title: Synthetic prostacyclin ONO-1301 Enhance Survival of Human Pluripotent Stem Cell-Derived Cardiomyocytes Tissue Transplantation in a Rat Myocardial Infarction Model

status: Public on Mar 26 2023

first: Daisuke

last: Motooka

summary: To investigate whether ONO-1301 activates angiogenesis-related signaling pathways in 253G1 derived cardiomyocytes

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 253G1 derived cardiomyocytes with or without the addition of ONO-1301.

first: Xiang

last: Qu

first: Junjun

first: Yoshiki

last: Sakai

first: Jingbo

last: Zhang

first: Ying

last: Hua

first: Kota

first: Akima

last: Harada

first: Li

last: Sawa

first: Shigeru

last: Miyagawa


title: Mapping of RNA Interactomes in Adenoma-carcinoma Sequence of Human Colorectal cancer

status: Public on Mar 23 2023

city: Jiaxing

first: Wu

last: Zhou

address: No 118, Rd Jiahang Avenue

country: China

institute: Jiaxing University

summary: To study the dynamics of RNA interactomes, RIC-seq was performed on several biological replicates of colorectal cancer patients, each including colorectal adenomas, cancerous tissues, and tissues distal to cancer

overall_design: Comparative RNA interaction profiling analysis of RIC-seq data for  colorectal adenomas, cancerous tissues, and tissues distal to cancer

first: Jing-Yu

last: Wang

first: Xiao-Ping

first: Hong-Kun

first: Hong-Xin

last: Cai

first: Jin-Biao

last: Xu

first: Bao-Gang

last: Xie


title: KRT13 is upregulated in pancreatic cancer stem-like cells and associated with radioresistance

status: Public on Mar 29 2023

city: Suita

first: Daisuke

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

type: Expression profiling by high throughput sequencing

summary: Pancreatic cancer is one of the most aggressive cancers and the seventh leading cause of cancer-associated death in the world. Radiation is performed as an adjuvant therapy as well as anti-cancer drugs. Because cancer stem-like cells (CSCs) are considered to be radioresistant and cause recurrence and metastasis, understanding their properties is required for the development of novel therapeutic strategies. To investigate the CSC properties of pancreatic cancer cells, we used a pancreatic CSC model, ZsGreen++ cells, which have low proteasome activity. ZsGreen++ cells displayed radioresistance in comparison with control cells. Using RNA sequencing, we successfully identified KRT13 as a candidate gene responsible for radioresistance. Knockdown of KRT13 sensitized the ZsGreen++ cells to radiation. Furthermore, a database search revealed that KRT13 is upregulated in pancreatic cancer cell lines and that high expression of KRT13 is associated with poorer prognosis. These results indicate that a combination therapy of KRT13 knockdown and radiation could hold therapeutic promise in pancreatic cancer.

overall_design: RNA-sequencing analyses were performed in two types of cell lines.

first: Y

last: Yokoyama

first: D

last: Okuzaki

first: H

last: Yamamoto


title: Hypoxic niches attract and sequester tumor-associated macrophages and cytotoxic T cells and reprogram them for immunosuppression.

status: Public on Mar 31 2023

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: Glioblastoma (GBM), a highly lethal brain cancer, is notorious for immunosuppression, but the mechanisms remain unclear. Here, we documented a temporospatial patterning of tumor-associated myeloid cells (TAMs) corresponding to vascular changes during GBM progression. As tumor vessels transitioned from the initial dense regular network to later scant and engorged vasculature, TAMs shifted away from perivascular regions and trafficked to vascular-poor areas. This process was heavily influenced by the immunocompetence state of the host. Utilizing a sensitive fluorescent UnaG reporter to track tumor hypoxia, coupled with single-cell transcriptomics, we revealed that hypoxic niches attracted and sequestered TAMs and cytotoxic T lympho- cytes (CTLs), where they were reprogrammed toward an immunosuppressive state. Mechanistically, we identified chemokine CCL8 and cytokine IL-1b as two hypoxic-niche factors critical for TAM trafficking and co-evolution of hypoxic zones into pseudopalisading patterns. Therefore, perturbation of TAM patterning in hypoxic zones may improve tumor control.

overall_design:
Single cell sequencing of mouse brain carrying GL261 intracranial GBM transplant engineered with HIF reporter HRE-UnaG.

**Please note that the records have been updated on June 12, 2024 as the previous files and information were incorrect***

first: A

last: Sattiraju

first: S

last: Kang

first: B

last: Giotti

first: Z

last: Chen

first: V

middle: J

last: Marallano

first: C

last: Brusco

first: L

last: Shen

first: AM

last: Tsankov

last: Hambardzumyan

first: R

middle: H

last: Friedel

last: Zou


title: Comprehensive Analysis of Transcriptome in Dorsal Root Ganglia Following Chronic Constriction Injury.

status: Public on Mar 15 2023

city: Changchun

first: yao

last: qu

state: Jilin

address: NO1 Xinmin Street

department: Department of Anesthesiology

institute: The First Hospital of Jilin Univeristy

summary: To investigate mechanisms underlying neuropathic pain, we established sciatic nerve chronic constriction injury (CCI) neuropathic pain model in rats, and performed RNA-seq on ipsilateral bulk L4-L6 dorsal root ganglia from CCI rats and sham rats 11 days after surgery. By comprehensive analysis, we identified several key mRNAs and miRNAs, especially those associated with inflammatory immune response, may serve as promising targets, facilitating further investigation and eventually developing better therapeutic strategies for NP.

overall_design: Comparative and comprehensive analysis of gene expression profiling of CCI rats and sham rats.

first: Yao

last: Qu

first: Laijin

last: Lu

first: Han

last: Wang

first: Qiao

last: Li

first: Ruirui

last: Cai


title: Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPα [CRISPRi]

status: Public on Mar 08 2023

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

address: 1 Barker Hall #3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the hematopoietic transcription factor C/EBPα produced from different start sites exert opposing effects during myeloid cell development. This alternative initiation depends on sequence features of the CEBPA transcript, including a regulatory upstream open reading frame (uORF), but the molecular basis is not fully understood. Here we identify trans-acting factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescence reporter coupled with CRISPRi screening. Our screen uncovered a role for the ribosome rescue factor PELOTA (PELO) in promoting expression of the longer C/EBPα  isoform, by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin (mTOR) kinase. Our work provides further mechanistic insights into coupling between ribosome recycling and translation reinitiation in regulation of a key transcription factor, with implications for normal hematopoiesis and leukemiagenesis.

overall_design: Sublibrary CRISPR-dCas9 knockdown (CRISPRi) screens were performed in two color reporter cell lines to identify trans-factors that drive translation start site choice on CEBPA. CRISPRi sublibrary screens were performed using four, compact BFP-tagged CRISPRi sublibraries containing 5 sgRNAs per TSS (Addgene, #83971-3 and #83975) expressed in the pCRISPRi-v2 expression vector (Addgene, #84832). Plasmid sublibraries were separately packaged in HEK 293T Lenti-X cells and transduced into the CRISPRi dual color reporter line at an MOI < 1 where the percentage of transduced cells by BFP expression after 2 days post-transduction was 20%-30%. At 2 days post-transduction, we performed fluorescence activated cell sorting (FACS) using an Aria Fusion (BD Biosciences) to select for cells expressing BFP. Cells with the highest (20%) BFP expression were collected and recovered in RPMI 1640 for 6 days post-FACS. Approximately 10 million cells were collected per sublibrary, maintaining an average sgRNA coverage of at least 500 cells per sgRNA. At 6 days post-BFP selection, cells were again sorted using a FACS Aria Fusion based on the ratio of green/red fluorescence from our CEBPA dual color reporter line. Approximately 40 million cells per sublibrary transduction were sorted into four, distinct green/red bins (20-25% of cells in each bin), with each bin containing 8-10 million cells to ensure an average sgRNA/cell coverage of at least 500. Genomic DNA was immediately harvested from these cells using the DNeasy Blood and Tissue kit (Qiagen, 69504) and sgRNA fragments were isolated by SbfI (New England Biolabs) restriction digestion and Ampure bead size selection then amplified by PCR for deep sequencing using custom sequencing primers. The sgRNAs were sequenced on an Illumina HiSeq-4000 using custom primers.

first: Samantha

middle: G

last: Fernandez

first: Lucas

last: Ferguson


title: Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPα

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

overall_design: Refer to individual Series


title: Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPα [riboprofiling]

summary: Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the hematopoietic transcription factor C/EBPα produced from different start sites exert opposing effects during myeloid cell development. This alternative initiation depends on sequence features of the CEBPA transcript, including a regulatory upstream open reading frame (uORF), but the molecular basis is not fully understood. Here we identify trans-acting factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescence reporter coupled with CRISPRi screening. Our screen uncovered a role for the ribosome rescue factor PELOTA (PELO) in promoting expression of the longer C/EBPα isoform, by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin (mTOR) kinase. Our work provides further mechanistic insights into coupling between ribosome recycling and translation reinitiation in regulation of a key transcription factor, with implications for normal hematopoiesis and leukemiagenesis.

overall_design: To determine the impact of reduced PELO levels on ribosome occupancy transcriptome-wide and on a CEBPA, we established a CEBPA fluorescent reporter in K562 cells. We then depleted PELO by sgRNA (CRISPRi). We determined changes in translation on our reporter (and transcriptome-wide) by ribosome profiling using the nucleases, RNAse1 and P1. A nontargeting sgRNA was used as a control and both sgRNA conditions (nontargeting and PELO KD) were performed in triplicate. Samples from each condition and replicate were also taken for matched RNA-seq gene expression analysis.


