title: Sex differences in cardiac aging in mice and development of a female murine model of hypertensive disease in the elderly

city: Quebec

first: Jacques

last: Couet

state: QC

address: 2725 Chemin Sainte-Foy

department: Medicine

institute: Université Laval

summary: C57Bl6/J male and female mice were gonadectomized or not at the age of 12 months and then euthanized 12 months later at the age of 24 months. Half of the females received for 28 days an angiotensin II (AngII; 1.5 mg/kg/day) continuous infusion starting at the age of 23 months. The mice were provided with a running wheel during the 12 months after gonadectomy with the exception of the last month before euthanasia.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse left ventricle samples of both sexes (M or F) from various groups (Controls (Ctr) or Gonadectomised (Gx)) at the age of 24 months. Half of the females were treated for with Angiotensin II(AngII) 4 weeks before euthanasia .

first: Elisabeth

last: Walsh-Wilkinson

first: Audrey

last: Morin-Grandmont


title: IGHMBP2 deletion suppresses translation and activates the integrated stress response

status: Public on Dec 18 2023

city: San Francisco

first: Jesslyn

last: Park

state: CA

address: 513 Parnassus Ave

department: Cell and Tissue Biology

country: USA

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The effects of host-microbe interactions on the transcriptomic signatures of cervicovaginal epithelial cells [RNA-seq]

status: Public on Dec 14 2023

city: New York

first: Michal

middle: A

last: Elovitz

state: NY

address: 1468 Madison Ave

department: Obstetrics, Gynecology and Reproductive Sciences

institute: Icahn Mount Sinai

summary: To elucidate the molecular pathways altered by host-microbe interactions in cervicovaginal epithelial cells we performed whole genome RNA-sequencing. We identified genes and functional pathways that were altered in cervicovaginal epithelial cells after exposure to G. vaginalis or L. crispatus or their supernatant.

overall_design: We performed functional pathways analysis using the transcriptomic data from RNA-seq on three cell types treated with live bacteria or bacterial supernatants from different bacterial strains.

first: Lauren

last: Anton

first: Briana

last: Ferguson


title: Inhibition of IL-6 signaling attenuates vascular damage caused by HIF1α activation

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

summary: Protection against endothelial damage is recognized as a frontline approach to preventing the progression of cytokine release syndrome (CRS). Accumulating evidence has demonstrated that interleukin-6 (IL-6) promotes vascular endothelial damage during CRS, although the molecular mechanisms remain to be fully elucidated. Targeting IL-6 receptor signaling delays CRS progression; however, current options are limited by persistent inhibition of the immune system. Here, we show that endothelial IL-6 trans-signaling promoted vascular damage and inflammatory responses via hypoxia-inducible factor-1α (HIF1α)‒induced glycolysis. Using pharmacological inhibitors targeting HIF1α activity or mice with the genetic ablation of gp130 in the endothelium, we found that inhibition of IL-6R‒HIF1α signaling in endothelial cells protected against vascular injury caused by septic damage and provided survival benefit in a mouse model of sepsis. In addition, we developed a short half-life anti-IL-6R antibody (silent anti-IL-6R antibody) and found that it was highly effective at augmenting survival for sepsis and severe burn by strengthening the endothelial glycocalyx and reducing cytokine storm, and vascular leakage. Together, our data advance the role of endothelial IL-6 trans-signaling in the progression of CRS and indicate a potential therapeutic approach for burns to address the lack of burn-specific treatments.

overall_design: HUVECs were stimulated by 100 ng/ml of LPS plus 100 ng/ml of soluble IL-6R for 6 hours, and then  total RNA were extracted.

first: Sujin

last: Kang

first: Shinya

last: Onishi

first: Zhenzhen

last: Ling

first: Hitomi

last: Inoue

last: Okuzaki

first: Yingying

last: Zhang

first: Hao

last: Chang

first: Hui

last: Zhao

first: Tong

last: Wang

first: Toshio

last: Tanaka

first: Tadamitsu

last: Kishimoto


title: The effects of host-microbe interactions on the epigenetic signatures of cervicovaginal epithelial cells [ATAC-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To identify chromatin alterations by host-microbe interactions in cervicovaginal epithelial cells we performed ATAC-sequencing. We identified regions of chromatin that were altered in cervicovaginal epithelial cells after exposure to  L. crispatus supernatant.

overall_design: We performed chromatin accessibility analysis using the data from ATAC-seq on three cell types treated with bacterial supernatants from L. crispatus.

first: Anton

last: Lauren

first: Elovitz

last: Michal

first: Cristancho

middle: G

last: Ana

first: Ferguson

last: Briana


title: The effects of host-microbe interactions on cervicovaginal epithelial cells

first: Michal

last: Elovitz


title: Effects on left ventricle gene expression of a metabolo-hypertensive stress in mice and the myocardial thereafter.

first: Jacques

last: Couet

country: Canada

summary: In order to study the capacity of the myocardium to recover from a stress causing several features of heart failure with preserved ejection fraction, C57Bl6/J male and female mice received or not for 28 days an angiotensin II (AngII; 1,5 mg/kg/day) continuous infusion in combination with a high fat diet (HFD). Half of the animals were then euthanized. The remaining ones had the AngII infusion stopped and their diet normalized. In addition, voluntary exercise was initiated by introducing a running wheel in the animals cage for an additional 28 days.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse left ventricle samples of both sexes from various groups (Controls, metabolo-hypertensive stress (MHS) and left ventricle reverse remodeling (RR).

first: Elisabeth

last: Walsh-Wilkinson

first: Mohamed

middle: L

last: Aidara


title: Sex differences in cardiac aging in mice and development of a female murine model of hypertensive disease in the elderly: Study of the left atrial tissue

summary: C57Bl6/J female mice were ovariectomized or not at the age of 12 months and then euthanized 12 months later at the age of 24 months. Half of the females received for 28 days an angiotensin II (AngII; 1.5 mg/kg/day) continuous infusion starting at the age of 23 months. The mice were provided with a running wheel during the 12 months after gonadectomy with the exception of the last month before euthanasia.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse left atrial samples from various groups (Controls or Ovariectomized) at the age of 24 months. Half of the females were treated for with Angiotensin II(AngII) 4 weeks before euthanasia .

first: Audrey

last: Morin-Grandmont


title: Inseparable RNA binding and chromatin modification activities of a nucleosome-interacting surface in EZH2 [ChIP-seq]

status: Public on Dec 11 2023

city: Clayton

first: Evan

last: Healy

state: VIC

address: 23 Innovation Way, Building 77,, Monash University

country: Australia

institute: Monash University

summary: Polycomb repressive complex 2 (PRC2) interacts with RNAs in cells, but there is no consensus on how RNA regulates its canonical functions, including chromatin modification and the maintenance of transcription programs in lineage-committed cells. We assayed two separation-of-function mutants of the catalytic subunit EZH2, defective in RNA binding but active in methyltransferase. We find that part of the RNA-binding surface of EZH2 is required for chromatin modification, yet this activity is independent of RNA. Mechanistically, the RNA-binding surface within EZH2 is required for chromatin modification in vitro and in cells, through interactions with nucleosomal DNA. Contrarily, an RNA-binding defective mutant exhibited normal chromatin modification activity in vitro and in lineage-committed cells, accompanied by normal gene repression activity. Collectively, we show that part of the RNA-binding surface of PRC2, rather than the RNA-binding activity per se, is required for the histone methylation of chromatin in vitro and in cells.

overall_design: Quantitative ChIP sequencing with exogenous mouse reference genome spike in (ChIP-Rx) in human K562 cells for PRC2 components, EZH2 & SUZ12, as well as histone modification H3K27me3. Cas9 expressing K562 cells were transduced with lentiviruses containing gRNAs targeting EZH2 as well as rescue constructs to express EZH2-WT, -mt1, -mt2 and -dEZH2.

first: Qi

first: Emma

middle: H

last: Gail

first: Sarena

middle: F

last: Flanigan

first: Natasha

last: Jones

first: Xiao

last: Ng

first: Michael

last: Uckelmann

first: Vitalina

last: Levina

first: Chen

last: Davidovich


title: Gene expression profile at single cell level of macrophages in PDAC liver metastasis

city: Liverpool

first: Kim

last: Clarke

address: Crown Street

country: United Kingdom

institute: University of Liverpool

summary: We used single cell RNA sequencing to investigate macrophage heterogeneity and their temporal and spatial distributions in PDAC liver metastasis

overall_design: Macrophages from naïve liver, day 5 metastasis (early), and day 10 metastasis (advanced) at proximal and distal locations to tumour were labelled with F4/80 antibodies, isolated using fluorescence activated cell sorting (FACS), and analysed using scRNAseq

first: Yuliana

last: Astuti

last: Schmid


title: Inseparable RNA binding and chromatin modification activities of a nucleosome-interacting surface in EZH2

last: Zhang

address: 23 Innovation Walk


overall_design: CUT&TAG-Seq (H3K27me3, H3K27ac, IgG) of 6 cell lines with 3 independent replicates and RNA-Seq of 6 cell lines with 4 independent replicates.

first: Sam

last: Aigus


title: Cellular Decoding of Simultaneous Cranial Mesenchyme and Osseous Architecture Reconstruction by Scaffolds

status: Public on Dec 07 2023

city: Chengdu

first: Fanyuan

last: Yu

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

country: China

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

summary: In this study, RNA sequencing was employed to investigate the differences in gene expression levels and patterns of cells recruited into suture-bony combined calvarial injury following the implatation of distinct types of commonly used calvarial scaffolds including gelatin methacryloyl hydrogel (GelMA), porous chitosan scaffold (CTS), and polylactic acid eletrospinning membrane (PLA).

overall_design: Nascent tissue from the suture-bony composite defects, where GelMA (3 samples), CTS (3 samples), PLA (2 samples), or no scaffold (NC, 3 samples) was implanted, were harvested 6 weeks after surgery. Flow cytometry was used to isolate Cd45- cells from digested tissue for RNA-seq.

first: Jiayi

last: Wu

first: Chuyi

last: Han


title: Primase excites the competition of templating transcription and lagging replication to boost DNA damage

status: Public on Dec 06 2023

city: Beijing

first: Weifeng

address: Zhongguancun Street

institute: Tsinghua University

summary: Head-on transcription-replication conflicts (HO-TRCs) cause R-loops and DNA damage. We realized that HO-TRCs are the natural competition for templating transcription and lagging replication in the same DNA strand (termed TemLag competition), however, the regulatory mechanisms behind are unclear. We previously identified a chloroplast-localized RNase H1 protein AtRNH1C that can remove R-loops and relax HO-TRCs for genome integrity. Through the mutagenesis screen, we identified that the chloroplast-localized primase ATH exacerbates TemLag competition in the atrnh1c mutant. A mutation in ATH weakens the binding affinity of DNA, thus slowing down DNA replication and relieving TemLag competition. Overexpression of ATH boosts TemLag competition and intensifies DNA damage. Interestingly, strand-specific DNA damage sequencing reveals that TemLag competition induces single-strand DNA damage of the competitive strand at the end of transcription. These results illustrated a potentially conserved mechanism among organisms, of which the primase antagonizes R-loop clearance machinery to exaggerate TemLag competition and genome instability.

