title: Single-Cell Analysis Uncovers Dramatic Alteration of Microglia Heterogeneity after Ischemic Stroke

status: Public on Jun 14 2023

city: Shanghai

first: Yueman

last: Zhang

address: 160 Pujian Rd

institute: Department of Anesthesiology,  Renji Hospital, School of Medicine Shanghai Jiao Tong University, China

summary: Microglia are resident myeloid cells in the central nervous system (CNS) that regulate homeostasis and protect CNS from damage and infection. The phenotype of microglia is critical in regulating the propagation and resolution of inflammatory responses after ischemic stroke. However, little is known of its complexity and heterogeneity in the above context. Here, using single-cell RNA sequencing (scRNA-seq) of over 11,000 cells from the mice ischemic brain tissues, we demonstrated a previously undefined molecular heterogeneity among microglia clusters following ischemic stroke.

overall_design: To characterize the cell types and phenotypic changes involved in ischemic injury, we sorted a total of 11,226 single cells from sham or MCAO mice brain (n=3/group). All cells were sequenced using a modified BD Rhapsody scRNA-seq protocol after filtering

first: Yunlu

last: Guo

first: Tingting

last: Huang


title: Evidence for glutamate excitotoxicity that occurs before the onset of striatal cell loss and motor symptoms in an ovine Huntington’s Disease model.

status: Public on Jul 06 2023

city: Auckland

first: Andrew

last: Jiang

address: 3 Symonds Street

country: New Zealand

institute: The University of Auckland

type: Expression profiling by high throughput sequencing

summary:
Background
Huntington’s disease (HD) is a neurodegenerative genetic disorder caused by an expansion in the CAG repeat tract of the huntingtin (HTT) gene resulting in a triad of behavioural, cognitive, and motor defects. Current knowledge of disease pathogenesis remains incomplete, and no disease course-modifying interventions are in clinical use. We have previously reported the development and characterisation of the OVT73 transgenic sheep model of HD. OVT73 captures an early prodromal phase of the disease with an absence of motor symptomatology even at 5-years of age and no detectable striatal cell loss.

Methods
To better understand the disease-initiating events we have undertaken a single nuclei transcriptome study of the striatum of an extensively studied cohort of 5-year-old OVT73 HD sheep and age matched wild-type controls.

Results
We have identified transcriptional upregulation of genes encoding N-methyl-D-aspartate (NMDA), α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and kainate receptors in OVT73 medium spiny neurons, the cell type preferentially lost early in HD. This observation supports the glutamate excitotoxicity hypothesis as an early neurodegeneration cascade-initiating process. Moreover, we also observed the downstream consequences of excitotoxic stress, including a downregulation of transcription of components for the oxidative phosphorylation complexes. We also found that pathways whose activity has been proposed to reduce excitotoxicity, including the CREB family of transcription factors (CREB1, ATF2, ATF4 and ATF7) were transcriptionally downregulated.

Conclusions
To our knowledge, the OVT73 model is the first large mammal HD model that exhibits transcriptomic signatures of an excitotoxic process in the absence of neuronal loss. Our results suggest that glutamate excitotoxicity is a disease-initiating process. Addressing this biochemical defect early may prevent neuronal loss and avoid the more complex secondary  consequences precipitated by cell death.

overall_design: Single nuclei RNA-seq of ovine striatal tissue


title: CTLA-4 tail fusion enhances CAR-T anti-tumor immunity [bulk RNA-seq]

status: Public on Jun 09 2023

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

country: USA

institute: Yale University

summary: To gain further insight into how CCT fusion engineering impacts their function, we characterized CAR-T cells using transcriptome profiling. We performed mRNA-seq from all four groups of CAR-T cells, either without stimulation (baseline) or with 2 rounds of NALM6GL stimulation. For CAR-T cells that were cocultured with 2 rounds of NALM6GL cells, we sorted the pure CAR-T populations (CAR+; GFP-) before subjecting them to RNA sequencing

overall_design: Bulk RNA sequencing of anti-CD22 CAR-T cells with 0 or 2 rounds of NALM6GL stimulation. In each treatment, there were four different CAR-T groups with three biological repeats per group.

first: Xiaoyu

last: Zhou

first: Hanbing

last: Cao

first: Paul

last: Renauer


title: Effect of Nogo deficiency on the insulin signaling pathway

status: Public on Jul 24 2023

city: Hefei

first: Ke

last: Gong

address: 193 Tunxi Road, Baohe District

country: China

institute: Hefei University of Technology

summary: The elevation of Nogo-B expression in T2DM mice and Nogo-B knockdown alleviated diabetic symptoms in db/db mice prompted us to further investigate the involvement of Nogo-B in the insulin signaling pathway and T2DM. The three isoforms of Nogo are derived from various RNA splicing events, so deleting Nogo-B exons 2-4 results in the deficiency of other Nogo members, resulting in Nogo knockout (Nogo-/-) mice. As the liver is the key organ in the systemic response to insulin and controls glucose and lipid metabolism, we conducted RNA-seq of livers isolated from 8-week-old Nogo-/- mice and WT littermates.

overall_design: We conducted RNA-seq of livers isolated from normal chow fed 8-week-old Nogo-/- mice (NC) and WT littermates (CC). Each group is set up in three parallels.


title: Cell type- and time-dependent biological responses in ex vivo perfused lung grafts

status: Public on Jun 20 2023

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

summary: Ex vivo lung perfusion (EVLP) is a largely employed technique in transplantation that permits the reassessment of marginal lungs, thereby increasing the graft pool. However its biological effects on the different lung cell types are not known. In order to advance our mechanistic understanding and further improve EVLP, we conducted a pioneer study involving single-cell RNA-seq (scRNA-seq) on two human lungs declined for transplantation. We integrated data sets generated at 4 h (clinical duration) and 10 h (prolonged duration) and revealed functional changes common to both lungs that include inflammation in most cell types, loss of barrier function in epithelial and endothelial cells especially at 10 h, and reduction of migration properties in immune cells. In addition to providing insights into the biological effects of EVLP, scRNA-seq applied to EVLP offers a highly powerful way to evaluate novel EVLP therapeutic advances that will benefit to lung transplantation.

