title: Profiling the Cannabis-Sclerotinia pathosystem at the mRNA level using dual RNA sequencing

city: Winnipeg

first: Mark

last: Belmonte

state: MB

address: 50 Sifton Road

institute: University of Manitoba

summary: Known to infect more than 600 plant species worldwide, Sclerotinia sclerotiorum is a necrotrophic fungal pathogen, and the causative agent of white mold. With recent infection reports documented across North America, Cannabis sativa is known to be susceptible to Sclerotinia infection. Resulting from legal constraints associated with C. sativa, little is known about the Cannabis-Sclerotinia pathosystem, particularly in how the plant responds to pathogen attack at the cellular and molecular levels. Anatomical study revealed initial infection and degradation of the epidermis and cortical parenchyma, followed by widespread infection of the vascular phloem. Dual RNA sequencing provided a detailed transcriptomic profile of this pathosystem directly at the site of infection. Differential gene expression analysis revealed large-scale transcriptional shifts resulting from rapid infection. We identified the upregulation of 97 genes at 1 day post inoculation (dpi) and 6733 genes 5 dpi in C. sativa, while 3186 genes were identified in S. sclerotiorum 7 dpi. Gene ontology term enrichment identified processes associated with plant defense and signal transduction cascades during C. sativa infection while processes associated with redox control and sugar catabolism were enriched in S. sclerotiorum. Taken together, this study revealed transcriptional reprogramming in both the host plant and fungal pathogen associated with degradation of host cortical and vascular phloem tissues.

sample_organism:
Cannabis sativa
Sclerotinia sclerotiorum

overall_design: Cannabis sativa (cultivar 'Kona') inflorescences were inoculated with Sclerotinia sclerotiorum. Infected and uninfected tissues were collected at 1 day post inoculation (dpi), 3 dpi, 5 dpi and 7 dpi.

first: Natalie

middle: L

last: Cale

first: Rylee

middle: E

last: Swiderek

first: Philip

last: Walker

first: Sean

last: Robertson

first: Dylan

last: Ziegler


title: RNA-seq Analysis of Acute myeloid leukemia (AML) primary samples

status: Public on Mar 01 2025

city: Jena

first: Faezeh

last: Ghazvini Zadegan

address: Hans-Knoll-Strase 2

department: Department of Hematology/Oncology, Clinic of Internal Medicine II

country: Germany

institute: Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB)

type: Expression profiling by high throughput sequencing

summary: In this study, we examined gene expression in 69 primary samples from patients with Acute Myeloid Leukemia (AML), a complex hematologic malignancy, aiming to uncover potential avenues for novel treatment strategies.

overall_design: Primary human AML samples were isolated from peripheral blood mononuclear cells utilizing StemSep columns (STEMCELL Technologies, Canada). These samples were subsequently cultured in Stemline II Medium (Sigma, Hamburg, Germany) prior to harvesting for gene expression experimentation.


title: The new cohort of EMT genes are activated by benzo(a)pyrene and/or SATB1 during the malignant transformation of breast epithelial cells

status: Public on Feb 28 2025

city: San Francisco

first: Terumi

last: Kohwi-Shigematsu

state: CA

address: 513 Parnassus Ave (HSW810)

department: Department of Orofacial Sciences

country: USA

institute: UCSF

summary: Tumor metastasis, the migration of tumor cells from a primary site to distant organs, is the leading cause of death among cancer patients. Despite significant advancements in cancer research, much remains to be learned about how tumor cells acquire invasive properties at the molecular level. Here, we investigated the transcriptional program that enables breast epithelial cells to develop highly invasive malignant phenotypes. We focused on genes that promote epithelial-to mesenchymal transition (EMT), a process critical for both embryogenesis and cancer cell invasion, and we compiled a cohort of 339 genes associated with EMT functions with many identified in recent literature. Using an immortalized, non-malignant breast epithelial cell line, MCF10A, we analyzed changes in the transcriptional activity of these genes through Global Run-On Sequencing (GRO-seq) and RNA-seq following stable SATB1 transduction. SATB1 is a nuclear protein with genome-organizing functions that promotes metastatic cancer, including breast cancer. SATB1-expressing MCF10A cells acquire both tumorigenic and metastatic properties. We identified a total of 98 EMT promoting genes that were upregulated in SATB1-expressing MCF10A cells compared to control cells. Additionally, we investigated the effects of the chemical carcinogen benzo[a]pyrene (B[a]P), known to induce malignancy in MCF10A cells. Our findings revealed that B[a]P significantly upregulated 54 EMT genes after 3 hours. By day 3, this number increased to 72 genes, with 36 genes being common between those elevated by SATB1. Notably, the significant effects of B[a]P on EMT gene expression observed in MCF10A cells were largely diminished in SATB1 expressing MCF10A cells, suggesting that the pre-existing SATB1-regulated transcriptional program is dominant. Our results indicate that, despite the distinct causes of breast cancer, both the chemical carcinogen B[a]P and SATB1 activate many common EMT genes during the malignant transformation of breast epithelial cells. This suggests a key network of gene expression that drives the malignant phenotypes of these cells.

overall_design: We investigated the changes in the transcriptional program of breast epithelial cells using the MCF10A-1 cell line by stably expressing SATB1 compared to control cells, or by exposing MCF10A-1 cells to benzo[a]pyrene (B[a]P) compared to non-treated controls. We focused on studying a particular group of genes that function in promoting epithelial-to-mesenchymal transition (EMT), which is essential during embryogenesis as well as during cancer metastasis, as it promotes cell motility. We compiled a gene set consisting of 300 EMT genes from recent literature and from gene ontology (GO) lists, and we studied which of these genes are activated or upregulated when MCF10A-1 cells undergo malignant transformation and acquire metastatic phenotypes. We employed a method called GRO-seq, which detects nascent transcripts genome-wide to capture the early transcriptional response to environmental stimuli, as well as RNA-seq, which measures accumulated levels of mRNAs.

first: Yoshinori

last: Kohwi

first: Yelena

last: Vayn

first: Mari

last: Grange

first: Bao

last: Ho


title: A Study of Allostery Within Liganded RARα:RXR Heterodimers at the Genome Scale [CUT&Run]

status: Public on Feb 24 2025

city: Knoxville

first: Conner

last: Hawkins

state: TN

address: 309 Ken and Blaire Mossman Bldg.

department: BCMB

institute: University of Tennessee

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We provide evidence of coordination between heterodimeric nuclear hormone receptor ligands at the genome scale to reveal three unique transcriptional outcomes. First, when stimulated in pancreatic acinar cells, distinct doubly-liganded complexes of the retinoic acid receptor-α (RARα) and retinoid-X-receptor (RXR) bind divergent DNA hormone response elements (HRE). Furthermore, the link between ligand pairs and HRE specificity is correlated with RNA transcript formation.  Second, RXR ligands can function as either silent partners or as cooperative effectors on distinct HREs, also with correlated transcriptional outcomes. Third, the absence of unique binding sites on DNA by unliganded RARα:RXR suggests that productive HRE recognition and binding is an exclusive feature of the agonist-bound heterodimer. To achieve the above, DNA-bound heterodimers of RARα:RXR were isolated separately with an RARα-specific antibody,  RARα-specific and RXR-specific agonists and the pan-ligand, 9-cis retinoic acid, using the CUT&RUN technique. At each liganded state, transcriptional activity was detected by mRNA sequencing.

overall_design: CUT&RUN against retinoic acid receptor alpha in mouse acinar pancreatic tissue (266-6) with differing agonistic treatment

first: William

last: Blaner

first: Elias

last: Fernandez


title: A Study of Allostery Within Liganded RARα:RXR Heterodimers at the Genome Scale [RNA-seq]

overall_design: RNA-seq Profiling in mouse acinar pancreatic tissue (266-6) with differing agonistic treatment of the retinoic acid receptor alpha


title: Single-cell multiomics of neuron activation reveals context-specific genetics of brain disorders [029]

status: Public on Feb 18 2025

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: Most causal variants for neuropsychiatric disorders (NPD) remain unknown. A major hurdle is that disease variants may act in specific contexts, such as during neuronal activation, which is difficult to study in vivo at the population level. We profiled single-nucleus neuron-activation multiomics in human induced pluripotent stem cell-derived neurons from 100 donors, revealing the NPD-relevant transcriptomic and epigenomic landscape of neuronal activation. We identified abundant genetic variants associated with activity-dependent gene expression and chromatin accessibility, the latter explaining larger proportions of NPD heritability. Integrating multiomics data with genome-wide association studies further revealed NPD risk variants and genes with effects detected only upon stimulation, such as activity-dependent cholesterol metabolism. Our work highlights the power of cell stimulation to reveal context-specific "hidden" genetic effects.

overall_design: Raw FASTQ files complies 10x Genomics multiome scARC (scRNA-seq + scATAC-seq) standard. Library generated using cultured glutamatergic and GABAergic neurons derived from iPS cells with Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit. The output folders, including all matrices files, of Cell Ranger 2.0.2 were packaged and compressed sample-wise in according to their BioSample and SRA metadata

first: Siwei

last: Zhang


title: Single-cell multiomics of neuron activation reveals context-specific genetics of brain disorders [022] [030]


title: Single-cell multiomics of neuron activation reveals context-specific genetics of brain disorders [024]


title: Host-microbiome response to hyperbaric oxygen treatment in ulcerative colitis

status: Public on Feb 19 2025

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Pre- and post-hyperbaric oxygen sequencing of mucosal biopsies of ulcerative colitis patients to understand host response to hyperoxia

overall_design: In this post-hoc analysis of a phase 2A sham-controlled double-blind randomized trial, we aimed to understand the hyperbaric oxygen therapy specific mucosal effects in ulcerative colitis patients hospitalized for moderate-severe flares. Pre- and post-intervention mucosal biopsies were obtained through lower endoscopy at study day 10 among ulcerative colitis patients receiving hyperbaric oxygen therapy (2.4 atmospheres, 100% oxygen, 90 minute sessions) and compared against patients receiving sham hyperbaric air (1.34 atmospheres, room air, 90 minutes). In total we included, 5 hyperbaric treated and 8 sham treated patients. bulk-RNA sequencing was performed with replicates and compared between groups.

