therapy with GVAX, anti-PD1, and CD137 agonist with enhanced CD8+ T cell function while inducing alternative immunosuppressive pathways in patients with PDAC.

overall_design:
Single-cell RNA-seq and single-cell TCR-seq data were collected from tumor-infiltrating leukocytes in primary human pancreatic cancer tumors following neoadjuvant immunotherapy. Treatments included  seven patients receiving cyclophosphamide (Cy)/GVAX alone (Arm A), four patients receiving the combination of Cy/GVAX and anti-PD1 (nivolumab, Arm B), and four patients receiving Cy/GVAX, anti-PD1, and CD137 agonist (urelumab, a human IgG4 agonistic monoclonal antibody, Arm C).

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Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
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dbGaP (phs003002.v2.p1)

first: Janelle

last: Montagne

first: Jacob

middle: T

last: Mitchell

first: Joseph

last: Tandurella

first: Eric

middle: S

last: Christenson

first: Ludmila

middle: V

last: Danilova

first: Atul

last: Deshpande

first: Melanie

last: Loth

first: Dimitrios

last: Sidiropoulos

first: Emily

last: Davis-Marcisak

first: Daniel

last: Bergman

first: Qingfeng

last: Zhu

first: Hao

last: Wang

first: Luciane

last: Kagohara

first: Logan

last: Engle

first: Benjamin

last: Green

first: Alexander

last: Favorov

first: Won Jin

last: Ho

first: Su Jin

last: Lim

first: Rui

last: Zhang

first: Pan

last: Li

first: Jessica

last: Gai

first: Guanglan

last: Mo

first: Sarah

first: Rulin

first: Ajay

last: Vaghasia

first: Wenpin

last: Hou

first: Yao

last: Xu

first: Jacquelyn

middle: W

last: Zimmerman

first: Jennifer

last: Elisseeff

first: Srinivasan

last: Yegnasubramanian

first: Robert

last: Anders

first: Elizabeth

last: Jaffee

first: Lei

last: Zheng


title: Decoding the immune checkpoint signatures in human atherosclerosis: implications of type 2 diabetes and lipid-lowering intervention

status: Public on Oct 07 2024

first: Michael

last: Gildea

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


title: Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols [scRNA-seq]

city: Vienna

first: Julia

last: Naas

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

country: Austria

institute: University of Vienna

summary: Systematic analysis of the cellular and transcriptional landscape of brain organoids grown from multiple cell lines using four different protocols recapitulating dorsal and ventral forebrain, midbrain, and striatum via single-cell RNA sequencing.

overall_design:
Single-cell RNA-sequencing of brain organoids at day 120 grown in four distinct growth protocols designed to generate dorsal (D) and ventral (V) forebrain, midbrain (M) and striatum (S) tissue using eight different pluripotent stem cell lines. Per cell line-protocol combination two organoids (biological replicates) were grown. For cell line 176 the experiment was conducted in two independent biological replicates (repetitions E1 and E2).

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Submitter states that missing raw data are being made available for controlled access in EGA.
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Raw data have been deposited at the European Genome-phenome Archive (EGA), under series numbers EGAS50000000662, and are available through controlled access.