overall_design:
Donor lungs used in this study were from donation after brain death and were determined to be unsuitable for transplantation. Donor lung retrieval was carried out according to current clinical practice. After transportation at 4°C, lungs were processed to EVLP. Lung biopsies were taken just before EVLP (0 h), after 4 and 10 h EVLP, and analyzed using scRNAseq.
***Raw data for human samples not available due to patient privacy concerns***

first: Isabelle

last: Schwartz

first: Marc

last: Dalod

first: Edouard

last: Sage


title: CTLA-4 tail fusion enhances CAR-T anti-tumor immunity

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

overall_design: Refer to individual Series


title: chromatin accessibility assay at single-cell level (scATAC-seq) of the K562 cells with CRISPR-Cas9 KO of either HUB162 or HUB161

status: Public on Jun 01 2023

city: La Jolla

first: Peiyao

last: Wu

state: CA

address: 9500 Gilman Dr

department: Chemistry

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: HUB162 (chr11:42,878,450-42,883,450, hg38) was identified as an essential locus in the quiescent region in the K562 cells, and HUB161 (chr11:42,873,450-42,878,450, hg38) as a nonessential one. We used scATAC-seq of 10x Genomics Chromium to study chromatin accessibiliy after CRISPR-Cas9 deletion of either HUB162 (Ess) or HUB161 (Noness)

overall_design: K562 cells stably-expressing Cas9 (mCherry) were infected with pgRNA-expressing lentivirus (EGFP) and then cultured for 10 days. GFP+/mCherry+ cells were sorted and scATAC-seq was performed according to the procedures desrcibed in 10x Genomics Chromium Next GEM Single Cell ATAC Reagent Kits (v1.1) User Guide

first: Wei

last: Wang


title: gene profiling at single-cell level of the K562 cells with CRISPR-Cas9 KO of either HUB162 or HUB161

summary: HUB162 (chr11:42,878,450-42,883,450, hg38) was identified as an essential locus in the quiescent region in the K562 cells, and HUB161 (chr11:42,873,450-42,878,450, hg38) as a nonessential one. We used scRNA-seq of 10x Genomics Chromium to study gene expression after CRISPR-Cas9 deletion of either HUB162 (Ess) or HUB161 (Noness)

overall_design: K562 cells stably-expressing Cas9 (mCherry) were infected with pgRNA-expressing lentivirus (EGFP) and then cultured for 10 days. GFP+/mCherry+ cells were sorted and scRNA-seq was performed according to the procedures desrcibed in 10x Genomics chromium GEM Single Cell 3ʹ RNA library manual (v3)


title: Hi-C of the K562 cells with CRISPR-Cas9 KO of either HUB162 or HUB161

summary: HUB162 (chr11:42,878,450-42,883,450, hg38) was identified as an essential locus in the quiescent region in the K562 cells, and HUB161 (chr11:42,873,450-42,878,450, hg38) as a nonessential one. We used Arima Hi-C to study chromosomal structure after CRISPR-Cas9 deletion of either HUB162 (Ess) or HUB161 (Noness)

overall_design: K562 cells stably-expressing Cas9 (mCherry) were infected with pgRNA-expressing lentivirus (EGFP) and then cultured for 10 days. GFP+/mCherry+ cells were sorted and Hi-C was performed according to Arima Hi-C kit for Mammalian cell lines user guide (A160134 v01)


title: HUB162 and HUB161


title: IRF8 defines the epigenetic landscape in postnatal microglia, thereby directing their transcriptome programs

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

type: Methylation profiling by high throughput sequencing


title: Gene expression alteration in murine chondrogenic cell line ATDC5 cells by IL-1β and Fascin1 inhibitor NP-G2-044 treatment

status: Public on May 27 2023

city: Guangzhou

first: Kai

last: Li

address: 183 Zhongshan Avenue West

institute: The Third Affiliated Hospital of Southern Medical University

summary: To investigate the protective effect of Fascin1 inhibitor NP-G2-044 against chondrocyte dedifferentiation, we  stimulated murine chondrogenic cell line ATDC5 cells with  IL-1β to induce dedifferentiation, and with or without  NP-G2-044 treatment. Gene expression profiling analysis was performed using data obtained from RNA-seq of three independent experiments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ATDC5 cells treated with IL-1β or IL-1β plus Fascin1 inhibitor NP-G2-044 (IL, ILN).

first: Panpan

last: Yang

first: Yun

last: Xiao

first: Liangyu


title: Mapping the daily rhythmic transcriptome in the diabetic retina

status: Public on May 31 2023

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

summary: Retinal function changes dramatically from day to night. Yet, clinical diagnosis, treatments, and experimental sampling occur during the day, leaving a significant gap in our understanding of the pathobiology occurring at night. While there is evidence that diabetes disrupts the circadian system that optimizes our physiology to the environmental light/dark cycle, the impact of such disruption is not well understood. This study investigates whether diabetes affects the retina's daily rhythm of gene expression to understand the pathobiology of diabetic retinopathy, a common complication of diabetes. Control and hyperglycemic littermate mice (Ins2Akita/J) were kept under a standard 12h:12h light/dark cycle until four months of age.  Bulk mRNA sequencing was conducted in retinas collected every 4 hours throughout the 24 hr light/dark cycle. Computational approaches were used to detect rhythmicity, predict acrophase, identify differential rhythmic patterns, analyze phase set enrichment, and predict upstream regulators. The retinal transcriptome exhibited a tightly regulated rhythmic expression with a clear 12-hr axis of transcriptional rush, peaking at midday and midnight. The functions of day-peaking genes were enriched for DNA repair, RNA splicing, and ribosomal protein synthesis, whereas night-peaking genes were enriched for metabolic processes and growth factor signaling. Although the 12-hr transcriptional axis is retained in the diabetic retina, it was phase advanced by approximately 1-3 hours with a wider distribution. Upstream regulator analysis for the genes that showed phase shifts identified oxygen sensing mechanisms and HIF1alpha as regulators, but not the circadian clock, which remained in phase to the light/dark cycle. We propose a model in which early in diabetes, the diabetic retina experiences a ‘jet lag’ caused by the entrained circadian clock and its output being in one phase and metabolic pathways related to neuronal dysfunction and hypoxia driving advancement of gene expression to a different phase. Further studies are now required to evaluate the chronic implications of such internal jet lag for development of diabetic retinopathy.

overall_design: Control and hyperglycemic C57BL/6-Ins2Akita/J (Ins2Akita) mice were selected randomly at four months of age, and euthanized at one of six time-points over a 24hour light/dark cycle (ZT: 1, 5, 9, 13, 17, 21 where ZT0 is indicative of lights on and ZT12 lights off), with 4-5 biological replicates for each time-point

first: Ryan

middle: P

last: Silk

first: Hanagh

middle: R

last: Winter

first: Ouria

last: Dkhissi-Benyahya

first: Carmella

last: Evans-Molina

middle: A

first: Eleni

last: Beli


title: Transcriptome analysis of hepatocellular carcinoma and adacent non-tumor liver tissues

status: Public on May 25 2023

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio


title: Whole transcriptome sequencing of 50 laryngeal squamous cell carcinoma and paired adjacent normal tissues

status: Public on May 24 2023

city: Taiyuan

first: Yongyan

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

summary: Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. However, the mechanism underlying the pathogenesis of LSCC remains unclear. We performed high throughout transcriptome sequencing to identify lncRNA, mRNA, and circRNA that associated with LSCC progression.Transcriptome sequencing were performed on a cohort of LSCC tissues (50 samples) and paired adjacent normal mucosa tissues (50 samples).

