title: Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAs (RNA-Seq)

first: Anastasia

last: Hains

summary: Rhabdoid tumors, characterized and driven by the loss of the mSWI/SNF (mammalian SWItch/Sucrose Non-Fermentable) subunit SMARCB1, are very aggressive childhood cancers that can arise in the brain, the kidney, or soft tissues. Cell lines derived from these tumors are specifically sensitivity to the translation inhibitor homoharringtonin (HHT). Having recently demonstrated mSWI/SNF roles in translation, we assessed SMARCB1 potential roles in translation in rhabdoid tumor cells. We first revealed by cell viability assays that rhabdoid tumor cells’ sensitivity to HHT were dependent on the absence of SMARCB1. Polysome profiling and immunoprecipitation experiments demonstrated the interaction of SMARCB1 with the translation machinery. Global translation assays and ribosome profiling experiments further revealed that SMARCB1 re-expression increased global translation and altered translation efficiency of specific mRNAs. Most regulated mRNAs presented an increased translation efficiency and were involved in differentiation. In comparison with the entire transcriptome, these mRNAs presented a longer coding sequence and were enriched in GC. Finally, we demonstrated that SMARCB1 re-expression increased cytoplasmic localization of these mRNAs and that gene encoding these transcripts were bound by SMARCA4 and SMARCC1. In conclusion, this study reveals that the loss of SMARCB1 in rhabdoid tumors has specific consequences on mRNAs translation with potential to unveil new dependencies.

overall_design: G401 rhabdoid kidney tumor cells which carries either Tet-On dox-inducible SMARCB1 or GFP were treated with either 0.1ug/mL doxycycline or equivalennt DMSO for 12hrs, followed by harvesting for experiments

first: L

last: Nguyen

first: A

first: M

middle: O

last: Azizzanjani

last: Dalsass

first: B

last: Farooqee

first: Y

last: Lu

first: P

last: Jackson

first: C

last: Van Rechem


title: Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAsn (Ribo-Seq)

status: Public on Oct 31 2024

city: Stanford

email: hainsa@uchicago.edu, hains@stanford.edu

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

middle: E

middle: K


title: Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair.

status: Public on Oct 30 2024

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary: Analysis of single cell RNA-seq, CITE-seq data and bulk RNA-seq data on cells isolated from the livers of mice following PBS and APAP (paracetamol/acetaminophen) administration. Spatial Transcriptomics analysis was performed using 10x Visium platform on mouse livers 48hrs post PBS or APAP administration. We also analysed single cell RNA-seq data on CD64+F4/80+ macrophages isolated from the livers of Trem2 fl/fl mice and CD64CRE Trem2 fl/fl mice.

overall_design:
Single cell RNA Seq = Total liver cells derived from mice following PBS and APAP administration and CD64+F4/80+ macrophages from Trem2 fl/fl mice and CD64CRE Trem2 fl/fl mice.
Bulk RNA seq on KCs and LAM-like KCs isolated from livers 48hr post PBS or APAP administration
10 Visium Spatial Seq = mouse liver 48h post PBS or APAP administration.

first: Federico

middle: F

last: De Ponti

first: Anna

last: Bujko

first: Zhuangzhuang

last: Liu

first: Paul

middle: J

last: Collins

first: Sara

last: Schuermans

first: Christian

last: Maueroder

first: Seraja

last: Amstelveen

first: Tinne

last: Thoné

first: John

middle: G

last: McKendrick

first: Pieter

middle: A

last: Louwe

first: Ana

last: Sànchez Cruz

first: Wouter

last: Saelens

first: Kylie

middle: P

last: Matchett

first: Kathryn

last: Waller

last: Zwicker

first: Aimée

last: Buglar-Lamb

first: Bavo

last: Vanneste

first: Fleur

last: Parmentier

first: Mushida

last: Binte Abdul Latib

first: Anneleen

last: Remmerie

first: Lenard

last: Kertesz

first: Anneke

last: Kremer

first: Jeremy

last: Verbeke

first: David

last: Højland Ipsen

first: Dominik

last: Reinhard Pfister

first: Zhaoyuan

first: Martin

last: Guilliams

first: Neil

middle: C

last: Henderson

first: Kodi

last: Ravichandran

first: Pedro

last: Marques

first: Charlotte

last: Scott


first: Liesbet

last: Martens

first: Federico

last: De Ponti

first: Anna

last: Bujko

first: Zhuangzhuang

last: Liu

first: Paul

last: Collins

first: Sara

last: Schuermans

first: Christian

last: Maueroder

first: Seraja

last: Amstelveen

first: Tinne

last: Thoné

first: John

last: McKendrick

first: Pieter

last: Louwe

first: Ana

last: Sànchez Cruz

first: Wouter

last: Saelens

first: Kylie

last: Matchett

first: Kathryn

last: Waller


title: Structural and molecular properties of inclusion bodies of mumps virus

city: Bunkyo-ku

first: Hiroshi

last: Katoh

state: Tokyo

country: Japan

institute: The University of Tokyo

summary: Viral RNA synthesis of mononegaviruses occurs in the cytoplasmic membrane-less organelles called as inclusion body (IB). Here, we reported that the IBs of mumps virus (MuV), which is the causative agent of mumps and belongs to the family Paramyxoviridae, had properties of liquid organelles formed by liquid-liquid phase separation. Super-resolution microscopic analysis of the MuV IBs demonstrated that nucleocapsid and phospho-(P) proteins formed the cage-like structure and that viral polymerase was in a reticular pattern and partially co-localized with viral mRNA. In addition, we characterized host RNAs localized in the MuV IBs by a spatial transcriptome analysis and found that G-quadruplex motif sequences containing RNAs (G4-RNAs) were concentrated. In vitro phase separation assay showed that the G4-RNAs interacted with the P protein and enhanced condensation in the P droplets. Taken together, our data show that MuV generates the IBs with a characteristic cage-like structure and host G4-RNAs play an important role in the formation of MuV IBs

overall_design: To characterize host RNAs recruited into the MuV IBs, cDNA libraries were prepared from each sample for IB regions, cytoplasmic regions except for IBs, and cytoplasm of uninfected cells using PIC (Photo Isolation chemistry). The sequences were determined by NGS (Next-Generation Sequencing). Based on the expression profiles obtained from each group, RNAs that were significantly concentrated in the MuV IBs were identified.

first: Ryuichi

last: Kimura

first: Shinya

last: Oki

first: Yasuyuki

last: Ohkawa


title: m6Am sequesters PCF11 to suppress premature termination and drive neuroblastoma differentiation [fPAR-CLIP]

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

country: China

institute: Shenzhen Bay Laboratory

summary: N6,2’-O-dimethyladenosine (m6Am) is an abundant mRNA modification that impacts multiple diseases but its function remains controversial since the m6Am reader is unknown. Using quantitative proteomics, we identified transcriptional terminator PCF11 as a m6Am-specific reader. Direct quantification of mature versus nascent RNAs reveals m6Am does not regulate mRNA stability but promotes nascent transcription. Mechanistically, m6Am functions by sequestering PCF11 away from proximal RNA Pol II. This suppresses PCF11 from dissociating Pol II near transcription start sites, thereby promoting full-length transcription of m6Am-modified RNAs. m6Am’s unique relationship with PCF11 means m6Am function is enhanced when PCF11 is reduced, which occurs during all-trans-retinoic-acid (ATRA) induced neuroblastoma-differentiation therapy. Here, m6Am promotes expression of ATF3, a repressor of the neuroblastoma biomarker MYCN. Depleting m6Am suppresses MYCN-repression in ATRA-treated neuroblastoma and maintains their tumour stem-like properties. Collectively, we characterize m6Am as an anti-terminator RNA modification that suppresses premature termination and modulates neuroblastoma therapeutic response.

overall_design: UV crosslinking of s4U labelling of RNA to protein, followed by immunoprecipitation and RNA sequencing

first: W

middle: S

last: Sho Goh


title: NF-kB associated markers of PD-1 immunotherapy response in early and metastatic triple negative breast cancer

city: Providence

first: Payton

last: De La Cruz

state: Rhode Island

address: 200 Chestnut St

department: Division of Biology and Medicine

institute: Brown University

overall_design:
770 genes as well as pathways were analyzed in E0771-derived mouse tumors treated with monoclonal antibodies targeting PD-1, LAG-3, or TIM-3, or IgG isotype control
A total of 12 tumor samples were included in this experiment; 3 mice treated with anti-PD-1 therapy, 3 mice treated with anti-LAG-3, 3 mice treated with anti-TIM-3,  and 3 mice treated with IgG isotype control. Treatments were administered via IP injection every 4 days for a total of 3 treatments. Mice and tumors were collected one day following the final treatment.

first: Nicole

last: James

first: Christoph

last: Schorl


title: Single-cell transcriptome analysis reveals CD34 as a marker of human sinoatrial node pacemaker cardiomyocytes [CITE-seq]

city: Toronto

first: Stephanie

last: Protze

state: Ontario

address: 101 College Street

department: McEwen Stem Cell Institute

country: Canada

institute: University Health Network

summary: The sinoatrial node regulates the heart rate throughout life. Failure of this primary pacemaker results in life-threatening, slow heart rhythm. Despite its important function, the cellular and molecular composition of the human sinoatrial node is not resolved. Particularly, no cell surface marker to identify and isolate sinoatrial node pacemaker cells has been reported. Here we use single-nuclei/cell RNA sequencing of fetal and human pluripotent stem cell-derived sinoatrial node cells and show that they consist of three subtypes of pacemaker cells, including Core Pacemaker, Sinus Venosus, and Transitional Cells. Our study identifies a host of sinoatrial node pacemaker markers including MYH11, BMP4, and the cell surface antigen CD34. We demonstrate that sorting for CD34+ cells from stem cell differentiation cultures enriches for sinoatrial node cells with a functional pacemaker phenotype. This sinoatrial node pacemaker cell surface marker is highly valuable for stem cell-based disease modelling, drug discovery, cell replacement therapies, as well as the delivery of therapeutics to sinoatrial node cells in vivo using antibody-drug conjugates.

overall_design: Examining the heterogenity and global transcriptome of the cells present in the endogenous sinoatrial node and human pluripotent stem cell derived sinoatrial node-like pacemaker cells.

first: Amos

last: Lim

first: Delaram

last: Pouyabahar

first: Mishal

last: Ashraf

first: Kate

last: Huang

first: Michelle

last: Lohbihler

first: Brandon

middle: M

last: Murareanu

first: Matthew

middle: L

last: Chang

first: Maggie

last: Kwan

first: Faisal

last: Alibhai

first: Thinh

last: Tran

first: Amine

last: Mazine

first: Michael

last: Laflamme

first: Gary

middle: D

last: Bader

first: Zachary

last: Laksman


title: m6Am sequesters PCF11 to promote full-length transcription [anabolicSLAM]

first: Wee Siong Sho

last: Goh

summary: RNA modifications regulate how RNAs metabolize and function to impact development and diseases. N6,2’-O-dimethyladenosine (m6Am) is one such modification and despite being abundant, m6Am function remains unclear. Here, we identified cleavage and polyadenylation factor, PCF11 as a m6Am-specific binding protein. Direct quantification of mature versus nascent RNAs revealed that m6Am does not regulate mRNA stability but promotes transcription of nascent RNAs. m6Am caused RNA Polymerase II (Pol II) to be more processive when transcribing m6Am-modified RNAs. Rather than PCF11 regulating m6Am-modified RNA, m6Am sequesters PCF11 away from proximal Pol II, suppressing premature dissociation of elongating Pol II and promoting Pol II full-length transcription of m6Am-modified RNAs. This establishes a mechanism through which an RNA modification regulates transcription.