title: Impaired polyamine metabolism causes behavioral and neuroanatomical defects in a novel mouse model of Snyder-Robinson Syndrome

status: Public on Mar 06 2023

city: Pittsburgh

first: Dwi

last: Kemaladewi

state: PA

address: 4200 Fifth Avenue

department: Pediatrics

institute: University of Pittsburgh

summary: The polyamines (putrescine, spermidine, and spermine) are essential molecules for normal cellular functions and are subject to strict metabolic regulation. Mutations in the gene encoding spermine synthase (SMS) lead to accumulation of spermidine in an X-linked recessive disorder known as Snyder-Robinson syndrome (SRS). Presently, no treatments exist for this rare disease that manifests with a spectrum of symptoms including intellectual disability, developmental delay, thin habitus, and low muscle tone. The development of therapeutic interventions for SRS will require a suitable disease-specific animal model that recapitulates many of the abnormalities observed in patients. Here, we characterize the molecular, behavioral, and neuroanatomical features of a mouse model with a missense mutation in the Sms gene that results in a glycine-to-serine substitution at position 56 (G56S) of the SMS protein. Mice harboring this mutation exhibit a complete loss of SMS protein and elevated spermidine/spermine ratio in skeletal muscles and the brain. In addition, the G56S mice demonstrate increased anxiety, impaired learning, and decreased explorative behavior in fear conditioning, Morris water maze, and open field tests, respectively. Furthermore, these mice failed to gain weight over time and exhibit abnormalities in brain structure and bone density. Transcriptomic analysis of the cerebral cortex revealed downregulation of genes associated with mitochondrial oxidative phosphorylation and ribosomal protein synthesis. Our findings also revealed impaired mitochondrial bioenergetics in fibroblasts isolated from the G56S mice, indicating a correlation between these processes in the affected mice. Collectively, our findings establish the first in-depth characterization of an SRS preclinical mouse model that identifies cellular processes that could be targeted for future therapeutic development

overall_design: Transcriptomic profile by RNA-seq from isolated brain cortex in diseased mice that carry a pathogenic mutation in the Sms gene causing Snyder-Robinson Syndrome was compared to healthy wildtype control mice

first: Oluwaseun

last: Akinyele


title: Expression data for Vanderbilt triple-negative breast cancer subtype classification

status: Public on Mar 04 2023

city: Seoul

first: Kyungsoo

last: Kim

address: 50 Yonsei-ro, Seodaemun-gu

department: Biotechnoloty

country: South Korea

institute: Yonsei University

summary:
This study developed a triple-negative breast cancer (TNBC) surrogate subtype classification that represents TNBC subtypes based on the Vanderbilt subtype classification
The web-based subtyping tool TNBCtype was used to classify the TNBC cohort into Vanderbilt subtypes

overall_design: Patients who underwent breast cancer surgery between January 2009 and October 2017 at Seoul St. Mary’s Hospital were included

first: Tae-Kyung

last: Yoo

first: Byung

last: Chae


title: A nucleosome switch primes Hepatitis B Virus infection [RNA-Seq]

status: Public on Mar 03 2023

first: Andres

last: Mansisidor

state: NY

address: 1230 York Ave Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: Rockefeller University

summary: Chronic hepatitis B virus (HBV) infection is an incurable global health threat capable of causing liver disease and hepatocellular carcinoma. During the genesis of infection, HBV establishes an independent chromosome, cccDNA, consisting of the circular viral genome and host histones. The first viral protein expressed, HBx, induces degradation of a host silencing factor to facilitate infection. However, the relationship between cccDNA’s chromatin and early HBx transcription state remains poorly understood. Using reconstituted viral chromosomes, we found that nucleosomes in cccDNA drive HBx transcription. We corroborated these findings in cells and further showed that chromatin destabilizing drugs inhibit viral transcription and antigen expression in hepatocytes. Our results shed new light on a long-standing paradox and represent a novel therapeutic avenue for the treatment of chronic HBV.

overall_design: We performed RNA-seq and MNase-seq on HEK293T cells that were transfected with hepatitis B virus (HBV) cccDNA over different timepoitns post transfection. We also performed MNase-seq on HBV cccDNA that was reconstituted with nucleosomes at different levels of saturation.

middle: A

last: Prescott

first: Andrés

first: Yaron

last: Bram

first: Abigail

last: Lemmon

first: Christine

last: Lim

first: Viviana

middle: I

last: Risca

first: Robert

middle: E

last: Schwartz

first: Yael

last: David

first: Rendleman

last: Justin

first: Faulkner

middle: C

last: Sarah

first: Hamard

last: Pierre-Jacques

first: Koche

last: Richard


title: GM-CSF drives immune-mediated glomerular disease by licensing monocyte-derived cells to produce MMP12

status: Public on Mar 01 2023

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: Glomerulonephritis is a group of immune-mediated diseases that cause inflammation within the glomerulus and adjacent compartments of the kidney and is a major cause of end-stage renal disease. T cells are among the main drivers of glomerulonephritis. However, the T cell subsets, cytokine networks, and downstream effector mechanisms that lead to renal tissue injury are largely unknown, which has hindered the development of targeted therapies. Here, we identify a population of granulocyte-macrophage colony-stimulating factor (GM-CSF)–producing T cells that accumulates in the kidneys of patients with antineutrophil cytoplasmic antibody (ANCA)–associated glomerulonephritis, infiltrates the renal tissue in a mouse model of glomerulonephritis, and promotes tissue destruction and loss of renal function. Mechanistically, we show that GM-CSF–producing T cells license monocyte-derived cells to produce matrix metalloproteinase 12 (MMP12), which cleaves components of the glomerular basement membrane and exacerbates renal pathology. Moreover, targeting GM-CSF or MMP12 reduced disease severity in mice with glomerulonephritis. Together, these findings provide a mechanistic rationale for the immunopathology of T cell–mediated diseases and identify this GM-CSF monocyte–derived cells–MMP12 axis as a promising therapeutic target for the treatment of glomerulonephritis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell sequencing of C57BL6 and Csf2-/- mice, single cell sequencing of patients

first: Hans-Joachim

last: Paust

first: Ning

last: Song

first: Nariaki

last: Asada

first: Selma

last: Tuzlak

first: Donatella

last: De Feo

first: Jan-Hendrik

last: Riedel

first: Malte

last: Hellmig

first: Amirrtavarshni

last: Sivayoganathan

first: Anett

last: Peters

first: Anna

last: Kaffke

first: Alina

last: Borchers

first: Ulrich

middle: O

last: Wenzel

first: Oliver

middle: M

last: Steinmetz

first: Gisa

last: Tiegs

first: Elisabeth

last: Meister

first: Maja

last: Lindenmeyer

first: Elion

last: Hoxha

first: Rolf

last: Stahl

first: Tobias

middle: B

last: Huber

first: Stefan

last: Bonn

first: Catherine

last: Meyer-Schwesinger

first: Thorsten

last: Wiech

first: Jan-Eric

last: Turner

first: Burkhard

last: Becher

first: Christian

middle: F

last: Krebs

first: Ulf

last: Panzer


title: Expression data of newly diagnosed multiple myeloma and extramedullary myeloma

city: Wuhan

first: Chunyan

last: Sun

state: HUBEI

address: 1277 Jiefang Dadao, Wuhan 430022, China

department: Hematology

institute: Wuhan Union Hospital

summary: Despite the development of novel therapeutic agents, multiple myeloma (MM) remains incurable, owing mainly to inevitable relapse in almost all patients. Some relapses occur as extramedullary disease (EMD), which is rare but is the most aggressive event in MM patients. Extramedullary myeloma (EMM) has extraordinary heterogeneous biological and clinical features. Previous studies have shown that expression levels of LncRNAs and mRNAs in different stages of MM are different. This study analyzes the expression levels of LncRNAs and mRNAs in primary plasma cells (PCs) from MM and EMM patients.

overall_design: Collecting primary PCs of multiple myeloma patients and extramedullary myeloma patients, extract total RNA and hybridize on Agilent microarrays.

first: Yu

last: Hu


title: The role of Activin A in the development of heterotopic ossification

status: Public on Mar 14 2023

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University


title: Adolescent binge ethanol impacts H3K36me3 regulation of synaptic genes

status: Public on Feb 21 2023

city: Richmond

first: JENNIFER

last: WOLSTENHOLME

state: VA

address: 1217 E Marshall Street, KMSB Rm 536

institute: Virginia Commonwealth University

type: Genome binding/occupancy profiling by high throughput sequencing


title: Adolescent binge ethanol impacts H3K36me3 regulation of synaptic genes [RNA-Seq]

summary: Adolescence is marked in part by the ongoing development of the prefrontal cortex (PFC). Binge ethanol use during this critical stage in neurodevelopment induces significant structural changes to the PFC, as well as cognitive and behavioral deficits that can last into adulthood. Previous studies showed that adolescent binge ethanol causes lasting deficits in working memory, decreases in the expression of chromatin remodeling genes responsible for the methylation of histone 3 lysine 36 (H3K36), and global decreases in H3K36 in the PFC. H3K36me3 is present within the coding region of actively-transcribed genes, and safeguards against aberrant, cryptic transcription by RNA Polymerase II. We hypothesize that altered methylation of H3K36 could play a role in adolescent binge ethanol-induced memory deficits. To investigate this at the molecular level, ethanol (4g/kg, i.g.) or water was administered intermittently to adolescent mice. RNA- and ChIP-sequencing were then performed within the same tissue to determine gene expression changes and identify genes and loci where H3K36me3 was disrupted by ethanol. We further assessed ethanol-induced changes at the transcription level with differential exon-use and cryptic transcription analysis – a hallmark of decreased H3K36me3. Here, we found ethanol-induced changes to the gene expression and H3K36me3-regulation of synaptic-related genes in all our analyses. Notably, H3K36me3 was differentially trimethylated between ethanol and control conditions at synaptic-related genes, and Snap25 and Cplx1 showed evidence of cryptic transcription in males and females treated with ethanol during adolescence. Our results provide preliminary evidence that ethanol-induced changes to H3K36me3 during adolescent neurodevelopment may be linked to synaptic dysregulation at the transcriptional level, which may explain the reported ethanol-induced changes to PFC synaptic function.

overall_design: Male and female adolescent DBA/2J mice were treated with water or 4g/kg of ethanol from PND 29-42 and PFC tissue was harvested 24 hours after the last dose for RNA-seq and ChIP-seq. RNA-seq data was subjected to differential gene expression, differential exon use, and cryptic transcription analyses. H3K36me3 ChIP-seq data was subjected to differential binding analysis. n= 5-6/group

first: Brocato

last: Emily R.

first: Wolstenholme

last: Jennifer T.


title: CD11c+ macrophages are pro-angiogenic and necessary for experimental choroidal neovascularization

status: Public on Feb 27 2023

city: Chicago

first: Jeremy

middle: Arin

last: Lavine

state: Illinois

address: McGaw M343

department: Ophthalmology

institute: Northwestern University

summary: Patients with neovascular AMD (nAMD) suffer vision loss from destructive angiogenesis, termed choroidal neovascularization (CNV). Macrophages are found in CNV lesions from nAMD patients. Additionally, Ccr2-/- mice, which lack classical monocyte-derived macrophages, show reduced CNV size. However, macrophages are highly diverse cells that can perform multiple functions. We performed single-cell RNA-sequencing on immune cells from wildtype and Ccr2-/- eyes to uncover macrophage heterogeneity during the laser-induced CNV mouse model of nAMD. We identified 12 macrophage subtypes, including Spp1+ macrophages. Spp1+ macrophages were enriched from wildtype lasered eyes and expressed a pro-angiogenic transcriptome via multiple pathways, including vascular endothelial growth factor signaling, endothelial cell sprouting, cytokine signaling, and fibrosis. Additionally, Spp1+ macrophages expressed the marker CD11c, and CD11c+ macrophages were increased by laser and present in CNV lesions. Finally, CD11c+ macrophage depletion reduced CNV size by 40%. These findings broaden our understanding of ocular macrophage heterogeneity and implicate CD11c+ macrophages as a potential therapeutic target for treatment-resistant nAMD patients.

overall_design: Ocular CD45+ immune cells were isolated by FACS and scRNA-seq was performed on sham and laser-treated wildtype and Ccr2-/- eyes.