overall_design: Expression of lncRNA, mRNA and circRNA in 50 LSCC and 50 paired adjacent normal mucosa tissues was examination by high throughout sequencing.

last: Gao

first: Binquan

first: Qinli

last: Zhao

first: Xiwang

last: Zheng


title: Therapeutic immune cell engineering with an mRNA : AAV-Sleeping Beauty composite system [Splinkerette]

status: Public on May 18 2023

city: New Haven

first: Chuanpeng

last: Dong

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

summary: We evaluated the insertion site profile of the MAJESTIC (mRNA : AAV-Sleeping Beauty) CAR generation method.

overall_design: Genomic DNA was extracted from CAR-T cells, and then a two step Splinkerette PCR was performed to generate an insertion site library that was sequenced by a Miseq sequencer.

first: Stanley

last: Lam

first: Sidi


title: Generating human neural diversity with a multiplexed morphogen screen in organoids

status: Public on May 30 2023

city: Stanford

first: Kevin

last: Kelley

address: 318 Campus Drive, W200

institute: Stanford University

summary: Morphogens choreograph the generation of remarkable cellular diversity in the developing nervous system. Differen-tiation of stem cells toward particular neural cell fates in vitro often relies upon combinatorial modulation of these signaling pathways. However, the lack of a systematic approach to understand morphogen-directed differentiation has precluded the generation of many neural cell populations, and knowledge of the general principles of regional specification remain incomplete. Here, we developed an arrayed screen of 14 morphogen modulators in human neu-ral organoids cultured for over 70 days. Leveraging advances in multiplexed RNA sequencing technology and anno-tated single cell references of the human fetal brain we discovered that this screening approach generated consid-erable regional and cell type diversity across the neural axis. By deconvoluting morphogen-cell type relationships, we extracted design principles of brain region specification, including critical morphogen timing windows and combinatorics yielding an array of neurons with distinct neurotransmitter identities. Tuning GABAergic neural sub-type diversity unexpectedly led to the derivation of primate-specific interneurons. Taken together, this serves as a platform towards an in vitro morphogen atlas of human neural cell differentiation that will bring insights into hu-man development, evolution, and disease.

overall_design:
single-cell RNA-sequencing of human neural organoids cultured in various conditions and primary human fetal striatum

***Please note that raw data is not provided (for the 'fetal striatum; 21 PCW' sample) due to patient privacy***

first: Neal

middle: D

last: Amin

middle: W

first: Jin

last: Hao

first: Yuki

last: Miura

first: Genta

last: Narazaki

first: Tommy

first: Patrick

last: McQueen

first: Shravanti

last: Kulkarni

first: Sergey

last: Pavlov

first: Sergiu

last: Pasca


title: Moderate intrinsic phenotypic alterations in C9orf72 ALS/FTD iPSC-microglia despite the presence of C9orf72 pathological features

status: Public on May 23 2023

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N 5th St

institute: TGen

summary: To differentiate, characterize and examine intrinsic phenotypes of C9orf72 ALS/FTD patient-derived induced pluripotent stem cells into microglia (iPSC-MG). Moderate molecular and functional differences were observed in C9orf72 iPSC-MG mono-cultures despite the presence of C9orf72 pathological features.

overall_design:
Gene expression profiling analysis of control and C9orf72 ALS/FTD iPSC derived MG mono-cultures.  For figure 1 - we compared the iPSC-MG gene expression profile to iPSC derived cortical neurons.
We also performed gene expression profiling analysis of LPS and Ab treated control and C9orf72 ALS/FTD iPSC derived MG mono-cultures.

first: Ileana

last: Lorenzini

first: Ryan

last: Pevey


title: Circulating Plasma miRNA Homologs in Mice and Humans Reflect Familial Cerebral Cavernous Malformation Disease[Mouse]

status: Public on May 09 2023

city: Chicago

first: Issam

last: Awad

state: IL

address: 5841 S Maryland Avenue MC 3026, J 341 MC 3026, J 341

department: Neurological Surgery

institute: University of Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary:
Patients with familial cerebral cavernous malformation (CCM) inherit germline loss of function mutations and are susceptible to progressive development of brain lesions and neurological sequelae during their lifetime. To date, no homologous circulat- ing molecules have been identified that can reflect the presence of germ line pathogenetic CCM mutations, either in animal models or patients.
We hypothesize that homologous differentially expressed (DE) plasma miRNAs can reflect the CCM germline mutation in preclinical murine models and patients. Herein, homologous DE plasma miRNAs with mechanistic putative gene targets within the transcriptome of preclinical and human CCM lesions were identified.
Several of these gene targets were additionally found to be associated with CCM-enriched pathways identified using the Kyoto Encyclopedia of Genes and Genomes. DE miRNAs were also identified in familial-CCM patients who developed new brain lesions within the year following blood sample collection.
The miRNome results were then validated in an independent cohort of human subjects with real-time-qPCR quantification, a technique facilitating plasma assays. Finally, a Bayesian-informed machine learning approach showed that a combination of plasma levels of miRNAs and circulating proteins improves the associa- tion with familial-CCM disease in human subjects to 95% accuracy.
These findings act as an important proof of concept for the future development of translatable circulating biomarkers to be tested in preclinical studies and human trials aimed at monitoring and restoring gene function in CCM and other diseases.

overall_design: 41 micro RNA samples from plasma from 26 subjects with human cerebral cavernous malformations and 15 healthy controls

first: Sharbel

last: Romanos

first: Abhinav

last: Srinath

first: Ying

last: Li

first: Bingqing

last: Xie

first: Chang

last: Chen

first: Yan

first: Thomas

last: Moore

first: Dehua

last: Bi

first: JeYoung

last: Sone

first: Rhonda

last: Lightle

first: Nick

last: Hobson

first: Dongdong

last: Zhang

first: Janne

last: Koskimäki

first: Le

last: Shen

first: Sara

last: McCurdy

first: L

middle: C

last: Chinhchu

first: Agnieszka

last: Stadnik

first: Kristina

last: Piedad

first: Julián

last: Carrión-Penagos

first: Abdallah

last: Shkoukani

first: Daniel

last: Snellings

first: Robert

last: Shenkar

first: Dinanath

last: Sulakhe

first: Yuan

last: Ji

first: Miguel

last: Lopez-Ramirez

first: Mark

middle: L

last: Kahn

first: Douglas

last: Marchuk

middle: H

last: Ginsberg

first: Romuald

last: Girard


title: Single cell mRNA sequencing of Peyer's patch CD11c+ phagocytes from unstimulated or R848- or CpG-stimulated mice

status: Public on May 04 2023

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

institute: CNRS

summary: We deciphered the transcriptional landscape of Peyer's patch CD11c+ phagocytes from their emergence in the tissue to their final maturation state at homeostasis and under stimulation with the TLR7 ligand R848 and the TLR9 ligand CpG.