first: Robert

middle: H

last: Mills

first: Marvic

last: Carrillo-Terrazas

first: Yash

last: Mittal

first: Brian

middle: A

last: Yee

first: Christella

last: Widjaja

first: Fernando

last: Vargas

first: Kevin

last: Nguyen

first: Kelly

last: Weldon

first: Julia

last: Gauglitz

first: Gail

last: Ackerrmann

first: Gregory

last: Humphrey

first: Lindsay

last: DeRight-Goldasich

first: Tara

last: Schwartz

first: Austin

middle: D

last: Swafford

first: Corey

last: Siegel

first: Pradipta

last: Ghosh

first: Pieter

middle: C

last: Dorrestein

first: Rob

last: Knight

first: David

middle: J

last: Gonzalez

middle: W

first: John

last: Chang

first: Parambir

middle: S

last: Dulai


title: Gene expression profile at single cell level of cells isolated from the bone fracture gap and un-injured bone marrow in mouse osteotomy models

status: Public on Feb 14 2025

city: Dresden

first: Annemarie

last: Lang

address: Fetscherstrasse 74

institute: TU Dresden

summary: We investigated the cell composition in the bone fracture (osteotomy) gap under two different ambulatory loading conditions (stiif vs. compliant - external fixator). In addition, we applied an receptor inhibitor or respective isotype control to understand the role of a specific progenitor subpopulation during the onset of bone fracture repair.  Un-injured bone marrow was used as control. Some samples were combined prior to library prep as indicated in the sample titles

overall_design: Cells from the bone fracture (osteotomy) gap and contralateral bone marrow were isolated 3 days post-osteotomy. Erythrocyte lysis and live cells sorting was performed before scRNAseq. Female C57BL/6J mice (Jackson Laboratory) aged 14-16 weeks were used.

first: Joel

last: Boerckel

first: Joseph

middle: M

last: Collins


title: A p53-CCF circuit integrates genome integrity with senescence phenotypes [WGS 2]

status: Public on Feb 11 2025

first: Peter

middle: D.

last: Adams

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Genomic instability and inflammation are distinct hallmarks of aging, but the connection between them is poorly understood. Understanding their interrelationship will help unravel new mechanisms and therapeutic targets of aging and age-associated diseases. Here we report a novel mechanism directly linking genomic instability and inflammation in senescent cells, through a mitochondria-regulated molecular circuit that connects the p53 tumor suppressor and cytoplasmic chromatin fragments (CCF), a driver of inflammation through the cGAS-STING pathway. Activation or inactivation of p53 by genetic and pharmacologic approaches showed that p53 suppresses CCF accumulation and the downstream inflammatory senescence-associated secretory phenotype (SASP), independent of its effects on cell cycle arrest. p53 activation suppressed CCF formation by promoting DNA repair, reflected in maintenance of genomic integrity, particularly in subtelomeric regions, as shown by single cell genome resequencing. Activation of p53 by pharmacological inhibition of MDM2 in old mice decreased features of SASP in liver, indicating a senomorphic role in vivo. Remarkably, mitochondria in senescent cells suppressed p53 activity by promoting CCF formation and thereby restricting ATM-dependent nuclear DNA damage signaling. These data provide evidence for a mitochondria-regulated p53-CCF circuit in senescent cells that controls DNA repair, genome integrity and inflammatory SASP, and is a potential target for senomorphic healthy aging interventions.

overall_design: To better understand the genomic structure of senescent cells, as well as identify potential genomic deletions associated with CCF formation, we performed single-cell genome resequencing of irradiation-induced senescent cells.

first: Karl

middle: N

last: Miller

first: Hannah

middle: R

last: Pierce-Hoffman

first: Xue

last: Lei


title: Transcriptional Control of C. elegans Male Tail Tip Morphogenesis by DMD-3

status: Public on May 07 2025

city: New York

first: Porfirio

last: Fernandez

state: NY

address: 29 Washington Place

department: Biology

institute: New York University

summary: How transcriptional regulators are linked to cell biological effectors of morphogenesis is not fully understood. To elucidate this linkage, we use the C. elegans male tail-tip as a model. The tail-tip is made of four cells that, in males, undergo changes in shape and position during the L4 stage. The transcription factor DMD-3 is the master regulator of this Tail-Tip Morphogenesis (TTM). To identify other genes involved in TTM, the lab has previously performed a genome-wide RNAi screen and conducted an RNA-seq differential expression (DE) analysis using tail tips isolated from L4 wild-type and dmd-3 mutant males. This yielded candidates for genes downstream of and regulated by DMD-3 directly or indirectly. To identify the direct targets of DMD-3, we conducted male-specific DMD-3 ChIP-seq on whole worms during TTM. We identified 1755 DMD-3 binding peaks representing 6061 genes and a de novo DMD-3-associated binding motif, sharing similarity to the chromatin binding factor, EOR-1. Integrating this data with the previous RNAi screen and the DE analysis, we found 270 candidates for direct DMD-3 targets in tail-tip cells. To validate these candidates, we inserted GFP into the endogenous loci using CRISPR and evaluated the expression of the fusion proteins. We then deleted the sequences associated with DMD-3 ChIP peaks or the DMD-3-associated binding motif and assessed if this resulted in a protein expression change or defective TTM. We found four genes where deletion of a peak had an effect: The transcription factor FOS-1 is expressed in nuclei of male tail tips during TTM and in the vulva. Deletion of a DMD-3 peak or DMD-3-associated motif sites abolishes expression in male tail-tip nuclei. NMY-2 is localized as a “cap” at the tip of the tail during TTM. Removal of the peak reduces the level of tail tip NMY-2 expression. The pan-1 locus has two peaks. PAN-1::GFP is first seen in puncta at the cell surface, then at basal lateral membranes. Removal of the distal peak causes TTM defects in 10% of screened males, while removal of both peaks leads to global, previously reported,  pan-1 phenotypes. HMR-1 is expressed at adherens junctions at the onset of TTM and later forms puncta at the cell surface. Deleting the peak has little effect on expression but results in epidermal bulges in both sexes, including the mail tail region. Because of the global phenotypes observed in peak mutants, we hypothesize the peak regions contain binding sites for other factors. Additionally, using extrachromosomal arrays, we tested and confirmed the DMD-3-associated motif’s contribution to wild-type TTM.

overall_design: ChIP-seq of GFP::DMD-3 in C. elegans L4-stage males using a GFP antibody non-antibody treated input DNA samples were used as a control

first: Karin

last: Kiontke

first: Sevinc

last: Ercan

last: Fitch


title: A p53-CCF circuit integrates genome integrity with senescence phenotypes [WGS 1]

overall_design: To confirm genomic copy number variations in senescent cells with an alternative approach, and to and test whetherMDM2 inhibitor-associated DNA repair improves genome integrity, we treated irradiation-induced senescent IMR90 with the MDM2i RG7388 and performed single-cell genome resequencing.

first: Yoav

last: Altman


title: A p53-CCF circuit integrates genome integrity with senescence phenotypes

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: A p53-CCF circuit integrates genome integrity with senescence phenotypes  [RNA-Seq 2]

overall_design: To test the effect of p53 activation on senescence-associated inflammation, we treatedirradiation-induced senescent IMR90 cells with MDM2 inhibitor (RG7388 or HDM201) or DMSO control for 7 days.


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity

status: Public on Apr 22 2025

city: New York City

first: Andrew

middle: Wayne

last: Daman

address: 1300 York Avenue

department: Pathology

institute: Weill Cornell Medical College


title: A p53-CCF circuit integrates genome integrity with senescence phenotypes [RNA-Seq 3]

overall_design: To test whether the effects of MDM2 inhibitors we observed in culture translated to an in vivo model, we treated aged C57BL6  mice (20 month female, 24 month male) with HDM201 at 10 mg/kg once daily by oral gavage for 14 days, or vehicle control.  An additional young (5 month) vehicle control for each sex was included to assess the effect of age.  We assessed gene expression in whole liver.

first: Aaron

middle: P

last: Havas


title: Single cell RNAseq of iPSC tri-cultures treated with necroptosis inducer

status: Public on Feb 10 2025

city: Cambridge

first: Timothy

last: Hammond

state: MA

address: 350 Water Street

institute: Sanofi

summary: Transcriptomic analysis of iPSC tri-culture (microglia, neurons, astrocytes) stimulated with Tnf, Smac, and Zvad (TSZ) to trigger necroptosis pathway activation, in the presence or absence of a Ripk1 inhibitor

overall_design: Cells were pre-treated for 1 hour with 1 μM Smac mimetic LCL161 (Selleck Chem, S7009), 20 μM zVAD-fmk (Enzo Life Sciences, ALX-260-020), and 1 μM RIPK1 inhibitor GSK’547 prior to a 4 hour incubation with 50 ng/mL recombinant human TNF (R&D Systems, 210-TA). Four hours after treatment, cells were collected and sequenced using the 10x Genomics platform.


title: Single cell RNAseq of SOD1 mouse spinal cords

summary: Sequencing was performed to better understand the role of neuroinflammation and glial RIPK1 signaling in ALS pathogenesis in the SOD1G93A transgenic mouse model.

overall_design: Starting on postnatal day 70, before noticeable motor deficits, female mice were treated prophylactically with the tool compound GSK’547 (RIPK1i), a highly selective CNS-penetrant RIPK1 kinase inhibitor. The inhibitor was initially dosed in chow and as motor symptoms became more severe, RIPK1i was administered via oral gavage. Spinal cords were removed at day 120 for analysis.


title: A p53-CCF circuit integrates genome integrity with senescence phenotypes [RNA-Seq 1]

overall_design: To test the ability of the DNA repair regulator 53BP1 to suppress senescence-associated inflammation, we  exogenously expressed 53BP1 on a modest PGK promoter or empty vector in IMR90 human fibroblasts by lentivirus, then induced senescence by 20 Gy irradiation, and analyzed gene expression 10 days after irradiation.

last: N Miller


title: Spinal cord single-nuclei RNA sequencing of human ALS spinal cords [ALS human snRNAseq]

summary: Transcriptomic analysis of postmortem cervical spinal cord samples from 8 people with ALS (6 sporadic and 2 familial cases) and 4 age-matched non-neurological controls using snRNA-seq

overall_design: Spinal cords were acquired from the NIH brain biobank, nuclei were isolated by FACS, and sequenced using 10x Genomics and Illumina platforms.


title: Bulk RNA sequencing of human ALS spinal cords

summary: There remains a poor understanding of cell-specific responses in the human ALS spinal cord, including differences in cell type composition, changes in cell state, and contribution of various cell types to neuroinflammation.

overall_design: Transcriptomic analysis of postmortem cervical spinal cord samples from 8 people with ALS (6 sporadic and 2 familial cases) and 4 age-matched non-neurological controls


title: TNBC organoid sc-multiome seq data treated with epigenetic drugs

status: Public on Feb 06 2025

city: Chapel Hill

first: Elizabeth

last: Brunk

state: NC

address: 250 Bell Tower Dr.  4352 Genome Sciences Bldg.

department: Pharmacology, Lineberger Comprehensive Cancer Center, UNC School of Medicine

institute: University of North Carolina at Chapel Hill

summary: Identifying biologically relevant signals from single-cell omics data to ultimately promote precision medicine is one current grant challenge. To address this challenge, we focused on triple-negative breast cancer (TNBC), integrated bulk and single-cell RNA-seq data from a large global population, and identified subpopulation identities that were able to provide responsive trajectories upon treatment. As a proof of principle, we applied our computational frame work on a TNBC organoid treated with two epigenetic drugs, JQ1 and MS177. We used this model to highlight how different components within the tumor responded molecularly differently to drug treatment.