first: Steven

last: Droho

first: Amrita

last: Rajesh

first: Carla

last: Cuda

first: Harris

last: Perlman


title: Single-cell RNA-seq analysis identifies distinct myeloid cells in COVID19 vaccination- associated encephalitis (set 2)

status: Public on Feb 20 2023

first: Daisuke

last: Motooka

summary: Background and Objectives  Recently accumulating evidence demonstrates the rare occurrence of COVID19 vaccination- induced inflammation in the central nervous system. However, the precise immune dysregulation related to the COVID19 vaccination-associated autoimmunity remains elusive. Here we report a case of COVID19 vaccination-associated encephalitis, where single-cell RNA sequencing (scRNA-seq)  analysis identified a distinct myeloid cell population in the blood during the acute phase of the disease.  Methods  Peripheral blood mononuclear cells (PBMCs) were analyzed by scRNA-seq to clarify the cellular components of the patients at both the acute and remission phases of the disease. The data obtained were compared to those acquired from a healthy cohort.  Results  In this study, scRNA-seq analysis of PBMCs identified a distinct myeloid cell population observed at the acute phase of encephalitis. The specific myeloid population was not detected both at the remission phase of the disease and the samples fromof a healthy cohort.  Discussion  Our findings illustrate the induction of a unique myeloid subset in COVID19 vaccination-associated encephalitis. Further accumulation of reports investigating the dysregulated immune signature of COVID19 vaccination-associated autoimmunity is warranted to clarify the pathogenic role of the myeloid subset observed in our study.

overall_design: Comparative gene expression profiling analysis of single cell RNA-seq data for PBMCs of COVID19 vaccination-associated encephalitis patient and healthy donors.

first: Masakazu

last: Ishikawa

last: Okuzaki


title: Single-cell RNA-seq analysis identifies distinct myeloid cells in COVID19 vaccination- associated encephalitis (set 1)


title: Meis1 establishes the pre-hemogenic endothelial state prior to Runx1 expression [CITE-seq]

status: Public on Feb 22 2023

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

summary: Hematopoietic stem and progenitor cells (HSPCs) originate from an endothelial-to-hematopoietic transition (EHT) during embryogenesis. Characterization of early hemogenic endothelial (HE) cells is required to understand what drives hemogenic specification and to accurately define cells capable of undergoing EHT. Using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), we defined the early subpopulation of pre-HE cells based on both surface markers and transcriptomes. We identified the transcription factor Meis1 as an essential regulator of hemogenic cell specification in the embryo prior to Runx1 expression. Meis1 is expressed at the earliest stages of EHT and distinguishes pre-HE cells primed towards the hemogenic trajectory from the arterial endothelial cells that continue towards a vascular fate. Endothelial-specific deletion of Meis1 impaired the formation of functional Runx1-expressing HE which significantly impeded the emergence of pre-HSPC via EHT. Our findings implicate Meis1 in a critical fate-determining step for establishing EHT potential in endothelial cells.

overall_design: CITE-Seq profiles of CD31+ cells FACS-isolated from dissected mouse AGM at embryonic day 10.5. Each replicate represents a pool of 2-5 embryos.

first: Patrick

last: Coulombe

first: Amanda

last: Fentiman

middle: D

last: Parker

first: Derek

last: Tam

first: Eric

last: Yung

first: R

middle: K

last: Humphries


title: Adolescent binge ethanol impacts H3K36me3 regulation of synaptic genes [ChIP-Seq]

last: WOLSTENHOLME

last: Emily R.


title: Aldh1a2+ fibroblastic reticular cells regulate lymphocyte recruitment in omental milky spots (stromal fraction of wild-type)

status: Public on Feb 14 2023

summary: Milky spots, lymphoid clusters present in visceral adipose tissue omentum, play central roles in the regulation of abdominal immunity. Milky spots exhibit hybrid nature between secondary lymph organs and ectopic lymphoid tissues, yet the mechanism of their development and maturation is poorly understood. Here, we identified a subset of fibroblastic reticular cells (FRCs) that are uniquely present in omental milky spots. These FRCs were characterized by the expression of retinoic acid converting enzyme, Aldh1a2, and endothelial cell marker, Tie2, in addition to canonical FRC-associated genes. Diphtheria toxin-mediated ablation of Aldh1a2+ FRCs resulted in the alteration in milky spot structure with a significant reduction in size and cellularity. Mechanistically, Aldh1a2+ FRCs regulated the display of chemokine CXCL12 on high endothelial venules (HEVs), which recruit blood-borne lymphocytes from circulation. We further found that Aldh1a2+ FRCs are required for the maintenance of peritoneal lymphocyte composition. These results illustrate the homeostatic roles of FRCs in the formation of non-classical lymphoid tissues.

overall_design: RNA from sorted omental stromal fractions from WT C57BL/6 mice were analyzed by RNA sequencing.

first: Tomomi

last: Yoshihara

first: Yasutaka

last: Okabe


title: Functional genomic analysis of adult and pediatric brain tumor isolates

status: Public on Feb 07 2023

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Despite in-depth knowledge of the molecular features and oncogenic drivers associated with adult and pediatric brain tumors, identifying effective targeted therapies for these cancers remains challenging. To identify novel gene dependencies in adult and pediatric brain tumor isolates, we integrated data from functional genomic lethality screens in primary brain tumor isolates with machine learning network models from lethality screens performed in >900 cancer cell lines.  Integrated network models revealed molecular and phenotypic features that predict candidate genetic dependencies in multiple brain tumor types, including: atypical teratoid rhabdoid tumors, diffuse intrinsic pontine gliomas, ependymomas, medulloblastomas, and glioblastomas (primary and recurrent).  Some examples of dependencies and predictors include: ADAR and MX1 protein expression; EFR3A and low EFR3B expression; FBXO42 and spindle assembly checkpoint activation; FGFR1 and high FGF2 expression; and SMARCC2 in SMARCB1 mutated ATRT tumors. In general, the results demonstrate that large functional genetic data sets can be leveraged to identify, validate, and categorize gene dependencies and their associated biomarkers in primary tumor isolates. The results also highlight some of the challenges and limitations of this approach.

overall_design: RNASeq data for adult and pediatric brain tumor isolates.

first: Pia

last: Hoellerbauer

first: Matt

last: Biery

last: Paddison


title: Aldh1a2+ fibroblastic reticular cells regulate lymphocyte recruitment in omental milky spots

last: Motooka

overall_design: RNA from whole omenta of WT and Postn-DTR mice at 5 days post DT injection was analyzed by RNA sequencing.


title: Aldh1a2+ fibroblastic reticular cells regulate lymphocyte recruitment in omental milky spots (single cell RNA-Seq)

overall_design: single cell RNA-Seq of omental leukocytes of WT and Postn-DTR mice at 5 days post DT injection


title: RNA-seq analysis for OVSAHO cells with upregulated SMARCA2 and downregulated SMARCA4 expression

summary: The goal of this study is to explore the underlying mechanism which contributes to chemoresistance in high-grade serous carcinoma (HGSC) with low SMARCA4 and high SMARCA2 expression.

overall_design: RNA-seq data were obtained from OVSAHO-Ctrl-siNC cells (control) and OVSAHO-A2-siA4 cells (upregulated SMARCA2 and downregulated SMARCA4 expression). Cells were cultured in medium containing carboplatin at 25 μM for 2 days.

first: Kansuke

last: Kido

first: Satoshi

last: Nojima

last: Okuzaki


title: ATAC-seq and RNA-seq analyses for OVSAHO cells with upregulated SMARCA2 and downregulated SMARCA4 expression


title: Dissecting 16p11.2 hemi-deletion to study sex-specific striatal phenotypes of neurodevelopmental disorders

status: Public on Feb 12 2023

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 169 Newton Road

department: Neuroscience and Pharmacology

institute: University of Iowa

summary: We report two bulk transcriptomic datasets of striatum from male and female mice carrying either the 16p11.2 hemideletion of 3 genes hemideletion knockout within this region.

overall_design: We performed bulk RNA sequencing gene expression analysis obtained from mouse striatum for two paradigms in both males and females: the full 16p11.2 hemideletion of 27 genes (16pdelhet vs. 16pdelhetWT) and the 3 genes knockout (3geneKOMut vs 3geneKOWT).

first: Jaekyoon

last: Kim

first: Zeru

last: Peterson

first: Benjamin

last: Kelvington

first: Marie

last: Gaine

first: Thomas

last: Nickl-Jockschat

first: Ted

last: Abel


title: Direct transposition of native DNA for sensitive multimodal single-molecule sequencing

city: San Francisco

first: Arjun

middle: S

last: Nanda

state: California

address: 1700 Owens St

department: Gladstone Institute for Data Science & Biotechnology

institute: Gladstone Institutes / UCSF

overall_design: Refer to individual Series


title: XCR1+ Dendritic Cell-Induced CD4+ T Helper-1 Activation Leads to Exacerbation of Remodeling after Myocardial Infarction (T cell research)

status: Public on Feb 06 2023

first: Daisuke

summary: Th1 is the predominant phenotype during the early stage of MI. XCR1+ cDC1 activated CXCR3+ Th1 could be a novel therapeutic target for ischemic cardiac remodeling.

overall_design: Examination of  tissue factors affecting charctrization of CD4+ T cell subsets after HFD-MI.

first: Michiko

last: Ichii

first: Makoto

last: Nishida


title: A single-cell atlas of immunocyte in spleen of a mouse model of Wiskott-Aldrich Syndrome

status: Public on Feb 05 2023

city: shanghai

first: george

last: yue

address: Room 4B, the 3rd Building, No. 401, Caobao Road, Xuhui District, Shanghai, China, 200233

institute: Genergy Bio-technology (Shanghai) Co., Ltd

summary: Wiskott-Aldrich syndrome (WAS) is a disorder characterized by rare X-linked genetic immune deficiency with mutations in the was gene, a gene expressed specifically in hematopoietic cells, and the spleen plays a major role in hematopoiesis and the clearance of red blood cell. However, till now, comprehensive analyses of the spleen between wild type (WT) and WASp-deficient (WAS-KO) mice, especially at the transcriptomic level, have not been studied. Here, single-cell RNA sequencing (scRNA-seq) was adopted to identify various types of immune cells and investigate the mechanism of immune deficiency. We identified 30 clusters and 10 major cell subtypes among 11, 269 cells, including B cell, T cell, dendritic cell (DC), Natural Killer (NK) cell, monocyte, macrophage, granulocyte, stem cell and erythrocyte. Meanwhile, we evaluated the gene expression differences of cell subtypes, and analyzed the differential gene expression (DEGs) and enrichment analyses to reveal the reasons for the dysfunction of these different cell populations in WAS. Furthermore, some key genes were screened out by comparing the DEGs of each cell type during specific and non-specific immunization, and further analysis showed that these key genes were newly discovered pathologically related genes in WAS-KO mice. In summary, we present a detailed single cell resolution landscape of immune cells in spleen of WAS-KO mice. These unprecedented data uncovered the transcriptional characteristics of specific and non-specific immune cells, and the key genes were identified to lay a foundation for future studies of WAS, especially in discovering novel and underexplored mechanisms to improve gene therapies for WAS.

overall_design: Single cells were encapsulated in droplets using 10 × Genomics GemCode Technology and processed according to the manufacturer’s instruction. scRNA-seq was adopted to identify various types of immune cells and investigate the mechanism of immune deficiency.