overall_design: siRNA treatment and s4U labelling of nascent RNA for 3'end mRNA sequencing

first: Wee Siong


title: Single-cell transcriptome analysis reveals CD34 as a marker of human sinoatrial node pacemaker cardiomyocytes [hPSC_SAN]

first: Stephanie


title: m6Am sequesters PCF11 to promote full-length transcription [PCT]

overall_design: Enrich for PCT by siRNA knockdown of Dis3, enrichment of nuclear RNA and 3'end mRNA sequencing


title: m6Am sequesters PCF11 to promote full-length transcription [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for PCF11 in HEK293T cells.


title: Comparison of FACS-isolated mammary epithelial populations (CD49f/CD61)

city: South San Francisco

first: Jackson

last: Liang

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

summary: To validate the CD49f/CD61 flow cytometry panel for resolving the three major mammary epithelial lineages, mammary epithelial cells from MMTV-Cre mice were collected by FACS and analyzed by RNA-seq for comparison to previously published single-cell RNA-seq studies, which non-biasedly identified the three major lineages: basal, alveolar progenitor (AP), and hormone-sensing luminal (HSL) cells.

overall_design: Six nulliparous MMTV-Cre animals were raised to 12 weeks of age. Mammary tissues were collected from these animals, then minced and treated with collagenase/hyaluronidase/DNaseI for 1hr at 37C. Then, resulting parenchymal cells were isolated by centrifugation and further digested by dispase and trypsin successively. Cells were pipetted through a 40um filter, then blocked and stained with antibodies for FACS. FACS markers: CD49f, CD61, EpCAM, Lin (CD31/CD45/Ter119). By FACS, individual populations were isolated - basal cells, alevolar progenitors (AP, also called 'luminal progenitors'), and hormone-sensing luminal cells (HSL, HR+ population, also called 'mature luminal cells'). See Sample Characteristics 'cell population' field for FACS markers per cell type.

first: Ciara

last: Metcalfe

first: Marc

last: Hafner


title: Endothelial-secreted Endocan protein acts as a PDGFR alpha ligand and regulates vascularity, radioresistance, and regional phenotype in glioblastoma [2]

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: One of the hallmarks of glioblastoma (GBM) is extensive neovascularization. In addition to supplying blood and nutrients, vascular endothelial (VE) cells provide trophic support to GBM cells via paracrine signaling, the precise mechanisms of which are being unraveled. Here, using patient-derived GBM and VE cells as well as orthotopic GBM mouse models, we report that Endocan (ESM1), an endothelial-secreted proteoglycan, confers enhanced proliferative, migratory, and angiogenic properties to GBM cells and regulates their spatial identity. Mechanistically, Endocan exerts at least part of its functions via direct binding and activation of the PDGFRA receptor. Subsequent downstream signaling enhances chromatin accessibility of the Myc promoter and upregulates Myc expression inducing highly stable phenotypic changes in GBM cells. Furthermore, Endocan confers a radioprotection phenotype in GBM cells, both in vitro and in vivo. Inhibition of Endocan-PDGFRA signaling with ponatinib increases survival in the Esm1 wild-type but not in the Esm1 knock-out mouse GBM model. Our findings identify Endocan and its downstream signaling axis as a potential target to subdue the recurrence of GBM and further highlight the importance of vascular to tumor cell signaling for GBM biology.

overall_design: 1051 GBM cells were treated with either esm1/endocan (10ng/ml) or conditioned media (CM) from HBEC cells and incubated for 3 days, cells were then irradiated with 8Gy dose of gamma radiaiton. Cells were collected on Day 5 after radiation. RNA was extracted and we then performed RNAseq of these samples and performed gene expression analyses.

first: Soniya

last: Bastola

first: Marat

last: Pavlyukov

first: Fuying

last: Gao

first: Rik

first: Harley

last: Kornbmum


title: Endothelial-secreted Endocan protein acts as a PDGFR alpha ligand and regulates vascularity, radioresistance, and regional phenotype in glioblastoma

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

overall_design: Refer to individual Series


title: Endothelial-secreted Endocan protein acts as a PDGFR alpha ligand and regulates vascularity, radioresistance, and regional phenotype in glioblastoma [1]

overall_design: There are three groups: Control only (n=4), 1079 cells treated with 10ng/ml Endodcan (n=4) or 10ng/ml of PDGFBB for 72 hours. We then performed RNAseq of these samples and performed gene expression analyses.


title: Gene expression profile at single cell levels from glomerulus in wild type (WT) and inhibitor of MyoD family A(I-mfa) knock out mice

city: Fort Worth

first: Rong

last: Ma

state: TX

address: 3500 Camp Bowie Blvd

department: Integrative Physiology

institute: University of North Texas Health Science Center

summary:
Background: Inhibitor of MyoD family A (I-mfa) is a cytosolic protein and its function in kidney is unknown. In this study we used scRNAseq technique to study the diversity at single cell levels in kidney glomerulus from both wild types and I-mfa  knockout mice seperately.

Translational Project Award from American Heart Association (20TPA35500045, to R. Ma)

overall_design: 4 Wild type (WT) mice and 4 I-mfa knock out (I-mfa KO) mice (12-13 weeks) were used for the study. All kidneys from WT mice and KO mice were pooled, respectively for sample preparation so that sufficient cell numbers could be obtained for single cell analysis. Single cells from kidney glomerulus in each mouse were isolated. Cell number count in the final cell suspension was achieved using a hemocytometer. Additionally, cell viability (>80% for both groups) was examined and determined using trypan blue staining. The cell suspension from both the WT and KO groups were further evenly divided into 3 aliquots of 100 μl each with a concentration of 600 cells/μl and 900 cells/μl, respectively. single cells in each sample were analyzed by scRNAseq.

first: Yu

last: Tao

first: Muyi

last: Liu


title: Evaluating an Esr1-mutant novel cell population emerging upon ERα-antagonism by bulk ATAC-seq

summary: To examine the effects of ERα antagonism (giredestrant) on Esr1-wildtype and Esr1-mutant mammary glands, animals were treated with hormone pellets (E2, P4), then dosed daily with vehicle (MCT) or giredestrant (30 mg/kg, p.o.) for four days. Following dosing, individual mammary epithelial cell populations were FACS-isolated and sequenced.

overall_design: To examine the effects of ERα antagonism (giredestrant) on Esr1-wildtype and Esr1-mutant mammary glands, animals were treated with hormone pellets (E2, P4), then dosed daily with vehicle (MCT) or giredestrant for four days. 51 samples are included, 3 biological replicates per condition.


title: Transcriptomic landscape of mammalian ventral pallidum at single-cell resolution

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

summary: The ventral pallidum (VP) is critical for motivated behaviors. While contemporary work has begun to elucidate the functional diversity of VP neurons, the molecular heterogeneity underlying this functional diversity remains incompletely understood. We used snRNA-seq and in situ hybridization to define the transcriptional taxonomy of VP cell types in mice, macaques, and baboons. We found transcriptional conservation between all three species, within the broader neurochemical cell types. Unique dopaminoceptive and cholinergic subclusters were identified and conserved across both primate species but had no homolog in mice. This harmonized consensus VP cellular atlas will pave the way for understanding the structure and function of the VP and identified key neuropeptides, neurotransmitters, and neuro receptors that could be targeted within specific VP cell types for functional investigations.

sample_organism:
Macaca mulatta
Papio anubis
Mus musculus

overall_design: VP tissues were dissected from C57Bl6J mice, olive baboons, and rhesus macaque. Nuclear suspension was isolated by FACS based on 7-AAD signal and processed by 10X Genomics.

first: Lisa

last: Fang

first: Michelle

middle: R

last: Lynch

first: Chang

last: Xu

first: Hannah

last: Hahm

first: Yufen

last: Zhang

first: Monique

last: Heitmeier

first: Vincent

last: Costa

first: Vijay

last: Samineni

first: Meaghan

last: Creed


title: NG2/CSPG4 regulates the transcriptional profile of mandibular fibrochondrocytes during serum starvation [RNAseq-immortalized cells]

city: Chicago

first: David

last: Reed

state: IL

address: 801 South Paulina Street

department: Department of Oral Biology

institute: University of Illinois at Chicago

summary: Changes in the mechanical homeostasis of the temporomandibular joint (TMJ) can lead to the initiation and progression of degenerative arthropathies such as osteoarthritis (OA). Cells sense and engage with their mechanical microenvironment through interactions with the extracellular matrix. In the mandibular condylar cartilage, the pericellular microenvironment is composed of type VI collagen. NG2/CSPG4 is a transmembrane proteoglycan that binds with type VI collagen, and has been implicated in the cell stress response. The objective of this study is to define the role of NG2/CSPG4 in the cell stress response during serum starvation. To evaluate the role of the NG2/CSPG4, primary mandibular fibrochondrocytes from c57 BL/6 J and NG2/CSPG4 knockout mice (mixed sex) were cultured in normal and serum starvation conditions. To evaluate the role of the NG2/CSPG4 ectodomain, primary mandibular fibrochondrocytes were immortalized using hTERT. CRSIPR/Cas9 was used to truncate the NG2/CSPG4 ectodomain by targeting the type VI collagen binding region. Normal culture conditions were AMEM growth media supplemented with 10% FBS, penicillin, L-Glut, and plasmocin.  Serum starvation conditions were Optimem media with no FBS, supplemented with penicillin, L-Glut, and plasmocin. Serum starvation was induced for 24 hours. RNA from the cells was isolated using the RNeasy kit (Qiagen). poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system. Sequencing was done by LC Sciences. These data illustrate that in serum starvation conditions, NG2/CSPG4 knockout mandibular fibrochondrocytes and targeted truncation of the NG2/CSPG4 ectodomain alters the transcriptional profile of the cell, promoting biological processes associated with cell stress, migration, and ossiciation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data comparing c57/BL6J and NG2/CSPG4 knockout primary mandibular fibrochondrocytes collected from 10-14 day old pups in normal and serum starvation conditions and immortalized primary mandibular fibrochondrocytes with and without genetic truncation of the ectodomain in normal and serum starvation conditions.


title: Single-cell transcriptome analysis reveals CD34 as a marker of human sinoatrial node pacemaker cardiomyocytes [fetal SAN]

first: Stephanie

last: Protze

first: Amos

last: Lim

first: Delaram

last: Pouyabahar

first: Mishal

last: Ashraf

first: Kate

last: Huang

last: Lohbihler

first: Brandon

last: Murareanu

first: Matthew

last: Chang

first: Maggie

last: Kwan

first: Faisal

last: Alibhai

first: Thinh

last: Tran

first: Amine

last: Mazine

first: Michael

last: Laflamme

first: Gary

last: Bader

first: Zachary

last: Laksman


title: Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair.