overall_design: 10X sc-multiome sequencing was performed on the TNBC organoid in the control, JQ1-treated and MS177-treated conditions

first: Yue

last: Wang

first: Santiago

last: Haase

first: Austin

last: Whitman

first: Adriana

last: Beltran

first: Philip

last: Spanheimer


title: Effect of High Glucose on the Gene Expression Profiling in Cardiac Fibroblasts from Rats at Different Ages

status: Public on Feb 04 2025

city: Guangzhou

first: Quqian

last: Mo

state: Guangdong Province

address: No.280, Outer Ring East Road, University Town

department: Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine

country: China

institute: Guangdong Pharmaceutical University

summary:
Background: Cardiac fibroblasts (CFs) play a vital role in the physiological and pathological processes of the heart. Previous studies have demonstrated that high glucose stimulation induces the transformation of CFs into myofibroblasts, contributing to cardiac fibrogenesis. However, in vivo experiments have predominantly utilized adult animals, whereas most in vitro studies have focused on CFs derived from neonatal animals. The responses of CFs from different age groups to high glucose levels remain unclear. This study aimed to investigate transcriptional alterations in CFs at distinct developmental stages in response to high glucose exposure.
Methods: CFs were isolated from neonatal (S1, 0–3 days), juvenile (S2, 3–4 weeks), adult (S3, 10–13 weeks), and aged (S4, 20 months) rats. CFs were exposed to normal (5.5 mM, NG) or high glucose (33 mM, HG). The cellular RNA was extracted for sequencing and analysis. Differentially expressed genes (DEGs) were validated by quantitative real-time PCR. Results: After NG treatment, fibrosis and inflammation-related gene expression in CFs (e.g., Col8a1, Col8a2, IL-6, Ccl2, Ccl20, Mmp2 and Mmp9) increased with age, while proliferation-related genes (MCM family, Sox10, Sox11) decreased. HG treatment most affected S3-CFs, showing 228 DEGs; it suppressed growth-related genes (Adra1d, Htr2b) and enhanced inflammatory genes (IL-6, Olr1). In S1-CFs, 197 inflammation-rich genes were upregulated under HG. S4-CFs displayed 166 DEGs, mostly metabolic downregulation (G6pc). S2-CFs had the fewest DEGs (112), focusing on cell metabolism. Conclusions: Fibrosis- and inflammation-associated gene expression in CFs showed an age-dependent stepwise elevation. CFs from distinct developmental stages responded differently to HG stimulation, with S3-CFs exhibiting the most pronounced response. These findings highlight the developmental characteristics of CFs and provide implications for the selection of appropriate CFs to investigate diabetes-associated cardiac fibrosis.

overall_design: To investigate the difference of gene expression profile of rat cardiac fibroblasts at different ages under normal glucose and high glucose conditions, we extracted primary rat cardiac fibroblasts at four different age groups and cultured them in DMEM containing 5.5mM or 33mM glucose.

first: Angyu

last: Zhan

first: Ruining

last: Bai

first: Shaoling

last: Lin

first: Jiaojiao

last: Feng

first: Tongjun

last: Li

first: Zijian

last: Lao

first: Xiao

last: Yang

first: Keke

first: Xianglu

last: Rong

first: Lexun


title: RNA-seq Analysis of OCI-AML3 Cells Treated with Different Compounds

status: Public on Feb 01 2025

first: Faezeh

last: Ghazvini Zadegan

summary: Acute myeloid leukemia (AML) remains a challenging hematologic malignancy, necessitating the exploration of novel treatment strategies. In this study, we investigated the effects of all-trans retinoic acid (ATRA), AM80, and their combination treatments with GSK-LSD1 and MB3 on gene expression in OCI-AML3 cells.

overall_design: This study evaluates the effects of ATRA, AM80, and combination treatments with GSK-LSD1 and MB3 on OCI-AML3 cells, compared to untreated cells.


title: Effect of Lactobacillus salivarius HHuMin-U on gene expression of VK2/E6E7 human vaginal cell lines.

city: Seoul

first: Juwon

last: Choi

address: 50 Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

summary: Vulvovaginal candidiasis (VVC) is a common mucosal infection caused by Candida albicans, characterized by inflammation and disruption of epithelial immunity. Probiotic therapy has emerged as a promising approach for managing VVC by modulating host immune responses and enhancing mucosal defenses. In this study, we investigated the therapeutic potential of Lactobacillus salivarius HHuMin-U (HMU) against VVC using in vitro and in vivo models. HMU treatment enhanced the expression of antimicrobial peptides (AMPs) such as DEFB1 and S100A8 and modulated cytokine production (e.g., IL-6, IL-8) in vaginal epithelial cells. Furthermore, RNA sequencing of HMU-treated VK2/E6E7 cells revealed significant transcriptional changes, including upregulation of epithelial barrier function and immune-enhancing pathways. Gene Set Enrichment Analysis (GSEA) identified the NF-κB pathway as a critical regulator of HMU-induced immunity. In vivo, HMU administration significantly reduced fungal burden, mitigated tissue inflammation, and improved epithelial integrity in a murine model of VVC. The sequencing data presented in this report provide a comprehensive transcriptomic landscape of HMU-treated vaginal epithelial cells and offer insights into its underlying mechanisms. These findings support the therapeutic potential of HMU as a probiotic agent for VVC management.

overall_design: To investigate the effects of Lactobacillus salivarius HHuMin-U (HMU) on vaginal epithelial cells, VK2/E6E7 cells were seeded and divided into two groups. Control: PBS-treated; HMU: HMU-treated at a concentration of 1×10^8 CFU/mL. Cells were treated with PBS or HMU for 6 hours before total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Three biological replicates were prepared for each group.

first: Sanguine

last: Byun

first: Jay-Young

last: Jo


title: Single cell transcriptomic profiling reveals a dynamic molecular landscape and the importance of ligand-receptor genes and transcription factors during the progression of colorectal cancer

city: Nanchang

first: Pan

last: Zheng

address: 17 of Yongwaizhengjie Street

institute: The Affiliated Hospital of Nanchang University

summary: By analyzing the scRNA-seq data from ten human colorectal specimens, which represent the four kinds of colorectal tissues (normal colorectal mucosa, inflammatory polyps, Adenomatous polyps and colorectal cancer), in combination with validation by immunofluorescence staining using expanded clinical samples, and together with verification using large scale TCGA and Kaplan–Meier data, we reveal a dynamic molecular landscape and the importance of ligand-receptor genes and transcription factors driving the colorectal carcinogenesis.

overall_design: Under informed consent and ethical review, a total of 10 colorectal specimens were collected from colon or rectum from patients who underwent endoscopy examination (non-CRC colorectal mucosa samples) or surgery (CRC samples) at Yichun People’s Hospital, Jiangxi, China

first: Huizhen

last: Fan

first: Jianwen

last: Sheng

first: Jianping

last: Liu

first: Yin

last: Zhu

first: Nianshuang


title: Chemical perturbations impacting histone acetylation regulate colorectal cancer differentiation

status: Public on Jan 30 2025

city: Boston

first: Zhixin

state: Massachusetts

address: 450 Brookline Avenue, D742

institute: Dana-Farber cancer institute

summary: Histone acetylation governs broad gene expression programs in normal tissue and disease states. By applying a small chemical compound library targeting epigenetic regulators to a dual endogenous reporter system, we found that inhibiting histone deacetylase (HDAC) 1/2 initiates colorectal cancer (CRC) differentiation. Inhibiting the enzymatic pocket of HDAC1/2 induced differentiation and reduced proliferation across in vitro and in vivo models. On-target HDAC1/2 inhibition was validated using biochemical, chemical, and genetic approaches. A survey of histone posttranslational modifications from HDAC1/2 selective inhibition nominated acetylation of specific H3 and H4 lysine (K) residues as potential regulators of differentiation. Genome-wide profiles of these histone acetylation marks indicated that gains in histone 3 lysine 27 acetylation (H3K27ac) most strongly correlated to opening of chromatin and upregulation of genes associated with differentiation upon HDAC1/2 inhibition. Blocking acetylation of H3K27 by degrading its writer EP300 rescued the differentiation phenotype induced by HDAC1/2 inhibition in a patient-derived CRC model by single cell RNA-sequencing among other readouts. These results highlight the importance of specific chemically targetable histone modifications in governing cancer cell states and implicate precision targeting of H3K27ac as a potential therapeutic approach for CRC.

overall_design: To define the mechanism(s) by which MRK60 promotes CRC differentiation, we started with the analysis of gene expression profiles from CRC cells treated with MRK60.

first: Pornlada

last: Likasitwatanakul

first: Paul

last: Doan

first: Nilay

last: Sethi


title: The Role of Interferon-γ in Autoimmune Polyendocrine Syndrome Type 1

status: Public on Jan 28 2025

city: Bethesda

first: Behdad (Ben)

last: Afzali

state: MD

address: 10 Center Drive, Building 10

department: NIDDK

institute: National Institutes of Health

summary:
Background: Autoimmune polyendocrine syndrome type 1 (APS-1) is a life-threatening, autosomal recessive syndrome caused by autoimmune regulator (AIRE) deficiency. In APS-1, self-reactive T cells escape thymic negative selection, infiltrate organs, and drive autoimmune injury. The effector mechanisms governing T-cell-mediated damage in APS-1 remain poorly understood.

Methods: We examined whether APS-1 could be classified as a disease mediated by interferon-γ. We first assessed patients with APS-1 who were participating in a prospective natural history study and evaluated mRNA and protein expression in blood and tissues. We then examined the pathogenic role of interferon-γ using Aire-/-Ifng-/- mice and Aire-/- mice treated with the Janus kinase (JAK) inhibitor ruxolitinib. On the basis of our findings, we used ruxolitinib to treat five patients with APS-1 and assessed clinical, immunologic, histologic, transcriptional, and autoantibody responses.

Results: Patients with APS-1 had enhanced interferon-γ responses in blood and in all examined autoimmunity-affected tissues. Aire-/- mice had selectively increased interferon-γ production by T cells and enhanced interferon-γ, phosphorylated signal transducer and activator of transcription 1 (pSTAT1), and CXCL9 signals in multiple organs. Ifng ablation or ruxolitinib-induced JAK-STAT blockade in Aire-/- mice normalized interferon-γ responses and averted T-cell infiltration and damage in organs. Ruxolitinib treatment of five patients with APS-1 led to decreased levels of T-cell-derived interferon-γ, normalized interferon-γ and CXCL9 levels, and remission of alopecia, oral candidiasis, nail dystrophy, gastritis, enteritis, arthritis, Sjögren's-like syndrome, urticaria, and thyroiditis. No serious adverse effects from ruxolitinib were identified in these patients.