overall_design: Detail-seq performed using chloroplasts embedded in low-melting-point agarose. ssDRIP performed  with S9.6 antibody in atrnh1c mutant. ATH ChIP performed with GFP antibody using ATH-GFP tagged transgenic plants, and Col-0 with no tag as control.

first: Zhuo

last: Yang

first: Wenjie

last: Wang

first: Qianwen

last: Sun


title: The homeobox transcription factor DUXBL controls exit from the totipotent 2C state [Cut&Run]

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: Upon exit from the totipotent 2-cell (2C) embryo stage, the 2C-associated transcriptional program needs to be efficiently silenced. However, the molecular mechanisms involved in this process remain mostly unknown. Here, we determined that the 2C-specific transcription factor DUX directly induced the expression of DUXBL to promote this silencing. CUT&RUN analysis revealed that DUXBL gained accessibility to DUX-bound regions in DUX-induced ESC while it was unable to bind those regions in uninduced cells. Importantly, DUX expression in Duxbl-knockout ESC caused increased induction of the 2C-transcriptional program, whereas DUXBL overexpression impaired 2C-associated transcription. Mechanistically, we determined that DUXBL interacted with TRIM24 and TRIM33, two members of the tripartite motif superfamily involved in gene silencing, and co-localized with them in nuclear condensates upon DUX expression. Importantly, DUXBL downregulation in mouse zygotes led to a penetrant 2C-stage arrest. Our data revealed an unexpected role for DUXBL in controlling the exit from totipotency.

overall_design: Cut&Run experiments of DUXBL, FLAG and H3K27ac in untreated or DOX-treated WT control, DUXBL or DUX/DUXBL expressing ESC. In addition, untreated or DOX-treated WT DUXBL-expressing ESC incubated with Pladienolide B for 24 hours.

first: Sergio

last: Ruiz

first: Maria

last: Vega-Sendino

first: Teresa

last: Olbrich


title: The homeobox transcription factor DUXBL controls exit from the totipotent 2C state

status: Public on Dec 05 2023


title: A functional genomics process for systematic dissection and mutation-specific target discovery in breast cancer PIK3CA hotspot mutations [CRISPR KO Screen Data]

status: Public on Dec 01 2023

city: Nashville

first: Adam

middle: Xavier

last: Miranda

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University

summary: Despite the general understanding that different mutations impart different phenotypic changes within a cell, the majority of targeted therapies in cancer treatment are used to treat all mutations in the same gene regardless of location or phenotypic effects. There is a significant unmet need to distinguish distinct changes in cellular signaling which may provide opportunities for mutation-specific treatment with reduced toxicity to patients. Herein, we describe a series of functional genomic analysis with a unique isogenic cell line panel to accurately identify targetable differences between mutations within the same gene.  Using an isogenic cell line model bearing two distinct hotspot PIK3CA mutations found in breast cancer, we were able to identify many gene expression and chromatin accessibility differences. These findings allowed us to identify mutation specific molecular targets, specifically AREG as well as a proximal gene regulatory region, that may provide clinically relevant targets. When disrupted, these targets induce a mutation-specific decrease in proliferation and survival in vivo. These findings suggest new mutation-specific modes of treatment for PIK3CA mutant breast cancer and provide a means with which to find mutation-specific targets for the treatment of other oncogenic mutations.

overall_design:
A modified CRISPR screen was performed with a select cohort of gene targets selected based on two criteria: 1. genes exhibited significantly increased RNA expression (log2 fold change greater than 1.5 and p-adjusted value less than 0.05) in either PIK3CA-mutant cell lines and 2. gene demonstrated significantly increased accessibility in either mutant cell line. Differential accessibility was performed using DESeq2 and nearest neighbor annotation was performed using ChIPseeker (version 1.30.3) with the default annotation conditions of +/- 3kb from the TSS. Based on this selection criteria, 312 genes were selected, for which 280 guides were available in the Brunello whole genome single guide RNA (sgRNA) library. The Brunello whole genome sgRNA library was modified for these 280 genes and prepared by the Vanderbilt Functional Genomics core in the lentiCRISPRv2 plasmid background (Full list of guides Mageck_Guide.csv).
MCF-10A cells were cultured in the maintenance media conditions at a density of 500,000 cells/well in a 6-well plate. 24 hours after seeding, cells were infected with viral supernatant in maintenance media containing 5 ug/mL polybrene. 24 hours post-infection cells were placed in selection media containing 1 ug/mL of puromycin and maintained for two weeks. Following two weeks of selection, libraries were prepared and sequenced following the protocol described in Sanjana et al. Libraries were sequenced by the VANTAGE core and analysis was performed using the maximum likelihood estimation (MLE) algorithm within the MAGeCK software package(version 0.5.9.5).

first: Miranda

last: Adam


title: The homeobox transcription factor DUXBL controls exit from the totipotent 2C state [RNA-seq]

overall_design: RNAseq experiments of WT, DUXBL-KO, TRIM24-KO, and TRIM33-KO embryonic stem cells with and without DOX treatment.


title: A functional genomics process for systematic dissection and mutation-specific target discovery in breast cancer PIK3CA hotspot mutations [RNA-seq]

overall_design: The first stage of our discovery platform is the evaluation of the transcriptional environment of isogenic cells bearing either the PIK3CA E545K or H1047R mutation using RNA-seq. The development of this isogenic model was described in Gustin et al 2009 PNAS.


title: Acyloxyacyl Hydrolase Protects against Kidney Injury via Inhibition of Tubular CD74-Macrophage Crosstalk

city: Shanghai

first: Zhenkai

address: No. 639, Zhizaoju Road, Huangpu District, Shanghai, China.

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

summary: Renal fibrosis is the common pathway in the progression of chronic kidney disease (CKD). Acyloxyacyl hydrolase (AOAH) is expressed in various phagocytes and is highly expressed in proximal tubular epithelial cells (PTECs). Research shows that AOAH plays a critical role in infections and chronic inflammatory diseases, although its role in kidney injury is unknown. Here, we found that AOAH deletion led to exacerbated kidney injury and fibrosis after folic acid (FA) administration, which was reversed by overexpression of Aoah in kidneys. ScRNA-seq revealed that Aoah-/- mice exhibited increased subpopulation of CD74+ PTECs, though the percentage of total PTECs were decreased compared to WT mice after FA treatment. Additionally, exacerbated kidney injury and fibrosis seen in Aoah-/- mice was attenuated via administration of methyl ester of (S, R)-3-(4-hydroxyphenyl)-4,5-dihydro-5-isoxazole acetic acid (ISO-1), an inhibitor of macrophage inhibition factor (MIF) and CD74 binding. Finally, AOAH expression was found positively correlated with estimated glomerular filtration rate while negatively correlated with the degree of renal fibrosis in kidneys of CKD patients. Thus, our work indicates that AOAH protects against kidney injury and fibrosis by inhibiting renal tubular epithelial cells CD74 signaling pathways. Targeting kidney AOAH represents a promising strategy to prevent renal fibrosis progression.

overall_design: scRNA-seq was performed for kidneys from folic acid (FA)-treated WT and Aoah-/- mice.

first: Bo

last: Deng

first: Yu

last: Pan

first: Feng

last: Ding


title: A functional genomics process for systematic dissection and mutation-specific target discovery in breast cancer PIK3CA hotspot mutations


title: A functional genomics process for systematic dissection and mutation-specific target discovery in breast cancer PIK3CA hotspot mutations [ATAC-Seq]

overall_design: The second stage is assessment of chromatin accessibility using assay for transposase-accessible chromatin with sequencing (ATAC-seq). ATAC-seq utilizes tn5 transposase to identify accessible regions of the genome and provides additional insight into how genes and transcription factors are different in their regulation between mutants


title: Effect of deficiency of Siglec-15 during osteoclast differentiation of murine bone marrow macrophages

city: Sapporo

first: Hideyuki

last: Kobayashi

department: epartment of Orthopaedic Surgery, Faculty of Medicine and Graduate School of Medicine

institute: Hokkaido university

summary:
To investigate the  function of Siglec-15 in the regulation of osteoclast differentiation, Siglec-15 deficient mice was established.
Then gene expression profiling analysis using data obtained from RNA-seq of  bone marrow macrophages with M-CSF and RANKL at two different time points was performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Bone mrrow macrophages and pre-osteoclasts in wild type and Siglec-15 deficient mouse.

first: Masahiro

last: Ota

first: Tomoka

last: Hasegawa

first: Tomomaya

last: Yamamoto

first: Mohamed

last: Terkawi

first: Tomohiro

last: Shimizu

first: Dai

last: Sato

first: Ryo

last: Fujita

first: Norio

last: Amizuka

first: Norimasa

last: Iwasaki

first: Masahiko

last: Takahata


title: Single-cell gene expression analysis of pulmonary immune cells from BCG-vaccinated and CoMtb mice [scRNAseq]

status: Public on Nov 30 2023

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: The aim of this study was to measure effect of BCG vaccination or contained Mtb infection (CoMTB) on the expression profile of pulmonary immune cells.

overall_design: Mice were vaccinated sub-cutaneously with BCG-Pasteur (1e6 CFU), or inoculated in the dermis of the ear with H37Rv (1e4 CFU)  and allowed to rest for 8 weeks. Pulmonary immune cells were isolate by bronchoalveolar lavage and analyzed by single-cll RNA-sequencing.

first: Alissa

middle: C

last: Rothchild

first: Alan

last: Diercks

last: Aderem


title: Gene expression analysis of mouse alveolar macrophages infected with Mycobacterium tuberculosis isolated from BCG-vaccinated mice [balRNAseq]

summary: The aim of this study was to measure the immune response of alveolar macrophages (AMs) from BCG-vaccinated mice to intracellular Mtb infection in vivo. We characterized the transcriptional profile of murine Mtb-infected AMs after aerosol infection by sorting cells from bronchoalveolar lavage fluid and performing low-input RNA-sequencing.