first: Liesbet

last: Martens

first: Federico

last: De Ponti

first: Anna

last: Bujko

first: Zhuangzhuang

last: Liu

first: Paul

last: Collins

first: Sara

last: Schuermans

first: Christian

last: Maueroder

first: Seraja

last: Amstelveen

first: Tinne

last: Thoné

first: John

last: McKendrick

first: Pieter

last: Louwe

first: Ana

last: Sànchez Cruz

first: Wouter

last: Saelens

first: Kylie

last: Matchett

first: Kathryn

last: Waller

last: Zwicker

first: Aimée

last: Buglar-Lamb

first: Bavo

last: Vanneste

first: Fleur

last: Parmentier

first: Mushida

last: Binte Abdul Latib

first: Anneleen

last: Remmerie

first: Lenard

last: Kertesz

first: Anneke

last: Kremer

first: Jeremy

last: Verbeke

last: Højland Ipsen

first: Dominik

last: Reinhard Pfister

first: Zhaoyuan

first: Martin

last: Guilliams

first: Neil

last: Henderson

first: Kodi

last: Ravichandran

first: Pedro

last: Marques

first: Charlotte

last: Scott


title: ATAC-seq of Keratinocytes and Langerhans cells in normal and hyperproliferative epithelium

city: Brisbane

first: Janin

last: Chandra

state: Queensland

address: 37 Kent st., Woolloongabba

department: Faculty of Medicine

country: Australia

institute: The University of Queensland

summary: In an HPV-induced hyperplastic epithelium mouse model, hyperproliferative Keratinocytes (KCs) showed reduced Interleukin 34 (IL34) expression and chromatin accessibility, associating disturbing cell-cell interaction and immune response genes. Correspondingly, Langerhans cells (LCs) exhibited altered chromatin accessibility, including increased accessibility of IL34's receptor - the colony-stimulating factor 1 receptor (Csf1r) and reduced accessibility in antigen uptake and presentation genes.

overall_design: Bulk the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) on Keratinocytes and Langerhans cells sorted from single cell suspension derived from the epithelium of a murine model of squamous epithelial hyperplasia and the wildtype control. Epithelial samples from 4 independent experiments.

first: Kevin

last: Gillinder

first: Ian

middle: H

last: Frazer

first: Thi

last: Dang


title: MicroRNA Profiling to Inform Disease Classification, Severity, and Treatment Response in Pediatric Pulmonary Hypertension

city: San Francisco

first: Michael

last: Smith

address: 550 16th St, 5th Floor

department: Pediatrics

institute: UC San Francisco

type: Non-coding RNA profiling by high throughput sequencing

summary: Pediatric pulmonary hypertension is a heterogeneous disease associated with significant morbidity and mortality. MicroRNAs have been implicated as both pathologic drivers of disease and potential therapeutic targets in pediatric pulmonary hypertension. We sought to characterize the circulating microRNA profiles of a diverse array of pediatric pulmonary hypertension patients using high throughput sequencing technology. Peripheral blood samples were drawn from patients recruited at the time of a clinically indicated cardiac catheterization and microRNA sequencing followed by differential expression and target/pathway enrichment analyses were performed. Among 63 pediatric pulmonary hypertension patients, we identified specific microRNA signatures that uniquely classified patients by disease subtype, correlated with indicators of disease severity including invasive hemodynamic metrics, and changed over the course of treatment for pulmonary hypertension. These microRNA profiles include a number of specific microRNA molecules known to function in signaling pathways critical to pulmonary vascular biology and disease, including TGFβ beta, VEGF, PI3K/Akt, cGMP-PKG, and HIF-1 signaling. Circulating levels of miR-122-5p, miR-124-3p, miR-204-5p, and miR-9-5p decreased over the course of treatment in a subset of patients who had multiple samples drawn during the study period. Our findings support the further investigation of specific microRNAs as mechanistic mediators, biomarkers, and therapeutic targets in pulmonary hypertension.

overall_design: Peripheral blood samples were drawn from pediatric pulmonary hypertension patients and plasma was processed for RNA sequencing to identify circulating miRNA using the miRNeasy Advanced Kit (Qiagen). The QIAseq miRNA Quantification workflow of the CLC Genomics Server was used to map reads to miRBase version 22.

first: Sam

last: Chiacchia

first: Jason

last: Boehme

first: Sanjeev

last: Datar

first: Emily

last: Morell

first: Roberta

last: Keller

first: Amy

last: Romer

first: Elizabeth

last: Colglazier

first: Claire

last: Parker

first: Jasmine

last: Becerra

first: Jeffrey

last: Fineman


title: Single-Cell RNA Sequencing Pinpoints Exocrine Bipotentiality of Human Pancreatic Organoids

city: Milano

first: Alessandro

last: Cherubini

address: via F. Sforza 35

country: Italy

institute: IRCCS Ca' Granda Ospedale Maggiore Policlinico

summary:
Objective: Despite organoid formation and characterization from different tissues have been extensively studied, pancreas remains one among the least investigated organs. Here we proposed a multifaced characterization of cell types present in human pancreatic organoids (hPO) and starting from their progenitor we described their maturation and their lineage relationships.
Design: We performed unbiased transcriptome-wide scRNA-seq analysis on 3187 cells of human pancreatic organoids obtained from 3 healthy islet-depleted tissue. To support our results, we strengthened these findings with proteomic and qRT-PCR analyses performed during the long-term culture of hPO.
Results: First, we described hPO focusing on their morphology and long-term culture molecular aspects and showing a well-defined epithelial organization supported by a genetic stability through all cell passages. Successively, based on single-cell RNA sequencing technology, we defined all cell types present in hPO confirming that our pancreatic organoid methodology is highly reproducible. Moreover, exploiting the latest bioinformatic tools and comparing our data with recently published ones we reshaped the conventional theory of univocal ductal nature of hPO. Finally, we defined a new strategy to sort a refined multipotent progenitor from hPO and we gave a new definition of pancreatic progenitor demonstrating its capacity to renew the hPO stem population while maintaining its heterogeneity.
Conclusions: Taken together, our results give a new definition of human pancreatic organoids, which reveals the complex nature of these structures and provides a strong basis to pave the way for future study in the pancreatic field.

overall_design: Single cell RNA-seq profile of human pancreatic organoids obtained from 3 healthy islet-depleted tissue

first: Lorenza

last: Lazzari

first: Francesco

last: Rusconi


title: Genome-wide profiling of Kdm2a binding and H3K36me2 of hypoxia-cultured B cells derived from miR-155-sufficient and -deficient mice [ChIP-seq]

city: London

first: Rinako

last: Nakagawa

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: To investigate the impact caused by miR-155 ablation, B cells from miR-155-sufficient and -deficient mice were cultured in hypoxic conditions and analyzed for profiling the binding of a miR-155 target, Kdm2a, to genomic loci and the distribution pattern of H3K36me2, which Kdm2a demethylates.

overall_design: Splenic B cells derived from miR-155-sufficient or -deficient mice were cultured in hypoxic conditions.

first: Dinis

last: Calado


title: PKC modulator bryostatin-1 therapeutically targets CNS innate immunity to attenuate neuroinflammation and promote remyelination [invitro]

status: Public on Oct 29 2024

city: Baltimore

first: Matthew

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

summary: In multiple sclerosis (MS), microglia and macrophages within the central nervous system (CNS) play an important role in determining the balance between myelin repair and demyelination/neurodegeneration. Phagocytic and regenerative functions of these CNS innate immune cells support remyelination, whereas chronic and maladaptive inflammatory activation promotes lesion expansion and disability, particularly in the progressive forms of MS. No currently approved drugs convincingly target microglia and macrophages within the CNS, contributing to the critical lack of therapies promoting remyelination and slowing progression in MS. Here, we found that the protein kinase C (PKC)-modulating drug bryostatin-1 (bryo-1), a CNS-penetrant compound with an established human safety profile, produces a shift in microglia and CNS macrophage transcriptional programs from pro-inflammatory to regenerative phenotypes, both in vitro and in vivo. Treatment of microglia with bryo-1 stimulated scavenger pathways, phagocytosis, and secretion of factors that prevent the activation of neuroinflammatory reactive astrocytes while promoting neuroaxonal health and oligodendrocyte differentiation. In line with these findings, systemic treatment with bryo-1 augmented remyelination following a focal demyelinating injury in vivo. Our results demonstrate the potential of bryo-1 and possibly a wider class of PKC modulators as myelin regenerative and supportive agents in MS and other neurologic diseases through therapeutic targeting of microglia and CNS-associated macrophages.

overall_design: Mixed glia cultures (MGC) from C57BL/6 mouse neonates were cultured and treated for 24 hours prior to RNA collection and RNAseq analysis. The different conditions were: no treatment control, LPS, LPS+Bryostatin, LPS+IFNγ, LPS+IFNγ+Bryostatin, IL4, and IL4+Bryostatin. Each condition has three replicates except for No Treatment which has 6

first: Efrat

last: Abramson

first: Payam

last: Gharibani

first: Peter

last: Calabresi

last: Kornberg

first: Paul

last: Kim


title: SARS-CoV-2 infection elucidates unique features of pregnancy-specific immunity [ADT]

city: Boston

first: Alexandra-Chloe

last: Villani

state: MA

institute: MGH, Harvard

summary: Pregnancy is a risk factor for increased severity of SARS-CoV-2 and other respiratory infections. The mechanisms underlying this risk have not been well-established, partly due to limited understanding of how pregnancy shapes and modulates immune responses. To gain insight into the roles of pregnancy in shaping the immune responses we collected peripheral blood mononuclear cells (PBMC) from 17 non-pregnant and 9 pregnant donors with various COVID severities and compared their immunological profiles.

overall_design:
Hashed PBMC single cell libraries were generated with the Chromium Single Cell 5’ kit (10X Genomics) together with the 5’ Feature Barcode library kit. TCR and BCR-enriched cDNA libraries were generated with the Chromium Single Cell V(D)J Enrichment kit (10x Genomics). Library quality was assessed with an Agilent 2100 Bioanalyzer.