Conclusions: Our findings indicate that APS-1, which is caused by AIRE deficiency, is characterized by excessive, multiorgan interferon-γ-mediated responses. JAK inhibition with ruxolitinib in five patients showed promising results. (Funded by the National Institute of Allergy and Infectious Diseases and others.).

overall_design:
RNA-seq analysis of human oral mucosal tissues in APECED patients and healthy donors.
Genomics andComputational Biology Core (contributor)

first: Vasileios

last: Oikonomou

first: Grace

last: Smith

first: Monica

last: Schmitt

first: Gregory

last: Constantine

first: Elise

last: Ferré

first: Julie

last: Alejo

first: Deanna

last: Riley

first: Dhaneshwar

last: Kumar

first: Yannis

last: Hadjiyannis

first: Daniel

last: Martin

first: Marine

last: Besnard

first: Brendan

last: Snarr

first: Shiva

last: Deljookorani

first: Chyi-chia

last: Lee

first: Lindsey

middle: B

last: Rosen

first: Aristine

last: Cheng

first: Andre

last: Rastegar

first: Adrianna

last: Almeida de Jesus

first: Hyesun

last: Kuehn

first: Timothy

last: Break

first: Theo

last: Heller

first: Karen

last: Winer

first: Heidi

last: Kong

first: Leslie

last: Castelo-Soccio

first: Mikko

last: Seppanen

first: Sergio

last: Rosenzweig

first: Anthony

middle: F

last: Suffredini

first: Mark

last: Anderson

first: Carole

last: Guillonneau

first: Luigi

last: Notarangelo

first: Raphaela

last: Goldbach-Mansky

first: Olaf

last: Neth

first: Maria

middle: T

last: Monserrat-Garcia

first: Justo

last: Valderde-Fernandez

first: Jose

last: Lucena

first: Ana

last: Gomez-Gila

first: Angela

last: Garcia Rojas

first: Hero

last: Matti

first: Saila


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

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

last: Dou

first: Kelly

last: Bakulski

first: Justin

last: Colacino

first: Vasantha

last: Padmanabhan

first: Sean

last: Harris


title: Transcriptional memory is conferred by combined heritable maintenance and local removal of selective chromatin modifications

status: Public on Jan 20 2025

city: Oxford

first: Pawel

last: Mikulski

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Interferon-γ (IFNγ) transiently activates genes involved in inflammation and innate immunity. A subset of targets maintain a mitotically heritable memory of prior IFNγ exposure resulting in hyperactivation upon reexposure. Here we discovered that the active chromatin marks H3K4me1, H3K14Ac and H4K16Ac are established during IFNγ priming and selectively maintained on a cluster of GBP genes for at least 7 days in dividing cells in the absence of transcription. The histone acetyltransferase KAT7 is required for the accelerated GBP reactivation upon reexposure to IFNγ. In naïve cells, we find the GBP cluster is maintained in low-level repressive chromatin marked by H3K27me3 limiting priming in a PRC2-dependent manner. Unexpectedly, IFNγ results in transient accumulation of this repressive mark but is then selectively depleted from primed GBP genes during the memory phase facilitating hyperactivation of primed cells. Furthermore, we identified a cis-regulatory element that makes transient, long-range contacts across the GBP cluster and acts as a repressor, primarily to curb the hyperactivation of previously IFNγ-primed cells.  Combined our results identify the putative chromatin basis for long-term transcriptional memory of interferon signalling that may contribute to enhanced innate immunity.

overall_design:
Cut&Run-seq with immunoprecipitation for H3K4me1, H3K4me3, H3K14ac, H4K16ac, followed by Illumina short-read sequencing (NextSeq 500)

This work was funded by a Senior Wellcome Research Fellowship 210645/Z/18/Z to L.E.T.J., Goodger and Schorstein Scholarship from the University of Oxford, NAWA Polish Returns (BPN/PPO/2022/1/00014), National Science Centre Sonata (2022/47/D/NZ2/01219) and Komponent badawczy grants (2023/02/1/NZ2/00005) to P.M. S.S.H.T. was supported by Fundação para a Ciência e a Tecnologia (FCT) doctoral fellowship (PD/BD/128438/2017). A.K. is a Clarendon Scholar supported by the Hill Foundation.

first: Lars

middle: E

last: Jansen


title: Interferon gamma-induction of TH1-like regulatory T cells controls anti-viral responses

status: Public on Jan 19 2025

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

institute: University of Pittsburgh

summary: Abstract: Regulatory T cells (Tregs) are an immunosuppressive population that are required to maintain peripheral tolerance and prevent tissue damage during immunopathology, via anti-inflammatory cytokines, inhibitor receptors and metabolic disruption. We report that Tregs acquire an effector-like state, yet remain stable and functional, when exposed to IFNγ during chronic infection with lymphocytic choriomeningitis (LCMV) and Influenza A virus (IAV). Mechanistically, Treg-restricted-deletion of the IFNγ receptor 1 (IFNGR1), but not the IL12 receptor, prevented TH1-like polarization (decreased expression of T-bet, CXCR3 and IFNγ) and promoted TH2-like polarization (increased expression of GATA-3, CCR4 and IL4). TH1-like Tregs limited CD8+ T cell effector function, proliferation and memory formation during chronic and acute infection. These findings provide fundamental insights into how Tregs sense inflammatory cues from the environment (IFNγ) during viral infection to provide immune guidance to the effector T cell response, to prevent prolonged immunoinflammatory responses and shape the quality of the memory response.

overall_design: Splenic Tregs and Tetramer+ CD8+ T cells were harvested from Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP mice that remained naïve or were infected with lymphocytic choriomeningitis virus (LCMV) Clone 13 (Cl 13) for 16d

last: Gocher-Demske

first: Dario

last: Vignali


title: RNA sequencing analysis of genes related to manganese toxicity in Vibrio parahaemolyticus

city: Yangzhou

first: Yu

last: Zhang

address: No. 48, Wenhui East Road

institute: Yangzhou University

summary: RNA sequencing analysis was used to compare the transcriptome of the wild strains under normal conditions and manganese stress conditions. The data showed that some genes, such as mneA and terC, were significantly differentially expressed under manganese stress.

overall_design: The transcription profiles of wild type strains incubated under H2O and 1 mM Mn2 + conditions were compared. Three biological replicates were set for each condition.

first: Chengkun

last: Zheng

first: Xiaoya

last: Zhu

first: Furong

last: Ma


title: Generation of Bona Fide Human Induced Trophoblast Stem Cells from Term Umbilical Cord

status: Public on Jan 15 2025

city: Amsterdam

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Amsterdam UMC

summary: Placentation disorders such as severe fetal growth restriction and preeclampsia have their origin in the first trimester of pregnancy, whereas symptoms typically present later on. To be able to study the pathogenesis of these diseases, there is a need for a reliable model system of early placenta development with known pregnancy outcomes. Therefore, we aimed to optimize the generation of human induced trophoblast stem cells (iTSCs) from term umbilical cord using a direct reprogramming approach. In this, we added three supplements—A-485 (CREBBP/EP300 inhibitor), BMP4 or EPZ-6438 (PRC2 inhibitor)—that could potentially boost iTSC induction. The generated iTSCs fulfilled the criteria for bona fide first-trimester trophoblasts and exhibited transcriptional similarity to TSCs derived from first-trimester placental tissue, while the supplements tested did not substantially enhance iTSC induction.

overall_design: Mesenchymal stem cells were isolated from a term umbilical cord, and transduced with the OSKM reprogramming factors. Seven days post-transduction, reprogramming intermediates were transited into human TSC medium to induce TSC conversion, with or without supplementation of A-485, BMP4 or EPZ-6438 for 1-3 days. Transcriptome sequencing was performed to assess the similarity between the generated iTSCs and TSCs derived from first-trimester placental tissue. The dataset contains 1-3 experimental replicates of each iTSC condition, 3 TSC lines, and TSCs differentiated into extravillous trophoblast for reference.

first: Jantine

last: van Voorden

first: Souad

last: Boussata

first: Marloes

last: Vermij

first: Muriel

last: Wagner

first: Wessel

last: Ganzevoort

first: Gijs

last: Afink


title: SFPQ protects DNA repeat stability by recruiting histone H3.3 chaperon activity to R-loop structures [ChIP-seq]

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired single stranded DNA loop. R-loops control physiologically processes, however when unscheduled or persistent they drive genome instability by creating conflicts with transcription and replication. The human genome is composed of up to 75% of repetitive sequence elements that can also hold transcriptional activity. Thus R-loop surveillance at repetitive elements is central for the maintenance of genome integrity.  Here we show that the RNA binding protein SFPQ suppresses R-loop mediated replication stress and DNA damage at repeat elements such as telomeres, (peri)-centromeres, LINE-1 and SINE elements. SFPQ shows in-vitro R-loop binding activity, uses its RNA-recognition motif (RRM) domains to bind chromatin containing R-loops and uses its proline-rich (P) domain to recruit the histone H3.3 chaperon DAXX to maintain a correct nucleosome template that antagonizes R-loop formation. Loss of SFPQ results in DAXX delocalization from repeat elements, reduction of histone H3.3 incorporations, replication stress mediated DNA damage in repeat elements resulting and centromere defects resulting the formation of cytoplasmatic DNA species that activate the cGAS/STING pathway and innate immunity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U2-OS cells transfected with Control or SFPQ siRNAs, with 3 replicates.

first: Stefan

last: Shoeftner

first: Alessandro

last: Ferrando

first: Alice

last: Gambelli

first: Giulia

last: Canarutto

first: Andrea

last: Parlante


title: SFPQ protects DNA repeat stability by recruiting histone H3.3 chaperon activity to R-loop structures [RNA-seq]


title: The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity [karpas-cutrun]

status: Public on Jan 13 2025

first: Agata

middle: Lemiesz

last: Patriotis

state: New York

address: 1230 York ave

institute: Rockefeller University

summary: Polycomb group proteins maintain gene expression patterns established during early development, with Polycomb Repressive Complex 2 (PRC2) methyltransferase a key regulator of cell differentiation, identity and plasticity. Consequently, extensive somatic mutations in PRC2, including gain- or loss- of function (GOF or LOF), are observed in human cancers. The regulation of chromatin structure by PRC2 is critically dependent on its EZH2 (Enhancer of Zeste Homolog 2) subunit, which catalyzes the methylation of histone H3 lysine 27 (H3K27). Recent structural studies of PRC2 revealed extensive conformational changes in the non-catalytic EZH2 N-terminal SANT-Binding Domain (SBD) during PRC2 activation, though the functional significance remains unclear. Here, we investigate how the SBD regulates PRC2 function. The domain is highly conserved in metazoans, dispensable for PRC2 assembly and chromatin localization, yet required for genome-wide histone H3K27 methylation. Further, we show that an intact SBD is necessary for the proliferation of EZH2-addicted lymphomas, and its deletion in the presence of EZH2 GOF mutations inhibits cancer cell growth. These observations provide new insights to the regulation of PRC2 activity in normal development and malignancy.