first: Fangfang

last: Liang

first: Cheng

last: Peng


title: Gene expression of brain cells from wild type and Gba flox/flox; Nestin-Cre mice

status: Public on Feb 03 2023

last: Motooka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: To investigate neuronopathic Gaucher disease brain cell gene expression, we established Gba flox/flox; Nestin-Cre mice and performed scRNA sequencing of whole brain cells from these and wild type mice. Unbiased clustering analysis revealed that most remarkable change between wild type and Gba flox/flox; Nestin-Cre mice was the appearance of an activated microglia cluster, which exclusively expressed Tnf. Our further study elucidated the mechanism by which activated microglia and TNF contribute to Gaucher disease pathology.

overall_design: Whole brain cells from 2-week-old wild type and Gba flox/flox; Nestin-Cre mice were analyed using scRNA sequencing.

first: Takashi

last: Shimizu

first: Charles

last: Schutt

first: Yu-Chen

last: Liu

first: Sho

last: Yamasaki


title: ATAC-seq analysis for OVSAHO cells with upregulated SMARCA2 and downregulated SMARCA4 expression

overall_design: ATAC-seq data were obtained from OVSAHO-Ctrl-siNC cells (control) and OVSAHO-A2-siA4 cells (upregulated SMARCA2 and downregulated SMARCA4 expression). Cells were cultured in medium containing carboplatin at 25 μM for 2 days.

first: Kansuke

last: Kido

first: Satoshi

last: Nojima

last: Okuzaki


title: Gene expression of microglia from wild type, Gba flox/flox; Nestin-Cre, and Gba flox/flox; Nestin-Cre; Mincle-/- mice

summary: To investigate the contribution of Mincle in neuronopathic Gaucher disease, we established Gba flox/flox; Nestin-Cre mice and crossed them with Mincle deficient mice. RNA sequencing of microglia from these mice revealed Axl, a phaogocytic receptor was upregulated in Gba flox/flox; Nestin-Cre mice. In addition, Tnf was upregulated in Gba flox/flox; Nestin-Cre mice in a Mincle-dependent manner. Our further study elucidated that Mincle, Axl and TNF are involved in the pathology of Gaucher disease.

overall_design: Microglia from 2-week-old wild type, Gba flox/flox; Nestin-Cre, and Gba flox/flox; Nestin-Cre; Mincle-/- mice were isolated by magnetic cell sorting and analyzed using RNA sequencing.


title: XCR1+ Dendritic Cell-Induced CD4+ T Helper-1 Activation Leads to Exacerbation of Remodeling after Myocardial Infarction


title: Multimodal decoding of human liver regeneration [snrna_human]

status: Public on Feb 01 2023

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

summary: Using snRNA-seq combined with spatial profiling of healthy and ALF explant human livers, we uncover a novel migratory hepatocyte subpopulation. We discover a corollary subpopulation in a mouse model of APAP-induced liver regeration, and demonstrate that this subpopulation meidates wound closure following liver injury.

overall_design: Single nuclei were isolated from human liver explants (n=9 healthy, n=11 APAP, n=12 NonAE)

first: Kylie

middle: P

last: Matchett

first: Jordan

middle: R

last: Portman

first: Chantriolnt-Andreas

last: Kapourani

first: Neil

last: Henderson


title: Multimodal decoding of human liver regeneration [st_mouse]

overall_design: Spatial transcriptomics was performed on mouse livers along an APAP-induced liver regeneration timecourse.


title: Toxoplasma IWS1 determines fitness in interferon-γ-activated host cells and mice by regulating ROP18 mRNA expression

status: Public on Jan 30 2023

city: Suita

first: Daisuke

address: 3-1, Yamadaoka

summary: Toxoplasma gondii secretes various virulence effector molecules into host cells to disrupt host interferon-γ (IFN-γ)-dependent immunity. Among the effectors, ROP18 directly phosphorylates and inactivates IFN-inducible GTPases, such as immunity-related GTPases (IRGs) and guanylate-binding proteins (GBPs), leading to subversion of IFN-inducible GTPase-induced cell-autonomous immunity. The modes of action of ROP18 have been studied extensively; however, little is known about the molecular mechanism of how ROP18 is produced in the parasite itself. Here, we report a role of T. gondii transcription factor IWS1 in ROP18 mRNA expression in the parasite. Compared with wild-type virulent type I T. gondii, IWS1-deficient parasites showed dramatically increased loading of IRGs and GBPs onto the parasitophorous vacuole membrane (PVM). Moreover, IWS1-deficient parasites displayed decreased virulence in wild-type mice but retained normal virulence in mice lacking the IFN-γ receptor. Furthermore, IWS1-deficient parasites showed severely decreased ROP18 mRNA expression. Ectopic expression of ROP18 in IWS1-deficient parasites restored the decreased loading of effectors onto the PVM and in vivo virulence in wild-type mice. Taken together, these data demonstrate that T. gondii IWS1 regulates ROP18 mRNA expression to determine fitness in IFN-γ-activated host cells and mice.

overall_design: We compared global gene expression profiles in freshly isolated tachyzoites of wild-type and IWS1-deficient type I T. gondii as triplicate.

first: Emi

last: Hashizaki

first: Masahiro

last: Yamamoto


title: Multimodal decoding of human liver regeneration [st_human]

overall_design: Spatial transcriptomics was performed on human liver explants (n=3 healthy, n=3 APAP, n=2 NonAE)


title: Metabolic subtyping based on dynamic network biomarker reveals potential therapeutic targets in hepatocellular carcinoma

status: Public on Jan 31 2023

city: Shanghai

first: Qi

last: Feng

address: 180 Fenglin Street, Xuhui District

institute: Zhongshan Hospital

summary: The purpose of this study is to identify the characteristics of different HCC subtypes through next generation  sequencing and metabolome analysis.The samples for transcriptome sequencing were collected from 60 cases of HCC, 30 of which were also used for whole exome sequencing and LC-MS/MS.

overall_design: Transcriptome sequencing, whole exome sequencing and LC-MS / MS were used to obtain the multi omic characteristics of HCC samples.The characteristics of different subtypes were obtained by data analysis and experiment.

first: Feng

last: Qi

first: Jia

last: Li

first: Zhuoran

first: Bei

last: Lv

first: Yongde

last: Luo

first: Jian

last: Zhang

first: Bin

last: Zhou

first: Biwei

last: Yang

first: Wenxing

last: Qin

first: Jinglin

last: Xia


title: Multimodal decoding of human liver regeneration

first: John

last: Wilson-Kanamori

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


title: Investigating microenvironment in MDS

status: Public on Jan 25 2023

city: Taipei

first: Yu-Hung

last: Wang

address: N0 7, Chung-Shan South Rd

country: Taiwan

institute: National Taiwan University Hospital

summary: High BM plasma S100A8/A9 is associated with a perturbed microenvironment and poor prognosis in myelodysplastic syndromes

overall_design: mRNA profiles of 215 MDS patients using RNA-seq

first: Hwei-Fang

last: Tien

first: Wen-Chien

last: Chou

first: Chien-Chin

last: Lin


title: Canagliflozin combined with aerobic exercise protects against chronic heart failure in rats via regulating the retinol metabolism signaling pathway.

status: Public on Feb 17 2023

city: Jinan

first: Bingyu

last: Du

state: 请选择省

address: Jingshi Road

institute: 山东省千佛山医院

summary: To determine the efficacy and potential protective mechanism of canagliflozin combined with aerobic exercise in treating chronic heart failure (CHF).During 10 days, isoproterenol (5 mg/kg/d) was injected into rats to create CHF models. The rats were then randomized into four groups and administered with saline, canagliflozin (3 mg/kg/d), aerobic exercise training, and canagliflozin combined with aerobic exercise training. Then, we performed gene expression profiling using the data obtained by RNA-seq in the Control, HF, LC and LC-AE groups.

overall_design: Comparative gene expression profiling of RNA-seq data from the control, HF, LC and LC-AE groups.

first: Yanyan

last: Yin

first: Hui

last: Fu

first: Zhaodi

last: Yue

first: Helin

last: Sun

first: Xueyin

first: Shaohong

last: Yu

first: Zhongwen


title: Multimodal decoding of human liver regeneration [snrna_mouse]

overall_design: Single nuclei were isolated from mouse livers along an APAP-induced liver regeneration timecourse.

first: Kylie

last: Matchett

first: Jordan

last: Portman

first: Chantriolnt-Andreas

last: Kapourani

first: Neil

last: Henderson


title: Effect of genomic and cellular environments on gene expression noise [pools]

status: Public on Jan 23 2023

city: Saint Louis

first: Barak

last: Cohen

state: MO

address: 4515 Mckinley Ave

institute: Washington University in St. Louis

summary: Individual cells from isogenic populations often display large cell-to-cell differences in gene expression. This “noise” in expression derives from several sources, including the genomic and cellular environment in which a gene resides. Large-scale maps of genomic environments have revealed the effects of epigenetic modifications and transcription factor occupancy on mean expression levels, but leveraging such maps to explain expression noise will require new methods to assay how expression noise changes at locations across the genome. To address this gap, we present Single-cell Analysis of Reporter Gene Expression Noise and Transcriptome (SARGENT), a method that simultaneously measures the noisiness of reporter genes integrated throughout the genome and the global mRNA profiles of individual reporter-gene-containing cells. Using SARGENT, we performed the first comprehensive genome-wide survey of how genomic locations impact gene expression noise. We found that the mean and noise of expression correlate with different histone modifications. We quantified the intrinsic and extrinsic components of reporter gene noise and, using the associated mRNA profiles, assigned the extrinsic component to differences between the CD24+ “stem-like” sub-state and the more “differentiated” sub-state. SARGENT also reveals the effects of transgene integrations on endogenous gene expression, which will help guide the search for “safe-harbor” loci. Taken together, we show that SARGENT is a powerful tool to measure both the mean and noise of gene expression at locations across the genome, and that the data generated by SARGENT reveals important insights into the regulation of gene expression noise genome-wide.

overall_design: K562 clonal cells containing reporter genes integrated in different locations were pooled and used for 10x scRNA-seq. We performed four sets of this experiment that we call pool1, pool2, pool3 and pool4. For pool1 we used cells from a clonal cell-line we call LP3, For pool2, pool3 and pool4 we used cells from another clonal cell-line called LP1. Both LP1 and LP3 are derived from the K562 cell-line. We performed 2 replicates for each pool, Rep1 and Rep2. For Pool2 we also captured the RNA molecules in two ways: using polyA (named pa) and using a capture sequence (named cs)

first: Clarice

last: Hong

first: Avinash

last: Ramu

first: Siqi

last: Zhao


title: Effect of genomic and cellular environments on gene expression noise


title: Effect of genomic and cellular environments on gene expression noise [bulk-mapping]

overall_design: K562 clonal cells containing reporter genes integrated in different locations were pooled and used for 10x scRNA-seq. LP3 and LP1 are two different clonal cell-lines (derived from K562) that we used for these experiments.