>>>Submitter states: Due to patient privacy concerns, raw data will be submitted to dbGaP.<<<

first: Rachelly

last: Normand

first: Pritha

last: Sen

first: Dongsun

last: Oh

first: Eunha

first: Guangqing

last: Lu

first: Andrea

last: Edlow

first: Jun

last: Huh


title: PKC modulator bryostatin-1 therapeutically targets CNS innate immunity to attenuate neuroinflammation and promote remyelination [exvivo]

last: Smith

overall_design: C57BL/6J Female mice were immunized with myelin peptide and pertussis toxin to induce EAE. Starting at day 19, mice were treated 3 times per week with vehicle or bryostatin 19 days after immunization. On day 35, myeloid cells were sorted from enzymatically dissociated CNS. Data are from two independent experiments. There are 3 replicates for each condition.

first: Michael


title: PKC modulator bryostatin-1 therapeutically targets CNS innate immunity to attenuate neuroinflammation and promote remyelination


title: SARS-CoV-2 infection elucidates unique features of pregnancy-specific immunity [GEX]


title: Effects of BT-11 treatment on hippocampal gene expression in Female Fisher transgenic 344-AD rats. [Female RNAseq]

city: NY

first: Emily

last: Birnbaum

state: NY

address: 200 West 93rd Street, 6J

institute: CUNY Graduate Center

summary: 5 month old Female Fisher transgenic 344-AD (Tg-AD) rats expressing human Swedish amyloid precursor protein (APPsw) and Δ exon 9 presenelin-1 (PS1ΔE9) were treated with BT-11  (cat. no. HY-102013, MCE) at 8.5 mg/kg body weight administered in rodent chow. Following 6 months of BT-11  treatment, rats (11 months of age) were tested for cognitive behavior prior to sacrificing. Hippocampal Brain region were dissected and  RNA sequencing (RNAseq) analyses was done on the Isolated sample. Taken together we showed that BT-11  treatment enriched pathways for females included passive transmembrane transporter activity, G protein-coupled receptor activity, G protein-coupled peptide receptor activity.

overall_design: To show the effects of BT-11-treatment on gene expression levels, Hippocampi of 5 BT-11 -treated and 5 untreated transgenic rats of male rats were analysed for gene expression by RNAseq. At 11 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis. Left hemisphere of the hippocampus.  F1 – F5 (untreated female transgenic rats), FBT1 – FBT5 (transgenic female AD rats treated with the drug BT-11). Female Rats started BT-11 treatment at 5-months of age and were treated for 6 months untli they were 11 months old.  For this experiment, the gene expression for the drug treated transgenic rats will be compared to that of the untreated transgenic group  (FBT/F)

first: Birnbaum

last: Emily

first: Patricia

last: Rockwell

last: Serrano

first: Maria

last: Figueiredo-Pereira

first: Lei

last: Xie


title: Effects of BT-11 treatment on hippocampal gene expression in Male Fisher transgenic 344-AD rats. [Male RNAseq]

summary: 5 month old Male Fisher transgenic 344-AD (Tg-AD) rats expressing human Swedish amyloid precursor protein (APPsw) and Δ exon 9 presenelin-1 (PS1ΔE9) were treated with BT-11  (cat. no. HY-102013, MCE) at 8.5 mg/kg body weight administered in rodent chow. Following 6 months of BT-11  treatment, rats (11 months of age) were tested for cognitive behaviour prior to sacrificing. Hippocampal Brain region were dissected and  RNA sequencing (RNAseq) analyses was done on the Isolated sample. Taken together we showed that BT-11  treatment enriched pathways in males including salt transmembrane transporter activity, signaling receptor regulator receptor ligand activity, signaling receptor activator activity, and transmembrane transporter activity.

overall_design: To show the effects of BT-11-treatment on gene expression levels, Hippocampi of 5 BT-11 -treated and 5 untreated transgenic rats of male rats were analysed for gene expression by RNAseq. At 11 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis. Left hemisphere of the hippocampus. M1 – M5 (untreated male transgenic rats), MBT1 – MBT5 (transgenic male AD rats treated with the drug BT-11). Male  Rats started BT-11 treatment at 5-months of age and were treated for 6 months untli they were 11 months old. For this experiment, the gene expression for the drug treated transgenic rats will be compared to that of the untreated transgenic group (MBT/M)


title: Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer

city: Tampere

first: Matti

last: Nykter

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

summary: Prostate cancer treatment resistance is a significant challenge facing the field. Genomic and transcriptomic profiling have partially elucidated the mechanisms through which cancer cells escape treatment, but their relation toward the tumor microenvironment (TME) remains elusive. Here we present a comprehensive transcriptomic landscape of the prostate TME at multiple points in the standard treatment timeline employing single-cell RNA-sequencing and spatial transcriptomics data from 120 patients. We identify club-like cells as a key epithelial cell subtype that acts as an interface between the prostate and the immune system. Tissue areas enriched with club-like cells have depleted androgen signaling and upregulated expression of luminal progenitor cell markers. Club-like cells display a senescence-associated secretory phenotype and their presence is linked to increased polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) activity. Our results indicate that club-like cells are associated with myeloid inflammation previously linked to androgen deprivation therapy resistance, providing a rationale for their therapeutic targeting.

overall_design:
We used the Visium Spatial Transcriptomics assay to generate data from 52 prostate tumors, including benign prostate tumors, treatment-naïve, neadjuvant-treated, castration-resistant, and metastatic castration-resistant prostate cancer tumors.

***************************************************************
the raw sequencing data cannot be shared due to privacy concerns
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first: Alfonso

last: Urbanucci


title: Single-nucleotide-resolution genomic maps of O6-methylguanine from the glioblastoma drug temozolomide

city: Zurich

first: Shana

middle: J.

last: Sturla

address: Schmelzbergstrasse 9

department: D-HEST

country: Switzerland

institute: ETH Zurich

summary: Temozolomide kills cancer cells by forming O6-methylguanine (O6-MeG), which leads to cell cycle arrest and apoptosis. However, O6-MeG repair by O6-methylguanine-DNA methyltransferase (MGMT) contributes to drug resistance. Characterizing genomic profiles of O6-MeG could elucidate how O6-MeG accumulation is influenced by repair, but there are no methods to map genomic locations of O6-MeG. Here, we developed an immunoprecipitation- and polymerase-stalling-based method, termed O6-MeG-seq, to locate O6-MeG across the whole genome at single-nucleotide resolution. We analyzed O6-MeG formation and repair with regards to sequence contexts and functional genomic regions in glioblastoma-derived cell lines and evaluated the impact of MGMT. O6-MeG signatures were highly similar to mutational signatures from patients previously treated with temozolomide. Furthermore, MGMT did not preferentially repair O6-MeG with respect to sequence context, chromatin state or gene expression level, however, may protect oncogenes from mutations. Finally, we found an MGMT-independent strand bias in O6-MeG accumulation in highly expressed genes in TMZ-exposed cells and naked DNA proposing an indirect influence of transcription to O6-MeG formation. These data provide high resolution insight on how O6-MeG formation and repair is impacted by genome structure and nucleotide sequence. Further, O6-MeG-seq is expected to enable future studies of DNA modification signatures as diagnostic markers for addressing drug resistance and preventing secondary cancers.

overall_design: We used a novel DNA modification sequencing stragegy, O6‑MeG‑seq, to assess O6-methylguanine in LN-229 cells exposed to temozolomide. We used an MGMT-transfected LN-229 cell line and the transfection control cell line further referred to as wild-type (WT). They were exposed to temozolomide or solvent control once (1x) or repetitively (3x).  Additionally, naked DNA from LN-229 WT and MGMT-transfected cells was exposed to temozolomide.There are 3 biological replicates per condition

first: Jasmina

last: Kubitschek

first: Cécile

last: Mingard

first: Vakil

last: Takhaveev

first: Martha

middle: I

last: Rochlitz

middle: B

last: Reinert

first: Giulia

last: Keller

first: Tom

last: Kloter

first: Raúl

last: Fernández Cereijo

first: Sabrina

last: Huber

first: Maureen

last: McKeague


title: scRNA-seq analysis of murine TECs after depleting RANKL and CD40L signaling

city: Yokohama

first: Taishin

last: Akiyama

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN

summary: the molecular mechanisms behind the turnover of medullry thymic epithelial cells remain unclear.  We performeds single cell RNA-seq of TECs from mice 15 days after depleting cytokine RANKL and CD40L signaling.

overall_design: Thymic epithelial cells (EPCAM+, CD45-, reticulocyte negative ) were isolated from the thymus of wild-type and CD40-deficient mice after injection of RANKL neutralizing antibody

first: Mio

last: Hayama

first: Maki

last: Miyauchi

first: Nobuko


title: Effects of tofacitinib and takinib on autoimmune pancreatitis in mice

city: Rostock

first: Robert

last: Jaster

address: Ernst-Heydemann-Str. 6

department: Dept. of Medicine, Div. of Gastroenterology

country: Germany

institute: Rostock University Medical Center

summary:
Using a mouse model of autoimmune pancreatitis (AIP), we investigated two potential alternatives to steroid treatment, the transforming growth factor-β-activated kinase 1 (TAK1) inhibitor takinib, and the Janus kinase (JAK) inhibitor tofacitinib. The drug effects were assessed histopathologically and by RNA sequencing (RNA-seq).
MRL/MpJ mice that received injections of polyinosinic-polycytidylic acid developed severe AIP with inflammation, destruction of acinar tissue, and fibrosis. The steroid dexamethasone significantly attenuated the disease, while takinib or tofacitinib had no effects. In the principal component analysis of pancreatic RNA-seq data, poly I:C-injected mice treated with tofacitinib, takinib, and solvent formed a common cluster whereas completely untreated and dexamethasone-treated mice clustered separately. We conclude that inhibition of TAK1 or JAKs alone is not sufficient to improve AIP in mice.

overall_design: MRL/MpJ mice received injections of polyinosinic-polycytidylic acid (poly I:C) for six weeks to trigger AIP. During the last four weeks, they were also treated with takinib (75 mg/kg body weight), tofacitinib (15 mg/kg), dexamethasone (1 mg/kg), or solvent only. RNA was isolated from pancreatic tissue and subjected to RNA seq analysis.


title: Nucleo-cytoplasmic distribution of SAP18 reveals its dual function in splicing regulation and heat-stress response in Arabidopsis

city: Bellaterra

first: Alvaro

middle: Santiago

last: Larran

state: Barcelona

address: C/ de la Vall Moronta s/n, Campus UAB

country: Spain

institute: CRAG

summary: RNA-seq experiment of Col0, sr45, sap18sr45 and asap (sap18sr45acinus) mutants

overall_design: Col0, sr45, sap18 sr45 and asap plants were grown on MS medium under 16:8 photoperiod at 22 °C for 11 days. RNA was extracted from 100 mg of seedlings using RNeasy plant mini kit (Qiagen) following manufacturer’s instructions. RNA was quantified in a Qubit 2.0 fluorometer using Qubit RNA Assay Kit and following by an integrity check on Bioanalyzer. 2 μg of RNA per sample was sent to Macrogen for library preparation and sequencing performing (Truseq stranded mRNA Library + NovaSeq6000, 150 x 2bp, 30M reads/sample, 4.5Gb/sample).

first: Julia

last: Qüesta

first: Guiomar

last: Martín


title: To elucidate the role of Protein Kinase C in Urothelial Bladder Carcinoma.

city: New Delhi

first: DEEPIKA

last: TREHAN

state: Delhi

address: ICMR- National Institute of Pathology, Safdarjung Hospital Campus, Ansari Nagar

country: India

institute: ICMR-NATIONAL INSTITUTE OF PATHOLOGY

summary: Comprehensive evaluation of human cell lines for the transcription dynamics in response to the inhibition of PKC isozymes ε & ζ in bladder cancer.