first: Meritxell

last: Balmãna

first: Laurenz

last: Holcik

first: Maria

last: Novatchkova

first: Lina

last: Dobnikar

first: Thomas

last: Krausgruber

first: Sabrina

last: Ladstätter

first: Christoph

last: Bock

first: Arndt

last: von Haeseler

first: Christopher

last: Esk

first: Jürgen

last: Knoblich


title: CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation

status: Public on Sep 24 2024

city: Bethesda

first: Elena

last: Pugacheva

state: Maryland

address: 9000 Rockville Pike

department: NIAID

institute: NIH

type: Methylation profiling by high throughput sequencing

summary: CTCF binding sites serve as anchors for the 3D chromatin architecture in vertebrates. The functionality of these anchors is influenced by the residence time of CTCF on chromatin, which is determined by its binding affinity and its interactions with nucleosomes and other chromatin-associated factors. In this study, we demonstrate that CTCF occupancy is driven by CTCF motifs strategically positioned at the entry sites of well-positioned nucleosome, such that, upon binding, the N-terminus of CTCF is oriented towards the nucleosome. We refer to this nucleosome as the CTCF priming nucleosome (CpN). CTCF recognizes its binding sites as long as they are not methylated. It can then displace the CpN, provided the nucleosome is not marked by CpG methylation or repressive histone modifications. Under these permissive conditions, the N-terminus of CTCF recruits SMARCA5 to reposition the CpN downstream, thereby creating nucleosome-free regions that enhance CTCF occupancy and cohesin stalling. In contrast, when CpNs carry repressive epigenetic marks, CTCF binding is transient, without nucleosome displacement or chromatin opening. In such cases, cohesin is not effectively retained at CTCF binding sites. We propose that the epigenetic status of CpNs governs cell-specific CTCF binding patterns, ensuring the maintenance of chromatin architecture throughout the cell cycle.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) in combination with nucleosome positioning by MNase-Seq Assisted H3 ChIP-seq and CpG methylation by 5mC MeDIP-seq

middle: M

first: Md

last: Tajmul


title: The spatial transcriptomic landscape of fibrosing ILDs [Nanostring]

status: Public on Sep 30 2024

city: London

first: Marco

last: Mura

state: Ontario

address: 800 Commissioners Road E

department: Medicine, Respirology

institute: Western University

summary: Fibrosing interstitial lung diseases (ILDs) encompass a diverse range of scarring disorders that lead to progressive lung failure. Previous gene expression profiling studies focused on idiopathic pulmonary fibrosis (IPF) and bulk tissue samples.  We employed digital spatial profiling to gain new insights into the spatial resolution of gene expression across distinct lung microenvironments (LMEs) in IPF, chronic hypersensitivity pneumonitis (CHP) and non-specific interstitial pneumonia (NSIP). We identified differentially expressed genes between LMEs within each condition, and across histologically similar regions between conditions. Uninvolved areas in IPF and CHP were remarkably distinct from normal controls, and displayed potential therapeutic targets. Hallmarks LMEs of each condition retained a distinct gene signature, but these could not be reproduced in matched lung tissue samples. Based on these gene expression signatures and unsupervised clustering, we grouped previously unclassified ILD cases into NSIP or CHP. Lastly, we characterized a gene expression pattern associated with poor outcome .  Overall, our work uniquely dissects gene expression profiles between LMEs within and across different types of fibrosing ILDs. This new spatial transcriptomics approach has the potential to reclassify unclassifiable cases, to qualify the transcriptional relevance of smaller biopsies for clinical use, and to predict outcome at the time of diagnosis.

overall_design: Treatment-naïve cases of IPF, idiopathic NSIP, CHP and unclassifiable ILD (3 cases for each condition) were selected. Four types of ROIs that coincided with lung microenvironments (LMEs) of interest were chosen for each of the four conditions under investigation: IPF: 3 fibroblastic foci; 3 areas of fibrosis; 3 areas of lymphoid aggregates; 3 areas of uninvolved lung for each case.  NSIP: 3 areas of peripheral fibrosis; 3 areas of central fibrosis; 3 areas of inflammation; 3 airways for each case. CHP: 3 granulomas; 3 areas of airway inflammation; 3 areas of fibrosis; 3 areas of uninvolved lung for each case.  Unclassifiable: 3 areas of fibroblasts; 3 areas of fibrosis; 3 lymphoid aggregates; 3 areas of uninvolved lung for each case.  Normal controls: 3 central areas; 3 peripheral areas; 3 airways; 3 pleural regions for each case.