overall_design: Mice were vaccinated sub-cutaneously with BCG-Pasteur and allowed to rest for 4 weeks. To characterize the early macrophage transcriptional response to Mtb infection, we infected mice with 2000-4000 CFU of mEmerald-H37Rv, and isolated AMs (CD45+, Zombie Violet-, CD3-/CD19-, Siglec-F+, CD11bmid, and CD64+) from BAL by fluorescence activated cell sorting at 24 hours following infection. Three populations were sorted for analysis by RNA-seq: Mtb-infected AMs (mEmerald+), bystander AMs (mEmerald-), and AMs from naïve mice.


title: Gene expression analysis of BCG-vaccinated and CoMtb mice

overall_design: Refer to individual Series


title: Environmental monobutyl phthalate exposure promotes liver cancer via reprogramming cholesterol metabolism and activation of the IRE1α-XBP1s pathway

city: Wuhan

first: Faming

last: Zhao

state: Hubei

address: Hangkong road 13

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: In this study, we applied a long-term cell culture model by treating the liver cancer cell HepG2 and normal hepatocyte L02 to environmental dosage of monobutyl phthalate (MBP), the main metabolite of phthalates. By RNA-seq, ATAC-seq and CUT&Tag-seq analysis, we found that long-term MBP exposure triggered reprogramming of lipid metabolism in HepG2 cells, which was causal to the activation of the IRE1α-XBP1s axis of the unfolded protein response. Furthermore, the XBP1s-regulated gene sets and pathways contributed to the increased aggressiveness of HepG2 cells.

overall_design: RNA-seq, ATAC-seq and CUT&Tag-seq analysis upon a long-term cell culture model mimicking chronic MBP exposure.

first: Tingting

last: Zhang

first: Xia

last: Sheng


title: Single cell analyses reveal the transient emergence of retinal progenitor cells in the ciliary margin zone during human retinal development

status: Public on Nov 29 2023

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

institute: Newcastle University

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


title: Gene expression analysis of alveolar macrophages from BCG-vaccinated and CoMtb mice stimulated ex vivo [exvivoRNAseq]

summary: The aim of this study was to measure the response of alveolar macrophages (AMs) from BCG-vaccinated mice and mice with CoMtb to LPS, PAM3CSK4, and Mtb stimulation ex vivo.

overall_design: Mice were vaccinated sub-cutaneously with BCG-Pasteur (1e6 CFU), or inoculated in the dermis of the ear with H37Rv (1e4 CFU)  and allowed to rest for 8 weeks. To characterize the  macrophage transcriptional response to each stimulus, AMs were isolated by bronchoalveolar lavage followed by plate adherence for 24 hours. AMs were stimulated with either LPS (10 ng/mL), Pam3CSK4 (10 ng/mL), or Mtb-H37Rv for 6 hours prior to RNA isolateion.


title: Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis and atopic dermatitis [MPRA]

status: Public on Nov 26 2023

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

summary: Eosinophilic esophagitis (EoE) is a rare atopic disorder associated with esophageal dysfunction, including difficulty swallowing, food impaction, and inflammation.  EoE develops in a small subset of people with food allergies under the influence of environmental and genetic risk factors.  Genome wide association studies (GWAS) have identified 31 independent risk loci for the disease, and linkage disequilibrium (LD) expansion of these loci nominates a set of 531 variants that are potentially causal.  These risk variants are non-coding, suggesting a likely role in altered gene regulatory mechanisms. To systematically interrogate the gene regulatory activity of these variants, we designed a massively parallel reporter assay (MPRA) containing the alleles of each variant within their 170 bp genomic sequence context cloned into a GFP reporter library.  Transfection of the MPRA library into TE-7 esophageal epithelial cells, HaCaT skin keratinocytes, and Jurkat T cells revealed cell-type-specific gene regulation.  We identify 32 allelic enhancer variants (allelic enVars) that regulate reporter gene expression in a genotype-dependent manner in at least one cellular context.  By annotating these variants with expression quantitative trait loci (eQTL) and chromatin looping data in related tissues and cell types, we identify putative target genes affected by genetic variation in EoE patients, including TSLP and multiple genes at the HLA locus. Transcription factor enrichment analyses reveal possible roles for cell-type specific regulators, including GATA-3, a key regulator of type 2 inflammation. Collectively, our approach reduces the large set of EoE-associated variants to a set of 32 with allelic regulatory activity, providing new functional insights into the effects of genetic variation in this disease.

overall_design: Massively parallel reporter assays to study EoE and atopic dermatitis-associated variants for allele-dependent transcriptional enhancer activity, 5 replicates, 2 conditions, 3 cell types

first: Parameswaran

last: Sreeja

first: Shook

last: Molly

first: Ernst

last: Kevin


title: Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis and atopic dermatitis


title: Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis and atopic dermatitis [RNA-Seq]

overall_design: RNA-seq to identify genes differentially expressed in unstimulated versus IL-13 stimulated cells, 2-3 replicates, 2 conditions, 2 cell types


title: Single cell analyses reveal the transient emergence of retinal progenitor cells in the ciliary margin zone during human retinal development [ATAC]

summary: Retina is the innermost, light-sensitive layer that lines the back of the eye and is vital for light sensing and image processing. All the retinal cells types are derived from retinal progenitor cells (RPCs) in an orderly spatio-temporal manner that has been well studied in vertebrates. To better understand the emergence of RPCs, their localisation and differentiation to retinal lineages, we performed single cell (sc) RNA-Seq of 24 samples spanning 13 time points from 10-21 post-conception weeks of human development. Several types of progenitors were identified, including early and late RPCs which in turn gave rise the transient neurogenic progenitors that differentiated to all retinal neurones. Spatial transcriptomic analyses combined with scRNA-Seq revealed localisation of early RPCs in the ciliary margin of developing human retinas up to 10 PCW of development and propagation of neural retina differentiation from the centre to the periphery. Single cell ATAC-Seq analyses of 11 samples spanning 8-21 PCW of human development identified Hippo-Yap signalling as key pathway regulating RPC proliferation and cell cycle exit. These results provide the molecular map of human retinal development which may help guide generation of RPCs from human pluripotent stem cells and the design of cell-based replacement therapies for treating retinal dystrophies

overall_design: 12 samples of developing human eyes and neural retina from 10-21 post-conception weeks

first: Birthe

last: Dorgau

first: Joseph

last: Collin

first: Agata

last: Rozanska

first: Darin

last: Zerti

first: Moira

last: Crosier

first: Rafiqul

last: Hussain

first: Jonathan

last: Coxhead

first: Tamilvendhan

last: Dhanaseelan

first: Jane

last: Sowden

first: David

last: Fitzpatrick

first: Rachel

last: Queen


title: Pro-inflammatory T cells-derived cytokines enhance the maturation of the human fetal intestinal barrier

status: Public on Nov 24 2023

city: Amsterdam

first: Vanesa

last: Muncan

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

summary: In this data set we aimed to interrogate the milestones of human functional gut development from 13-20 weeks post gestation for proximal intestinal segments and 15-35 weeks gestation for distal intestinal segments

overall_design: gut tissue was isolated from fetuses 13-20 wk of gestation (n=20) or patients undergoing bowel resection at 35wk of gestation  (n=5).

first: Francesca

last: Giugliano


title: Single cell analyses reveal the transient emergence of retinal progenitor cells in the ciliary margin zone during human retinal development [Spatial]

first: Majlinda

last: Lako

overall_design: 4 fetal retina samples from 8,10,11 and 13PCW


title: Single cell analyses reveal the transient emergence of retinal progenitor cells in the ciliary margin zone during human retinal development [scRNA-seq]

overall_design: 24 samples of developing human eyes neural retina from 7.5-21 post-conception weeks


title: Targeting SOX13 inhibits the assembly of respiratory chain supercomplexes to overcome ferroptosis-resistance in gastric cancer

status: Public on Nov 17 2023

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

summary: Therapeutic resistance represents a bottleneck to treatment in advanced gastric cancer (GC). Ferroptosis is an iron-dependent form of non-apoptotic cell death and is associated with anti-cancer therapeutic efficacy. Further investigations are required to clarify the underlying mechanisms. Ferroptosis-resistant GC cell lines were constructed. Dysregulated mRNAs between ferroptosis-resistant and parental cell lines were identified. The expression of SOX13/SCAF1 was manipulated in GC cell lines where relevant biological and molecular analyses were performed. Molecular docking and computational screening were performed to screen potential inhibitors of SOX13. We showed that SOX13 boosts protein remodeling of electron transport chain (ETC) complexes by directly transactivating SCAF1. This leads to increased supercomplexes (SCs) assembly, mitochondrial respiration, mitochondrial energetics, NADPH production and chemo- and immune-resistance. Zanamivir, reverted the ferroptosis-resistant phenotype via directly targeting SOX13 and promoting TRIM25-mediated ubiquitination and degradation of SOX13. Overall, SOX13/SCAF1 are important in ferroptosis-resistance, and targeting SOX13 with zanamivir has therapeutic potential.

overall_design: To identify which genes binds directly to SOX13 and the genes with SOX13-bound transcription sites

first: Mingzhe

first: Hui

last: Yang


title: Control of a gene transfer agent cluster in Caulobacter crescentus by transcriptional activation and anti-termination

status: Public on Nov 14 2023

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

summary: Gene transfer agents (GTA) are domesticated prophages that cannot self-multiply and be infectious but might have been co-opted to perform biological functions for the host bacteria. Recently, Caulobacter crescentus, a bacterium best known as a model organism to study bacterial cell biology and cell cycle regulation1, has been demonstrated to produce bona fide GTA particles (CcGTA). Two direct activators of the CcGTA biosynthetic gene cluster, GafY and GafZ, have been identified, however, it is unknown how GafYZ controls transcription mechanistically or how they coordinate gene expression of the CcGTA gene cluster with other accessory genes elsewhere on the genome for an ultimate CcGTA synthesis. Here, we show that the CcGTA gene cluster is transcriptionally co-activated by GafY and an integration host factor (IHF), and by a GafZ-mediated transcription anti-termination. We present evidence that GafZ is a novel transcription anti-terminator that likely forms an anti-termination complex with RNA polymerase, NusA, NusG, and NusE to bypass transcription terminators within the 14kb CcGTA cluster. Overall, we reveal a two-tier regulation (by transcription activation and anti-termination) that coordinates the synthesis of GTA particles in C. crescentus.

overall_design: Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on stationary phase Caulobacter crescentus (see the supplementary Materials and Methods for the exact treatment that were applied to each strain).

first: Ngat

middle: T

last: Tran

middle: B


title: Deciphering cell states and genealogies of human hematopoiesis with single-cell multi-omics

status: Public on Nov 18 2023

city: Boston

first: Chen

last: Weng

state: OH

address: 415 Main St, Cambridge

department: Genetics

institute: Broad Institute and Whitehead Institute

summary:
This SuperSeries is composed of the SubSeries listed below.
The main processed data are organized in the following two Figshare links:
Seurat objects: https://doi.org/10.6084/m9.figshare.23290004
ReDeeM-V output: https://doi.org/10.6084/m9.figshare.24418966.v1