overall_design: The bladder cancer cells were knockdown with siRNA for PKC ε & ζ, followed by microarray analysis

first: Deepika

last: Trehan

first: Usha

last: Agrawal


title: New weapons explosive exhibits persistent toxicity in plants

city: York

first: Elizabeth

last: Rylott

address: Wentworth Way

department: Department of Biology

institute: University of York

summary: Explosives are widespread, toxic and persistent environmental pollutants. 2,4-Dinitroanisole (DNAN) is being phased in to replace 2,4,6-trinitrotoluene (TNT) in munitions. Here we demonstrate that only low levels of DNAN are detoxified in Arabidopsis, leaving it to remain as a substrate for monodehydroascorbate reductase 6 mediated chronic phytotoxicity. Enhancing the potential for environmental toxicity, DNAN is readily transported to the aerial tissues exposing this toxin to herbivores and the wider food chain.

overall_design: To investigate genes differentially expressed in reposnse to the presence of DNAN, Arabidopsis plants in shake flasks were dosed with either 0, 60, 120, 240 or 480 μM DNAN. RNAseq was performed on RNA extracted from five replicate plants for each concentration of DNAN. Differential expression analysis carried out across the range of DNAN concentrations.

first: Nicola

last: Oates

first: Edward

last: Nay

first: Tim

last: Cary

first: Neil

last: Bruce


title: H3.3K122A results in a neomorphic phenotype in mouse embryonic stem cells (TT-Seq)

city: Pittsburgh

first: Sarah

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

summary: The histone variant H3.3 facilitates mRNA transcription activation and suppression at cis-regulatory elements such as promoters and enhancers, with histone epigenetic modifications including acetylation or methylation as context-defining features. Canonical histone H3 and histone variant H3.3 are post-translationally modified with the genomic distribution of these marks denoting transcription features and with more recent evidence suggesting that these modifications may influence transcription. While the majority of posttranslational modifications occur on histone tails, there are defined modifications with the globular domain, such as acetylation of H3K122/H3.3K122. To understand the function of the residue H3.3K122 in transcriptional regulation, we attempted to generate H3.3K122A mES cells, but were unsuccessful. Through multi-omic profiling of mutant cell lines harbor two of four or three of four H3.3 targeted alleles, we have uncovered that H3.3K122A is neomorphic and results in lethality while H3.3-null mES cells are viable and pluripotent, albeit with reduced differentiation capacity. Together, these studies have uncovered a novel dependence of a globular domain residue of H3.3 for viability and broadened our understanding of how histone variants contribute to transcription regulation and pluripotency in mES cells.

overall_design: Nascent RNA-seq samples (TT-seq) from mutant or wildtype murine embryonic stem cells. Five mutant lines (H3f3a_AA_H3f3b_WTWT,H3f3a_WTWT_H3f3b_AA,H3f3a_AA_H3f3b_WTA_clone1,H3f3a_AA_H3f3b_WTA_clone2,H3f3a_WTA_H3f3b_AA) profiled once and wildtype cells (WT1,WT2,WT3) profiled in biological triplicate.

first: Benjamin

last: Patty

first: Cailin

last: Jordan

first: Santana

last: Lardo

first: Kris

last: Troy


title: Identification of molecular mechanisms promoting long-term cytopenia after BCMA CAR-T therapy in Multiple Myeloma

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

institute: CIMA

summary: Hematological toxicity is a common side effect of CAR-T cell therapies, being particularly severe in relapsed/refractory multiple myeloma (MM) patients treated with CAR-T cells. In this work, we analyzed a cohort of 48 patients treated with BCMA CAR-T cells to characterize the kinetics of cytopenia, identify predictive factors and determine potential mechanism underlying these toxicities. The overall incidence of cytopenia was 95.74%, and grade ≥3 thrombopenia and neutropenia persisting one month after infusion was reported in 57% and 53% of the patients, respectively. Presence of cytopenia at baseline and high peak inflammatory markers highly correlated with cytopenia persisting up to three months. To determine potential mechanisms underpinning cytopenias, we evaluated the paracrine effect of BCMA CAR-T cells on the differentiation of HSPCs using an ex-vivo myeloid differentiation model. Phenotypic analysis showed that supernatants from activated CAR-T cells (spCAR) halted HSPCs differentiated promoting more immature phenotypes, with reduced expression of granulocytic, monocytic and erythroid markers. Single-cell RNAseq demonstrated an upregulation of transcription factors associated with early stages of hematopoietic differentiation in the presence of spCAR (GATA2, RUNX1 or CEBPA) and a decrease activity of key regulons involved in neutrophil and monocytic maturation (ID2 and MAFB). Overall, our study contributes to the understanding of severe cytopenia observed after CAR-T cell treatment of MM patients, providing potential molecular drivers. Our results suggest that CAR-T cell activation would negatively influence hematopoietic differentiation through paracrine effects inducing arrest of HSPCs maturation. Identification of regulatory mechanism involved in alter hematopoiesis could led to new therapeutic strategies.

overall_design: In the current study, we characterized the kinetics of cytopenia in a cohort of patients with R/R MM receiving BCMA CAR-T cell treatment, evaluating their correlation with clinical and laboratory parameters. To dwell into the mechanisms of these cytopenias, we studied the effect of activated CAR-T cell supernatant on ex-vivo hematopoietic differentiation. Our results using phenotypic and single cell transcriptional studies allowed us to identify abnormal transcriptional and regulatory programs involved in hematopoietic differentiation, providing molecular mechanistic insights driving prolonged cytopenia.

first: Maria

last: Luisa Palacios-Berraquero

first: Paula

last: Rodriguez-Marquez

last: Erendira Calleja-Cervantes

first: Juan

last: Roberto Rodriguez-Madoz

first: Felipe

last: Prosper


title: H3.3K122A results in a neomorphic phenotype in mouse embryonic stem cells (CUT&RUN)

overall_design: CUT&RUN assays for select targets in either wildtype or mutant murine ES cells. Conditions (Targets): Wildtype ES cells done in biological duplicate (K27ac, K122ac, H3.3, and No antibody) and mutants for one biological replicate: H3f3a_AA_H3f3b_WTWT (K27ac, K122ac, H3.3, and No antibody, H3f3a_WTWT_H3f3b_AA (K27ac, K122ac, H3.3, and No antibody, H3f3a_AA_H3f3b_WTA_clone1 (K27ac, K122ac, H3.3, and No antibody, H3f3a_AA_H3f3b_WTA_clone2 (K27ac, K122ac, H3.3, and No antibody, H3f3a_WTA_H3f3b_AA (K27ac, K122ac, H3.3, and No antibody)


title: SARS-CoV-2 infection elucidates unique features of pregnancy-specific immunity

first: Alexandra-Chloe

last: Villani

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

overall_design: Refer to individual Series


title: SARS-CoV-2 infection elucidates unique features of pregnancy-specific immunity [VDJ]

first: Rachelly

last: Normand

first: Pritha

last: Sen

first: Dongsun

last: Oh

first: Eunha

last: Kim

first: Guangqing

last: Lu

first: Andrea

last: Edlow

first: Jun

last: Huh


title: Enhanced combination treatment on osteosarcoma by mitigating drug-induced oncogenic signaling pathway activation

city: Changsha

first: Lin

last: Qi

address: 139 Renmin Road

institute: The Second Xiangya Hospital, Central South University

summary: Osteosarcoma is a prevalent primary malignant bone tumor in children and young adults, with limited progress in improving survival rates for metastatic or recurrent cases. Kinase inhibitors emerged as potential treatment for osteosarcoma due to the critical role of kinases regulating network. However, single-agent kinase inhibitors often face challenges due to the activation of compensatory oncogenic signaling pathways, which can undermine treatment efficacy. In this study, a systematic combination screening of kinase inhibitors was further conducted in osteosarcoma cells. Among 190 pair-wise combinations, 44 exhibited strong synergistic antitumor efficacy. Notably, the combination of the ALK inhibitor Ceritinib and the FLT3 inhibitor Crenolanib showed significant synergistic effects against osteosarcoma cell lines, patient-derived organoids in vitro, and xenograft models in vivo. This combination also effectively mitigated the compensatory activation of oncogenic signaling pathways, a common resistance mechanism to single-agent therapies. Our findings provide compelling evidence that dual kinase inhibition targeting ALK and FLT3 can effectively exploit pharmacological vulnerabilities in osteosarcoma, suggesting a promising therapeutic strategy for clinical application. This combinatorial approach could potentially overcome the limitations of single-agent therapies and improve outcomes for patients with osteosarcoma. Further clinical evaluation is warranted to confirm these preclinical results.

overall_design: 143B osteosarcoma cells were treated with DMSO,1.0 μM Ceritinib, 1.0 μM Crenolanib, and the combination of 1.0 μM Ceritinib and 1.0 μM Crenolanib for 48 hours and subjected to NGS.

first: Zhihong

last: Li

first: Chao

last: Tu

first: Wenchao

last: Zhang


title: Transient promoter interactions modulate developmental gene activation [CaptureC]

city: Heidelberg

first: Angelika

last: Feldmann

address: Im Neuenheimer Feld 581

institute: German Cancer Research Center

summary: Transcriptional induction coincides with the formation of various chromatin topologies, including loss and gain of physical interactions between promoters and distal regulatory elements (DREs). Strong evidence supports that gene activation is accompanied by a general increase in promoter-enhancer interactions. However, it remains unclear how these topological changes are coordinated across time and space to collectively enable transcription. Here we combine chromatin conformation capture with profiling of histone modifications, RNA polymerase II and transcription during an embryonic stem cell differentiation time-course to determine how 3D genome restructuring is related to transcriptional transitions. Using this approach, our data identifies distinct topological alterations that are associated with the magnitude of transcriptional induction. We detect transiently formed interactions between gene promoters and DREs and demonstrate by genetic deletions that these DREs can contribute to the transcriptional induction of associated genes. Finally, by acutely depleting cohesin, we interfere with early transient promoter-enhancer interactions, and show that this impairs the activation of linked genes. Taken together, our study identifies typical topological alterations during gene activation, links them to the magnitude of transcriptional induction, and detects an uncharacterized type of transcriptional enhancers. Our data are compatible with a model where the type of topological pattern that a promoter displays during developmental transitions and the dynamics and magnitude of its transcriptional induction are interdependent.

overall_design: For the time-course analysis of promoter differentiation mouse embryonic stem cells (E14) were differentiated using retinoic-acid treatment and samples were collected at 0, 2, 4, 6, 24, 48 and 72 hours of treatment in biological duplicates to conduct Capture-C. A total of four sets of view points were assessed (sets 1-3 deeply sequenced, set4 shallow sequencing). To assess how transient interactions are affected by cohesin depletion, mESCs with and without acute depletion of SCC1 were differentiated for four hours. Samples were collected in triplicates. To assess how interactions are affected by the absence of the transient DRE DRE.H5.100 samples were collected at 0, 24 and 72 hours.