title: Immunotoxicity Evaluation of Trihalophenolic Disinfection By-Products in Mouse and Human Mononuclear Macrophage Systems: The Role of RNA Epitranscriptomic Modification in Mammalian Immunity

status: Public on Jan 20 2023

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

summary: Purpose: Detect transcriptome-wide mapping of m6A modifications of mouse macrophage RAW264.7 cells by MeRIP-seq after 24 h-treatment with 100 μM 2,4,6-trichlorophenol (TCP), 100 μM 2,4,6-tribromophenol (TBP) and 100 μM 2,4,6-triiodophenol (TIP).   Methods: Total RNA was extracted using TRIzol Reagent. Poly (A) RNA was purified from 50 μg total RNA using Dynabeads. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module.The fragmented RNA was incubated with m6A-specific antibody. The desired m6A-enriched RNA eluate was used to construct cDNA library in parallel with input control.   Conclusion: Our study revealed the difference of gene expression at transcriptional level and m6A-methylated RNA among TCP, TBP and TIP treated RAW264.7 cells by RNA-seq and MeRIP-seq technologies.

overall_design: Compare the difference of gene expression at transcriptional level and m6A-methylated RNA among TCP, TBP and TIP treated RAW264.7 cells.

first: Meishuang

last: Li

first: Qing

last: Zhou

first: Jingfan

last: Qiu

first: Jun

last: Zhang


title: Effect of genomic and cellular environments on gene expression noise [10x-transcriptomes]

overall_design: K562 clonal cells containing reporter genes integrated in different locations were pooled and used for 10x scRNA-seq.


title: Depletion of miR-144/451 alleviates anemia in β-thalassemic mice

status: Public on Jan 13 2023

city: Yangzhou

first: Fangfang

last: Wang

state: Jiangsu

address: No. 98 of Nantong Road

institute: Clinical medical college, Yangzhou university

summary:
Tto investigate whether ablation of miR-144/451 is deleterious for th3+/- mice, we crossed miR-144/451 knockout (mKO) mice (with mild anemia at baseline)13 with th3+/- mice (with severe anemia). We found that mKO/th3+/- double-mutant mice exhibited dramatic improvement in anemia.
To explore the mechanism of anemia improvement in mKO/th3+/- mice, we fractionated erythroblasts from bone marrow of four genotypes mice, including WT,mKO, th3+/-,mKO/th3+/- mice,for microarray analysis.

overall_design: We used microarrays to detail the comparative gene expression profiling analysis  for  erythroblastsand of th3+/- and mKO/th3+/- mice.

first: Duonan


title: Disruption of dNTPs Homeostasis by Ribonucleotide Reductase Hyperactivation Overcomes AML Differentiation Blockade II

status: Public on Jan 11 2023

city: Arcadia

first: WEI

last: CHEN

state: CA

address: 655 e huntington dr

department: Shared Resource

institute: City of Hope National Medical Center

summary: We assessed global gene expression changes in nelarabine (NEL)-treated AML cell lines (U937 and KG1A)

overall_design: Expression profiling data in NEL-treated cells (4 replicates) were compared to vehicle (VEH) control cells (4 replicates) by RNA sequencing

first: Ling

first: Hanying

first: Xin

last: He

first: Wei

last: Chen


title: OX40 agonism enhances efficacy of PD-L1 checkpoint blockade by shifting the cytotoxic T cell differentiation spectrum

status: Public on Jan 10 2023

city: Leiden

first: Ramon

last: Arens

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Center

summary: Immunotherapy effect on T cells in C57BL/6 mice

overall_design: Single cell RNA-sequencing of 4 different blood samples withdrawn from 4 different treated mice treadted by : UNT (Untreated), PDL1 (PD-L1 treated), OX40 (OX40 treated) and PDOX (PDOX treated)

first: Tetje

last: van der Sluis

first: Guillaume

last: Beyrend

first: Esmé

middle: T

last: van der Gracht

first: Tamim

last: Abdelaal

first: Simon

last: Jochems

first: Robert

last: Belderbos

first: Thomas

middle: H

last: Wesselink

first: Suzanne

last: van Duikeren

first: Floortje

middle: J

last: van Haften

first: Anke

last: Redeker

first: Elham

last: Nejad

first: Marcel

last: Camps

first: Kees

middle: L

last: Franken

first: Margot

last: Linssen

first: Peter

last: Hohenstein

first: Noel

last: de Miranda

first: Hailiang

last: Mei

first: Adriaan

last: Bins

first: John

last: Haanen

first: Joachim

last: Aerts

first: Ferry

last: Ossendorp

first: Laura

last: Ouboter


title: Spectinomycin Analogs for the Treatment of Mycobacterium abscessus Infections

status: Public on Jan 09 2023

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

summary: Non-tuberculous mycobacteria (NTM) are emerging pathogens with high intrinsic drug resistance. Among rapidly growing NTM species, Mycobacterium abscessus is among the most pathogenic. Standard of care therapy has led to unacceptable outcomes and demonstrates the urgent need to develop effective, broad-spectrum antimycobacterial regimens. Through synthetic modification of spectinomycin (SPC), an aminocyclitol antibiotic, we have identified a distinct structural subclass of ethylene linked aminomethyl spectinomycins (eAmSPC) that are up to 64-fold more potent against M. abscessus when compared to SPC. Lead eAmSPC retain activity against other NTM species and multi-drug resistant M. abscessus clinical isolates. Sequencing of eAmSPC-resistant mutants revealed nucleotide changes in the distinct helix-34 spectinomycin binding site and X-ray crystallography further demonstrated the derivatives mode of ribosomal inhibition remained on target. The eAmSPC displayed increased intracellular accumulation compared to SPC and transcriptional profiling indicate that eAmSPC’s induce whiB7 resistance responses, however, the series maintains potency despite its expression.  These leads display favorable pharmacokinetic profiles and robust efficacy in M. abscessus mouse infection models. The results of these studies suggest that eAmSPCs have the potential to be developed into clinical treatments for M. abscessus and other NTM infections.

overall_design: RNA-sequencing of mid-log cultures of M. abscessus ATCC19977 treated for 3 hours with AmSPC molecules 2593 (1mg/L) and 2694 (1 and 10 mg/L), spectinomycin (1 and 10 mg/L) and vehicle (DMSO).

middle: E

first: Gregory

middle: A

last: Phelps

first: Dinesh

last: Fernando


title: Gene regulation in activated microglia by adenosine A3 receptor agonists. A transcriptomics analysis.

status: Public on Jan 01 2023

city: Barcelona

first: Rafael

last: Franco

address: Avinguda Diagonal, 643

country: Spain

institute: Universitat de Barcelona

summary: Most neurodegenerative disorders, including the two most common, Alzheimer’s disease (AD) and Parkinson’s disease (AD), course with activation of microglia, the resident innate immune cells of central nervous system. A3 adenosine receptor (A3R) agonists have been proposed to be neuroprotective by regulating the phenotype of activated microglia. RNAseq was performed using samples isolated from lipopolysaccharide/interferon-γ activated microglia treated with 2-Cl-IB-MECA, a selective A3R agonist. The results showed that the number of negatively regulated genes in the presence of 2-Cl-IB-MECA was greater than the number of positively regulated genes. Gene ontology enrichment analysis showed regulation of genes participating in several cell processes, including those involved in immune-related events. Analysis of known and predicted protein-protein interactions showed that Smad3 and Sp1 are transcription factors whose genes are regulated by A3R activation. Under the conditions of cell activation and agonist treatment regimen, 2-Cl-IB-MECA did not lead to any tendency to favor the expression of genes related to neuroprotective microglia (M2).

overall_design: Cells were maintained in a humid atmosphere of 5% CO2 at 37ºC and were used for RNA extraction after 15 days of culture. Cells were activated for 48 h with 0.01% (v/v) LPS and 0.002% (v/v) IFN-γ in Dulbecco's modified Eagle medium and, at 24, 32 and 40 h, vehicle or 200 nM 2-Cl-IB-MECA was added.

first: Alejandro

last: Lillo

first: Joan

last: Serrano-Marín

first: Jaume

first: Iu

last: Raïch

first: Gemma

last: Navarro


title: Transcriptome analysis after treatment with recombinant Sparcl1 protein in primary mouse chondrocyte (mcc)

first: Yu

last: Miao

address: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

summary: In order to analyze the mechanism of Sparcl1, we conducted RNA-sequencing in mouse chondrocytes treated with or without recombinant Sparcl1 protein.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary mouse chondrocyte (treated with or without recombinant Sparcl1 protein).


title: Decline in IGF1 in CXCL12-Abundant Reticular (CAR) Cells Causes Myeloid-Biased Hematopoiesis Observed During Aging

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

summary: Decline in hematopoietic function in aged individuals is associated with expansion of phenotypic hematopoietic stem cells (HSCs) and a shift in their lineage potential toward production of myeloid cells. Both HSC-intrinsic changes, and extrinsic changes in the bone marrow (BM) microenvironment, have been identified in old mice and humans. However, to extend healthy and robust hematopoietic function from youth into older age, we need to understand and effectively target the processes that initiate functional hematopoietic decline. We recently identified decline in Insulin-Like Growth Factor 1 (IGF1) in the BM microenvironment as early as middle age to be an HSC-extrinsic initiating driver of HSC aging (Young et al., Cell Stem Cell 2021). As systemic IGF1 administration has significant undesirable side effects, we sought to comprehensively interrogate the cell population(s) in the BM microenvironment that are responsible for IGF1 decline, towards the goal of cell type-specific targeted therapy. We performed single cell RNA-seq to comprehensively profile hematopoietic and non-hematopoietic fractions of the BM in young (2-4mo; n = 5 biological replicates) and middle-aged (12-14mo; n = 10) mice. In young mice, we find Igf1 to be nearly entirely detected in the mesenchymal stromal cell populations Adipo-CAR and Osteo-CAR, and Igf1 is significantly reduced in expression in both populations in middle-aged mice. Using two independent mesenchymal stromal cell Cre mouse lines, Lepr-Cre and Prx1-CreERT2, we found that knockout of Igf1 resulted in myeloid-biased hematopoiesis that replicated aging phenotypes. This result was similar to our published work showing that knockout of Igf1 using Nestin-CreER causes myeloid-biased hematopoiesis. While these Cre models generally do not mark similar cell types, it has been shown that Lepr-Cre-expressing perisinusoidal stromal cells include cells that express certain Nestin transgenes. Using fluorescent reporters, we find that all three lines (Lepr-Cre, Prx1-CreERT2, and Nestin-CreER) overlap in expression in the CAR populations that abundantly express Igf1 in young mice. Taken together, our work identifies a new role for Cxcl12-abundant reticular cells in sustaining hematopoietic function through local IGF1 production and suggests that specifically targeting CAR cells to maintain or restore Igf1 expression during aging will have beneficial effects on lymphoid cell production and adaptive immunity.

overall_design: Hematopoietic and bone marrow microenvironment cell populations were enriched for using cell sorting from 5 young and 9 middle age mice for single cell RNA-seq.