overall_design: cDC1s, cDC2s, LysoDCs and macrophages were isolated from Peyer's patches of 12 untreated, 12 R848-treated and 12 CpG-treated C57BL/6Rj female mice and processed using the Chromium Single Cell 3’ kit from 10X genomics (California, USA) for the library preparation and the NextSeq 500/550 High Output Kit v2 (75 cycles) cartridges from Illumina for the sequencing. FASTQ raw files were processed using Cell Ranger software, which performs alignment, filtering, barcode counting and UMI counting. Reads were aligned to the mouse mm10 genome.

first: Cynthia

last: Arroyo Portilla

first: Camille

last: Wagner

first: Cécilia

last: Luciani

first: Margaux

last: Lagier

first: Lionel

last: Spinelli

first: Hugues

last: Lelouard


title: Circulating Plasma miRNA Homologs in Mice and Humans Reflect Familial Cerebral Cavernous Malformation Disease [Human]

first: Issam

last: Awad

overall_design: 30 micro RNA samples from plasma from 23 subjects with human cerebral cavernous malformations and 7 healthy controls

first: Sharbel

last: Romanos

first: Abhinav

last: Srinath

first: Ying

last: Li

first: Bingqing

last: Xie

first: Chang

last: Chen

first: Yan

first: Thomas

last: Moore

first: Dehua

last: Bi

first: JeYoung

last: Sone

first: Rhonda

last: Lightle

first: Nick

last: Hobson

first: Dongdong

last: Zhang

first: Janne

last: Koskimäki

first: Le

last: Shen

first: Sara

last: McCurdy

first: L

last: Chinhchu

first: Agnieszka

last: Stadnik

first: Kristina

last: Piedad

first: Julián

last: Carrión-Penagos

last: Shkoukani


title: CTLA-4 tail fusion enhances CAR-T anti-tumor immunity [single-cell RNA-seq]

first: Sidi

summary: To systematically investigate the effect of CCT engineering on CAR-T cell phenotypes in vivo, we used single-cell RNA sequencing (scRNA-seq) to characterize the full spectrum of engineered CAR-T cells and their transcriptomic profiles

overall_design: NSG mice were inoculated with 0.5 million NALM6GL cells intravenously (i.v.) on day 0 and treated with 1 million CAR-T cells (i.v.) on day 4. Relapse was modeled by re-challenging all mice with 0.5 million NALM6GL cells(i.v.) on day 12. To better model the clinical response to CAR-T cells in NSG mice45, 2.5µg human recombinant IL2 (Peprotech) was administered subcutaneously (s.c.) everyday starting on  from day 4 to day 14. All mice were sacrificed on day 15.  Spleen and bone marrow tissues were collected and processed into single cell suspension. CAR-T cells were sorted using Aria II cell sorter (BD) based on mScarlet expression. For all four groups (CAR, CAR-1CCT, CAR-2CCT and CAR-3CCT), samples from 3 individual mice within the same group were pooled together to minimize sampling bias.

first: Xiaoyu

last: Zhou

first: Hanbing

last: Cao

first: Paul

last: Renauer


title: Regulation of Parietal Cell Homeostasis by Bone Morphogenetic Protein signaling

status: Public on May 01 2023

city: Ann Arbor

first: Andrea

last: Todisco

state: MI

address: 1150 West Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

summary: Loss of BMP signaling in the stomach, achieved by transgenic expression of the BMP inhibitor noggin (H+/K+-Nog mice), causes parietal cells (PC) loss, SPEM, a marker of pre-neoplasia, and activation of cell proliferation.  Purpose:  We examined if specific inhibition of BMP signaling in PCs leads to aberrations in epithelial homeostasis

overall_design: Isolation of PCs from control and Nog-expressing mice, was achieved by crossing H+/K+-Nog mice to Rosa26-tdTomato (Tom) mice to generate H+/K+-Nog;Rosa26-tdTom mice.  H+/K+-Cre mice were then crossed to H+/K+-Nog;Rosa26-tdTom mice to generate H+/K+-Cre;H+/K+-Nog;Rosa26-tdTom mice.  Tom-labeled PCs were purified by flow-cytometry.

first: Hidehiko

last: Takabayashi

first: Tuo

last: Ji

first: Lei

last: Peng

first: Xuan

last: Li

first: Masahiko

last: Shinoara

first: Maria

last: Mao

first: Kathryn

last: Eaton

first: Yatrik

middle: M

last: Shah


title: Distinct tumor architectures for metastatic colonization of the brain [Flura-seq]

status: Public on May 02 2023

city: New York

first: Siting

last: Gan

state: NY

address: 417 East 68th Street

department: SKI

institute: MSKCC

summary: Brain metastasis is a dismal complication of cancer that hinges on the initial survival and outgrowth of disseminated cancer cells. To better understand these crucial early stages of brain metastatic colonization, we investigated two prevalent sources of cerebral relapse in the clinic, triple-negative breast cancer (TNBC) and HER2+ breast cancer (HER2BC). We elucidated distinctive early tumor architectures, physical and functional stromal interfaces, and autocrine growth programs employed by these two tumor types to colonize the brain. TNBC cells form extensive perivascular sheath colonies with diffusive contact with astrocytes and microglia. In striking contrast, heightened autonomous deposition of several extracellular matrix components prompts HER2BC cells to colonize the brain as compact, spheroidal colonies, segregating stromal cells to the periphery of the colony. Single-cell dissection of the spatially resolved tumor microenvironment (TME) reveals that brain metastases activate – to different degrees – the canonical stages of the disease-associated microglia (DAM) response previously defined in Alzheimer’s disease. Differential engagement of paracrine tumor-DAM signaling through the receptor AXL suggests specific pro-metastatic functions of the tumor architecture in both TNBC perivascular and HER2BC spheroidal colonies. Collectively, our findings illuminate the distinct stereospatial features of two different yet highly efficient modes of brain colonization, and the relevance of these features in future efforts to leverage the TME to treat brain metastasis.