overall_design:
EZH2, SUZ12, H3K27me3, H3K27me2 ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESCs, EZH2 KO and EZH2 ΔSBD.
MTF2, JARID2 ChIP-seq experiment of A1 (WT) mESCs, EZH2 KO and EZH2 ΔSBD.
Cut and Run experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF)
RNA-seq experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF), 72 hours after EZH2-KO induction.
H3K27me3 ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESC with the expression of  EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF)

middle: L

first: Douglas

last: Barrows

first: C. David

last: Allis


title: The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity [delSBD-ChIP-Rx]

overall_design:
EZH2, SUZ12, H3K27me3, H3K27me2, H3K27ac ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESCs, EZH2 KO and EZH2 ΔSBD.
MTF2, JARID2 ChIP-seq experiment of A1 (WT) mESCs, EZH2 KO and EZH2 Î?SBD.
Cut and Run experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-Î?SBD-Y641N (Î?SBD-GOF)
RNA-seq experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-Î?SBD-Y641N (Î?SBD-GOF), 72 hours after EZH2-KO induction.
H3K27me3 ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESC with the expression of  EZH2-Y641 (GOF) and EZH2-Î?SBD-Y641N (Î?SBD-GOF)


title: The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity [MTF2-JARID2]

overall_design:
EZH2, SUZ12, H3K27me3, H3K27me2 ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESCs, EZH2 KO and EZH2 ΔSBD.
MTF2, JARID2, EPOP, AEBP2 ChIP-seq experiment of A1 (WT) mESCs, EZH2 KO and EZH2 ΔSBD.
Cut and Run experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF)
RNA-seq experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF), 72 hours after EZH2-KO induction.
H3K27me3 ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESC with the expression of  EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF)


title: The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity [Karpas-rna-seq]


title: Modeling retinal ganglion cell axonal pathology associated with glaucoma using human pluripotent stem cell-based microfluidic platforms

city: Portland

first: Chi

last: Zhang

state: Oregon

address: 3303 S.W. Bond Avenue

department: Biomedical Engineering

institute: Oregon Health & Science University

summary: Retinal ganglion cells (RGCs) are highly compartmentalized cells, and previous studies have demonstrated that RGC degeneration in glaucoma occurs in a compartmentalized manner, with distinct injury responses in axonal and somatodendritic compartments. Thus, the goal of this study was to establish a novel microfluidic-based platform for the analysis of RGC compartmentalization in health and disease states. Human pluripotent stem cell (hPSC)-derived RGCs were seeded into microfluidics, enabling the recruitment and isolation of axons apart from the somatodendritic compartment. Initial studies explored axonal outgrowth and compartmentalization of axons and dendrites. We then compared the differential response of RGCs differentiated from hPSCs carrying the OPTN(E50K) glaucoma mutation with isogenic control RGCs in their respective axonal and somatodendritic compartments, followed by analysis of axonal transport. Further, we explored the axonal transcriptome via RNA-seq, focusing on disease-related axonal differences. Finally, we established models to uniquely orient astrocytes along the axonal compartment combined with modulation of astrocyte reactivity as a pathological feature of neurodegeneration. Overall, RGC culture within microfluidic chips allowed enhanced cell growth and maturation, including long-distance axonal projections and proper compartmentalization. OPTN(E50K) RGCs exhibited axonal outgrowth deficits as well as decreased rate of axonal transport, compared to isogenic controls. Finally, upon introduction of astrocytes into the proximal axonal compartment, the induction of astrocyte reactivity led to the onset of neurodegenerative phenotypes in RGCs. These results represent the first study to effectively recapitulate the highly compartmentalized properties of hPSC-derived RGCs in healthy and disease states, providing a more physiologically relevant in vitro model for neuronal development and degeneration.

overall_design: RNA was extracted from the somatodendritic and axonal compartments of the microfluidic devices and RNA-sequencing was performed to assess transcriptional differences between (1) the somatodendritic and axonal compartments of RGCs, as well as (2) within the axonal compartment of OPTN(E50K) RGCs versus isogenic controls (axon-sequencing).

first: Catia

last: Gomes

first: Yue

last: Fang

first: Jason

last: Meyer


title: The cationic liposome of  trehalose dimycolate (TDM) inducees antitumor immunity in bladder.

status: Public on Jan 10 2025

city: Tsukuba city

first: Kozaburo

last: Tanuma

state: Ibaraki

address: Tennodai 2-1-1

department: Urology

country: Japan

institute: University of Tsukuba

summary: BCG therapy is the most effective immunotherapy for bladder cancer, but it sometimes causes serious adverse events because of infection with live BCG bacteria. To develop more effective and less toxic immunotherapeutic agents, we have developed formulations using BCG cell wall components. Trehalose dimycolate (TDM) is a predominant glycolipid that constitutes the cell wall of BCG, and reported to show activation of innate immunity and have adjuvant effect. We already established hydrophilic cationic liposomes incorporating TDM, and reported that local administration of the cationic liposome TDM (Lip-TDM) exerted antitumor effect to subcutaneously inoculated tumors by inducing activation of CD8+ T cells via dendritic cell maturation. In present study, we demonstrated that intraperitoneal administration of Lip-TDM exerted antitumor effects in orthotopic bladder carcinogenesis mouse model induced by N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN). In this model, intraperitoneal administration of Lip-TDM enhanced the systemic activation of dendric cells and macrophages, and increased infiltration of adaptive immune cells such as CD8+ T cells. Furthermore, Lip-TDM treatment induced Natural Killer (NK) cells to be cytotoxic NK cells in tumors and regulatory NK cells in lymphoid tissues. Lip-TDM treatment induced activation of DCs and cytotoxic CD8+ T cells and exerted antitumor effect in WT mice, but not in NK cell-depleted mice. These results indicate NK cells are essential for Lip-TDM to induce sufficient acquired immune response. Our findings elucidate the mechanism of the antitumor effect by Lip-TDM and suggest that Lip-TDM is a non-infectious agent which can be administered intraperitoneally and has potential to be an alternative to BCG.

overall_design: RNA sequencing was performed using the bladders from the wild-type C57BL/6 mice treated with Lip-TDM or Lip-CON. Bladders were extracted from sacrificed animals at baseline and after 16 weeks of treatment.

first: Jun

last: Miyazaki

first: Masanobu

last: Shiga

first: Keisuke

last: Sano

first: Yoshiyuki

last: Nagumo


title: Epigenetic features support the diagnosis of B-cell prolymphocytic leukemia and identify two clinico-biological subtypes

status: Public on Jan 08 2025

city: Barcelona

first: Jose Ignacio

last: Martin-Subero

state: Barcelona

address: c/Rosselló, 149-153

country: Spain

institute: IDIBAPS

summary: The recognition of B-cell prolymphocytic leukemia (B-PLL) as a separate entity is controversial based on the current classification systems. Here, we analyze the DNA methylome of a cohort of 20 B-PLL cases diagnosed according to the ICC/WHO-HAEM4R guidelines, and compare them with chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MCL), splenic marginal zone lymphoma (SMZL), and normal B cell subpopulations. Unsupervised principal component analyses suggest that B-PLL is epigenetically distinct from CLL, MCL and SMZL, which is further supported by robust differential methylation signatures in B-PLL. We also observe that B-PLL can be segregated into two epitypes with differential clinico-biological characteristics. B-PLL epitype 1 carries lower IGHV somatic hypermutation and a less profound germinal center-related DNA methylation imprint than epitype 2. Furthermore, epitype 1 is significantly enriched in mutations affecting MYC and SF3B1 as well as gain 1q, and displays DNA hypomethylation and gene upregulation signatures enriched in MYC targets. Despite the low sample size, patients from epitype 1 have an inferior overall survival than those of epitype 2. This study provides relevant insights into the biology and differential diagnosis of B-PLL, and potentially identifies two subgroups with distinct biological and clinical features.

overall_design: Illumina Infinium MethylationEPIC v1.0 commercial kit

first: Stella

last: Charalampopoulou


title: Single-cell RNA sequencing of chronic idiopathic erythroderma defines disease-specific markers

status: Public on Jan 07 2025

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Background: Chronic erythroderma is a potentially life-threatening condition that can be caused by a variety of diseases, but approximately 30% of cases remain idiopathic, often with insufficient treatment options.

Objective: To establish a molecular disease map of chronic idiopathic erythroderma.

Methods: We performed single-cell RNA sequencing combined with T-cell receptor sequencing of blood and skin from 5 chronic idiopathic erythroderma (CIE) patients and compared results with 8 cases of erythrodermic cutaneous T-cell lymphoma (eCTCL), 15 moderate-to-severe atopic dermatitis (AD), 10 psoriasis and 20 healthy control (HC) individuals.

Results: In erythrodermic CTCL, we found strong expansion of CD4+ malignant clones with a CCR7+SELL+ central memory phenotype. By contrast, CIE exhibited a pattern of low-level, but consistent expansion of CD8A+KLRK1+ T-cell clones, both in blood and skin. KLRK1 was also expressed by CCR10+FUT7+ skin-homing CIE blood T-cells that had increased proliferation rates and were absent in all other conditions. While CIE and CTCL patients lacked the strong type 2 or type 17 immune skewing typically found in AD or psoriasis, respectively, they were characterized by upregulation of MHC II genes (HLA-DRB1, HLA-DRA, CD74) in keratinocytes and fibroblasts, most likely in an IFNG-dependent fashion. However, we found strongest upregulation of type 1 immune mediators in CIE samples, both in the expanded CD8A+ clones, as well as in the tissue microenvironment.

Conclusion: Despite the notion that CIE might be a mere bundle of various yet uncharacterized disease processes, we found specific pathogenic signatures in these patients, that were different from other forms of erythroderma. These data might help to improve our pathogenic understanding of the blood and skin compartments of CIE, aiding in discovery of future treatment targets.

overall_design:
Comparison of skin cells obtained from chronic idiopathic erythroderma (CIE), erythrodermic cutaneous T-cell lymphoma (CTCL), atopic dermatitis (AD) and healthy controls (HC).