title: Decoding epigenetic markers: implications of traits and genes through DNA methylation in resilience and susceptibility to mastitis in dairy cows

status: Public on Sep 27 2024

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: Cattle farming faces challenges linked to intensive exploitation and climate change, requiring the reinforcement of animal resilience in response to these dynamic environments. Currently, genetic selection is used to enhance resilience by identifying animals resistant to specific diseases; however, certain diseases, such as mastitis, pose difficulties in genetic prediction. This study introduced the utilization of enzymatic methyl sequencing (EM-seq) of the blood genomic DNA from twelve dairy cows to identify DNA methylation biomarkers, with the aim of predicting resilience and susceptibility to mastitis. The analysis uncovered significant differences between cows resilient and susceptible to mastitis, with 196,275 differentially methylated cytosines (DMCs) and 1,227 Differentially Methylated Regions (DMRs). Key genes associated with the immune response and morphological traits, including ENOPH1, MYL10 and KIR2DL5A, were identified by our analysis. Quantitative trait loci (QTL) were also highlighted and the body weight trait was the most targeted by DMCs and DMRs. Based on our results, the risk of developing mastitis can potentially be estimated with as few as fifty methylation biomarkers, paving the way for early animal selection. This research sets the stage for improved animal health management and economic yields within the framework of agricultural sustainability through early selection based on the epigenetic status of animals.

overall_design: To explore whole genome methylation and evaluate various potential sites involved in the immune system as predictors of resilience, we collected blood from cows raised under the same conditions .  A year later, we selected six cows that were culled during the year due to complications related to mastitis that were not identified  at the time of sampling, thus forming the Mastitis Susceptible Group (MSG). We selected a second group of six cows that were still in the herd one year after blood collection and had a similar age distribution as the cows from the MSG.  This second group represented the Mastitis Resilient Group (MRG).

first: Lotfi

last: Bouzeraa

first: Helene

last: Martin

first: Clement

last: Plessis

first: Pascal

last: Dufour

first: Jessica

middle: C

last: Marques

first: Sydney

last: Moore

first: Ronaldo

last: Cerri

first: Marc


title: Proton pump inhibitors modulate the barrier dysfunction caused by IL-13 in the epithelium in eosinophilic esophagitis

status: Public on Sep 13 2024

city: Philadelphia

first: Megha

last: Lal

state: PA

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: Eosinophilic esophagitis (EoE) is a chronic immune-mediated disorder triggered by specific food antigens, characterized by eosinophil-rich multicellular inflammation and structural changes in the epithelium. Treatment options for EoE include dietary therapy, pharmacological therapy, or a combination of both, chosen based on the patient's preference and clinical progression. Pharmacological options include proton pump inhibitors (PPIs), corticosteroids, and biologic therapy. Although PPI therapy is used for EoE management, its underlying mechanism of action remains unclear. To investigate the effects of omeprazole, an orally bioavailable PPI commonly used for EoE therapy, on the dynamics of esophageal epithelial barrier function and inflammation, we employed air-liquid interface (ALI) culture. We examined how omeprazole affects gene expression changes caused by IL-13 treatment. ALI cultures were treated with 100 ng/ml of IL-13 and/or 50 µM of acid-activated omeprazole for 96 hours, and bulk RNA sequencing was performed to analyze the epithelial-specific transcriptomes of IL-13 and/or omeprazole-treated ALI. Our findings suggest potential gene interactions where omeprazole may mitigate transcriptional changes induced by IL-13, indicating that omeprazole may attenuate IL-13 mediated epithelial dysfunction relevant to EoE pathophysiology by modulating pathways associated with inflammation, tissue repair, and cell-cell communication.

overall_design: Effect of Omeprazole on gene expression profiling of air-liquid interface (ALI) derived from telomerase-immortalized human esophageal keratinocyte cell line, EPC2-hTERT.

first: Ravi

last: Gautam

first: Melanie

last: Ruffner


title: Cell-type-specific RNA Pol II activity maps in intact-tissues: gateway to mammalian gene regulatory mechanisms in vivo.