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: miR-709 exerts an angiogenic effect through an FGF2 upregulation induced by a GSK3B downregulation

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: The aim of this study was to identify angiogenic microRNAs (miRNAs) that could be used in the treatment of hindlimb ischemic tissues. miRNAs contained in extracellular vesicles (EVs) deriving from the plasma were analyzed in C57BL/6 mice, which have ischemia tolerance, and in BALB/c mice without ischemia tolerance as part of a hindlimb ischemia model; as a result 43 angiogenic miRNA candidates were identified. An aortic ring assay was employed by using femoral arteries isolated from BALC/c mice and EVs containing miRNA; as a result, the angiogenic miRNA candidates were limited to 14. The blood flow recovery was assessed after injecting EVs containing miRNA into BALB/c mice with hindlimb ischemia, and miR-709 was identified as a promising angiogenic miRNA. miR-709-encapsulating EVs were found to increase the expression levels of the fibroblast growth factor 2 (FGF2) mRNA in the thigh tissues of hindlimb ischemia model BALB/c mice. miR-709 was also found to bind to the 3’UTR of glycogen synthase kinase 3 beta (GSK3B) in three places. GSK3B-knockdown human artery-derived endothelial cells were found to express high levels of FGF2, and were characterized by increased cell proliferation. These findings indicate that miR-709 induces an upregulation of FGF2 through the downregulation of GSK3B.

overall_design: To compare the expression levels of miRNAs in EVs isolated from plasma between hindlimb ischemia model C57BL/6 mice exhibiting a blood flow recovery after a ligation of their femoral vessels and hindlimb ischemia model BALB/c mice not exhibiting such a blood flow recovery, the left femoral artery in mice was ligated at two points, and was severed with an electric scalpel between the ligated points. In order to collect plasma at 24 h after the ligation of the left femoral artery, blood was drawn from the abdominal vena cava by using a 26-G syringe including 0.1 mL of 1% ethylenediaminetetraacetic acid (EDTA). The collected blood was transferred to a 1.5-mL tube, and was centrifuged at 1,200 g for 20 min, at 4℃. The supernatant was placed in a new 1.5-mL tube, and was stored at −80℃. EVs were isolated from the obtained plasma by using the total exosome isolation kit (# 4484450; Thermo Fisher Scientific, Waltham, Massachusetts, USA). miRNAs in the EVs were extracted with the use of a total exosome RNA and protein isolation kit (#4478545; Thermo Fisher Scientific). The miRNA expression levels were analyzed in each of the five-sample pools (n=5 in C57BL/6, and n=5 in BALB/c)

first: Koji

last: Ueno

first: Hiroshi

last: Kurazumi

first: Ryo

last: Suzuki

first: Masashi

last: Yanagihara

first: Takahiro

last: Mizoguchi

first: Takasuke

last: Harada

first: Noriyasu

last: Morikage

first: Kimikazu

last: Hamano


title: Effect of SMARCB1 loss in bladder cancer tumor growth and metastasis.

status: Public on Nov 15 2023

city: Houston

first: Wenbo

last: Chen

address: 7000 Fannin Street

institute: The University of Texas Health Science Center at Houston

summary: To investigate the loss of SMARCB1 , a critical component of SWI/SNF complex in bladder cancer tumorigenesis and metastasis. We investigated the loss by generating SMARCB1 KO cells by CRISPR and rescuing the expression of SMARCB1 by lentivirus in the KO cell line. The cell lines were implanted orthotopically into bladder wall to investigate its effects on tumor growth and metastatic phenotype.

overall_design: We performed human RNA-seq profiling of these mouse xenografts derived from control, SMARCB1 KO and SMARCB1 rescue cell lines (Four replicates each).

first: Amara

last: Chandra

first: Putluri

last: Nagireddy

first: Yuntao

first: Weijin

last: Zheng


title: METTL16 deficiency attenuates apoptosis through translational control of extrinsic death receptor during nutrient deprivation

status: Public on Nov 11 2023

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

summary: METTL16 is a well-characterized m6A methyltransferase that has been reported to contribute to tumorigenesis in various types of cancer. However, the effect of METTL16 on tumor progression under restricted nutrient conditions, which commonly occur in tumor microenvironment, has yet to be elucidated. Herein, our study initially reported the inhibitory effect of METTL16 depletion on apoptosis under amino acid starvation conditions.

overall_design: To investigate the potential role of METTL16 under nutrient deprivation, stable METTL16-knockdown (M16-KD) cell lines were initially constructed using two classic A549 NSCLC cells,  through a shRNA-based gene interference approach.

first: Qiujie

last: Li

first: Jun

last: Zhang


title: A cell atlas of the adult female Aedes aegypti midgut revealed by single-cell RNA sequencing

first: Han

last: Xia

department: Key Laboratory of pathogenic Viruses and Biosafety

institute: Wuhan Institute of Virology, CAS

summary: Midgut is an important immune organ of Aedes aegypti. To help further studies on host-pathogen interaction of midgut, we established a midgut cell atlas using scRNA-seq.

overall_design: Midguts from female Aedes aegypti at 7 days post eclosion were dissected. The midgut cellular population was analyzed using scRNA-Seq.


title: Depletion of mRNA cap-binding protein eIF4E1 drives bradyzoite formation in Toxoplasma gondii

status: Public on Nov 02 2023

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine


title: Depletion of mRNA cap-binding protein eIF4E1 drives bradyzoite formation in Toxoplasma gondii [CLIP-seq]

summary: Ingestion of Toxoplasma gondii results in life-long infection due to its ability to convert from the rapidly disseminating tachyzoite stage to the chronic, encysted bradyzoite stage.  The control of mRNA translation has been suggested to play a key role in the signaling required to trigger bradyzoite formation. In eukaryotes, translational control primarily operates at two key points during the assembly of translation initiation factors. The phosphorylation of eIF2 affects mRNA start codon recognition and promotes differentiation in a variety of parasites. Modulating eIF4F function is the second pan-eukaryote regulatory point but remains unexplored in Toxoplasma. Here, we uncover the role that eIF4F-centric regulation plays in regulating bradyzoite formation by targeting the cap-binding subunit, eIF4E1. We discover that eIF4E1 coordinates two eIF4F complexes and binds the 5’-end of all mRNAs transcribed in tachyzoites, many of which show evidence of stemming from heterogenous transcriptional start sites. Together, this indicates that eIF4E1 is the predominant cap-binding protein in Toxoplasma tachyzoites. We also demonstrate that eIF4E1 knockdown or its chemical inhibition triggers the efficient formation of bradyzoites in the absence of other stresses and that stress-induced bradyzoites reduce their eIF4E1 expression. This study unearths a role for eIF4F-centric translational control in controlling Toxoplasma differentiation, suggesting that control of cap-dependent translation regulates the process of bradyzoite formation.

overall_design: expression changes at the transcriptional and translational levels upon IAA-induced eIF4E1 depletion in Toxoplasma gondii tachyzoites

middle: J

first: William

last: Sullivan Jr


title: Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression

status: Public on Nov 06 2023

city: Austin

first: Can

last: Cenik

state: TX

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on polysome profiling to measure variant effects on translation at scale, uncovering single-nucleotide variants that increase and decrease ribosome load. By combining high-throughput ribosome load data with multiplexed mRNA and protein abundance readouts, we mapped the cis-regulatory landscape of thousands of catechol-O-methyltransferase (COMT) variants from RNA to protein and found numerous coding variants that alter COMT expression. Finally, we trained machine learning models to map signatures of variant effects on COMT gene expression and uncovered both directional and divergent impacts across expression layers. Our analyses reveal expression phenotypes for thousands of variants in COMT and highlight variant effects on both single and multiple layers of expression. Our findings prompt future studies that integrate several multiplexed assays for the readout of gene expression

overall_design: Amplicon targeted library preparation was used to assay variant abundance of thousands of COMT variants in gDNA, total RNA, and fractionated polysomal RNA by Next-Generation Sequencing

first: Ian

last: Hoskins

first: Shilpa

last: Rao

first: Charisma

last: Tante


title: An integrated toolkit for the analysis of synthetic cellular barcodes in the genome and transcriptome

status: Public on Nov 05 2023

city: Melbourne

first: Dane

middle: Aaron McKay

last: Vassiliadis

address: Parkville VIC 3000

institute: Peter MacCallum Cancer Centre

summary: Cellular barcoding using heritable synthetic barcodes coupled to high throughput sequencing is a powerful technique for the accurate tracing of clonal lineages in a wide variety of biological contexts. Recent studies have integrated cellular barcoding with a single-cell transcriptomics readout, extending the capabilities of these lineage tracing methods to the single-cell level. However there remains a lack of scalable and standardised open-source tools to pre-process and visualise both bulk and single-cell level cellular barcoding datasets. Here, we describe bartools, an open-source R-based toolkit that streamlines the pre-processing, analysis and visualisation of synthetic cellular barcoding datasets. In addition, we developed BARtab, a portable and scalable Nextflow pipeline that automates upstream barcode extraction, quality control, filtering and enumeration from high throughput sequencing data. In addition to population-level cellular barcoding datasets, BARtab and bartools contain methods for the extraction, annotation, and visualisation of transcribed barcodes from single-cell RNA-seq and spatial transcriptomics experiments, thus extending the analytical toolbox to also support novel expressed cellular barcoding methodologies. We showcase the integrated BARtab and bartools workflow through the analysis of bulk, single-cell, and spatial transcriptomics cellular barcoding datasets.

overall_design:
We generated three independent cellular barcoding datasets using the SPLINTR lineage tracing system comprising population-level DNA barcoding or expressed cellular barcoding approaches using single-cell RNA and spatial transcriptomics platforms.
For the population-level DNA barcoding dataset, Mouse MLL-AF9 fusion oncogene containing AML cells were barcoded with SPLINTR and cultured in vitro with increasing doses of IBET-151, Cytarabine or DMSO. At each dose escalation, cells were sampled for bulk barcode sequencing. The dose escalation dataset comprises bulk barcode-seq data per timepoint.
For the single-cell dataset, SPLINTR barcoded MLL-AF9 AML cells were cultured in vitro and sequenced using the 10X Genomics 3’ single-cell RNA-seq platform.
For the spatial dataset, SPLINTR barcoded MLL-AF9 AML cells were transplanted into a recipient C57BL6 mouse and BGI Stereo-seq spatial transcriptomics was performed on spleen cross sections isolated at the time of fulminant disease.