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Sumanth

last: Chennareddy

first: Katharina

last: Rindler

first: Shannon

last: Meledathu

first: Malini

last: Naidu

first: John

last: Ruggiero

first: Lisa

last: Szmolyan

first: Wolfgang

last: Weninger

last: Bauer

first: Johannes

last: Griss

first: Constanze

last: Jonak

first: Patrick

last: Brunner


title: Ifi27l2a regulates the microglial inflammation in the context of aging and stroke

status: Public on Jan 09 2025

city: Houston,

first: Gab Seok

last: Kim

state: TX

address: 6431 Fannin St.

department: Department of Neurology

institute: The University of Texas Health Science Center at Houston

summary: Microglia are key mediators of inflammatory responses within the brain, as they regulate pro-inflammatory responses while also limiting neuroinflammation via reparative phagocytosis. To facilitate identification of potential mediators of inflammation, we performed single-cell RNA sequencing of aged mouse brains following stroke and found that Ifi27l2a was significantly up-regulated, particularly in microglia.

overall_design: Sham and PDMCAO surgeries were performed on young and aged mice. At 14 days after surgery, brains were isolated. Both sexes were used for scRNA-seq. Fourteen days post PDMCAO (or sham surgery), anesthetized mice were transcardially perfused with heparinized PBS (10 U/mL). Brains were removed from the skull and sliced coronally into 3 mm-thick blocks (from a region spanning +1 to -2 mm from bregma), covering the cortical infarction and secondary thalamic injury site. The brain slice was then minced with a razor blade and subjected to the brain tissue dissociation protocol.The 10X Genomics Chromium™, Single-Cell RNA-SeqSystem (10X Genomics, Pleasanton, CA) was used to prepare cells for scRNA-seq.

first: Gab

first: Sean

last: Marrelli

first: Joshua

last: Wythe

first: Manuel

last: Gutierrez


title: Vostok:  A New Looping Factor for the Organization of the Regulatory Genome in the Drosophila Brain

city: Moscow

first: Maksim

last: Erokhin

state: Moscow

address: Vavilov

country: Russia

institute: IGB

summary: The Drosophila regulatory genome is organized in a hierarchical series of topological associating domains (TADs) and intra-TAD regulatory loops.  High-resolution Micro-C maps identified ~645 such loops in the larval brain of Drosophila, spanning distances of 25 kb to 250 kb.  Many of these loops are associated with genes encoding neural adhesion proteins implicated in the formation of specific synapses, including Dprs, Dips, Sides and Beats.  They are formed by interactions of pairs of tethering elements that contain simple repeated sequence motifs, such as GAGAG.  Approximately 10% (64/645) of the loops are lost or diminished in larval brains obtained from homozygous mutants lacking the GAF (GAGA-associated factor) POZ oligomerization domain.  We also present evidence for a second looping factor, the MADF-containing Vostok protein (CG11504), which recognizes a GCAACA motif that is over-represented in brain tethering elements.  There is a loss of 47 of the loops (7%) in larval brains obtained from Vostok mutants. These losses are associated with diminished expression of associated genes, suggesting impaired enhancer-promoter interactions.  Only 9 loops are disrupted in both Vostok and GAF mutants, raising the possibility of a combinatorial code for tether-tether interactions.  Support for this possibility stems from the observation that two previously identified meta-loops spanning 6 Mb rely on both GAF and Vostok. We discuss the prospects of using different combinations of looping factors to produce unlimited 3D associations of genetic loci in animal genomes.

overall_design: ChIP-Seq analyses were performed on the brains of wandering larvae (4-6h before puparium formation). All experiments were performed using wild type or Vostok null mutant larvae.

first: Jie

last: Hu

first: Xiao

last: Li

first: Dmitry

last: Lomaev

first: Nadezhda

last: Vorobyeva

first: Michael

last: Levine

first: Darya

last: Chetverina


title: Topical lubrication restores dry eye corneal stroma by producing  reparative  keratocytesacripep promotes corneal regeneration in autoimmune mediated dry eye disease (Bulk RNA-Seq).

status: Public on Jan 02 2025

city: San Francisco

first: Sarah

last: Knox

state: California

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

summary: Topical lubrication is the most common remedy for relieving the signs and symptoms of dry eye. However, the therapeutic value of lubricating the ocular surface remains relatively unknown. Here we reveal the restorative properties of the simplest form of lubrication in a mouse model of autoimmune-mediated dry eye. We show topical treatment with PBS rescues corneal stromal architecture through restoring the basement membrane and collagen fiber alignment essential for maintaining corneal transparency. At the single cell level we show keratocytes exhibit significant plasticity under chronic injury, with continuous transition from a homeostatic to inflammatory state, and that lubrication converts these inflammatory cells to a unique reparative phenotype. We further identify IL1b-IL1R1-MAPK signaling as a key pathway driving keratocyte inflammation, and that disruption of the IL1b autocrine amplification loop by lubrication is sufficient to reprogram the inflammatory keratocytes towards the reparative state. Thus, our study underscores the regenerative potential of topical lubrication in dry eye, and reveals fibroblast-targeted therapies as a novel approach to restoring ocular surface health.

overall_design: Comparative analysis of gene expression between wilt type, untreated Aire KO (dry eye disease) , Aire KO treated with PBS, and Aire KO treated with 4uM lacripep whole corneas at day 7 of treatment (6 wk of age).

first: Yael

last: Efraim

first: Feeling

last: Yu

first: Ting

last: Chen

first: Dylan

last: Pham

first: Vahid

last: Niknezhad

first: Ka

last: Cheong

first: Luye

last: An

first: Hanan

last: Sinada

first: Nancy

middle: A

last: McNamara


title: Topical lubrication restores dry eye corneal stroma by producing  reparative  keratocytesacripep promotes corneal regeneration in autoimmune mediated dry eye disease.

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

overall_design: Refer to individual Series


title: Breast cancer cell lines

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus


title: Effect of TDO2/IDO dual inhibitor AT0174 on  human MDA-MB-453 breast cancer cells

summary: To investigate global transcriptomics of human MDA-MB-453 breast cancer cells in response to the TDO2/IDO dual inhibitor AT0174 treatment in compared with the vehicle control

overall_design: Breast cancer cell line MDA-MB-453 at attached culture and forced suspension culture was treated with AT0174 or vehicle control (DMSO) for 48 hours, the cells were then collected for Bulk RNA sequencing. All conditions were performed with biological triplcates.

first: Li-Wei

last: Kuo

first: Lyndsey

last: Crump

first: Kathleen

middle: I

last: O'Neil

first: Michelle

last: Williams

first: Jessica

last: Christenson

first: Nicole

last: Spoelstra

first: Jennifer

middle: K

last: Richer

first: Meher

last: Boorgula


title: Topical lubrication restores dry eye corneal stroma by producing  reparative  keratocytesacripep promotes corneal regeneration in autoimmune mediated dry eye disease (snRNA-Seq).

first: Sarah

last: Knox

first: Yael

last: Efraim

first: Feeling

last: Yu


title: The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity [es-cells-gof-chip]

city: New York City

first: Agata

last: Patriotis

first: Douglas

middle: W

last: Barrows

first: C. David

last: Allis


title: Global transcriptomics analysis for TDO2 alteration in human triple-negative breast cancer cell lines

summary: To elucidate the downstream transcriptomics changes in reponse to TDO2 alteration including shRNA knockdown, overexpression and TDO2/IDO duak inhibitor treatments in human triple-negative breast cancer cell lines.

overall_design: Each condition with biological triplicates. Human triple-negative breast cancer cell line BT549 with TDO2 overexpression (OE) in compared with control empty vector (EV); BT549 with shRNA TDO2 knockdown (shTDO2-082 or shTDO2-098) vs. shNegative control (shNeg);  BT549 at forced suspension culture treated with TDO2/IDO dual inhibitor AT0174 for 48 hours ; SUM159PT at forced suspension culture treated with TDO2/IDO dual inhibitor AT0174 for 48 hours

middle: S


title: Polyamine metabolism dysregulation contributes to muscle fiber vulnerability in ALS

status: Public on Jan 01 2025

city: Rome

first: Andrea

last: Bracaglia

address: Via Antonio Scarpa 16

institute: University of Rome La Sapienza

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive paralysis due to primary and secondary degeneration of motor neurons. In spite of extensive biomedical research, no curative therapy has yet been established. One of the primary targets of ALS is skeletal muscle, which undergoes profound functional changes as the disease progresses. To better understand how altered innervation interferes with muscle homeostasis during disease progression, we generated the first spatial transcriptomics dataset of skeletal muscle in the SOD1G93A mouse model of ALS. Using this strategy, we identified polyamine (PA) metabolism as one of the main altered pathways in affected muscle fibers. By establishing a correlation between the vulnerability of muscle fibers and the dysregulation of this metabolic pathway, we show that disrupting polyamine homeostasis causes impairments similar to those seen in ALS muscle. Finally, we show that restoration of polyamine homeostasis rescues the muscle phenotype in SOD1G93A mice, opening new perspectives for the treatment of ALS.

overall_design: Spatial Transcriptomics of Tibialis anterior of transiently denervated mice 3 days and 30 days post-denervation, used as biological replicates for the already published samples od D'Ercole et al., 2022

first: Veronica

last: Ruggieri

first: Silvia

last: Scaricamazza

first: Cristina

last: Parisi

first: Paolo

last: D'Angelo

first: Chiara

last: D'Ercole

first: Daisy

last: Proietti

last: Cappelletti

first: Alberto

last: Macone

first: Lozanoska-Ochser

last: Biliana

first: Marina

last: Bouchè

first: Lucia

last: Latella

first: Cristiana

last: Valle

last: Ferri

first: Lorenzo

last: Giordani

first: Luca

last: Madaro


title: Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development [RNA-seq]

status: Public on Dec 30 2024

city: Bethesda

first: Sakshi

last: Chauhan

state: Maryland

address: Building 6A, Room 2A11,6 Center Drive

institute: NICHD

summary: Variant histone H3.3 is thought to be critical for survival of many cells, since it is deposited in expressed genes, a feature different from core histones. For example, H3.3 deletion leads to embryonic lethality in mice.  However, requirement of H3.3 in later stage of development has remained unclear.  The aim of this work was to elucidate the role of H3.3 for development of myeloid lineage, important for innate immunity.  We conditionally knocked out (cKO) the H3.3 genes in myeloid progenitor cells differentiating into bone marrow derived macrophages (BMDMs). Progenitor cells lacking H3.3 were defective in replication, suffered from extensive DNA damage, and underwent apoptosis.  Surviving H3.3cKO cells expressed many interferon stimulated genes (ISGs) throughout differentiation.  Further, H3.3cKO BMDMs possessed chromatin accessible sites, and histone posttranslational modifications consistent with the gene expression profiles, Accordingly, H3.3cKO BMDMs retained general  nucleosomal structure genome wide.  In summary, H3.3 is required for proliferation of myeloid progenitor cells, but is in large part dispensable for differentiation of BMDMs.

overall_design:
RNA seq of WT and H3.3 cKO cells on day3, 5 and day7 of M-CSF induced differentiation.
RNA seq of WT and H3.3 cKO BMDM on day8 of M-CSF induced differentiation under untreated and IFNγ treated (12 hrs) conditions
RNA seq of WT and H3.3 cKO  peritoneal macrophages.
RNA seq of WT and cKO BMDMs under no antibody, control antibody and IFNAR1 antibody conditions.
RNA seq of WT, H3.3cKO and H3.3cKO:Sting KO BMDMs.
RNA seq of WT, H3.3cKO and H3.3cKO:Mavs KO BMDMs.
RNA seq of WT, H3.3cKO and H3.3cKO:Irf7 KO BMDMs.