overall_design: Xenograph model mice were injected with MDA231-BrM or HCC1954-BrM cells and brains were harvested after 30 days of growth for flura-seq

first: Danilo

middle: G

last: Macalinao

first: Sayyed

last: Shahoei

first: Lin

last: Tian

first: Xin

last: Jin

first: Harihar

last: Basnet

first: James

middle: T

last: Muller

first: Pranita

last: Atri

first: Evan

last: Seffar

first: Walid

last: Chatila

first: Anna-Katerina

last: Hadjantonakis

first: Nikolaus

last: Schultz

first: Edi

last: Brogi

first: Tejus

last: Bale

first: Dana

last: Pe'er

first: Joan

last: Massagué


title: Distinct tumor architectures for metastatic colonization of the brain

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Single cell gene expression profiling of endothelial cells from the aorta of wild type and amotl2 ec-/ec- mice

status: Public on May 17 2023

city: Solna

first: Martin

last: Enge

address: Solnavägen 1

country: Sweden

institute: Karolinska Institutet

summary: Deletion of AmotL2 in endothelial cells has a pronounced effect on nuclear shape and subcellular positioning. Difference in the phenotype of WT and AmotL2 KO endothelial cells is elucidated by scRNA-seq on both populations.

overall_design: Aortae from 6 mice from WT and 6 AmotL2 KO mice were  dissociated. Single cell suspension was then depleted of Cd45+ cells with magnetic bead separation and Endothelial cells positively sorted out as Cd31+, CD45- cells. CD31-, CD45- cells were sorted as well as control. The dataset is from two separate preparations of cells (12 mice in total).

first: Sólrún

last: Kolbeinsdóttir

first: Yuanyuan

last: Zhang


title: RNA sequencing of Osteoblasts

status: Public on Apr 28 2023

city: Houston

first: Mo-Fan

last: Huang

state: TX

address: 6431 Fannin Street

department: Integrative Biology and Pharmacology

institute: University of Texas Health science center

summary: We utilized RNA sequencing to provide the gene expression profile of mesenchymal stem cells (MSCs) derived osteoblasts in different differentiation stages as well as the gene alteration profile of H9 MSCs-derived osteoblasts following different gene regulation treatments, including SDC1 overexpression, knockout of CEBPD, knockout of IL1R1, and knockdown of CORIN. The commitment of stem cells to an osteoblastic lineage is a complex and tightly regulated process, involving coordination between extrinsic signals and intrinsic transcriptional machinery. While many rodent osteoblast studies abound, human osteoblastic signaling networks are not as well-researched due to limitations in cell sources and existing models. Here, we generated human pluripotent stem cell (hPSC)-derived osteoblasts and used this modeling platform to identify functional osteoblastic surface receptors and their downstream transcriptional networks involved in human osteogenesis. We systematically dissected osteoblastic gene expression patterns and identified critical clusters associated with osteogenesis. The osteoblast surface receptor signature study revealed enriched CORIN expression in osteoblasts and enriched SDC1 expression in MSCs. In vitro calcified staining and 3D biomimetic GelMA/microCT (μCT) studies demonstrated that depletion of CORIN as well as ectopic expression of SDC1 significantly impaired osteogenesis. Transcriptome analyses revealed that dysregulation of CORIN or SDC1 alters biological processes and pathways mainly involved in bone formation associated signaling including TGFβ regulating extracellular matrix and Wnt signaling. Genome-wide ChIP enrichment analysis further indicated that CEBPD is a downstream transcription factor involved in CORIN and SDC1-modulated osteogenesis. CEBPD ChIP-seq and RNA-seq validated its role in controlling extracellular matrix organization, bone mineralization, and TGFβ, BMP, and Wnt signaling. Depletion of CEBPD led to impairment of osteoblastic differentiation. Differential expression analysis of single-cell transcriptomes revealed enriched expression of CEBPD and its transcriptional targets during the different stages of osteoblast differentiation. In summary, our findings elucidated the vital signaling in osteoblast lineage commitment.

overall_design:
OBs Differentiation: 44 samples. They are ad-HMSC, bm-HMSC, hFoB, H9, H1, RUES2, iPSC WT-1G, iPSC WT-1H, iPSC WT-1J, iPSC WT-F6 and iPSC WT-F37. For each cell line, we collect 4 samples at different differentiation stages: MSCs, pre-Osteoblasts (Pre-OBs), maturing OBs (Mat-OBs) and OBs.
OE-SDC1: 4 samples. We construct TetO-SDC1 vector and generate lentiviruses expressing SDC1 in osteoblasts derived from H9 MSCs. For RNA-seq, we have 2 replicates for SDC1 overexpression (SDC1-1 and SDC1-2) and 2 samples as vector controls (SDC1-1 Ctrl and SDC1-2 Ctrl) which had only Tet-On empty vectors transduction.
sgIL1R1: 4 samples. For RNA-seq, we have 2 replicates for sgIL1R1 (sgIL1R1-1 and sgIL1R1-2) and 2 replicates as vector controls (sgCtrl-1 and sgCtrl-2).
sgCEBPD: 2 samples. For RNA-seq, we have 2 replicates for sgCEBPD (sgCEBPD-1 and sgCEBPD-2) and 2 replicates as vector controls (sgCtrl-1 and sgCtrl-2).
shCORIN: 4 samples. For RNA-seq, we have 2 replicates for shCORIN (shCORIN-1 and shCORIN-2) and 2 replicates as vector controls (shCtrl-1 and shCtrl-2).

first: Dandan

last: Zhu

first: Yang

first: Ruiying

last: Zhao

first: Dung-Fang

last: Lee


title: Genome-wide CEBPD binding in human embryonic stem cell (H9) derived mesenchymal stem cells (MSCs) derived osteoblasts