first: Henrietta

last: Holze

first: Mark

last: Dawson


title: RNA Polymerase II Dynamics along the Intestinal Crypt-Villus Axis

status: Public on Nov 08 2023

city: Piscataway

middle: P

last: Verzi

state: NJ

address: 145 Bevier Rd

institute: Rutgers, the State University of New Jersey

summary: The mechanisms underlying intestinal epithelial differentiation are essential for maintaining intestinal health. Gene expression analysis reveals vast changes in the transcriptome as cells transition from crypts to villi, impacting nearly 4000 genes. The regulatory mechanisms driving transcriptome shifts during intestinal differentiation remain incompletely understood. Using ChIP-seq and multi-omic analyses, we have identified differential recruitment of Pol II to gene promoters as the primary driver of transcriptomic shifts during differentiation. Using genetic loss-of-function we show that HNF4, a crucial pro-differentiation transcription factor, is required for recruitment of Pol II to hundreds of genes that are activated during differentiation. Dynamic Pol II recruitment corresponds to dynamic enhancer-promoter looping and chromatin remodeling events, indicating a multi-step mechanism driving differentiation gene expression. Additional regulatory mechanisms, such as differential Pol II pause-release and post-transcriptional processes, may govern specific subsets of differentially expressed genes. In summary, our findings emphasize the central role of Pol II recruitment as the major regulator of intestinal differentiation and highlight the significance of HNF4 in this complex process.

overall_design: ChIP-seq of RNA Polymerase II (Pol II) was employed to survey its binding patterns in crypt and villus cells of the intestinal epithelium. Pol II ChIP-seq was also applied to Hnf4DKO and littermate control mice to identify HNF4 dependent recruitment patterns of Pol II in the mouse duodenal epithelium.

first: Kiranmayi

last: Vemuri


title: RNA damage compartmentalization by DHX9 granules

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Cell division ensures that both genetic information and non-genetic contents are inherited by daughter cells. Whereas considerable detail has been learned about the processing of intact or damaged DNA during the cell cycle (Branzei & Foiani, 2008; Klaasen et al., 2022),(Bakhoum & Cantley, 2018),(Hustedt & Durocher, 2016), how daughter cells deal with other forms of inherited damage is unknown. Here we identified a special kind of cytoplasmic granules responsible for the compartmentalisation of parental RNA damage. We found that ultraviolet (UV)-induced RNA, but not DNA, damage triggered assembly of this unique type of granules characterized by the presence of RNA helicase DHX9. By developing a novel methodology, FANCI, we discovered that DHX9 granules are enriched in damaged intron RNA and pre-mRNA-binding proteins, which is in contrast to other classical stress granules (SGs) that are composed of mature mRNA. Intron damage impeded proper splicing and intron decay, and induced generation of circRNA and dsRNA in the granules. Moreover, we showed that intron damage induced DHX9 granules assembled specifically in postmitotic daughter cells and triggered a cellular dsRNA immune response. Condensation with dsRNA is crucial for DHX9 localization to the granules and the modulation of dsRNA in these granules by DHX9 was crucial for daughter cell survival. Our observations revealed that DHX9 granules constitute a dedicated non-membrane-bound cytoplasmic compartment that protects daughter cells from parental damaged RNA.

overall_design: We generated total RNA-Seq profiles of Hela cells and stress granules treated with different stresses. We performed FLASH to analyze endogenous RNA binding sites of DHX9 in HeLa cells.

first: Yilong

last: Zhou

first: Niyazi

last: Umut Erdogdu


title: Targeting autophagy and proteinopathy provides sweet relief for preeclampsia

status: Public on Nov 01 2023

city: Providence

first: Surendra

last: Sharma

state: RI

address: 200 Chestnut St

department: Pediatrics

institute: Women and Infants Hospital of Rhode Island

summary: We have demonstrated that the etiology of preeclampsia (PE) is associated with protein aggregation, a pathologic paradigm observed in neurodegenerative diseases, and that impaired autophagy contributes to accumulation of protein aggregates. In search of therapeutic options for preeclampsia that inhibit protein aggregation and restore autophagy, we screened several small molecules and identified a class of disaccharides that may prove to be highly efficacious to treat and prevent this severe pregnancy complication. We used the human serum-based humanized PE mouse model to assess the effect of disaccharides on the onset of the syndrome.  Mice were i.p. injected with vehicle, disaccharides (2g/kg) at gd9, gd11, and gd14. At gd17, urine was collected, blood pressure was measured, fetal weight was recorded, and placenta was collected and subjected to immunostaining and RNA sequencing. Trehalose and Lactotrehalose inhibited hypoxia-induced accumulation of aggregates and restored impaired autophagy-lysosomal machinery. Disaccharide administration significantly restored normal pregnancy features in PE mice as characterized by normalization of hypertension, proteinuria, growth restriction, and kidney injury. RNA-seq analysis identified some novel genes and pathways that are related to preeclampsia and normalized by disaccharides.

overall_design: RNASeq of mouse placenta exposed to NP Serum, PE Serum, PE + Trehalose, PE + Lactotrehalose

first: Zheping

last: Huang

first: Jaimie

last: Fierce

first: Shibin

last: Cheng

first: Akitoshi

last: Nakashima

first: Anthony

last: Agudelo

first: Shigeru

last: Saito

first: James

last: Padbury

first: Jessica

last: Schuster


title: miRNAs associated with breast cancer brain metastasis

city: La Jolla

first: Emily

last: Wang

state: CA

address: 9500 Gilman Dr

department: Vc-health Sciences-schools

institute: UC San Diego

type: Non-coding RNA profiling by high throughput sequencing

summary: The goal of this study is to determine the extracellular miRNAs associated with breast cancer metastasis to the brain.  By combining the small RNA-seq data of patient sera and cell culture models, we are able to select breast cancer cell-derived miRNAs that are associated with brain metastasis for further functional study.

overall_design: We first performed small RNA-seq using serum RNA from 42 patients with stage IV breast cancer.  These patients include 21 with brain metastases (cases) and 21 controls without brain metastases (but with metastases to other organs) that were selected to have matched age, time from diagnosis, and HER2/ER/PR status of the breast tumor.  We next peformed small RNA-seq using RNA extracted from extracellular vesicles (EVs, including exosomes) and from cell lysate, to compare the extracellular and intracellular miRNA profiles between two isogenic cell lines, the parental MDA-MB-231 human breast cancer cell line and a brain-tropic variant of MDA-MB-231 that was selected in vivo for its enhanced potential to form brain metastasis.

first: Shizhen

middle: E


title: Transient Induction of Actin Cytoskeletal Remodeling Associated With Dedifferentiation, Proliferation, and Redifferentiation Stimulates Cardiac Regeneration

status: Public on Oct 29 2023

city: Chongqing

first: Chunyu

last: Zeng

state: Chongqing

address: 10 Changjiangzhilu Road

institute: Third Military Medical University

summary: The formation of new and functional cardiomyocytes requires a 3-step process: dedifferentiation, proliferation, and redifferentiation, but the critical genes required for efficient dedifferentiation, proliferation, and redifferentiation remain unknown. In our study, a circular trajectory using single-nucleus RNA sequencing of the pericentriolar material 1 positive (PCM1+) cardiomyocyte nuclei from hearts 1 and 3 days after surgery-induced myocardial infarction (MI) at postnatal day (P) 1 was reconstructed and demonstrated that actin remodeling contributed to the dedifferentiation, proliferation, and redifferentiation of cardiomyocytes after injury. We identified four top actin-remodeling regulators, namely Tmsb4x, Tmsb10, Dmd, and Ctnna3, which we collectively referred to as 2D2P. Transiently expressed changes of 2D2P, using a polycistronic non-integrating lentivirus driven by Tnnt2 (cardiac-specific troponin T) promoters (Tnnt2-2D2P-NIL), efficiently induced transiently proliferative activation and actin remodeling in P7 cardiomyocytes and adult hearts. Furthermore, the intramyocardial delivery of Tnnt2-2D2P-NIL resulted in a sustained improvement in cardiac function without ventricular dilatation, thickened septum, or fatal arrhythmia for at least 4 months. In conclusion, this study highlights the importance of actin remodeling in cardiac regeneration and provides a foundation for new gene-cocktail-therapy approaches to improve cardiac repair and treat heart failure using a novel transient and cardiomyocyte-specific viral construct.

overall_design: snRNA-seq  was performed on post-MI hearts 7 days after Control-NIL or Tnnt2-2D2P-NIL injection.

first: Wenbin

last: Fu


title: Effect on gene expression of addition of N-acetylmannosamine to galactose grown Streptococcus pneumoniae.

city: Leicester

first: Richard

middle: David

last: Haigh

state: Leicestershire

address: Medical Sciences Building, University Road

department: Department of Respiratory Sciences

institute: University of Leicester

summary: RNA-seq analysis of N-acetylmannosamine upon growth and gene expression in pneumococci grown with galactose as sole sugar.

overall_design: Pneumocccal strain D39 was grown to mid exponetial phase in chemically defined media (CDM) containing 55 mM galactose (as sole sugar). N-acetylmannosamine was added at 3.5 mM and samples were taken for RNA analysis at 0, 15 and 30 minutes post addition. Additionally separate D39 cultures were grown with 3.5 mM N-acetyl-mannosamine as the sole sugar and RNA extracted at mid-exponential.

first: Megan

last: De Ste Croix

middle: D

first: Marco

middle: R

last: Oggioni


title: RNA accumulation in aged endothelial cells links an interferon gene signature to cellular senescence

status: Public on Oct 27 2023

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

summary: RNA-seq was performed on early passage and senescent human retinal microvascular endothel cells (HRMECs), to determine transcriptomic changes. Replicative and Etoposide-induced senescent HRMECs senescence-associated gene signature and upregulation of an interferon related gene signature.

overall_design: Sequencing of total mRNA from three independent clones, comparing early-passage human retinal microvascular endothelial cells (HRMECs) to replicative and Etoposide-induced senescent counterparts.

first: Pietro

middle: M

last: Bertelli

first: Jasenka

last: Guduric-Fuchs

first: Reinhold

last: Medina


title: Analysis of gene expression in Idasanutlin-arrested SIN3A and SIN3B depleated cells

status: Public on Oct 28 2023

city: Santa Cruz

first: Gerd

middle: Armin

last: Mueller

address: 1156 High Street

department: Chemistry and Biochemistry

institute: University of California, Santa Cruz

summary: mRNA expression analysis of arrested HCT116 cells (wild-type or SIN3B-/-) transfected with either non-targeting control siRNA or one of three SIN3A siRNAs and treated with Idasanulin to activate p53.