first: Valeriia

last: Smialkovska

first: Sylvia

last: Mahara

first: Helena

last: Borgers

first: Susannah

last: Holliman


title: Whole blood gene expression analysis of spontaneous hypertriglyceridemia in dogs suggests an underlying pro-thrombotic process

city: St. Paul

first: Eva

last: Furrow

state: MN

address: 1352 Boyd Ave, C339 VMC

department: Veterinary Clinical Sciences

institute: University of Minnesota

summary: Hypertriglyceridemia (HTG) is influenced by multiple genetic and environmental factors. Spontaneous, idiopathic HTG is common in the Miniature Schnauzer dog and presumed to have a strong genetic influence in this breed. To define genes that are differentially expressed in dogs with HTG, we performed RNA sequencing on peripheral blood of 13 Miniature Schnauzers with HTG and 18 controls. We identified 110 differentially expressed genes (DEGs). Pathway analysis suggests an ongoing pro-thrombotic, endothelial activation process in dogs with HTG. The gene with the largest fold change (5.4 ± 1.4, Padj=4.4E-04), SERPINE1, encodes plasminogen activator inhibitor 1 (PAI-1), a known risk factor for atherosclerosis and thrombosis. Other top DEGs, including SHANK3, MMRN1, and FZD7, are involved in endothelial activation. Two of the top DEGs, ARHGAP29 and ARHGAP21, inhibit pro-thrombotic pathways and are potentially protective of disease sequelae. Top DEGs, including SERPINE1 and ARHGAP21, have also been linked to metabolic syndrome or its features (e.g. insulin resistance) in humans and animal models. Our findings indicate that HTG in the Miniature Schnauzer dog has similar features to HTG and metabolic syndrome in humans, highlighting the potential use of the dog as a spontaneous model for further research into the etiology and effects of HTG.

overall_design: Gene expression profiling analysis of whole blood RNA-seq from 13 dogs with HTG and 18 control dogs

first: Lauren

last: Baker

first: Nicole

last: Tate


title: Analysis of transcriptomes of germinal center (GC) B cells derived from miR-155-sufficient and -deficient mice at the single-cell level [scRNA-seq]

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

summary: To investigate the impact caused by miR-155 ablation, GC B cells were sorted by flow cytometry and used to analyze transcriptomic profiles.

overall_design: Splenic B cells derived from miR-155-sufficient or -deficient mice expressing HEL-specific B cell receptor together with endogenous cMyc-GFP reporter cassette and AID-cre-hCD2 were adoptively transferred into congenic mice, followed by immunization with HEL3x mutant conjugated with sheep red blood cells (SRBCs). After seven days, Donor-derived GC-B cells were sorted and used for the scRNA sequencing library.

first: Rinako

last: Nakagawa

first: Hubert

last: Slawinski


title: Transient promoter interactions modulate developmental gene activation [RNA-Seq]

summary: Transcriptional induction coincides with the formation of various chromatin topologies, including loss and gain of physical interactions between promoters and enhancers. While strong evidence supports that gene activation is accompanied by a general increase in promoter-enhancer interactions, how these topological changes are coordinated across time and space with other types of interactions to collectively enable gene activation remains unresolved. Here we combine chromatin conformation capture with the profiling of histone modifications and transcription during a finely resolved time-course of embryonic stem cell differentiation to determine how genome restructuring in 3D correlates with and informs transcriptional transitions. Our data indicates that genome restructuring follows only a few common patterns that are related to the magnitude of transcriptional induction. Using this approach we identify transiently formed interactions between gene promoters and distal regulatory elements for which we demonstrate by genetic deletion that they can contribute to the transcriptional induction of associated genes. Finally, using acute depletion of cohesin, we prevent the formation of early promoter-enhancer interactions, and show that this impairs the activation of corresponding genes, compatible with the possibility that early topological changes are instructive for transcription.  Taken together, our study identifies the variety of typical topological changes during gene activation, detects an uncharacterized type of transcriptional enhancers and provides evidence that the earliest topological changes can affect the magnitude of gene activation. Our data agrees with the idea that the multitude of topological changes account for appropriate gene induction during cell differentiation.

overall_design: For the time-course analysis of promoter differentiation wildtype mouse embryonic stem cells (E14) were differentiated using retinoic-acid treatment and samples were collected at 0, 2, 4, 6, 24, 48 and 72 hours of treatment in biological duplicates to quadruplicates to conduct RNA-Seq. Transient enhancer within the Hoxb locus was deleted and two knockout clones (E3 and H12) as wella s one wildtuype clone (G4) were obtained with which the timecourse was also conducted. To assess how gene expression is affected by cohesin depletion, mESCs with and without acute depletion of SCC1 were differentiated for four hours. Samples were collected in triplicates.

first: Sonja

last: Pruessing


title: A p53-topoisome replaces the acutely genotoxic MYC- topoisome to empower DNA-damage repair in cells

city: ROCKVILLE

first: Subhendu kumar

last: Das

address: 9000 Rockville pike, Building 10, Bethesda, Maryland

department: Laboratory of Pathology

institute: NCI

summary: Hyperproliferation driven by the protooncogene MYC has been presumed to elicit a chain of event that leads to DNA damage and activates the tumor suppressor p53 response. This DNA damage has been presumed to derive from hypertranscription and overreplication. Here, we report that MYC-topoisome (MYC/Topoisomerase 1/Topoisomerase 2) formation is genotoxic within minutes of its formation. Topoisome mediated damage activates pATM and p53, that in turn shuts off MYC and dissociates the topoisome in vitro and in vivo. To manage topological and torsional stress generated at its targets, p53 assembles its own topoisome. Because topoisomerase activity is intrinsically DNA-damaging, the p53-topoisome creates initial burst of DNA damage but, because p53 (unlike MYC) upregulates the DNA damage response and activates TDP1 and TDP2, this damage is quickly suppressed. The novel coupling of TOP1 and TOP2 sponsored by p53, creates a tool to support the expression of p53 targets while braking MYC-accelerated cell growth.

overall_design: To pull down the "topisome" complex we designed cross CAD-seq method which involves trapping of TOP2A by etoposide treatment and then proceeding with a pull down against TOP1. TOP1cc cross-CAD-seq was performed in HO15.19 MYC-ER cells with and without p53 induction by nutlin to look at the formation of the p53-topisome.

first: Subhendu

middle: K

first: Sharmistha

last: Karmakar

first: Rajiv

last: Jha

first: Eric

last: Batchelor

first: David

last: Levens


title: Transient promoter interactions modulate developmental gene activation [ChIPseq]

first: Angelika

last: Feldmann

overall_design: Mouse embryonic stem cells (E14) were differentiated using retinoic-acid and samples were collected at 0, 2, 4, 6, 24, 48 and 72 hours of treatment to conduct ChIP-Sequencing.

first: Samuel

last: Krall


title: Characterisation of a novel covS SNP identified in Australian Group A Streptococcus isolates derived from the M1UK lineage

status: Public on Oct 28 2024

city: Saint Lucia

first: Johanna

last: Richter

address: Institute for Molecular Bioscience, QBP, Building 80, Services Road

institute: The University of Queensland

summary: Group A Streptococcus (GAS) is a human-adapted pathogen responsible for a variety of diseases. The GAS M1UK lineage has contributed significantly to the recently reported increases in scarlet fever and invasive infections, however the basis for its evolutionary success is not yet fully understood. During the transition to systemic disease, the M1 serotype is known to give rise to spontaneous mutations in the CovRS two-component transcriptional regulation system that confer a fitness advantage during invasive infections. Mutations that inactivate CovS function result in the de-repression of key GAS virulence factors such as Streptolysin O (SLO), a pore-forming toxin and major trigger of inflammasome/interleukin-1-dependent inflammation. Conversely, expression of the streptococcal cysteine protease SpeB, which is required during initial stages of colonisation and onset of invasive disease, is typically lost in such mutants. In this study, we identified and characterised a novel covS mutation detected in three separate invasive M1UK isolates. The resulting CovSAla318Val mutation caused a significant upregulation of SLO resulting in increased inflammasome activation in human THP-1 macrophages, indicating an enhanced inflammatory potential. Surprisingly, SpeB production was unaffected. Site-directed mutagenesis was performed to assess the impact of this mutation on virulence and global gene expression. We found that the CovSAla318Val mutation led to subtle, virulence-specific changes of the CovRS regulon compared to previously characterised covS mutations, highlighting an unappreciated level of complexity in CovRS-dependent gene regulation. Continued longitudinal surveillance is warranted to determine whether this novel covS mutation will expand in the M1UK lineage.

overall_design: RNA-seq

first: Amanda

middle: J

last: Cork

first: Yvette

middle: Y

last: Ong

first: Nadia

last: Keller

first: Andrew

last: Hayes

first: Mark

last: Schembri

first: Amy

middle: V

last: Jennison

last: Davies

first: Kate

last: Schroder

last: Walker

first: Stephan

last: Brouwer


title: Somatic mtDNA Mutation Burden Shapes Metabolic Plasticity in Leukemogenesis

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: The role of somatic mitochondrial DNA (mtDNA) mutations in leukemogenesis remains poorly   characterized. To determine the impact of somatic mtDNA mutations on the process, we assessed the   leukemogenic potential of hematopoietic progenitor cells (HPCs) from mtDNA mutator mice (Polg D257A)   with or without NMyc overexpression. We observed a higher incidence of spontaneous leukemogenesis   in recipients transplanted with heterozygous Polg HPCs and a lower incidence of NMyc-driven leukemia   in those with homozygous Polg HPCs compared to controls. Although mtDNA mutations in heterozygous   and homozygous HPCs caused similar baseline impairments in mitochondrial function, only  heterozygous HPCs responded to and supported altered metabolic demands associated with NMyc  overexpression. Homozygous HPCs showed altered glucose utilization with pyruvate dehydrogenase   inhibition due to increased phosphorylation, exacerbated by NMyc overexpression. The impaired growth   of NMyc-expressing homozygous HPCs was partially rescued by inhibiting pyruvate dehydrogenase   kinase, highlighting a relationship between mtDNA mutation burden and metabolic plasticity in   leukemogenesis.