summary: We carried out CEBPD chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) and revealed that the top motif enriched in CEBPD sites are identical to the CEBPD family motif and osteoblast differentiation/bone formation motifs like Fos1, Fra1, JUNB, RUNX and STAT3. The commitment of stem cells to an osteoblastic lineage is a complex and tightly regulated process, involving coordination between extrinsic signals and intrinsic transcriptional machinery. While many rodent osteoblast studies abound, human osteoblastic signaling networks are not as well-researched due to limitations in cell sources and existing models. Here, we generated human pluripotent stem cell (hPSC)-derived osteoblasts and used this modeling platform to identify functional osteoblastic surface receptors and their downstream transcriptional networks involved in human osteogenesis. We systematically dissected osteoblastic gene expression patterns and identified critical clusters associated with osteogenesis. The osteoblast surface receptor signature study revealed enriched CORIN expression in osteoblasts and enriched SDC1 expression in MSCs. In vitro calcified staining and 3D biomimetic GelMA/microCT (μCT) studies demonstrated that depletion of CORIN as well as ectopic expression of SDC1 significantly impaired osteogenesis. Transcriptome analyses revealed that dysregulation of CORIN or SDC1 alters biological processes and pathways mainly involved in bone formation associated signaling including TGFβ regulating extracellular matrix and Wnt signaling. Genome-wide ChIP enrichment analysis further indicated that CEBPD is a downstream transcription factor involved in CORIN and SDC1-modulated osteogenesis. CEBPD ChIP-seq and RNA-seq validated its role in controlling extracellular matrix organization, bone mineralization, and TGFβ, BMP, and Wnt signaling. Depletion of CEBPD led to impairment of osteoblastic differentiation. Differential expression analysis of single-cell transcriptomes revealed enriched expression of CEBPD and its transcriptional targets during the different stages of osteoblast differentiation. In summary, our findings elucidated the vital signaling in osteoblast lineage commitment.

overall_design: 4 samples. We prepared control samples (two replicates) and CEBPD samples (two replicates).  The two IgG Input samples are used as controls.They are ChIP CEBPD Input-1 and ChIP CEBPD Input-2. The two CEBPD samples are ChIP CEBPD-1 and ChIP CEBPD-2.


title: m6A modification segregates the stemness program from proliferation in ISCs

status: Public on Apr 13 2023

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

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

overall_design: Refer to individual Series


title: m6A modification segregates the stemness program from proliferation in ISCs [ATAC-seq]

summary:
Purpose: A method for mapping chromatin accessibility genome-wide, to reveal chromatin accessibility in  Intestinal stem cells.
Methods: Intestinal stem cells(Lgr5-high cells) were sorted by flow cytometry from wild type mice. The samples were prepared in duplicate. HISAT2 was used to align the sequences to the mouse genome and generate bam files.  bamCoverage was used to generate bigwig files from bam files. MACS2 (v2.2.5) was used for peak calling and to generate bed files from aligned reads.
Conclusions: ATAC-seq analysis confirmed that Fosb binding sites in Chip-seq assay were correlated with the chromatin accessibility .

overall_design: Examination of chromatin accessibility in intestinal stem cells.

first: Ye-Guang

first: Yuan

last: Liu

first: Meimei

first: Xiaodan

last: Wang

first: Zinan

first: Siqi

last: Li


title: m6A modification segregates the stemness program from proliferation in ISCs [ChIP-seq]

summary:
Purpose: A method for identifying genome-wide DNA binding sites for Fosb.
Methods: Alive cells were sorted from retro-Fosb-OE(over-expression) organoids. The samples were incubated with anti-Fosb antibody (Abcam, ab184938). Purified DNA was subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep Kit  and sequenced as paired-end with Illumina Novaseq 6000. HISAT2 was used to align the sequences to the mouse genome and generate bam files. bamCoverage (CPM normalized and extended reads) was used to generate bigwig files from bam files. MACS2 was used for peak calling and to generate bed files from aligned reads. HOMER annotatePeaks.pl was used to annotate the peaks.
Conclusions: Target genes of Fosb through ChIP assay were consistent with predicted target genes. Thus, we concluded that Fosb, which is a key TF could regulate most of ISC signature genes to maintain Lgr5+ ISCs.

overall_design: Examination of Fosb binding sites and target genes in Intestinal epithelial cells.


title: m6A modification segregates the stemness program from proliferation in ISCs [scRNA-seq]

summary:
Purpose: To monitor the different of ISCs and cell fate alteration upon Mettl3 deletion, we use single cell sequencing to examine the sequence information from individual cells with optimized next-generation sequencing (NGS) technologies, providing a single-cell resolution of cellular differences.
Methods:Alive intestinal epithelial cells were sorted from WT and Mettl3-KO mice at 4 dpt. ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000. Raw reads were aligned to the GRCm38/mm10 mouse genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs). Raw aligned features were loaded and processed using the Seurat package (v4.0.2). Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes.
Results: After cells with low information content and a high fraction of mitochondrial RNAs were excluded, 7865 cells (4467 WT and 3398 KO) were analyzed.
Conclusions: Mettl3 deletion reduced the expression of stem cell signature genes but unchanged proliferation profile in ISCs. Thus, we conclude that Mettl3 deletion leads to loss of stemness but not proliferation, and enhanced regeneration and apoptosis.

overall_design: Single cell profiles of intestinal epithelial cells from WT and Mettl3-KO mice at 4 dpt.


title: m6A modification segregates the stemness program from proliferation in ISCs [MeRIP-seq]

summary:
Purpose: To find m6A modified genes which were affected in Mettl3-KO (Mettl3fl/fl; Lgr5-EGFP-IRES-CreERT2; Villin-CreERT2) Intestinal stem cells, we used a method combining RNA-protein immunoprecipitation with high-throughput sequencing to achieve RNA methylation, exactly m6A, analysis at the full transcriptome level.
Methods: Intestinal stem cells (Lgr5-high cells) were sorted by flow cytometry in WT and Mettl3-KO intestinal epithelium at 4 dpt.  mRNA was purified using Dynabeads mRNA Purification kit (Invitrogen, 61006). Then, mRNA was fragmented into ~100-nucleotide-long fragments by RNA Fragmentation Reagents (Ambion, AM8740) at 94 ℃ for 45s. After that, mRNA were immunoprecipitation with m6A antibody (NEB, NO.E1610S) to enrich the m6A-marked mRNA followed by RNA extraction by RNA clean&concentrator-5 (ZYMO RESEARCH, 1013).  The cDNA libraries were generated using SMARTER Stranded Total RNA-seq kit v2. In each sample, reads were aligned to the mouse genome in Ensembl (release 95) with HISAT2. m6A peaks in each sample were identified using exomePeak (v2.17.0) R/Bioconductor package with default parameters.
Conclusions: We found that 2074 transcripts showed a reduced m6A modification in Mettl3-KO Lgr5-high ISCs at 4 dpt. The most of targets contained the common m6A motif “RRACH (GGACU)” in the protein-coding region and 3’UTR, especially enriched near the stop codon.

overall_design: Examination of m6A modification in Intestinal stem cells from WT and Mettl3-KO mice at 4 dpt.