overall_design: HCT116 cells were cultivated in 6-well plates and transfected with 20 nM SIN3A siRNAs (Horizon Discovery, #MQ-012990-00-0002; siRNAs #1, #2, and #4 for three biological replicates) or a non-targeting control siRNA (siGENOME Non-Targeting siRNA 5, Horizon Discovery; three biological replicates) and 5 µl Lipofectamine RNAiMAX (Invitrogen, #13778075) in a total volume of 2 ml in antibiotics free 10% DMEM. 24 h after transfection, cells were treated with either DMSO or 5 µM Idasanutlin (R&D Systems, #12-35-22-07) for an additional 24 h before cells were harvested RNA extraction. Total RNA was isolated with the Direct-zol RNA MiniPrep Kit (Zymo Research, #R2053).

middle: A

first: Alison

last: Barrett

first: Andreas

last: Rechtsteiner

first: Seth

last: Rubin

first: Tilini

middle: U

last: Wijeratne

first: Manisha

last: Shingare

first: Kelsie

last: Rodriguez


title: Effect of Lymph nodes removal on transcriptomic profile in iWAT of mice

status: Public on Oct 23 2023

city: Chicago

first: Jooman

last: Park

state: IL

address: 909 S Wolcott Ave COMRB 1120

department: Dept. of Physiology and Biophysics

institute: University of Illinois at Chicago

summary: There is a regional preference around lymph nodes (LNs) for adipose beiging upon cold exposure. However, the importance of this unique anatomical location remains poorly understood. In this study, the potential role of Lymph nodes in iWAT was investigated. to elucidate functional outcomes, we performed RNA-sequencing analysis using littermate sham and lymph nodes removal (LNR) mice upon cold exposure

overall_design: To investigate the cooperative function of lymph nodes in beige adipocytes in iWAT, we established lymph nodes removal and confirmed in respond with cold exposure. We performed gene expression analysis using data obtained from RNA-sequencing. comparative gene expression profiling between sham and LNR group.

first: Yexian

last: Yuan

first: Yuwei

last: Jiang


title: Retinoic  acid modulation guides human-induced pluripotent stem cell differentiation towards left or right ventricle-like cardiomyocytes

status: Public on Oct 25 2023

city: Munich

first: Hengliang

last: Zhang

department: University Hospital

institute: LMU Munich

summary: Background: Cardiomyocytes (CMs) induced from human induced pluripotent stem cells (hiPSCs) by traditional methods are a mix of atrial and ventricular CMs and many other non-cardiomyocytes. Retinoic acid (RA) plays an important role in regulation of the spatiotemporal development of the embryonic heart and high concentrations of RA have been shown to steer differentiation towards atrial CMs, whereas lower concentrations of RA promote a more ventricular-like CM profile. Aim: Create engineered heart tissue (EHT) with left and right ventricular phenotype from hiPSCs by intervening with specific concentrations of retinoic acid (RA) during hiPSC differentiation towards CM. Methods: hiPSC were derived by reprogramming skin fibroblasts. Different concentrations of RA (Control group without RA, LRA group with 0.05 µM and HRA group with 0.1 µM) were administered during third to sixth days of the differentiation process. Engineered heart tissues (EHTs) were generated by assembling CMs derived from hiPSC (hiPSC-CM) at high cell density in a low collagen hydrogel. The maturation and growth of EHTs were induced in a customized biomimetic tissue culture system, that provides continuous electrical stimulation, medium agitation and stretch. The function of CMs and EHTs was analyzed under different conditions. Finally, RNA extraction and tissue fixation were performed on CMs and EHTs for RT-qPRC and immunofluorescence staining analysis. RNA sequencing was conducted on EHTs to examine how RA affects both the function and structure of EHT. Results: In the HRA group, hiPSC-CMs exhibited the first onset of beating and showed the highest expression of maturity genes MYH7 and cTnT. The expression of TBX5, NKX2.5 and CORIN, which are the marker genes for left ventricular CMs, was also the highest in the HRA group. The transcription factor MEF2C associated with RA and ventricular development genes, NPPA and MYH7, were highly expressed in the HRA group, while GATA4 was less expressed in the HRA group. In terms of EHT, the HRA group displayed the highest contraction force, the lowest beating frequency, and the highest sensitivity to hypoxia and isoprenaline, which means it was more functionally similar to the left ventricle. The expression of TBX5 and NKX2.5 was found to be the highest expression in the HRA group of EHT, while expression of TBX20 and ISL1 was found to be the highest expression in control group. When the electrical stimulation frequency of EHT in the HRA group was raised, it correspondingly increased its contractile force. The heightened contractility of EHT within the HRA group can be attributed to the promotion of augmented extracellular matrix strength by RA. Conclusion: By interfering with the differentiation process of hiPSC with a specific concentration of RA at a specific time, we were able to successfully induce CMs and EHT with a phenotype similar to that of the left ventricle or right ventricle. Our research paved the way for future studies on in vitro left ventricular or right ventricular function, personalized drug screening, and precision medicine.

overall_design: To investigate molecular changes underlying the improved organisation of the EHTs derived from hiPSC-CMs previously exposed to RA. Different concentrations of RA (Control group without RA, LRA group with 0.05 µM and HRA group with 0.1 µM) were administered during third to sixth days of the hiPSCs differentiation process. Comparative gene expression profiling analysis of RNA-seq data for EHT from different group.

first: Payel

last: Sen

first: Jules

last: Hamers

first: Theresa

last: Sittig

first: Brent

last: Woestenburg

first: Alessandra

last: Moretti

last: Dendorfer

first: Daphne

last: Merkus


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [bulkMPRA(promoters, cells v2)]

status: Public on Oct 17 2023

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 activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode circularization, these scalable single-cell quantitative expression reporters (scQers) provide high-contrast readouts, analogous to classic in situ assays, but entirely from sequencing. Screening >200 putative enhancers in a multicellular in vitro model of early mammalian development, we identified thirteen (eight previously uncharacterized) autonomous and cell-type-specific elements, such as constituents of the Sox2 control region exclusively active in pluripotent cells, endoderm-specific enhancers, including near Foxa2 and Gata4, and a compact pleiotropic enhancer at the Lamc1 locus. We further demonstrate that synthetic enhancer pairs generate cognate two-cell-type activity profiles and assess gain/loss-of-function multicellular expression phenotypes from enhancer variants with perturbed transcription factor binding sites. scQers can be applied in developmental systems to quantitatively characterise native, perturbed, and synthetic enhancers at scale, with high sensitivity and at single-cell resolution.

overall_design: Bulk MPRA from K562 & HEK293T bottlenecked populations with genome-integrated MPRA reporters (promoter series).

first: Jean-Benoît

first: Samuel

middle: G

last: Regalado

first: Silvia

last: Domcke

first: Tony

last: Li

first: Xiaoyi

first: Beth

last: Martin

first: Diego

last: Calderon

first: Chase

middle: C

last: Suiter

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: Microfluidics-free single-cell genomics reveals complex central-peripheral immune crosstalk in the mouse brain during peripheral inflammation

status: Public on Oct 18 2023

city: Gainesville

first: Jake

last: Boles

state: FL

address: LG-152, 1149 Newell Dr

department: Neuroscience

institute: University of Florida

summary: Inflammation is a realized detriment to brain health in a growing number of neurological diseases, but querying neuroinflammation in its cellular complexity remains a challenge. This manuscript aims to provide a reliable and accessible strategy for examining the brain’s immune system. We compare the efficacy of cell isolation methods in producing ample and pure immune samples from mouse brains. Then, with the high-input single-cell genomics platform PIPseq, we generate a rich neuroimmune dataset containing microglia and many peripheral immune populations. To demonstrate this strategy’s utility, we interrogate the well-established model of LPS-induced neuroinflammation with single-cell resolution. We demonstrate the activation of crosstalk between microglia and peripheral phagocytes and highlight the unique contributions of microglia and peripheral immune cells to neuroinflammation. Our approach enables the high-depth evaluation of inflammation in longstanding rodent models of neurological disease to reveal novel insight into the contributions of the immune system to brain health.

overall_design: Mice received a single intraperitoneal injection of lipopolysaccharide (LPS) or saline vehicle, and brains were collected 24 hours post-injection. Brains were dissociated using Miltenyi Biotec's Adult Brain Dissociation Kit, and some samples were treated with anisomycin D, actinomycin, and triptolide or DMSO vehicle during dissociation to inhibit the activation of artifactual gene signatures. Immune cells were then isolated from brain cell suspensions with magnetic separation using a CD45 magentic antibody.

first: Oihane

last: Uriarte Huarte

first: Malú

last: Tansey


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [scQer_mEB, v2)]

overall_design: Single-cell reporter on day 24 mouse embryoid bodies with high MOI genome-integrated dual RNA reporters with literature-selected CREs, mutated CREs (allelic series of transcription factor binding sites), and paired CREs. Three biological replicates. Gene expression and custom oBC, mBC libraries.


title: Choroid plexus defects in Down syndrome brain organoids enhance neurotropism of SARS-CoV-2

status: Public on Oct 16 2023

city: St Lucia

first: Andrii

last: Slonchak

state: QLD

address: MBS Bldg 76, Cooper Rd

department: School Of Chemistry And Molecular Biosciences

institute: The University of Queensland

summary: Why individuals with Down Syndrome (DS, trisomy 21) are particularly susceptible to SARS-CoV-2 induced disease remains largely unclear. The choroid plexus secrets the cerebrospinal fluid and strongly expresses the ACE2 receptor and the chromosome 21 encoded TMPRSS2 protease. To investigate the role of the choroid plexus in SARS-CoV-2 central nervous system infection in DS, we established a new type of brain organoid from DS and isogenic euploid control iPSC that consists of a core of appropriately patterned functional cortical neuronal cell types that is surrounded by a patent and functional choroid plexus (CPCOs). Remarkably, DS-CPCOs not only recapitulated abnormal features of DS cortical development but also revealed defects in ciliogenesis and epithelial cell polarity of the developing choroid plexus. We next demonstrate that the choroid plexus layer facilitates SARS-CoV-2 replication and infection of cortical neuronal cells, and that this is increased in DS-CPCOs. We further show that inhibition of TMPRSS2 activity in DS-CPCOs inhibits SARS-CoV-2 infectivity. We conclude that CPCOs are a useful model for dissecting the role of the choroid plexus in euploid and DS forebrain development and enables screening for therapeutics that can inhibit SARS-CoV-2 induced neuro-pathogenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for euploid (EU79) and down syndrome (DS) brain organoids with Choroid plexus (CP) upon infection with SARS-CoV-2.