first: Kira

last: Young


title: PFKFB3 overexpression in monocytes of patients with colon but not rectal cancer programs pro-tumor macrophages and is indicative for higher risk of tumor relapse [RNAseq]

status: Public on Dec 31 2022

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

summary: Circulating monocytes are main source for tumor-associated macrophages (TAMs) that control tumor growth, angiogenesis, metastasis and therapy resistance. We raised the questions how monocyte programming is affected by growing tumors localized in colon and rectal sections, and how treatment onsets affect monocyte programming in the circulation. Patients with rectal cancer and colon cancer were enrolled in the study. Peripheral blood monocytes were characterized by transcriptomic analysis using RNA sequencing. NGS analysis identified tumor-specific transcriptional programming of monocytes in all CRC patients compared to healthy individuals. The analysis also identified difference between colon and rectal cancer monocytes and chemotherapy effects on monocyte profile in rectal cancer.

overall_design: The study included patients with colorectal adenocarcinoma with morphologically verified diagnosis, treated in the Department of abdominal oncology, Cancer Research Institute of Tomsk National Research Medical Center (Tomsk, Russia) from 2019 to 2021, and healthy donors. The study was carried out according to Declaration of Helsinki (from 1964, revised in 1975 and 1983) and was approved by the local committee of Medical Ethics of Tomsk Cancer Research Institute (15 May 2019, the approval No. 6/1); all patients signed informed consent for the study. Patients were divided into two groups according to morphological diagnosis and treatment strategy: 1) patients with colon cancer who did not receive neoadjuvant chemotherapy (NAC) (T2-4N0-3M0, stages I–III), and 2) patients with rectal cancer underwent NAC (T2-4N0-3M0, stages II–III). Colon cancer included cancers of different sections of colon: the cecum, the ascending colon, the transverse colon, the descending colon, and the sigmoid colon. Rectal cancer combined localization of tumors in rectum and rectosigmoid junction. Patients with rectal cancer received 3 courses of neoadjuvant chemotherapy (NAC). Chemotherapeutic regimens included XELOX (Capecitabine plus Oxaliplatin) or FOLFOX-4 (oxaliplatin, L-leucovorin and fluorouracil). Whole-transcriptome sequencing was performed on total 62 (3 of only NAC treated samples were excluded from the study) samples of monocytes isolated from CRC patients. Prepared libraries were then pooled and sequenced on Illumina NextSeq 500 instrument (Illumina, USA) with NextSeq 500/550 High-Output v2.5 Kit (75 cycles) (#20024906, Illumina, USA). RNA sequencing study included patients with colon (n=17) and rectal (n=12) cancers, and healthy individuals (n=19)

first: Marina

last: Patysheva

first: Pavel

last: Iamshchikov

first: Elena

last: Kazakova

first: Anna

first: Militsa

last: Rakina

first: Evgeniya

last: Grigoryeva

last: Tarasova

first: Sergei

last: Afanasiev

first: Natalia

last: Bezgodova

first: Artem

last: KIselev

first: Alexey

last: Dobrodeev

first: Dmitriy

last: Kostromitskiy

first: Nadezhda

last: Cherdyntseva

first: Julia

last: Kzhyshkowska


title: Deciphering Tumor Cell Evolution in Cutaneous T-Cell Lymphomas: Distinct Differentiation Trajectories in Mycosis Fungoides and Sézary Syndrome

city: Pittsburgh

first: Oleg

last: Akilov

state: PA

address: 200 Lothrop Street

department: Dermatology

institute: University of Pittsburgh

summary: Cutaneous T-cell lymphomas are a heterogeneous group of neoplasms originating in the skin, with mycosis fungoides (MF) and Sézary syndrome (SS) representing the most common variants. The cellular origin of cutaneous lymphomas has remained controversial due to their immense phenotypic heterogeneity that obfuscates lineage reconstruction based on classical surface biomarkers. To overcome this heterogeneity and reconstruct the differentiation trajectory of malignant cells in MF and SS, T-cell receptor sequencing was performed in parallel with targeted transcriptomics at the single-cell resolution among cutaneous samples in MF and SS. Unsupervised lineage reconstruction showed that Sézary cells exist as a population of CD4+ T cells distinct from those in patch, plaque, and tumor MF. Further investigation of malignant cell heterogeneity in SS showed that Sézary cells phenotypically comprised at least three subsets based on differential proliferation potentials and expression of exhaustion markers. A Th1 polarized cell type, intermediate cell type, and exhausted Th2 polarized cell type were identified, with Th1 and Th2 polarized cells displaying divergent proliferation potentials. Collectively, these findings provide evidence to clarify the relationship between MF and SS, and reveal cell subsets in SS that suggest a possible mechanism for therapeutic resistance.

overall_design:
high-throughput TCR sequencing in parallel with targeted single-cell transcriptomics coupled with AbSeq

***raw data will be made available at dbGaP due to patient privacy concerns***


title: PFKFB3 overexpression in monocytes of patients with colon but not rectal cancer programs pro-tumor macrophages and is indicative for higher risk of tumor relapse

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Gene expression profile at single cell level of donor hematopoietic stem cells and multipotent progenitors 3 from bone marrow in control and Tet2 knockout mice.

city: Los Angeles

first: Jiya

last: Eerdeng

address: 1425 San Pablo St

department: DSR

institute: University of Southern California

summary: HSPCs cells exhibit heterogeneous clonal expansion upon Tet2 KO. We used scRNA-seq to analyze the molecular basis for clones exhibiting high levels of expansion.

overall_design: Baroced HSPCs (GFP+) from Tet2 KO and control mice were isolated 13-months post transplantation by Fluorescence-activated cell sorting (FACS) according to presence of relevant cell surface markers and GFP.

first: Charles

last: Bramlett


title: Phase 1 Trial With Challenge to Assess the Safety and Biomarkers of Protection in Malaria-naive Adults of Immunization Via Mosquito Bite With Radiation-Attenuated Plasmodium Falciparum Sporozoites (IMRAS) - Day 140-147

city: Seattle

first: Raphael

last: Gottardo

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutch

summary: This study is to assess the safety, tolerability, and biomarkers of protection in healthy malaria-naive adults, who will receive bites from Anopheles stephensi mosquitoes either infected with Plasmodium falciparum Sporozoites (PfRAS) (true-immunization) or noninfected (mock-immunization).

overall_design: Comparison of RNAseq results from two cohorts each with two treatments, true-immunization and mock-immunization, across multiple timepoints from challenge to post-challenge (Day 140, 141, 147) to assess biomarkers of clinically-defined protection. This Series includes the data from Cohort 1.

first: Ying

last: Du

first: Fergal

last: Duffy

first: Ken

last: Stuart


title: A dietary oxysterol, 7-ketocholesterol, exacerbates imiquimod-induced psoriasis-like dermatitis in steatohepatitic mice (Liver)

status: Public on Dec 27 2022

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Patients with psoriasis are at a higher risk of developing nonalcoholic fatty liver disease. We previously identified an oxidized derivative of cholesterol, 7-ketocholesterol (7KC), in diet-induced steatohepatitic mice. Here, we investigated whether 7KC exacerbates psoriasis-like dermatitis by accelerating steatohepatitis in mice. A high fat/high cholesterol/high sucrose/bile salt diet (NASH diet) with or without 0.0125% 7KC was fed to C57BL/6 mice (7KC or control group) for three weeks to induce steatohepatitis. 5% imiquimod cream was then applied to the ears and dorsal skin for four days to induce psoriasis-like dermatitis. Hepatic lipid accumulation and inflammatory cell infiltration were exacerbated in the 7KC group compared with the control group after three weeks. Serum tumor necrosis factor-α (TNF-α) levels were also elevated in the 7KC group (108.5±9.8 vs. 83.1±13.1 pg/ml, p<0.005). Imiquimod cream increased the psoriasis area severity index (PASI) score in mice in the 7KC group (9.14±0.75 vs. 5.17±1.17, p<0.0001). Additionally, Tnfa, Il23a, Il17a, and Il22 mRNA levels in the dorsal lesion were significantly upregulated. Finally, Th17 cell differentiation and the TNF signaling pathway were enhanced in the dorsal lesions and liver of mice in the 7KC group. These data suggest that steatohepatitis and psoriasis are linked by a potent, diet-related factor.

overall_design: Liver of C57BL/6 mice fed a high-fat, high-cholesterol, bile-salt diet (NASH diet) containing 7-ketocholesterol for 3 weeks (n=2). As a control, liver of C57BL/6 mice fed a NASH diet without 7-ketocholesterol for 3 weeks (n=2).

first: Ayami

last: Saga

first: Masahiro

last: Koseki

first: Kotaro

last: Kanno

first: Jiuyang

last: Chang

first: Tomoaki

last: Higo

last: Okuzaki

first: Takeshi

last: Okada

first: Hiroyasu

last: Inui

first: Masumi

last: Asaji

first: Katsunao

last: Tanaka

first: Takashi

last: Omatsu

first: Sae

last: Nishihara

first: Yinghong

last: Zhu

first: Kaori

last: Ito

first: Hiroaki

last: Hattori

first: Yoshihiro

last: Kamada

first: Ikuyo

last: Ichi

first: Tohru

last: Ohama

first: Shungo

last: Hikoso

first: Makoto

last: Nishida

first: Shizuya

last: Yamashita

first: Yasushi

last: Sakata


title: A dietary oxysterol, 7-ketocholesterol, exacerbates imiquimod-induced psoriasis-like dermatitis in steatohepatitic mice (Dorsal skin)

first: Daisuke

last: Motooka

overall_design: Dorsal skin of C57BL/6 mice fed a high-fat, high-cholesterol, bile salt diet (NASH diet) containing 7-ketocholesterol for 3 weeks followed by daily application of imiquimod cream (n=2). As a control, dorsal skin of C57BL/6 mice fed a NASH diet without 7-ketocholesterol for 3 weeks and then treated with imiquimod cream for 1 day (n=2).

first: Ayami

last: Saga

first: Masahiro

last: Koseki

first: Kotaro

last: Kanno

first: Jiuyang

last: Chang

first: Tomoaki

last: Higo

last: Okuzaki


title: A dietary oxysterol, 7-ketocholesterol, exacerbates imiquimod-induced psoriasis-like dermatitis in steatohepatitic mice

status: Public on Dec 26 2022

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


title: Phase 1 Trial With Challenge to Assess the Safety and Biomarkers of Protection in Malaria-naive Adults of Immunization Via Mosquito Bite With Radiation-Attenuated Plasmodium Falciparum Sporozoites (IMRAS) - Day 31-126

first: Raphael

last: Gottardo

overall_design: Comparison of RNAseq results from two cohorts each with two treatments, true-immunization and mock-immunization, across multiple timepoints from 2nd vaccination to post-5th vaccination (Day 31, 35, 42, 56, 59, 63, 70, 84, 87, 91, 119, 120, 122, 126) to assess biomarkers of clinically-defined protection. This Series includes the data from Cohort 1.

first: Ying

last: Du

first: Fergal

last: Duffy

first: Ken

last: Stuart


title: Next-generation sequence analysis of primary culture cells isolated from mouse inner ear vestibular or cochlear cells

status: Public on Dec 15 2022

summary: In the present research, we performed the gene expression analysis of cells isolated from vestibule or cochlea.