title: m6A modification segregates the stemness program from proliferation in ISCs [RNA-seq]

summary:
Purpose: One goal of this Bulk RNA-seq is to compare genome-wide transcriptome profiles in WT and Mettl3-KO mice intestinal stem cells at indicated time point.The other goal is to compare expression of stemness genes in WT, Mettl3-KO, Mettl3 KO and AKF-OE or AKFP-OE organoids.
Methods: For mice, intestinal crypts were isolated and digested with Tryple, Lgr5-high or Lgr5-low cells were sorted by flow cytometry. For organoids, organoids were digested with Tryple and alive cells were sorted by flow cytometry. Total RNA was extracted with RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. Bulk RNA-seq was performed using the Illumina Hiseq X. RNA-seq reads were aligned to the mouse genome available in Ensembl (release 95) with HISAT2.
Conclusions: Mettl3 deletion results in reduced expression of most of the stem cell signature genes in Mettl3-KO ISCs, including Lgr5, Olfm4, Ascl2, and Smoc2, but increased gene expression related to cell death, p53, MAPK, YAP and regeneration pathway. AKF and AKFP-overexpression could rescue the expression level of some ISC signature genes compared with Mettl3 detion organoids.

overall_design: mRNA profiles in Lgr5-high or Lgr5-low cells from WT and Mettl3-KO mice at indicated time; mRNA profiles in Intestinal epithelial cells from WT, Mettl3-KO, Mettl3-KO-AKF-OE, Mettl3-KO-AKFP-OE organoids.


title: Single-cell RNA-Seq resolves phenotypically heterogeneous subtypes in systemic juvenile idiopathic arthritis (SJIA)

status: Public on Apr 12 2023

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Systemic juvenile idiopathic arthritis (SJIA) is a clinically heterogenous systemic inflammatory disorder sometimes complicated by macrophage activation syndrome (MAS) and lung disease (LD), which are thought to be driven by IFN signaling. To identify cellular sources and novel gene programs underlying SJIA pathogenesis, we performed the first in-depth single-cell RNA Sequencing (scRNA-Seq) analysis of 21 SJIA, SJIA-LD, and SJIA-MAS patient PBMCs. To define novel heterogenous patient-subtypes associated with shared transcriptional responses and associate these with clinical and diagnostic metadata, we developed the tools UDON and SATAY-UDON. These tools identify hidden patient-subtypes, including a novel Complement and IFN signaling gene program expressed by SJIA-LD monocyte populations, unravel cellular sources of IFN signaling in SJIA-MAS as CD4 T cells and monocytic cell types, and identify a previously unknown role for platelets and S100 proteins as drivers of systemic inflammation. These data provide insights into new potential therapeutic targets for SJIA complications.

overall_design:
Single-cell RNA-Seq of PBMCs of 21 pediatric patients with SJIA from each of 4 clinical sub-types (Inactive SJIA, Active SJIA, SJIA-LD, and SJIA-MAS) and 5 age equivalent controls.
***Raw sequencing data is being submitted to dbGAP***

first: Emely

last: Verweyen

first: Kairavee

last: Thakkar

first: Sanjeev

last: Dhakal

first: Elizabeth

last: Baker

first: Kashish

last: Chetal

first: Daniel

last: Schnell

first: Scott

last: Canna

first: Alexei

last: Grom

first: Grant

middle: S

last: Schulert


title: Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [Cut&Tag]

status: Public on Apr 10 2023

city: Vienna

first: Jingkui

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary:
The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program.
Profiling histone marks of Axoltol limb connective tissue cells, and comparing among limb different limb segments and mature vs regeneration time points.

overall_design: We performed Histone mark profiling analysis using data obtained from CUT&Tag of different mature limb segments (mature UA vs LA vs hand). Therefore, we also performed libraries from the mature arm and 5, 9, 13 dpa regenerating arm blastema. Histone mark profiling analysis using IgG (negative control), H3K4me1 (Enhancer associate), H3K4me3 (Active promoter associate), and H3K27me3 (Repressive region associate). .

first: Akane

last: Kawaguchi

first: Dunja

last: Knapp

first: Prayag

last: Murawala

first: Sergej

last: Nowoshilow

first: Wouter

last: Masselink

first: Yuka

last: Taniguchi-Sugiura

first: Jifeng

last: Fei

first: Elly

last: Tanaka


title: Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration

last: Wang


title: Single nucleus RNA-sequencing  for 3 normal salivary glands

status: Public on Apr 01 2023

city: La Jolla

first: Takuya

last: Nakagawa

address: 3855 Health Sciences Dr

department: Moores Cancer Center

institute: UC San Diego

summary: Salivary glands are composed of several types of cells, and each cell type is predicted to be involved in the carcinogenesis of different types of cancers. In this study, we performed single nucleus RNA-seq on 3 human salivary gland samples to clarify the gene expression profile of each complex cellular component of the salivary glands.

overall_design: 30mg each pulverized salivary gland tissue was dissociated by gentleMACS (Miltenyi Bio, Auburn, CA).12,000 nuclei were loaded into the Chromium Controller (10x Genomics) and used for scRNAseq.

first: Chanond

last: Nasamran

first: Joseph

last: Califano


title: scRNAseq analysis of four populations sorted from midbrain organoids using Flow cytometry

status: Public on Mar 15 2023

city: Montreal

first: Rhalena

middle: Amber

last: Thomas

state: QC

address: 3801 rue University, Montreal Neurological Institute, NW B150

department: Neurology

country: Canada

institute: McGill University

summary: Midbrain organoid derived from human induced pluriopotent stem cells a new model of Parkinson's Disease.  Organ specific organoids can be used to model many diseases, however little is know about these models.  We created a flow cytometry workflow to identify cell types in midbrain organoids.  We then selected four populations and sorted these populations: Neurons1(CD24++), Neurons2(CD56++), Astrocytes and Radial Glia, using FACS and the antibody intensity gates defined by our workflow. We then performed scRNAseq on the sorted population and identified cell types within the sorted populations.

overall_design: Human midbrain organoids dervived from the iPSC line AIW002-02 were cultured 304 days in final differenation media. Three samples of 20 organoids were discociated. The single cell suspensions were labelled with a panel of 13 different antibodies.  Individual samples were hashtag labelled. Using the CelltypeR workflow gates for 4 populations were defined and cells were sorted using FACS. Technical replicates were pooled prior to single cell sequencing.

first: Edward

last: Fon

first: Thomas

last: Durcan


title: PdgfrB signaling alters the beige adipogenic niche

status: Public on Mar 06 2023

city: Ithaca

first: Abigail

last: Benvie

address: 526 Campus Rd

institute: Cornell University

summary: Ageing beige adipose progenitor cells overexpress platelet derived growth factor receptor beta (PdgfrB) to prevent beige adipogenesis. Genetically deleting PdgfrB in restores beige adipocyte generation whereas activating PdgfrB in juvenile mice blocks beige fat formation.