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [bulkMPRA (devCRE, mEB, v2)]

overall_design: Bulk MPRA time series on mouse embryoid body induction from cells harboring high MOI genome-integrated dual RNA reporters with different architectures (two pools of constructs A & B)


title: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [plasmid libraries subassembly, v2]

overall_design: Subassembly of plasmid barcoded reporter libraries.


title: mTOR promotes zebrafish larvae fin regeneration through regulating macrophages activation and CaM-mTOR-dnm1l axis

status: Public on Oct 13 2023

first: Gongyi

last: Xiao

address: 74 Linjiang Road

institute: Chongqing Medical University

summary: To investigate the functional and mechanistic roles of mTOR in zebrafish larvae fin regeneration, we firstly examined the spatiotemporal expression of mTOR in larvae fin and established a mTOR knockout (mTOR-KO)  transgenic fish line using CRISPER / Cas9 gene editing technology. Moreover, mTOR was essential for the activation of macrophages, which is a key factor in maintaining the regenerative repair process. We also demonstrated that mTOR knockdown attenuated the proliferative capacity of bud embryo cell during the regenerative phase, while cell apoptosis was not affected. RNA-sequence analysis showed changes in mitochondrial function and dnm1l was identified as the main regulatory factor during the fin regeneration stage. We further suggested that mTOR may promote mitochondrial fission to support bud embryo cell regeneration via CaM-mTOR-dnm1l axis.

overall_design: Sequencing samples for the micro-transcriptome were obtained from tail fin tissues regenerated for 24 h. Fifty regenerated tail fins were extracted for each sample from the control and experimental groups treated with 1 uM Rapamycin. Each group had 3 biological replicates and samples were lysed using Trizol. Sequencing technology was provided by UNIKAWA Biotechnology Co.Ltd (Hangzhou, China).

first: Huiping

last: Yang

first: Mao

last: Nie


title: Depletion of mRNA cap-binding protein eIF4E1 drives bradyzoite formation in Toxoplasma gondii [RIBO-seq]

first: Michael

last: Holmes

institute: Indiana University School of Medicine

summary: Ingestion of Toxoplasma gondii results in life-long infection due to its ability to convert from the rapidly disseminating tachyzoite stage to the chronic, encysted bradyzoite stage.  The control of mRNA translation has been suggested to play a key role in the signaling required to trigger bradyzoite formation. In eukaryotes, translational control primarily operates at two key points during the assembly of translation initiation factors. The phosphorylation of eIF2 affects mRNA start codon recognition and promotes differentiation in a variety of parasites. Modulating eIF4F function is the second pan-eukaryote regulatory point but remains unexplored in Toxoplasma. Here, we uncover the role that eIF4F-centric regulation plays in regulating bradyzoite formation by targeting the cap-binding subunit, eIF4E1. We discover that eIF4E1 coordinates two eIF4F complexes and binds the 5’-end of all mRNAs transcribed in tachyzoites, many of which show evidence of stemming from heterogenous transcriptional start sites. Together, this indicates that eIF4E1 is the predominant cap-binding protein in Toxoplasma tachyzoites. We also demonstrate that eIF4E1 knockdown or its chemical inhibition triggers the efficient formation of bradyzoites in the absence of other stresses and that stress-induced bradyzoites reduce their eIF4E1 expression. This study unearths a role for eIF4F-centric translational control in controlling Toxoplasma differentiation, suggesting that control of cap-dependent translation regulates the process of bradyzoite formation.

overall_design: expression changes at the transcriptional and translational levels upon IAA-induced eIF4E1 depletion in Toxoplasma gondii tachyzoites

first: William

last: Sullivan Jr.


title: Epithelial human NLRC4 promotes cancer survival by mediating Type-I Interferon signaling and immune infiltration

status: Public on Oct 09 2023

city: St. Louis

first: Emily

last: Landy

state: Missouri

address: 425 S. Euclid Ave

institute: Washington University in St. Louis

summary: The induction of a broad Type-I IFN gene signature by NLRC4 is confirmed with a NLRC4 GOF mutation (T337S), using a THP1-NLRC4 (T337)-expressing stable cell line versus WT NLRC4.These Type-I IFN stimulated genes were confirmed to be also upregulated in NLRC4 (T337S) patient monocytes versus healthy controls, but not in NLRP3 (G569R) patient monocytes. Unbiased gene set enrichment analysis of RNAseq revealed a top enrichment of the “interferon alpha response” pathway in THP1-NLRC4 (T337S) cells versus WT NLRC4

overall_design: Primary human monocyte-derived macrophages and NLRC4-transduced THP1 cells were generated, then stimulated with PMA for up to 72hrs. Control (2), CEG, and NOMID patient PBMC-derived monocytes were stimulated with LPS and DOTAP/flagellin.

first: Lindsey

last: Spiker

first: Scott

middle: W

last: Canna


title: scRNAseq of peripheral blood mononuclear cells in age-related macular degeneration

status: Public on Oct 06 2023

city: Saint Louis

first: Joseph

last: Lin

state: MO

address: 660 South Euclid Ave, MSC-8096-06-07

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine

summary: We profiled using single cell RNA sequencing the peripheral blood mononuclear cells from control patients and patients with age-related macular degeneration (AMD).

overall_design: We collected blood by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify peripheral blood mononuclear cells (PBMCs), we centrifuged the blood, isolated the buffy coat, and lysed red blood cells leaving nucleated cells behind. We performed single cell RNA sequencing using the 10x Genomics platform.

first: Philip

last: Ruzycki

first: Rajendra

middle: S

last: Apte


title: Microarray analysis of mRNA and long noncoding RNA expression profiles between multiple myeloma patients and control

city: Wuhan

first: Han

last: Yan

address: Jiefang  Avenue

institute: Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: To further investigate the differential expression gene of multiple myeloma.Three multiple myeloma samples and three normal samples were used for microarray.

overall_design: Bone marrow CD138+ cells were sorted from multiple myeloma patients and normal individuals. Samples were treated with TRIzol and RNA extracted.Gene expression profiling was carried out in three multiple myeloma patients and three controls.

first: Su

last: Gao

first: Chunyan

last: Sun

first: Yu

last: Hu


title: Early-to-mid stage idiopathic Parkinson’s disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Neuroinflammation in the brain contributes to the pathogenesis of Parkinson’s disease (PD), but the potential dysregulation of peripheral immunity has not been systematically investigated for idiopathic PD (iPD). Here we showed an elevated peripheral cytotoxic immune milieu, with more terminally-differentiated effector memory (TEMRA) CD8 T, CD8+ NKT cells and circulating cytotoxic molecules in fresh blood of early-to-mid iPD, especially in females, after analyzing >700 innate and adaptive features. This profile, also reflected by fewer CD8+FOXP3+ regulatory T cells, was confirmed in another subcohort. Co-expression between cytotoxic molecules was selectively enhanced in CD8 TEMRA and effector memory (TEM) cells. Single-cell RNA-sequencing analysis demonstrated the accelerated CD8 differentiation within CD8 compartments, enhanced cytotoxic pathways in CD8 TEMRA and TEM cells, while CD8 central-memory (TCM) and naïve cells were already more-active and transcriptionally-reprogrammed. Our work provides a comprehensive map of dysregulated peripheral immunity in iPD, proposing previously-unrecognized candidates for early diagnosis and treatments.

overall_design: We compared samples between patients with early-to-mid idiopathic Parkinson’s diseases (iPD) and age-matched healthy controls (HC). Four HC were 59-65 years old (mean=62.33) while five iPD were 56-68 years old (mean=63.14) when they were sampled. Considering our female-biased data in clinical diagnostic values, we only selected female iPD vs age-matched HC for scRNA-seq. All the iPD and HC are CMV seropositive (for other inclusion and exclusion criteria, please refer to the manuscript). All the iPD have a Hoehn and Yahr (H&Y) staging scale of 2. All the PBMC were cryopreserved at the Luxembourg biobank (IBBL) and thawed (for detailed procedures, please refer to the manuscript text). After thawing, PBMC from each participant were stained with marker Abs and sorted into four CD8 subsets: CD8 Naïve (CD45RO-CCR7+), CD8 TCM (CD45RO+CCR7+), CD8 TEM (CD45RO+CCR7-) and CD8 TEMRA (CD45RO-CCR7-). For each subset, we pooled the sorted samples from the same group (HC or iPD) prior to scRNA-seq. The processed files provided in this dataset are the starting point of our scRNA-seq analysis. For detailed analysis steps, please refer to the Methods section of our manuscript including all the code depository information.

first: Christophe

last: Capelle

first: Fanny

last: Hedin

first: Lukas

last: Pavelka

first: Kamil

last: Grzyb

first: Dimitrios

last: Kyriakis

first: Oliver

last: Hunewald

first: Vera

last: Tslaf

first: Alexander

last: Skupin

first: Antonio

last: Cosma

first: Rudi

last: Balling

first: Rejko

last: Krüger

first: Markus

last: Ollert

middle: Q


title: Heterogeneous gene expression during early arteriovenous fistula remodeling suggests that downregulation of metabolism predicts adaptive venous remodeling

status: Public on Oct 04 2023

city: New Haven

first: Yuichi

last: Ohashi

state: CT

address: 10 Amistad Street #414J

department: Surgery

institute: Yale University School of Medicine

summary: Background: Although clinical outcome of arteriovenous fistula (AVF) as a preferred vascular access for hemodialysis has been inadequate, biological mechanisms of AVF maturation and failure is still poorly understood. Since our mouse AVF model recapitulates human AVF maturation and partial failure, we hypothesized that high throughput RNA sequencing (RNA-seq) analysis would identify early changes in gene expression that might predict AVF maturation and failure. Method: Aortocaval fistula creation (AVF group) or sham operation (sham group) was performed with C57BL/6 mice (10 wk). Ultrasound was performed to confirm the AVF patency and to measure hemodynamics. Venous limbs were collected on postoperative day 7 and total RNA was extracted. After Poly-A mRNA libraries were constructed, RNA-seq was performed. Differentially expressed genes (DEG) were identified, and subsequent enrichment analyses of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed with bioinformatics techniques. Results: 1057 DEG were identified between the AVF and sham groups. Genes in metabolic pathways were significantly downregulated in the AVF. Since gene expression patterns among the AVF group were significantly heterogenous, the AVF group was divided into 2 groups (‘normal’ AVF group; nAVF and ‘outliers’ group; OUT), and subgroup analyses were performed. Although physiological data of body weight change and hemodynamics were not different between the nAVF and OUT groups, 413 DEG were identified between them. Enrichment analyses showed significant overrepresentation of metabolism, immunity, and coagulation in the OUT group. Comparing the nAVF group with the sham group, 403 DEG were identified. Enrichment analyses showed increase of gene expression related to cell cycle, extracellular matrix, and immunity. Comparing these results with previously published data, the gene expression patterns of the nAVF group was consistent with AVF maturation and adaptive remodeling, whereas the OUT group showed attenuated difference, suggesting the heterogeneity of the AVF group reflects early gene expression changes in the process of AVF maturation and failure. Significant sex differences were not observed in the AVF group. Conclusions: A small subset of AVF undergoes aberrant biological processes in the early phase including diminished ECM remodeling, activated coagulation and upregulated metabolism, that could lead to fistula failure. Detection of these processes might be a viable translational strategy to predict fistula failure and reduce patient morbidity.