title: Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development [ATAC-seq]

overall_design: ATAC seq with WT and H3.3 cKO BMDMs.


title: Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development [CUT&RUN]

overall_design:
CUT & RUN seq for histone variant H3.3 in H3f3b-HA tagged BMDM using HA antibody.
CUT & RUN seq for histone post translational modification H3K27ac in WT and H3.3 cKO BMDMs.
CUT & RUN seq for histone post translational modification H3K36me3 in WT and H3.3 cKO BMDMs.


title: Identification of adipo-osteoprogenitors in murine bone marrow

city: Chengdu

first: XUEYANG

last: LIAO

state: Sichuan

address: NO.14 3rd section of Renminnan Road

institute: Sichuan university

summary: The bone marrow in mammals house both hematopoietic and mesenchymal cells that are responsible for sustaining blood and bone cell production, respectively, throughout adult life. Although the hematopoietic system is well understood, the molecular identities, hierarchy of the marrow mesenchymal cells and their respective contribution to bone homeostasis are just beginning to be unraveled. By employing single-cell RNA sequencing (scRNA-seq) technology, we have discovered a subset of bone marrow mesenchymal cells co-expressing adiponectin (Adipoq) and osterix (Osx) which are traditionally considered adipocyte or osteoblast markers, respectively. Trajectory analyses predict the Adipoq+Osx+ bi-marker cells to be common progenitors for osteoblasts and marrow adipogenic lineage cells. Lineage tracing with Osx-CreERT2 or Adipoq-CreERT2 supports that the bi-marker cells give rise to both osteoblasts and adipocytes in vivo. Imaging studies localize the bi-marker cells to the endosteal bone niche. The data therefore support the hypothesis that Adipoq+Osx+ bi-marker cells are adipo-osteoprogenitors attuned to the physiological milieu in the bone marrow. The studies have shed light on the role of the adipo- osteoprogenitors in bone physiology and pathophysiology.

overall_design: Identification and illuminating of adipo-osteoprogenitors (Osteo-CAR) in murine bone marrow

first: Xueyang

last: Liao

first: Fanxin

last: Long


title: Asymmetric crosstalk between the BMP and TGFβ pathways resolves signaling ambiguity

city: Rehovot

first: Inbal

last: Eizenberg

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: The BMP and TGFβ signaling pathways control cellular fate decisions in diverse biological contexts, often playing opposing roles. Despite extensive knowledge of these pathways, understanding how cells respond to environments containing these opposing cues remains a challenge. Here, we systematically analyze the activation of these pathways under combinatorial signaling environments. We find that TGFβ ligands inhibit BMP signaling, while BMP ligands enhance TGFβ transcriptional response across concentrations, ligand variants, and cell types. This asymmetric crosstalk results in the activation of a TGFβ-biased transcriptional response, even under mixed signaling conditions, effectively reducing signal ambiguity, with implications for processes such as EMT. We show that this crosstalk originates downstream of SMAD proteins phosphorylation. Using mathematical models, we predict, and experimentally verify, that promiscuous interactions between SMAD proteins provide the mechanism for the observed crosstalk. Our findings challenge the canonical models, suggesting an active role for mediator proteins in determining biological responses.

overall_design:
To examine the activation of the BMP and TGFb pathways under complex signaling environment we established an NMuMG dual reporter cell line. Cells contained transcriptional reporters for BMP (Smad1/5/8 response element) controlling the expression of mCherry and TGFb (Smad2/3 response element) controlling the expression of mCitrine.
Gene expression profiles of the dual reporter cells were examined using bulk RNA-sequencing in cells cultured under four ligand conditions.
ChEC-seq was used to examine the genomic localization of SMAD1 and quantify its occupancy under different conditions in NMuMG cells transfected with SMAD1-MNASE

first: Johannes

middle: M

last: Auth

last: Eizenberg-Magar

first: Omer

last: Erez

last: Zachar

first: Merav

middle: D

last: Shmueli

last: Zigdon

first: Achinoam

last: Shoham

first: Vladimir

last: Mindel

first: Tsviya

last: Olender

first: Meytar

last: Asulin  Berrebi

first: Ariel

last: Tennenhouse

first: Neta

last: Bar-Hai

first: Rakefet

last: Ben-Yishay

first: Dana

last: Ishay-Ronen

first: Yaron

last: Antebi


title: Genotype and expression analyses of FTO and ALKBH5 in renal cell carcinoma cohort from MENA region

status: Public on Dec 29 2024

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

summary: RNA-modifying proteins significantly contribute to cancer progression. Fat mass and obesity-associated protein (FTO) and alkB homolog 5 RNA demethylase (ALKBH5) are RNA-demethylating proteins with opposing roles in renal cell carcinoma (RCC) across different populations. This study evaluates the genotype and expression of FTO and ALKBH5 in RCC patients from the Middle East and Northern Africa (MENA) region. Formalin-fixed paraffin-embedded samples from kidney biopsies of RCC patients and controls were analyzed through targeted DNA sequencing, whole transcriptome profiling, and immunohistochemistry.  Our findings indicated that the rs11075995T variant in FTO is linked to an increased risk of ccRCC. ALKBH5 and FTO protein expression were significantly downregulated in clear cell RCC (ccRCC) and chromophobe RCC (chRCC) but not in papillary RCC (pRCC) patients. In ccRCC, transcriptomic data revealed significant downregulation of FTO (log2FC = -5.2, q <0.001) and ALKBH5 (log2FC = -4.7, q <0.001) compared to controls. A significant negative correlation was found in ccRCC between FTO expression and T allele frequency in rs11075995, suggesting an impact on FTO expression. To our knowledge, this is the first study to examine FTO and ALKBH5 mutations and expression in RCC patients from the MENA region.

overall_design:
Formalin-fixed paraffin-embedded samples from kidney biopsies of RCC patients and controls were analyzed through targeted DNA sequencing to sequence common variant in FTO and ALKBH5 genes.
11 controls, 22  ccRCC, 6 chRCC, and 7 pRCC samples
Abbreviations: (RCC: Renal cell carcinoma, ccRCC: clear cell RCC, chRCC: chromphobe RCC, pRCC: papillary RCC)

first: Muna

last: Alhammadi

first: Burcu

middle: Y

last: Ilce

first: Poorna

last: Bhamidimarri

first: Amal

last: Bouzid

first: Nival

last: Ali

first: Reem

last: Alhamidi

first: Alaa

last: Hamad

first: Mona

last: Mahfood

first: Abdelaziz

last: Tlili

first: Iman

last: Talaat


title: Hi-C Calibration by Chemically Induced Chromosomal Interactions

status: Public on Dec 11 2024

city: State College

first: Yi

last: Li

address: 406 SOUTH FREAR, UNIVERSITY PARK

institute: Penn State University

summary: The genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and linearity, remain challenging to assess. Measuring these properties in vivo is difficult due to the heterogenous and dynamic nature of chromosomal interactions. Here, using Chemically Induced Chromosomal Interaction (CICI) method, we create stable intra- and inter-chromosomal interactions in G1-phase budding yeast across a broad range of contact frequencies. Hi-C analysis of these engineered cell populations demonstrates that static intra-chromosomal loops do not generate Topologically Associated Domains (TADs) and only promote 3D proximity within ~50kb flanking regions. At moderate sequencing depth, Hi-C is sensitive enough to detect interactions occurring in a few percent of cells. It also shows no inherent bias toward intra- versus inter-chromosomal interactions. Furthermore, we observe a linear relationship between Hi-C signal intensity and contact frequency. These findings illuminate the intrinsic properties of the Hi-C assay and provide a robust framework for its calibration.

overall_design: Hi-C experiments are performed on three yeast strains with intra-chromosomal CICI pairs and two yeast strains with inter-chromosomal CICI pairs. For each strain, 5 populations with different absolute contact frequencies between CICI loci are generated and their Hi-C contacts are measured.

first: Christoph

last: Fischer

first: Fan

last: Zou

first: Manyu

last: Du

first: Lu

last: Bai


title: scBiopsy-seq: a platform for temporal single-cell RNA-seq analysis

city: Xiamen

first: Xing

last: Xu

address: 422, Siming South Road

institute: Xiamen University

summary: The development of temporal single-cell RNA-seq (scRNA-seq) assay enabled us to systemically investigate the effects of various types of perturbations in a time course with single-cell resolution. However, the existing temporal scRNA-seq technologies have certain limitations in reliability, detection efficacy and detection diversity. In the current study, we develop scBiopsy-seq assay that combines a synergistic electroosmosis-electrophoresis extraction method for efficient RNA extraction and digital microfluidics with contamination-isolated hydrophobic interface for high-performance sample processing. scBiopsy-seq extracts the cytoplasm at well-controlled volume to detect >10K genes per extraction with 90% successful rate. Functional enrichment revealed that the genes robustly detected by scBiopsy-seq were associated to diverse biological processes, demonstrating its superb diversity of detection. scBiopsy-seq can perform the sequential extraction of the cytoplasm from the same cell multiple times, which allows us to associate the cell phenotypic responses with its transcriptic dynamics. We employed scBiopsy-seq to analyze the temporal response to BRD4 inhibition with single-cell resolution of SW480 cells and identified the key roles of fatty acid oxidation in this biological process. scBiopsy-seq with comparable data quality with scRNA-seq will dramatically expand the application of temporal scRNA-seq towards a broader spectrum of biological research.

sample_organism:
Danio rerio
Homo sapiens
Mus musculus

platform_organism:
Danio rerio
Homo sapiens
Mus musculus

overall_design: scRNA-seq profiles of different cell lines

first: Linfeng

last: Cai

first: Shiyan

last: Lin

first: Minghao

last: Qiu

first: Li

first: Fuyuan

first: Jiajia

last: Liu

first: Yuning

first: Dianyi

last: Liang

first: Shanshan

first: Jianhua

last: Guo

first: He

last: Huang

first: Chaoyong

last: Yang

first: Jin


title: Comparision of Differential methylation between Control and mutant Dnmt3a

status: Public on Dec 17 2024

city: Saint Louis

first: Andrew

middle: Lee

last: Young

state: MO

address: 660 South Euclid Ave

department: Medicine

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing

summary: Dnmt3a is the most recurrently mutated gene in clonal hematopoiesis (CH), and it is a critical regulator of hematopoietic stem cells (HSCs). Conditional deletion of Dnmt3a in mouse HSC results in enhanced self-renewal but impaired differentiation. Dnmt3a encodes for a de novo DNA methyltransferase enzyme but both mouse and human cells with loss of Dnmt3a show minimal change in DNA methylation levels which do not correlate with gene expression differences. To understand if there are methylation differences between control and mutant (R878H) Dnmt3a, we are performing WGBS.