overall_design: Analysis of differential gene expression in vestibular cells and cochlear cells.

first: Msaharu

last: Sakagami

first: Yukiteru

last: Ouji


title: Effect of TDB and PEG-TGL treatment on gene expression in BMDC from C57BL/6 mice

status: Public on Dec 14 2022

summary: There is much demand for more water-soluble Mincle ligands which is promissing adjuvants. We synthesized water-soluble Mincle ligad, PEG-TGL, and assessed its potential on adjuvanticity. Comparing to TDB, known ligand for Mincle, PEG-TGL induced less IL-1beta secretion. To elucidate the gene expression differenses leads to IL-1beta secretion, we performed RNA-seq analysis using bone marrow-derived dendritic cells, and revealed that PEG-TGL were less able to active phagocytic pathways.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TDB and PEG-TGL treated BMDC from wild type (C57BL/6) mice

first: M

last: Thathsaranie

first: P

last: Manthrirathna

first: Emma

last: Dangerfield

first: Shigenari

last: Ishizuka

first: Aodhamair

last: Woods

first: Brenda

last: Luong

first: Sho

last: Yamasaki

first: Mattie

last: Timmer

first: Bridget

last: Stocker


title: RNA sequencing of human monocytes stimulated with murine platelets from wild-type or Clec1b-/- mice

status: Public on Dec 20 2022

first: Daisuke

last: Motooka

summary: C-type lectin receptors (CLRs) recognize glycans present on the surface of pathogens or self and mediate host defense as well as homeostasis. Dectin-1 is the most well-characterized CLR which recognizes β-glucan on various pathogens and expressed on human myeloid cells. Recently, we screened various tissue-derived primary cells for Dectin-1 binding and found that human Dectin-1 selectively binds to platelets. By establishing anti-platelet monoclonal antibodies that inhibit human Dectin-1 binding, we identified that CLEC-2 is responsible for the interaction with human Dectin-1. CLEC-2 is critical for lymphangiogenesis in early embryonic stage. In this study, we evaluated the influence on CLEC-2 binding in human monocytes which highly expresses human Dectin-1 by RNA sequencing.

overall_design: RNAseq analysis was performed by using RNA extracted from human monocytes stimulated with murine platelets from wild-type or Clec1b-/- mice.

first: Shojiro

last: Haji

first: Masamichi

last: Nagae

first: Taiki

last: Ito


title: Gene expression profile at single cell level of the intestinal T cells from patients with inflammatory bowel disease

summary: T cells are key mediators of inflammation. Here we performed deep profiling of T cells in the gut of patients with inflammatory bowel disease to reveal  the functional specialization of lymphocytes under pathological conditions and provide comprehensive insights into the pathogenesis of this disease.

overall_design: Intestinal CD3+ T cells were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq. This technology was further combined to BD AbSeq system to measure protein and transcriptome levels simultaneously at a single cell level.

first: Takehito

last: Yokoi

first: Mari

last: Murakami

last: Okuzaki

first: Kiyoshi

last: Takeda


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [scQer_devCRE_mEBs]

status: Public on Dec 12 2022

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

institute: University of Montreal

summary: The inability to scalably and precisely measure the cell-type-specific activity of developmental enhancers is a bottleneck in genomics. To address this, we developed a “dual RNA”' system that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. Together with RNA barcode circularization, the resulting single-cell quantitative expression reporters (scQers) facilitate the robust detection of which reporter(s) are present in which single cells, thereby providing high contrast readouts analogous to classic in situ assays but entirely from sequencing. Our dual RNA strategy extends the range of expression measurement into a regime fundamentally inaccessible with traditional multiplex reporter systems, yielding an accurate readout of mRNA levels spanning four orders of magnitude and a precision approaching the limit set by Poisson (shot) noise. As a proof-of-concept experiment, we profile over two hundred putative developmental cis-regulatory elements (CREs) for cell-type-specific activity in a multicellular in vitro model of early mammalian development, identifying dozens of active elements, ten of which function in an autonomous, cell-type-specific manner. These include constituents of the canonical Sox2 control region, exclusively active in pluripotent cells, multiple parietal endoderm-specific enhancers, including at the Foxa2 and Gata4 loci, and a compact pleiotropic enhancer at the Lamc1 locus. Looking forward, we envision that scQers will be broadly useful in developmental systems to quantitatively profile the activity of native, perturbed, or synthetic enhancers at scale, with high sensitivity and at single cell resolution.

overall_design:
Single-cell reporter on day 21 mouse embryoid bodies with high MOI genome-integrated dual RNA reporters (devCRE series), three biological replicates. Gene expression and custom oBC, mBC libraries.

Experient type (submitter-provided): single-cell RNA-seq with expression reporters

first: Jean-Benoît

first: Samuel

middle: G

last: Regalado

first: Silvia

last: Domcke

first: Tony

last: Li

first: Beth

last: Martin

first: Diego

last: Calderon

first: Chase

middle: C

last: Suiter

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [scQer_promoters_cell_lines]

overall_design:
Single-cell reporter on mix of K562, HEK293T, HepG2 cells with high MOI genome-integrated dual RNA reporters (promoter series) in biological duplicates. Gene expression and custom oBC, mBC libraries

Experient type (submitter-provided): single-cell RNA-seq with expression reporters


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [bulkMPRA_promoters_cell_lines]

overall_design:
Bulk MPRA from (separate)  K562, HEK293T, HepG2 cells with high MOI genome-integrated dual RNA reporters (promoter series) in biological duplicates.

Experient type (submitter-provided): massively parallel reporter assay (bulk)


title: Single-cell RNA-sequencing of breast cancer cells growing in invasion permissive and non-permissive 3D matrices

status: Public on Dec 13 2022

city: Utrecht

first: Antoine

last: Khalil

address: Universiteitsweg 100

institute: UMC Utrecht

summary: Murine breast cancer organoids (MMTV-PyMT) were embeded in basement membrane extract (BME, invasion non-permissive) or collagen I (invasion-permissive). Organoids were harvested after 5days for single-cell RNA-sequencing (SORT-seq).

overall_design: Organoids were isolated from the 3D BME or 3D Collagen I, dissociated into single cells. Single cells from either BME or Collagen I were single cell sorted by FACS into 3 x 384 well plate each (3 replica per ECM condition) and analyzed by single cell RNA sequencing

first: Daan

last: Smits

first: Peter

last: Haughton

first: Thijs

last: Koorman

first: Karin

last: Jansen

first: Mirjam

last: van der Net

first: Lotte

last: Enserink

last: Visser

first: Milena

last: Pasoli

first: Max

last: Tak

first: Denise

last: Westland

first: M

last: Roukens

first: F

last: Zwartkruis

first: Patrick

middle: W

last: Derksen

first: Johan

last: de Rooij


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [bulkMPRA_PolIII_linBC_vs_oBC]

first: Jean-Benoit

last: Lalanne

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design:
Bulk MPRA data from genome-integrated PolIII driven oBC and linBC in K562 cells (two biological replicates).

Experient type (submitter-provided): massively parallel reporter assay (bulk)

first: Jean-Benoît

first: Samuel

last: Regalado

first: Silvia

last: Domcke

first: Tony

last: Li

first: Beth

last: Martin

first: Diego

last: Calderon

first: Chase

last: Suiter

last: Trapnell


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [scATAC_mEBs]

overall_design:
scATAC-seq from day 21 mouse embryoid bodies (two biological replicates)

Experient type (submitter-provided): single-cell chromatin accessibility (ATAC-seq)

first: Cole

first: Jay

last: Shendure


title: Histone monoaminylation dynamics are regulated by a single enzyme and promote neural rhythmicity

status: Public on Dec 06 2022

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Histone H3 monoaminylations at glutamine(Q) 5 represent important epigenetic markers in neurons that play critical roles in the mediation of permissive gene expression. We previously demonstrated that H3Q5 serotonylation(ser) and dopaminylation(dop) are catalyzed by the Transglutaminase 2 (TGM2) enzyme. Here, we identified a new class of histone monoaminylation, H3Q5 histaminylation(his), which displayed dynamic diurnal expression in brain and contributed to neural rhythmicity. We found that H3Q5his, unlike H3Q5ser, electrostatically inhibited recruitment of the “reader” protein WDR5 and attenuated MLL1 methyltransferase activity on H3 lysine(K) 4. We determined that H3Q5 monoaminylation dynamics are dictated by local monoamine concentrations, which are sensed by TGM2. This noncanonical mechanism indicated that histone monoaminylations can be established and removed by a single enzyme based upon its sensing of cellular microenvironments.

overall_design: Brain tissue was collected every 4 h across the 24 h zeitgeber, 21 d post viral-infusion, or following behavioral assays. For viral infused brains, Adeno-associated virus H3.3 constructs [empty vs. wildtype (WT) vs. (Q5A)- Flag-HA] were used - all three containing an IRES driven GFP fluorescent tag to allow visualization of the injection site during tissue dissection. Animals were anaesthetized with isoflurane (1-3%) and positioned in a stereotaxic frame (Kopf instruments) and 0.5 μl of viral construct was infused bilaterally into TMN using the following coordinates; anterior-posterior (AP) -2.3, medial-lateral (ML) +1.0, dorsal-ventral (DV) -5.5. All brains were immediately frozen following collection. For zeitgeber brains, tissues were sectioned at 1 mm thick and TMN was collected by tissue punch (1-2 mm). For virus-infused brains, tissue was sectioned at 150 μm on a cryostat, and GFP was illuminated using a NIGHTSEA BlueStar flashlight to microdissect virally infected tissues.

first: Qingfei

last: Zheng

first: Ryan

middle: M

last: Bastle

first: Yael

last: David

first: Ian

last: Maze


title: Transcript abundances associated with fertility in a case-control design including Angus and Holstein heifers

city: Blacksburg

first: Fernando

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: We carried out an experiment to test the hypothesis that differences in gene transcript abundance due to fertility fitness would be shared between heifers of different breeds. We produced transcriptome data from peripheral white blood cells from 22 heifers (purebred Angus heifers (n=12), purebred Holstein (n=10) heifers). We identified two genes whose transcript abundance differed (eFDR ≤ 0.002) between the two groups (Fertile and Sub-Fertile), namely Adipocyte Plasma Membrane Associated Protein (APMAP, 1.16 greater abundance in the Fertile group) and Dynein Axonemal Intermediate Chain 7 (DNAI7, 1.23 greater abundance in the Sub-Fertile group).

overall_design: We collected blood samples from purebred Angus heifers (n=12), averaging 14 months in age, at the time of their first artificial insemination (AI) service. Heifers were subjected to a 7-Day Co-Synch + CIDR estrus synchronization protocol prior to breeding. Additionally, we collected blood samples from purebred Holstein (n=10) heifers, averaging 12 months in age, at the time of the first AI service. Heifers were identified as either Fertile (Holstein, n=5; Angus, n=5) or Sub-Fertile (Holstein, n=5; Angus, n=7) based on their pregnancy outcome. Fertile animals were identified as those who became pregnant and subsequently delivered a calf following the first insemination service. Angus heifers were categorized as Sub-Fertile after failing to achieve pregnancy following two insemination services and exposure to a bull for natural breeding. Holsteins were identified as Sub-Fertile after receiving four or more inseminations before achieving pregnancy or not becoming pregnant.