overall_design: All animal experiments were performed in compliance with federal guidelines and with approval from the Institutional Animal Care and Use Committee of Yale University.  10-week-old wild-type female and male C57BL/6J mice were purchased from Jackson Laboratory (Bar Harbor, ME, USA). Infrarenal aortocaval fistulae were created. Briefly, inhaled 2 - 2.5 % isoflurane in 1.0 L/min 02 was used for general anesthesia, and extended-release buprenorphine (Ethiqa XR; North Brunswick, NJ, USA) was administered subcutaneously with a dosage of 3.25 mg/kg body weight for intraoperative and postoperative analgesia. The abdominal aorta and the inferior vena cava (IVC) were exposed with a midline laparotomy; the bowels were gently retracted. After the vessels were clamped at an immediately caudal level of the origins of the left renal artery and vein, a fistula between the vessels was created by using a 25-gauge needle to puncture the aorta and IVC, from a left lateral side of the aorta into a lumen of the IVC at a level cranial to the aortic bifurcation. Hemostasis of the puncture site on the lateral aortic wall was achieved by a gentle compression with a surrounding retroperitoneal tissue. A pulsatile bright-red blood flow visible intraoperatively through the IVC wall was considered as a primary technical success of the AVF creation. Sham-operated mice underwent all the same steps except the needle puncture.   After euthanasia and circulatory flushing with normal saline, the IVC was harvested on postoperative day 7. The range of the extracted IVC from mice with an AVF was from just above the fistula opening through just below the origin of the left renal vein. The tissues were immediately submerged in RNAprotect Tissue Reagent (QIAGEN, Hilden, Germany) and incubated overnight at 4°C, then stored at -20°C without the reagent. Total RNA was extracted using RNeasy Mini Kit with DNase I (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. Total RNA quality and concentration were estimated with A260/A280 and A260/A230 ratios measured using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA).  Preparation and sequencing of poly-A mRNA sequencing libraries were performed by the Yale Center for Genome Analysis (YCGA). RNA integrity was estimated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples with RNA integrity number (RIN) values of ≥ 8.0 were used for analysis.  Poly-A mRNA was purified from approximately 200 ng of total RNA and the stranded mRNA sequencing libraries were constructed using KAPA mRNA HyperPrep Kit for Illumina sequencing (Roche, Basel, Switzerland). Indexed libraries were quantified by qRT-PCR using KAPA Library Quantification Kits (Roche, Basal, Switzerland) and insert size distribution was determined using an Agilent 2100 Bioanalyzer. Samples with a yield of ≥ 0.5 ng/µL and a size distribution of 150 - 300 bp were sequenced. Sample concentrations were normalized to 1.2 nM and loaded onto an Illumina NovaSeq flow cell (Illumina, San Diego, CA, USA) at a concentration that yielded 25 million passing filter clusters per sample. Samples were sequenced using 101 bp paired-end sequencing on an Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA). Data generated during sequencing runs were simultaneously transferred to the YCGA high-performance computing cluster.  The FASTQ files of raw sequencing reads were imported into a computing cluster based on Red Hat Linux computing system and analyzed. For the purpose of quality control, poly A and poly T sequences, Illumina adaptor sequences and low-quality sequences in the reads were deleted using PRINSEQ v0.20.4 and Trimmomatic v0.39 software. The trimmed sequencing data were aligned to the GRCm39 reference genome with the gene annotation information  (Ensembl release 106) and expression values for each gene were counted using STAR v2.7.7a and RSEM v1.3.3 software.

first: Alan

last: Dardik


title: eQTL mapping of fetal-like pancreatic progenitor cells

status: Public on Oct 03 2023

first: Kelly

middle: Ann

last: Frazer

address: 9500 Gilman Drive

institute: UC San Diego

summary: The goal of this study is to understand the effects of genetic variation on gene expression in fetal-like pancreatic progenitor cells. We generated bulk RNA-seq from 107 iPSC-derived pancreatic progenitor cells (iPSC-PPC) from iPSC lines derived from 106 individuals from the iPSCORE resource. We then conducted genome-wide expression quantitative trait loci analyses to identify genetic variants associated with gene expression and isoform usage.

overall_design:
This repository provides bulk RNA-seq data generated from 107 iPSC-derived pancreatic progenitor samples from 106 individuals in the iPSCORE Resource (PMID: 28410642). 102 samples were sequenced twice to obtain sufficient number of reads while five samples were sequenced once because they already had sufficient reads.

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

first: Jennifer

last: Nguyen

first: Matteo

last: D'Antonio


title: Gene expression profiling of epithelial cells from human cervix cultured in Organ Chip and transwells

status: Public on Dec 12 2023

city: Boston

first: Donald

last: Ingber

state: Massachusetts

address: 3 Blackfan Circle, CLSB 5th Floor

institute: Wyss Institute for Biologically Inspired Engineering at Harvard University

summary: Modulation of mucus production by the human ecto- and endo-cervical epithelium by steroid hormones and associated interactions with commensal microbiome play a central role in the physiology and pathophysiology of the female reproductive tract.  Here, we show that in a human organ-on-a-chip model of cervix (Cervix Chip), use of continuous fluid flow promotes ecto-cervical differentiation, whereas use of periodic flow including periods of stasis stimulated endo-cervical specialization. Continuous flow exhibited significant upregulation of genes associated with ectocervical epithelial phenotype whereas the same cells cultured in the same medium under periodic flow or under static conditions in Transwell inserts upregulated genes more closely associated with the endocervical epithelial phenotype. Similar results with minor differences were obtained using epithelial cells isolated from three donors each from a different ethnic background (African American, Hispanic, and Caucasian).

overall_design: Epithelial cells from three donors have been cultured in two experimental arrangements: a) organ chips at low strain cycle (n = 2 technical replicates) and b) medium strain cycle (n = 3 technical replicates) and c) static transwells (n = 3 technical replicates). Gene expression in the epithelial cells was measured using RNAseq.

first: Zohreh

last: Izadifar

first: Viktor

last: Horvath


title: Multiple myeloma patients and control

first: Han

last: Yan

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

overall_design: Refer to individual Series


title: Heat stress responsive HvHSFA2e gene regulates the heat and drought tolerance in barley through modulation of phytohormone and secondary metabolic pathways

status: Public on Oct 02 2023

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

summary: High temperature and drought are the primary yield-limiting environmental constraints for staple food crops. Heat shock transcription factors (HSF) terminally regulate the plant abiotic stress responses to maintain growth and development under extreme environmental conditions. HSF genes of Subclass A2 predominantly express under heat stress (HS) and activate the transcriptional cascade of defense-related genes. In this study, a highly heat-inducible HSF, HvHSFA2e was constitutively expressed in barley (Hordeum vulgareL.) to investigate its role in abiotic stress response and plant development. Transgenic barley plants displayed enhanced heat and drought tolerance in terms of increased chlorophyll content, improved membrane stability, reduced lipid peroxidation, and less accumulation of ROS in comparison to wild-type (WT) plants. Transcriptome analysis revealed that HvHSFA2e positively regulates the expression of abiotic stress-related genes encoding HSFs, HSPs, and enzymatic antioxidants, contributing to improved stress tolerance in transgenic plants. The major genes of ABA biosynthesis pathway, flavonoid, and terpene metabolism were also upregulated in transgenics. Our findings show that HvHSFA2e mediated upregulation of heat-responsive genes, modulation in ABA and flavonoid biosynthesis pathways enhance drought and heat stress tolerance.

first: Sumit

middle: K

last: Mishra

first: Chanderkant

last: Chaudhary

first: Suchi

last: Baliyan

first: Anuj

last: Poonia

first: Parul

last: Sirohi

first: Meenakshi

last: Kanwar

first: Annu

last: Kumari

first: Debabrata

last: Sircar

first: Hugo

last: Germain


title: Responsiveness of hypomethylated and control tumor cells to canonical Wnt-signalling

city: Heidelberg

first: Moritz

last: Jakab

address: Im Neuenheimer Feld

institute: German Cancer Research Center

summary: During metastasis, cancer cells travel the circulation to colonize distant sites. Due to the rarity of these events, the immediate cell fate decisions of metastasizing tumor cells (mTC)  are poorly understood and the role of the endothelium, as dissemination interface, remains elusive. Using a novel combinatorial mTC enrichment approach, we provide a first transcriptional blueprint of the early colonization process

overall_design: 4T1 cancer cells were treated with SKL2001 (Ctrl samples) or SKL2001 and decitabine (Hypo samples) over-night and RNAseq was performed.

first: Hellmut

last: Augustin


title: Gene expression changes in cord blood-derived ECFCs in response to in vitro senescence stimuli

first: Edoardo

last: Pedrini

institute: Hospital San Raffaele

summary: Senescent endothelial cells accumulate in blood vessels during aging and produce the senescence-associated secretory phenotype (SASP).  Age-related cardiovascular disease is promoted by SASP chronic inflammation. SASP establishment has been attributed to DNA damage and cGAS activation through cytoplasmic chromatin fragments. Therefore, DNA sensing has been extensively studied in cellular senescence; RNA sensing, on the other hand, remains unexplored. Here, we uncover a pivotal role for RNA accumulation and sensing in endothelial senescence. Our study suggests that intracellular RNA accumulation is a hallmark of senescent endothelial cells. This is associated with activation of RIG-I RNA sensing, and IRF7-driven IFN innate immune response. Moreover, our results revealed that inhibition of IRF7 or RIG-I were sufficient to extend the lifespan and functionality of endothelial cells. These data link the IFN gene signature with RNA accumulation/sensing in senescent endothelium and suggest IRF7 and RIG-I as potential therapeutic targets to delay vascular aging.

overall_design: In this study, three biological replicates of cord-blood derived ECFCs were exposed to three different treatments to characterize senescence response in endothelial progenitors. Confluent ECFCs were exposed to one of the following treatments: A. 10gy X-ray, four days recovery, passaging, RNA extraction 4 days post-passage. B. 1uM Etoposide for four days, four days recovery, passaging, RNA extraction 4 days post-passage. C. ECFCs were passaged until Hayflick limit was reached/cells exhausted their replicative potential, RNA was then extracted. D. ECFCs were treated with 100 IU/ml Interferon-β for 24 h. RNA was then extracted.

first: Reinhold

middle: J

last: Medina

first: Jasenka

last: Guduric-Fuchs

first: Kiran

last: Mcloughlin