status: Public on Dec 04 2024

city: Ithaca

first: Tudorita

last: Tumbar

state: NY

address: 526 Campus Rd

department: Molecular biology and genetics

institute: Cornell University


title: Functional screen for mediators of onco-mRNA translation specificity [CLIP-seq]

status: Public on Nov 29 2024

first: Joanna

last: Kovalski

state: CA

institute: University of California San Francisco

summary: Oncogenic protein dosage is tightly regulated to enable cancer cells to adapt and survive. Whether this is regulated at the level of translational control and the key factors in cis and trans remain unknown. The Myc oncogene is a central paradigm of an exquisitely regulated oncogene and a major driver of pancreatic ductal adenocarcinoma (PDAC). Using a genome-wide 5’UTR CRISPRi screen in PDAC cells, we identified activators of selective MYC translation and validated four RNA binding proteins (RBPs), including epitranscriptome modifiers. Among these RBPs, RBM42 was our top hit, which is highly expressed in PDAC and predicts poor survival. Combining polysome sequencing and CLIP-seq analyses, we find that RBM42 binds and selectively regulates the translation of MYC and a precise, yet vital suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, employing IP-mass spectrometry analysis, we find that RMB42 is a novel ribosome-associated protein (RAP). Using DMS-Seq and mutagenesis analysis, we show that RBM42 directly binds and remodels the MYC 5’UTR RNA structure, facilitating the formation of the translation pre-initiation complex. Importantly, RBM42 is necessary for human PDAC cell growth and fitness and PDAC tumorigenesis in xenograft mouse models in a Myc-dependent manner in vivo. In PDAC patient samples, RBM42 expression is correlated with Myc protein levels and transcriptional activity. This work transforms our understanding of the translational code in cancer and offers a new therapeutic opening to target the expression of oncogenes.

overall_design: To investigate the function of RBM42 in PDAC cells, we conducted endogenous crosslinking immunoprecipiation of RBM42 from the cytoplasmic fractions. We then perfromed RNA sequencing on the bound transcripts in duplicate.

first: Vishvak

last: Subramanyam

first: Davide

last: Ruggero


title: scRNA-seq, snATAC-seq, and spatial transcriptomics analysis of mammary glands of aged female mice

status: Public on Sep 29 2024

city: Farmington

first: Olga

last: Anczukow

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

summary: Aging results in changes in mammary gland cell proportions, gene expression, and chromatin accessibility. Cell types captured include epithelial, immune, and stromal cell types.

overall_design: Mammary gland 3M and 18M old virgin female C57BL/6J mice were enzymatically and mechanically digested. Single cells were FACS-sorted based on viability prior to performing scRNA-seq (10X Chromium v.3 chemistry) and snATAC-seq (10X Chromium v.1)

first: Brittany

last: Angarola

first: Neerja

last: Katiyar

first: Siddhartha

last: Sharma

first: Hyeon

middle: G

last: Kang

first: Djamel

last: Nehar-Belaid

first: Duygu

last: Ucar


title: Lupus-prone NZM2328 mice exhibit enhanced UV-induced myeloid cell recruitment and activation in a type I interferon dependent manner

status: Public on Sep 03 2024

city: Ann Arbor

first: J. Michelle

last: Kahlenberg

state: MI

address: NCRC 20-1841, 2800 Plymouth Rd

department: Department of Internal Medicine – Division of Rheumatology and Department of Dermatology

institute: University of Michigan

summary: This study used the NZM2328 spontaneous murine model of lupus, iNZM mice, which share the NZM2328 background but harbor a whole-body knockout of the type I interferon (IFN) receptor, and wild-type BALB/c mice to examine transcription changes in murine skin after acute and chronic dosing of UVB.

overall_design: 10–13-week-old female mice of each strain were treated with acute (300mJ/cm2 x1), chronic (100mJ/cm2 daily x5 days), or no UVB followed by biopsy of skin 24 hours after the final dose of UVB.

first: Mitra

last: Maz