overall_design:
To investigate changes in gene expression associated with NMyc expression and accumulation of somatic mtDNA mutations
NMyc or Contol (Ctrl) vector transduced HPCs from mice with different genotype WT, Het, Hom

first: Xiujie

last: Li-Harms

first: Geoff

last: Neal

first: Mondira

last: Kundu


title: Transcriptomic and genetic analysis reveals a Zn2Cys6 transcription factor necessary for conidiation in submerged culture in Thermothelomyces thermophilus [RNA-seq 2]

city: Berkeley

first: Louise

middle: N

last: Glass

state: CA

address: Koshland Hall

department: PMB

institute: UC California

summary: Filamentous fungi are important producers of enzymes and secondary metabolites in the biotech industry. A relatively new but highly promising fungus for industrial production is Thermothelomyces thermophilus, which is closely related to the model fungus Neurospora crassa. Nevertheless, to fully exploit the potential of T. thermophilus, a deeper understanding of its biology is necessary. A critical aspect of the filamentous fungal life cycle is the production of asexual spores (conidia), regulated by various stimuli, including nutrient availability. Under certain submerged fermentation conditions, several filamentous fungi produce conidia, which can be detrimental to product expression. In this study, we utilized RNA-seq to map transcriptomic changes during conidia production under submerged conditions in T. thermophilus. We found that the essential genes for conidiation in Aspergillus sp. and N. crassa, fluG and fluffy (fl), are not essential for conidiation in T. thermophilus. However, we identified a transcription factor, res1, whose deletion resulted in a complete loss of conidia production under fermentation conditions. This deletion also led to increased biomass production without increasing enzyme secretion. Notably, the deletion of res1 did not affect spore production on solid media. Differential gene expression analysis between the wild type and the res1 deletion mutant revealed that res1 regulates a broad range of cellular and metabolic processes, including MAPK and spore production pathways. Overexpression of res1 caused a severe growth defect and early conidia production compared to the wild type. Using ChIP-seq, we identified 35 potential target genes of res1, including known conidiation-related genes such as acon3, MAPK genes, and transcription factors like cpc1, as well as genes with unknown functions. Overall, we identified res1 to be obligatory for submerged conidia production and lay the foundation for further work on the T. thermophilus conidiation pathway and its applications.

overall_design: We grew WT, ∆res1 and ∆res1 PH2A::res1-V5 (res1 overexpression) in submerged conditions in pre-culture medium as biological triplicates and took samples for RNAseq at 6, 7.5 and 9  hours post inoculation.

first: Florian

last: Drescher

first: Yang

last: Li

first: Jose

last: Villalobos-Escobedo

first: Stefan

last: Haefner

first: Lori

last: Huberman

first: N


title: Transcriptomic and genetic analysis reveals a Zn2Cys6 transcription factor necessary for conidiation in submerged culture in Thermothelomyces thermophilus [RNA-seq 1]

overall_design: We grew WT, ∆res1 and ∆res1 Pres1::res1-gfp (res1 complementation) in submerged conditions in pre-culture medium as biological triplicates and took samples for RNAseq at 11.5, 14, 16, 20 and 48 hours post inoculation.


title: Transcriptomic and genetic analysis reveals a Zn2Cys6 transcription factor necessary for conidiation in submerged culture in Thermothelomyces thermophilus [ChIP-seq]

overall_design: We grew WT, ∆res1 Pres1::res1-V5 (complementation) and ∆res1 PH2A::res1-V5 (res1 overexpression) in submerged conditions in VMM medium for 16 hours until conidiation was starting to be visible. Cultures were then harvested and ChIP was cnducted as described.


title: Sequencing of four types of RNA modifications in primary and liver metastatic samples of colorectal cancer

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

type: Methylation profiling by high throughput sequencing

summary: To detect the differential RNA modifications in primary and liver metastatic samples of colorectal cancer

overall_design: Eight samples were analyzed, divided into two groups with four samples each: the primary colorectal cancer group and the liver metastatic group.  Four types of RNA modifications were analyzed, including m1A, m5C, m6A, and m7G.

first: Feng

last: Qi

first: Jia

last: Gao


title: Quantification of N-acyl alanine methyl ester (NAME) production by Roseovarius tolerans EL-164 enables dose-dependant activity testing

city: Oldenburg

first: Janina

last: Leinberger

address: Ammerländer Heerstraße 114-118

department: Institute for Chemistry and Biology of the Marine Environment

institute: University of Oldenburg

summary: N-acyl amino acid methyl esters (NAMEs), which are structurally similar to the signalling compounds N-acyl homoserine lactones (AHLs), have been identified in culture extracts of Roseovarius tolerans EL-164. However, previous studies have shown that NAMEs do not participate in AHL-mediated signalling and thus their ecological role remains unclear. To enable dose-dependent bioactivity-testing of NAMEs, we have established a quantification method for NAMEs. The concentrations determined for the major NAMEs produced by EL 164, C16:1- and C17:1-NAME, ranged between 0.7-5.7 mg L-1 and 5.3-86.4 µg L-1, respectively. We observed opposing production patterns for NAMEs and AHLs, with a continuously increasing NAME production during exponential growth and an accumulation in the stationary phase. We further conducted a spike-in experiment, using the previously determined metabolite concentrations. By comparing the transcriptomes of pre- and post-NAME or AHL spikes, we identified distinct impacts on gene expression patterns. Different genetic neighbourhoods were significantly up- or downregulated in NAME and AHL-spiked cultures. Yet no synergetic effect was observed. These findings exemplify the broad application range of dose-dependent testing and highlight the different biological activities of NAMEs and AHLs.

overall_design: Three setups were compared: spike-in of NAME, spike-in of AHL, spike-in of both metabolites. For each setup, biological triplicates were sampled at three different time points (tS1=26 h (NAME spike), tS2=49 h, tS3=53 h (AHL spike)). All cultures were sampled at all time points, irrespective whether or not they did receive the respective metabolite at that time point. However, not all sequencing was successful, resulting in a reduced number of replicates for some time points and conditions.

first: Diana

last: Koteska

first: Judith

last: Boldt

first: Jörn

last: Petersen

first: Sahana

last: Shivaramu

first: Jürgen

last: Tomasch

last: Schulz

first: Thorsten

last: Brinkhoff


title: Transcriptional profile of the rat cardiovascular system at single-cell resolution

city: Cambridge

first: Stephen

middle: Jordan

last: Fleming

address: 415 Main St.

institute: Broad Institute

summary: We sought to characterize cellular composition across the cardiovascular system of the healthy Wistar rat, an important model in preclinical cardiovascular research. We performed snRNA-seq in 78 samples in 10 distinct regions including the four chambers of the heart, ventricular septum, sinoatrial node, atrioventricular node, aorta, pulmonary artery, and pulmonary veins, which produced 505,835 nuclei. We identified 26 distinct cell types and additional subtypes, with different cellular composition across cardiac regions and tissue-specific transcription for each cell type. Several cell subtypes were region-specific, including a subtype of vascular smooth muscle cells enriched in the large vasculature. We observed tissue-enriched cellular communication networks, including heightened Nppa - Npr1/2/3 signaling in the sinoatrial node. The existence of tissue-restricted cell types suggests regional regulation of cardiovascular physiology. Our detailed transcriptional characterization of each cell type offers the potential to identify novel therapeutic targets and improve preclinical models of cardiovascular disease.

overall_design: 78 samples which passed QC are included here. All samples are from healthy Wistar rat cardiovascular tissue, collected from specific tissue regions. The rats are all male 17 week old animals. Multiple tissue region samples were collected from each individual rat, and a total of 16 individual rats were used to collect the snRNA-seq data in this study.  Nuclei were isolated from each sample and were used to prepare a 10x 3' v2 library for snRNA-seq.

first: Alessandro

last: Arduini

first: Patrick

middle: T

last: Ellinor


title: Pembrolizumab, exemestane, and leuprolide in premenopausal estrogen receptor-positive/HER2-negative advanced breast cancer

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: We evaluated the efficacy of combining pembrolizumab (anti-PD1 antibody), exemestane (nonsteroidal aromatase inhibitor), and leuprolide (gonadotropin-releasing hormone agonist) for 15 patients with ER+/HER2− premenopausal MBC who had failed one to two lines of hormone therapy without chemotherapy.

overall_design: We performed transcriptome analysis on pre-treatment samples.

first: I-Chun

last: Chen

first: Yen-Shen

last: Lu


title: Fasting reshapes tissue-specific niches to improve the innate immune response to cancer

city: New York

first: Endi

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: Fasting has long been associated with the improved elimination of cancer cells. However, the distinctive role of specific immune subsets mediating these anti-tumor properties remain elusive. Using a cyclic fasting diet (CFD) after tumor initiation, we investigated the impact of fasting on NK cell anti-tumor immunity. We found that adherence to a CFD improved anti-tumor immunity against both solid and metastatic tumors in a NK cell-dependent manner. During periods of fasting, NK cells underwent tissue redistribution where NK cells in the spleen experienced tissue-specific metabolic rewiring. These NK cells were exposed to elevated concentrations of fatty acids and glucocorticoids which increased fatty acid metabolism via expression of CPT1A, and was essential for NK cell survival and anti-tumor functions. In parallel, a population of NK cells were redistributed to the bone marrow during CFD in a S1PR5- and CXCR4-dependent manner. These cells were primed by an increased pool of IL-12-expressing myeloid cells which improved IFN-g production. Together, these data uncover a novel dietary strategy to improve tumor clearance and identifies a previously unknown mechanistic link between dietary restriction and optimized innate immune responses.

overall_design: Natural Killer (NK) cells from the bone marrow, spleen and tumors of mice subjected to ad libitum or cyclic fasting diet conditions were isolated using fluorescence-activated cell sorting (FACS) and subjected to scRNA-seq.

first: Rebecca

last: Delconte

first: Joseph

middle: C

last: Sun


title: Small RNA sequencing of exosomes in breast cancer screening population

city: Shenzhen

first: Junluan

last: MO

address: Buxin Road, Luohu District

institute: Shenzhen Center for Chronic Disease Control

summary: The breast cancer screening population was selected for small RNA sequencing of plasma exosomes, one of several types of extracellular vesicles. The analysis included 728 piRNAs, 2656 miRNAs, and 154 tsRNAs.

overall_design:
Female residents aged 40-74 living in cities were recruited through public health programs to participate in free breast cancer screening. This screening includes clinical examinations, blood tests, imaging examinations, and pathological examinations. We selected blood samples from both screening positive and negative populations. Exosomes were isolated from plasma. Small RNA sequencing in exosomes was performed. The isolated exosomes were selected for identification using Transmission Electron Microscope (TEM), Nanoparticle Tracking Analysis (NTA), and Flow Cytometry (FCM) detection of exosome surface proteins. The sequencing identified 728 piRNAs, 2656 miRNAs, and 154 tsRNAs.