overall_design: To investigate the differential DNA methylation in hematopoietic cells expressing Dnmt3a mutant with reduced DNA methyltransferase activity, we established Cre-mediated knock in mouse model. Competitive HSC transplantation was performed.  Cells were isolated 18-weeks post-transplant for analysis of DNA methylation patterns by whole genome bisulfite sequencing.

first: Infencia

middle: X

last: Raj

first: Won

last: Koh

first: Jessica

last: Harrison

first: Christine

middle: R

last: Zhang

first: Barbara

last: Soares

first: Aishwarya

last: Krishnan

first: Hassan

last: Bjeije

first: Tyler

last: Parsons

first: Wentao

last: Han

first: Ting

last: Wang

first: Luis

last: Batista

first: Grant

last: Challen


title: Amphiregulin Upregulated in Esophageal Squamous Cell Carcinoma Cells upon Direct Contact with Cancer-Associated Fibroblasts

status: Public on Dec 04 2024

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
Cancer-associated fibroblasts (CAFs) are a pivotal component of the tumor microenvironment, significantly contributing to the progression of esophageal squamous cell carcinoma (ESCC). Direct co-culture of human bone marrow-derived mesenchymal stem cells (MSCs), one of the origins of CAFs, with ESCC cell line, led to increased amphiregulin (AREG) expression and secretion in the ESCC cells. Consequently, the expression and phosphorylation of the AREG receptor EGFR were upregulated in co-cultured ESCC cells. Moreover, AREG treatment enhanced ESCC cell survival and migration through the EGFR-Erk/p38 signaling pathway.
Immunohistochemical analysis of AREG using human ESCC tissues showed a positive correlation between the intensity of AREG expression in tumor invasive front and the expression level of the CAF marker FAP. Furthermore, bioinformatics database analysis confirmed a significant upregulation of AREG expression in ESCC tissues compared to normal tissues. These findings suggest that AREG is involved in CAF-mediated ESCC progression and could be a novel therapeutic target for ESCC.

overall_design: MSCs and ESCC cells were seeded in the same dish and co-cultured for 4 days. Monocultures of both cell types served as controls. Following co-culture or monoculture, cells were washed with phosphate-buffered saline (FUJIFILM Wako Pure Chemical Corporation) and detached themselves from the dish using trypsin (FUJIFILM Wako Pure Chemical Corporation) treatment. The harvested cells were then mixed with anti-CD326 (epithelial cell adhesion molecule; EpCAM) microbeads (130-061-101; Miltenyi Biotec) and subjected to magnetic separation using the autoMACS Pro Separator (Miltenyi Biotec) to isolate high-purity tumor cells. cDNA microarray analysis was performed on monocultured and co-cultured TE-9 cells.

first: T

last: Nakanishi

first: YI

last: Koma


title: Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes

status: Public on Nov 30 2024

city: Seville

first: Marta

middle: Silvia

last: Magri

address: Carretera de Utrera km1

institute: Centro Andaluz de Biología del Desarrollo

sample_organism:
Strongylocentrotus purpuratus
Patiria miniata


title: Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes [Hi-C]

summary: we generated new reference genome assemblies for two species belonging to two different echinoderm classes: the bat sea star Patiria miniata and  the purple sea urchin Strongylocentrotus purpuratus

platform_organism:
Strongylocentrotus purpuratus
Patiria miniata

overall_design: Hi-C assays in wild-type sea star and sea urchin whole embryos at late gastrula

first: Marta Silvia

first: Danila

last: Voronov

first: Saoirse

last: Foley

first: Pedro Manuel

last: Martínez-García

first: Martin

last: Franke

first: Gregory A

last: Cary

first: José M

last: Santos-Pereira

first: Carolyn

last: Ku

first: Claudia

last: Cuomo

first: Manuel

last: Fernández-Moreno

first: Alejandro

last: Gil-Galvez

first: Rafael D

last: Acemel

first: Periklis

last: Paganos

first: Jovana

last: Ranđelović

first: Maria Lorenza

last: Rusciano

first: Panos N

last: Firbas

first: Veronica F

last: Hinman

first: Maria Ina

last: Arnone

first: Ignacio

last: Maeso

first: José

last: Gómez-Skarmeta


title: Developmental dynamics of sea urchin and sea star cis-regulation and the evolution of echinoderm genome organization - ATAC-seq

first: Marta

last: Magri

summary: We identified conserved cis-regultaory elements based on their dynamic chromatin accessibility over the gastrula-larva stages

overall_design: ATAC-seq assays in wild-type sea urchin whole embryos

first: Marta Silvia

first: Danila

last: Voronov


title: An Omics approach on Marchantia polymorpha single FERONIA and MARIS homologs confirms links between cell wall integrity and abscisic acid

status: Public on Nov 26 2024

city: Sophia Antipolis

first: Aurélien

last: Boisson-Dernier

address: 400 route des Chappes, BP 167

department: SPE

country: France

institute: INRAE

summary: Plant cells are surrounded by an extracellular cell wall that shields them from their abiotic and biotic environment. To coordinate their growth with their cell wall status, they have developed cell wall integrity mechanisms at the center of which lies the transmembrane Malectin-like receptor kinase FERONIA (FER). FER controls a myriad of plant developmental processes including sexual reproduction, cell growth and morphogenesis, often intersecting with phytohormones-dependent pathways such as abscisic acid (ABA) or plant immunity. Interestingly, FER and its downstream receptor-like cytoplasmic kinase MARIS (MRI) were shown to cooperate similarly in the control of root hair and rhizoid integrity for the vascular model Arabidopsis and the early diverging bryophyte model Marchantia polymorpha, respectively. Here, we carried out comparative transcriptomics and proteomics approach on Mpfer-1 and Mpmri-1 knock-down mutant plants and the wild-type strains Tak-1 and Tak-2. Our -omics analyses revealed that globally, MpFER and MpMRI largely cooperate to negatively regulate transcriptional and translational networks in particular those related to plant defense and ABA responses. Moreover, Mpfer-1 plants were found to be hypersensitive to ABA-dependent growth inhibition indicating that FER’s function of negatively regulating ABA-related growth responses is conserved between bryophytes and vascular plants.

overall_design: To reveal pathways that could be regulated by the ancestral MpFER/MpMRI module or alternative compensatory ones that are up-regulated in the absence of the module in Marchantia, comparative transcriptomic (RNA-seq)  analyses of Mpfer-1 (male) and Mpmri-1 (female) lines with short bursting rhizoids and their respective wild-type male (Tak-1) and female (Tak-2) strains with intact rhizoids were carried out. For this purpose, 3-week-old Marchantia thalli grown on cellophane membranes were collected and RNA were extracted and submited to RNAseq.

first: Timothy

last: Jobe


title: Single-Cell Transcriptomic Analysis Reveals Differential Cell Subpopulations and Distinct Phenotype Transition in Normal and Acute Dissected Ascending Aorta

city: Shanghai

first: Jing

last: Zhang

address: No.241, west huaihai road, Xuhui district

department: Department of Cardiovascular Surgery

institute: Shanghai Chest Hospital, Shanghai Jiao Tong University

summary:
Background: Acute thoracic aortic dissection (ATAD) is a fatal condition characterized by tear of intima and formation of false lumen whereby leading to the rupture of aorta. To better understand the potential mechanism of ATAD, we analyzed characterization of different cell types between ATAD and control group and predicted interactions among different cell types which might promote the progression of ATAD.
Methods: Single-cell RNA sequencing (scRNA-seq) was performed including 5 patients with ATAD and 4 healthy controls. Cells were digested from ascending aortic tissues and subpopulations of most cell types were identified on the basis of scRNA-seq data. The gene expression profiles of each cell type and related changes between ATAD and control group were analyzed via bioinformatic analysis. We also predicted potential interaction among different cell types and verified the results by immunohistochemistry (IHC) and immunofluorescence (IF).
Results: We got 8 cell types from human ascending aorta and 50 subpopulations were identified after re-clustering including vascular smooth muscle cells (VSMCs), endothelial cells, fibroblasts, neutrophils, monocytes and macrophages. Higher proportion of synthetic VSMCs, dysfunctional neutrophils and monocytes were seen in ATAD group compared with control group. Next, we predicted cell differentiation trajectory of VSMCs, fibroblasts and neutrophils via CytoTRACE, then identified subpopulations with higher differentiation potential. Moreover, the hub genes of VSMCs, fibroblasts and neutrophils were examined by weighted gene co-expression network analysis. Further analysis revealed that six transmembrane epithelial antigen of prostate 4 metalloreductase (STEAP4) might be a new marker for isolation of synthetic VSMCs by verification with IHC and IF. We also found synthetic VSMCs-derived C-X-C motif chemokine ligand 12 (CXCL12) might interact with neutrophils and fibroblasts via combination with C-X-C motif chemokine receptor 4 (CXCR4) and atypical chemokine receptor 3 (ACKR3), respectively, which might recruit neutrophils and induce transdifferentitation of FBs into synthetic VSMCs.
Conclusion: In this study, we demonstrated integrative composition of different cell types in normal and dissected human ascending aorta and identified a new marker favorable to isolation of synthetic VSMCs. Furthermore, we also proposed a potential mechanism that synthetic VSMCs could interact with neutrophils and fibroblasts via CXCL12-CXCR4/ACKR3 axis whereby deteriorating the progression of ATAD. In total, these findings in our study might provide new insights to better understand the development and progression of ATAD.

overall_design: Examination of transcriptomic characteristics of normal and acute dissected ascending aortas

first: Yubin

last: He

first: Haizhen

last: Jin

first: Guanxin

first: Chong

last: Wang

first: Busheng

first: Wenrui

last: Ma

first: Jianfeng

first: Jie

last: Xing

first: Xiaobin

first: Yangyang

first: Huangdong

last: Dai

first: Naishi

last: Zhao

first: Dan

last: Zhu


title: Investigating the role of Paf1 in transcription by RNA polymerase I

status: Public on Nov 24 2024

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

summary: Polymerase-associated factor 1 complex (Paf1C) has been identified to promote transcription by Pols I and II and is conserved across eukaryotes. This transcription factor has been well-studied for Pol II, but its role in transcription by Pol I has not been fully characterized. Therefore, the goal of this study was to use a high-resolution technique, native elongating transcript sequencing (NET-seq), to investigate the effect of the loss of two of the five Paf1C subunits (Paf1 and Cdc73) on Pol I occupancy in yeast. Most notably, we found that in both paf1D and cdc73D mutants, there was a significant reduction in Pol I occupancy at the 5’ end of the rDNA template as compared to WT yeast. Overall, our results suggest that Paf1C is an important transcription elongation factor for Pol I.

overall_design: NET-seq libraries were prepared for two replicates each of WT, cdc73△, and paf1△ yeast.

first: Jinger

last: Yang

first: David

last: Schneider