title: Single cell RNA sequence analysis of murine alveolar macrophages in the presence of lung cancer cells

status: Public on Nov 23 2022

city: Suita

first: Daisuke

last: Motooka

summary: To classify the cell population of lung alveolar macrophages in the presence (or absence) of lung cancer cells in vivo, single cell RNA sequence analysis was performed using orthotopic tumor bearing animal model with C57BL/6 mice and Lewis Lung Carcinoma (LLC) cells. CD45+, F4/80+, Siglec-F+ population was sorted as alveolar macrophage population with fluorescence-activated cell sorting (FACS) technique.

first: Seiji

last: Taniguchi

first: Takahiro

last: Matsui

first: Masaru

last: Ishii


title: Functional genomic analyses of iPSC-derived pancreatic progenitor cells

status: Public on Dec 02 2022

city: La Jolla

first: Kelly

middle: Ann

last: Frazer

address: 9500 Gilman Drive

department: Pediatrics

institute: UC San Diego

summary: The goal of this study is to molecularly characterize regulatory variation in pancreatic progenitor cells (PPC). Here, we derived PPC from iPSCs of nine iPSCORE individuals (DeBoever et al., 2017; Panopoulos et al., 2017), and generated RNA-seq, ATAC-seq, scRNA-seq, and snATAC-seq. We strive to understand the role of functional genetic variation during fetal pancreatic development that later give rise to adult pancreatic diseases.

overall_design:
Transcriptome and chromatin accessibility maps of iPSC-PPCs.

**Submitter states that the raw data will be available in dbGaP (phs000924)**

first: Matteo

last: D'Antonio

first: Hiroko

first: Jennifer

last: Nguyen


title: Gene expression analysis of murine alveolar macrophages in the presence of lung cancer cells

summary: To investigate the interaction between lung alveolar macrophages and lung cancer cells in vivo, gene expression analysis was performed using orthotopic tumor bearing animal model with C57BL/6 mice and Lewis Lung Carcinoma (LLC) cells. CD45+, F4/80+, Siglec-F+ population was sorted as alveolar macrophage population with fluorescence-activated cell sorting (FACS) technique.


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [bulkMPRA_devCRE_mEBs]

first: Jean-Benoit

last: Lalanne

overall_design:
Bulk MPRA time series on mouse embryoid body induction from cells harboring high MOI genome-integrated dual RNA reporters (devCRE series), three biological replicates.

Experient type (submitter-provided): massively parallel reporter assay (bulk)

first: Jean-Benoît

first: Samuel

last: Regalado

first: Silvia

last: Domcke

first: Tony

last: Li

first: Beth

last: Martin

first: Diego

last: Calderon

first: Chase


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters

status: Public on Dec 11 2022

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Zygotic genome activation by the totipotency pioneer factor Nr5a2 [CUT&Tag]

city: Martinsried

first: Siwat

last: Ruangroengkulrith

state: Bavaria

address: Am Klopferspitz 18

department: Totipotency

institute: Max Planck Institute of Biochemistry

summary: Life begins with a switch in genetic control from the maternal to the embryonic genome during zygotic genome activation (ZGA). Despite its importance, the essential regulators of ZGA remain largely unknown in mammals. Based on de novo motif searches, we identified the orphan nuclear receptor Nr5a2 as a key activator of major ZGA in mouse 2-cell embryos. Nr5a2 is required for progression beyond the 2-cell stage. It binds to its motif within SINE B1/Alu retrotransposable elements found in cis-regulatory regions of ZGA genes. Chemical inhibition suggests that 72% of ZGA genes are regulated by Nr5a2 and potentially other orphan nuclear receptors. Nr5a2 promotes chromatin accessibility during ZGA and binds nucleosomal DNA in vitro. We conclude that Nr5a2 is an essential pioneer factor that regulates ZGA.

overall_design: CUT&Tag of H3K4me3 was performed on GV-stage oocytes for validation of CUT&Tag experiments in 2-cell embryos. Nr5a2 CUT&Tag on 2C-embryos was performed with normal high salt condition (300 mM NaCl). Esrrb CUT&Tag on 2C-embryo was performed with low salt condition (150 mM NaCl) due to its low binding affinity to the genome.

first: Johanna

last: Gassler

first: Wataru

last: Kobayashi

first: Imre

last: Gáspár

first: Adarsh

last: Mohanan

first: Laura

last: Gomez Hernandez

first: Pavel

last: Kravchenko

first: Maximilian

last: Kümmecke

first: Aleksandar

last: Lalic

first: Nikita

last: Rifel

first: Robert

last: Ashburn

first: Maciej

last: Zaczek

first: Antoine

last: Vallot

last: Cuenca Rico

first: Sabrina

last: Ladstätter


title: Analysis of tumor cell plasticity in endometrioid carcinoma using cancer stem cell marker aldehyde dehydrogenase (ALDH)

status: Public on Nov 30 2022

first: Daisuke

last: Motooka

summary: To investigate the tumor cell plasticity using aldehyde dehydrogenase (ALDH) 1A1 activity, we established two distinct HEC-1B sublines, in which ALDH1A1-high population accelerated such transition and ALDH1A1-high population did not show such acceleration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HEC-1B cells confirmed the presence or absence of acceleration of transition from ALDH1A1-low to ALDH1A1-high population by Fluorescence-activated cell sorting (FACS).

first: Jun-ichiro

last: Ikeda

first: Eiichi

last: Morii

first: Shinya

last: Kusumoto

first: Etsuko

last: Maeno-Fujinami


title: Space flight mouse plasma cell-free RNA seuqnencing in Mouse Habitat Unit-1 (MHU-1)

status: Public on Nov 16 2022

city: Tsukuba

first: Masafumi

last: Muratani

state: Ibaraki

address: 1-1-1 Tennodai

department: Faculty of Medicine

institute: University of Tsukuba

summary: Purpose: Sequencing analysis of plasma cell-free RNA was performed to study the effects of space flight and microgravity environment in mice. Methods: Plasma samples were collected during the JAXA MHU-1 mission as reported previously (Shiba et al., 2017, Scientific Reports). Total RNA was purified from plasma samples and processed for sequencing analysis, to compare RNA expression profiles in ground control, space flight and artificial 1-G control groups.

overall_design: Plasma cell-free RNA profiles were compared among ground control, space flight and artificial 1G control groups.

first: Rutter

last: Lindsay

first: Husna

last: Nailil

first: Fujita

last: Shin-Ichiro

first: Saito

last: Yoshika

first: Shiba

last: Dai

first: Kudo

last: Takashi

first: Takahashi

last: Satoru

first: Muratani

last: Masafumi


title: Zygotic genome activation by the totipotency pioneer factor Nr5a2

first: Siwat

last: Ruangroengkulrith

summary:
Life begins with a switch in genetic control from the maternal to the embryonic genome during zygotic genome activation (ZGA). Despite its importance, the essential regulators of ZGA remain largely unknown in mammals. Based on de novo motif searches, we identified the orphan nuclear receptor Nr5a2 as a key activator of major ZGA in mouse 2-cell embryos. Nr5a2 is required for progression beyond the 2-cell stage. It binds to its motif within SINE B1/Alu retrotransposable elements found in cis-regulatory regions of ZGA genes. Chemical inhibition suggests that 72% of ZGA genes are regulated by Nr5a2 and potentially other orphan nuclear receptors. Nr5a2 promotes chromatin accessibility during ZGA and binds nucleosomal DNA in vitro. We conclude that Nr5a2 is an essential pioneer factor that regulates ZGA.

This SuperSeries is composed of the SubSeries listed below.


title: Zygotic genome activation by the totipotency pioneer factor Nr5a2 [Omni ATAC-seq]

overall_design: Omni-ATAC-seq was performed on mouse 2-cell embryos that was treated either with DMSO or SR1848, an inhibitor of Nr5a2.

first: Johanna

last: Gassler

first: Wataru

last: Kobayashi

first: Imre

last: Gáspár

first: Adarsh

last: Mohanan

first: Laura

last: Gomez Hernandez

first: Pavel

last: Kravchenko

first: Maximilian

last: Kümmecke

first: Aleksandar

last: Lalic

first: Nikita

last: Rifel

first: Robert

last: Ashburn

first: Maciej

last: Zaczek

first: Antoine

last: Vallot

last: Cuenca Rico

first: Kikuë

last: Tachibana


title: Cytoplasmic Location of Translation Controls Protein Output [CLIP-seq]

status: Public on Nov 15 2022

first: Christine

last: Mayr

state: NY

address: 417 E 68th Street

department: Cancer Biology and Genetics

institute: MSKCC

summary: The cytoplasm contains membrane-bound organelles and membraneless compartments. The TIS granule network is formed through assembly of the RNA-binding protein TIS11B together with its bound mRNAs and associates with a portion of the rough endoplasmic reticulum (ER) – one of the major sites of protein synthesis. Subcellular mRNA localization is widespread in polarized cells. However, it is largely unknown if mRNA localization is also widespread in non-polarized cells and if the location of protein synthesis has biological consequences. To identify compartment-specific cellular functions, we used fluorescent particle sorting to isolate TIS granules, the ER surface, and the cytosol and determined their mRNA contents.

overall_design: iCLIP-sequencing in HEK293T cells transfected with GFP-TIS11B, three biological replicates.

first: Ellen

last: Horste

first: Mervin

last: Fansler

first: Ting

last: Cai

first: Xiuzhen

last: Chen

first: Sibylle

last: Mitschka

first: Gang

last: Zhen

first: Flora

middle: Y

last: Lee

first: Jernej

last: Ule


title: Cytoplasmic Location of Translation Controls Protein Output [RNA-seq]

overall_design: RNA-seq of different compartments from HEK293T cells


title: Cytoplasmic Location of Translation Controls Protein Output

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


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [plasmid_libraries_subassembly]

first: Jean-Benoit

last: Lalanne

overall_design:
Subassembly of plasmid barcoded reporter libraries.

Experient type (submitter-provided): barcode association for library construction

first: Jean-Benoît

first: Samuel

last: Regalado

first: Silvia

last: Domcke

first: Tony

last: Li

first: Beth

last: Martin

first: Diego

last: Calderon

first: Chase

last: Suiter

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: Analysis on SARS-CoV-2-M198-206-specific CD8+ T cells

status: Public on Oct 13 2022

first: Daisuke

last: Motooka

summary: Gene profiling and T cell clonotype analysis on SARS-CoV-2-M198-206-specific CD8+ T cells were performed by scRNA-seq and scTCR-seq.

overall_design: SARS-CoV-2-M198-206-specific CD8+ T cells from convalescents of moderate/severe COVID-19 were subjected to scRNA-seq and scTCR-seq.

first: Hideki

last: Ogura

first: Xiuyuan

last: Lu

first: Yu-Chen

last: Liu

last: Okuzaki

first: Sho

last: Yamasaki

first: Satoshi

last: Ishido