UPDATE: [Jan-30-2025] The "Positive" Sample titles were changed to "Negative" and vice versa.

last: Mo

first: Wenxu

last: Hong

first: Jiye

last: Yin

first: Xi

last: Li


title: Parallel single-cell metabolic analysis and extracellular vesicle profiling reveal vulnerabilities with prognostic significance in acute myeloid leukemia

city: Bologna

first: Dorian

last: Forte

address: Via Massarenti 9

department: Department of Medical and Surgical Sciences

institute: University of Bologna

summary: RNA extracted from CD34+ isolated from Acute Myeloid Leukemia patients at the diagnosis and co-cultured with extracellular vesicles from plasma of AML patients at the diagnosis. Gene expression profiling was analyzed on the nCounter system using the Human Metabolic Pathways Panel comparing the expression profiles of EV-treated CD34+ cells and control (vehicle) CD34+ cells.

overall_design: Gene expression profiles were analyzed from untreated AML CD34+ (n=9) and EV-treated AML CD34+ cells (n=10)


title: Yin Yang 1 and guanine quadruplexes protect dopaminergic neurons from cellular stress via transmissive dormancy

city: Dallas

first: Peter

middle: M

last: Douglas

state: Tx

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Multiparameter imaging reveals clinically relevant cancer cell – stroma interaction dynamics in head and neck cancer

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

summary: Epithelial tumors are characterized by abundant inter- and intra-tumor heterogeneity, which complicates diagnostics and treatment. The contribution of cancer-stroma interactions to this heterogeneity is poorly understood. Here we report a paradigm to quantify phenotypic diversity in head and neck squamous cell carcinoma (HNSCC) with single cell resolution. By combining cell state markers with morphological features, we identify phenotypic signatures that correlate with clinical features, including metastasis and recurrence. Integration of tumor and stromal signatures reveals that partial epithelial-mesenchymal transition (pEMT) renders disease outcome highly sensitive to stromal composition, generating a strong prognostic and predictive signature. Spatial transcriptomics and subsequent analyses of cancer spheroid dynamics identifies cancer-associated fibroblast–pEMT axis as a nexus for intercompartment signaling that reprograms pEMT cells into an invasive phenotype. Taken together, we establish a paradigm to identify clinically relevant tumor phenotypes, and discover a cell state-dependent interplay between stromal and epithelial compartments that drives cancer aggression.

overall_design: Human tongue squamous cell carcinoma cells UTSCC74a (isolated from a 31-year-old male with T3N1M0 G1-2 primary tumor) and UTSCC76a (isolated from a 52-year old male with T3N0M0 G2 primary tumor) were obtained from University of Turku. CAFs were isolated from a T2N2bM0 G1 primary tumor of the buccal mucosa. Cells were plated as single-cell suspensions into U-bottom ultra-low attachment 96-well plates (Corning 4520) in in DMEM (4500, mg/L glucose, 1x GlutaMAX, Gibco) supplemented with 1x non-essential amino acids (Gibco), 1x penicillin/streptomycin (Gibco) and 10% fetal bovine serum (Sigma-Aldrich). Cancer cells were cultured either alone or as co-cultures with CAFs. Cells were harvested after 48h.

first: Karolina

last: Punovuori

first: Kai

last: Kruse


title: Yin Yang 1 and guanine quadruplexes protect dopaminergic neurons from cellular stress via transmissive dormancy [TG timeline RNA-seq]

summary: Neurons deploy diverse adaptive strategies to ensure survival and neurotransmission amid cellular stress. Yet, when these adaptive pathways are overwhelmed, functional impairment or neurodegeneration follow. Herein we report a scenario where stressed neurons actively adopt a state of transmissive dormancy, despite rapid activation of stress response pathways, as a terminal protective measure. Examination of dopaminergic neurons surviving severe cellular stress, revealed decreased spontaneous activity accompanied by dynamic control of dopamine metabolism through the Yin Yang 1 (YY1) transcriptional regulator. Under conditions of ionic imbalance or oxidative stress, YY1 promotes expression of the SLC18A2 transporter with the capacity to enhance sequestration of dopamine into transport vesicles. Subsequent DNA damage represses the rate-limiting enzyme in dopamine synthesis, tyrosine hydroxylase (TH), through YY1 mediated stabilization of an intronic guanine quadruplex. This cascade has the potential to drive circuit inactivation and safeguard neurons by minimizing the toxic accumulation of cytosolic dopamine and reducing the energetic expenditure associated with cellular depolarization. In essence, neurons appear to actively prioritize viability over functionality.

overall_design: Differentiated LUHMES cells were treated with 10 nM thapsigargin or DMSO for 30 minutes and RNA samples were collected 3, 6, and 24 hours after drug removal.

first: Kielen

last: Zuurbier


title: Yin Yang 1 and guanine quadruplexes protect dopaminergic neurons from cellular stress via transmissive dormancy [YY1 CUT&RUN]

overall_design: Differentiated LUHMES cells were treated with 10 nM TG or DMSO and collected 24 hours later. 6 biological replicates were collected and combined for CUT&RUN in duplicate (3 each). CUT&RUN targets included YY1, H3K4me3, and input control


title: Epigenetic Dysregulation of H19/IGF2 in Hepatic Cells Exposed to Toxic Metal Mixtures In Vitro [RNA-seq]

status: Public on Oct 27 2024

city: Cheonan

first: Jihye

last: Park

address: 119 Dan-daero, Dongnam-gu

country: South Korea

institute: Dankook University

summary: Exposure to mixtures of toxic metals is known to cause adverse health effects through epigenetic alterations. Here we aimed to examine the unexplored area of aberrant DNA methylation in the H19/IGF2 domain following combined toxic metal exposure. An in vitro epigenotoxicity assay using the human normal liver epithelial cell line THLE-3 was conducted. When THLE-3 cells were exposed to specific concentrations of either organic arsenic or MeHgCl, an increase in the H19 lncRNA levels and a marked reduction in the IGF2 mRNA levels were observed. In contrast, combined exposures coupled with CdCl2 resulted in the transcriptional repression of H19 and transcriptional activation of IGF2. It should be noted that the correlation between the dysregulated expression of H19/IGF2 and the hypermethylated CpG sites within the H19 differentially methylated region (DMR) was statistically significant. Furthermore, we performed transcriptomic analysis of the hepatocytes exposed to toxic metal combinations indicating enrichment of pro-inflammatory and anti-proliferative pathways compared to the unexposed cells. Our results suggest that hazardous metal mixtures may trigger epigenetic aberrations at the H19/IGF2 locus. We propose that altered CpG methylation in the H19 DMR could be a candidate biomarker for hepatic epigenotoxicity, in part, due to environmental exposure.

overall_design: To explore the effects of toxic metal exposure on gene expression, we conducted transcriptome analysis using RNA-seq in control and metal-exposed cells. The study includes RNA-seq samples with paired-end sequencing data collected from four experimental conditions: TAC-0, TAC-6, TCH-0, and TCH-6.

first: Yehoon

last: Jo

first: Eugene

last: Lim

first: Keunsoo

last: Kang

first: Miyeon

last: shin

first: Jeongweon

last: Choi

first: Sungkyoon

last: Kim

first: Jaehyouk

last: Lee


title: ATAC-seq data of miR-195 transduced Ebf1-KO FL-ProB-cells.

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

institute: Saga University

summary: EBF1 is crucial transcription factor in B cell lineage and Ebf1 -/- hematopoietic stem cells are arrest in early B cell development and disable to express CD19. miR-195 transduction is able to overcome Ebf1 deficiency and cause CD19 positive cells. ATAC-seq data of these cells provided a new insight into relationship between early B cell differentiation and micro-RNA regulation.

overall_design: ATAC-seq was performed on more than 5000 transplanted cells of from bonemarrow of NOG mouse in which miR-195 transduced or not EBF1 -/- FL cells were injected. Data was aligned to mouse reference genome mm10 and peak summits were determined using MACS3.

first: Y

last: Miyatake

first: R

last: Maruyama

first: A

last: Kotani


title: RNAsequencing of plasma cells generated ex vivo upon 2 days of LPS stimulation on WT and Sec22B-KO plasma cells

city: PARIS

first: Marion

last: Espeli

address: 1 avenue Claude Vellefaux, Inserm U1160, Institut de Recherche Saint Louis

country: France

institute: Inserm U1160

summary: We report RNAseq data obtains from ex vivo generated plasma cell after 2 days of stimulation with LPS. We compare WT plasma cells to Sec22bB-KO plasma cells. Sec22b KO is specific of B cell lineage. We find over 6000 genes differentially regulated between both genotypes. Gene set enrichment analyses (GSEA) revealed that several pathways were significantly different between WT and Sec22bB-KO PCs.

overall_design: Examination of transcriptome of ex vivo generated plasma cells from WT or Sec22b B-KO mice.

last: Espéli

first: Amélie

last: Bonaud


title: Epigenetic Dysregulation of H19/IGF2 in Hepatic Cells Exposed to Toxic Metal Mixtures In Vitro [Bisulfite-seq]

overall_design: To investigate the effects of toxic metal exposure on DNA methylation, we performed bisulfite amplicon sequencing (BSAS) to assess the methylation status at the H19/IGF2 locus in control and metal-exposed cells. BSAS samples were collected under various experimental conditions, including control (no exposure), organoarsenic (oAs, 10 μM), cadmium chloride (CdCl2, 1 μM), and methylmercury (MeHgCl, 10 nM), either individually or in combination. The CpG sites within the H19 differentially methylated region (DMR) and imprinting control region (ICR) were analyzed to quantify methylation changes across these exposure conditions.


title: Intestine epithelial specific hypoxia-inducible factor-1α overexpression on ileum transcriptome

status: Public on Oct 26 2024

city: Louisville

first: MING

last: SONG

state: KY

address: 505 S. Hancock St.

institute: University of Louisville

summary:
Background: Intestine epithelial hypoxia-inducible factor-1α (HIF-1α) plays a critical role in maintaining gut barrier function. The aim of this study was to determine genetic activation of intestinal HIF-1α ameliorates western diet-induced metabolic dysfunction–associated steatotic liver disease (MASLD).
Methods: Male and/or female intestinal epithelial-specific Hif1α overexpression mice (Hif1α LSL/LSL;VilERcre) and wild-type littermates (Hif1α LSL/LSL) were fed with regular chow diet, high fructose (HFr) or high-fat (60% Kcal) high-fructose diet (HFHFr) for 8 weeks. Metabolic phenotypes were profiled.
Results: Male Hif1α LSL/LSL;VilERcre mice exhibited markedly improved glucose tolerance compared to Hif1α LSL/LSL mice in response to HFr diet. Eight weeks HFHFr feeding led to obesity in both Hif1α LSL/LSL;VilERcre and Hif1α LSL/LSL mice. However, male Hif1α LSL/LSL;VilERcre mice exhibited markedly attenuated hepatic steatosis along with reduced liver size and liver weight compared to male Hif1α LSL/LSL mice. Moreover, HFHFr-induced systemic inflammatory responses were mitigated in male Hif1α LSL/LSL;VilERcre mice compared to male Hif1α LSL/LSL mice and those responses were not evident in female mice. Ileum RNA-seq analysis revealed that glycolysis/gluconeogenesis was up in male Hif1α LSL/LSL;VilERcre mice accompanied by increased epithelial cell proliferation.
Conclusion: Our data provide evidence that genetic activation of intestinal HIF-1α markedly ameliorates western diet-induced MASLD in a sex-dependent manner. The underlying mechanism is likely attributed to HIF-1α activation induced upregulation of glycolysis, which, in turn, leading to enhanced epithelial cell proliferation and augmented gut barrier function.

overall_design:
To understand the mechanisms of intestine HIF-1α overexpression on gut barrier function, we performed ileum bulk RNA-seq analysis in male and female Hif1α LSL/LSL and Hif1α LSL/LSL;VilERcre  mice [n=3(2 male, 1 female)/group].
Gene expression profile in the mouse ileum was compared between the two groups (Hif1α LSL/LSL versus Hif1α LSL/LSL;VilERcre ie. FLOX_IL versus IECOE_IL)

first: Ming

last: Song