overall_design: Comparative gene expression profile analysis of RNA-Seq data between 2 and 12 month old control mice, as well as 12 month old control and SMA-PdgfrB knock out mice

first: Daniel

last: Berry


title: Distinct tumor architectures for metastatic colonization of the brain [RNA-seq]

first: Siting

last: Gan

overall_design: Xenograph model mice were injected with MDA231-BrM or HCC1954-BrM cells and brains were harvested after 30 days of growth

first: Danilo

last: Macalinao

first: Sayyed

last: Shahoei

first: Lin

last: Tian

first: Xin

last: Jin

first: Harihar

last: Basnet

first: James

last: Muller

first: Pranita

last: Atri

first: Evan

last: Seffar

first: Walid

last: Chatila

first: Anna-Katerina

last: Hadjantonakis

first: Nikolaus

last: Schultz

first: Edi

last: Brogi

first: Tejus

last: Bale

first: Dana

last: Pe'er

first: Joan

last: Massagué


title: Microarray profiling analysis of whole transcriptome expression in osteosarcoma

status: Public on Mar 01 2023

city: BEIJING

first: Ben

last: Wan

state: 北京

address: Xinjiekou street No.31

institute: Beijing Research Institute of Traumatology and Orthopaedics

summary: Osteosarcoma (OS)is a rare primary malignant bone tumor in adolescents and children with a poor prognosis. Identification of prognostic genes lags far behind the advance of the treatments.  We identified differential genes by  microarray analysis from  paired OS tissues. Hub genes, gene set enrichment analysis, and pathway analysis were performed to gain an insight into the pathway alterations of OS.  These results showed CPE could be served as a prognostic factor in osteoblastic OS and should be further investigated as potential therapeutic target. The present study evaluated the whole transcriptome expression of osteosarcoma progression and provided novel therapeutic targets for advanced osteosarcoma.

overall_design: This study was carried out on osteosarcoma tissues and adjacent normal tissue that were collected from the Depatment of Orthopaedic Oncology Surgery of the Beijing JiShuiTan Hospital. All of the patients received the four cycles of standard preoperative adjuvant chemotherapy (high dose methotrexate, ifosfamide, cisplatin and doxorubicin, MAP + IFO). The Agilent Human lncRNA Microarray 2019 (4*180k,Design ID:086188) was used in this experiment and data analysis of the 12 samples were conducted by OE Biotechnology Co., Ltd.

first: Renxian

last: Wang


title: Neural transcriptomic responses to endotoxin challenge across social treatments

city: Orange

first: Patricia

last: Lopes

address: 450 N Center St

department: Biological Sciences

institute: Chapman University

summary: The aim of this experiment was to test whether the social setting changed neural transcriptomic responses to an endotoxin challenge in zebra finches

overall_design: Male zebra finches were given an LPS (L) or control (C) injection and then placed in 4 possible social settings: isolated (ISO), continuously with a known female (KFC), reunited with a known female (KF), and paired with a novel female (NF). Brains from these males were dissected for hypothalamus, bed nucleus of the stria terminalis and nucleus taenea. RNA from each brain region was extracted and transcript levels were obtained using an RNA-seq pipeline.


title: The RNA-seq for the kidneys injected with cisplatin and NAD precursors.

status: Public on Feb 03 2023

city: philadelphia

first: tomohito

last: doke

state: Pennsylvania

address: smilow, 3400 Civic Center Blvd STRC 12-188

department: Medicine

institute: University of Pennsylvania

summary: To investigate the molecular mechnism of NAD precursors. We then performed gene expression profiling analysis using data obtained from RNA-seq of the kidneys of mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for different 4 groups (PBS, Cisplatin, Cisplatin with NMN, Cisplatin with NR)

first: Tomohito

last: Doke

first: Amin

last: Abedini


title: Interferon dependent genes of intrathymic antigen presenting cells

city: Minneapolis

first: Kristin

last: Hogquist

state: MN

address: 2101 6th St SE

institute: University of Minnesota

summary: The activation of thymic B cells is critical for their licensing as antigen presenting cells and resulting ability to mediate central tolerance. The processes leading to licensing are still not fully understood. By comparing thymic B cells to activated Peyer’s Patch B cells at steady state, we found that thymic B cell activation starts during the neonatal period and is characterized by TCR/CD40 dependent activation, followed by immunoglobulin class switch recombination (CSR) without forming germinal centers. Transcriptional analysis also demonstrated a strong interferon signature, which was not apparent in the periphery. Thymic B cell activation and CSR were primarily dependent on type III IFN signaling, and loss of type III IFN receptor in thymic B cells resulted in reduced thymocyte regulatory T cell (Treg) development. Finally, from TCR deep sequencing, we estimate that licensed B cells induce development of a substantial fraction of the Treg cell repertoire. Together, these findings reveal the importance of steady state type III IFN in generating licensed thymic B cells that generate T cell tolerance to activated B cells

overall_design: MHC-II-expressing cells sorted from the thymus of 5-week-old wildtype (WT), Ifnar1-/- (IFNAR-KO) and Ifnar1-/-/Ifnlr1-/- (IFNAR/IFNLR-DRKO) mice were submitted for scRNA sequencing.

first: Oscar

last: Salgado

first: S

last: Lee

first: Ryan

last: Martinez

first: Elise

last: Breed

first: Christine

last: O'Connor

first: Dan

last: Stetson


title: RNAseq analysis on metastatic Colorectal Cancer

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

summary:
In this study we want present a bank of metastatic colorectal cancer (mCRC) Patient Derived Organoids (PDOs) obtained from Patient Derived Xenografts (PDXs).
These models are annotated with different omics to advance our understanding of CRC.
We wanted to create a resource for the scientific community to assess the predictive reliability of these preclinical models.
We performed comparative analyses between PDOs and matched PDXs to assess the similarities of these two platforms regarding molecular profiles and transcriptional classification.
Moreover, we analyzed how these models respond to Cetuximab, a chimeric monoclonal antibody, normally given to patients after chemotherapy, that inhibits EGFR.
After having assessed models’ reliability with Cetuximab, we aimed at identifying potential synergistic drugs to individuate new possible therapeutic prospects.

overall_design:
Transcriptional profiles were obtained with RNA sequencing – we aligned reads with STAR on a hybrid human-mouse genome, in order to remove the mouse derived reads without requiring a pre-filtering step.
Reads were assigned to human genes with FeatureCounts, then we used DESeq2 to obtain normalized expression values and perform differential expression analyses.
All analytical pipelines have been implemented with Snakemake as a workflow management system, to ensure portability and reproducibility.
----------------------------------------------
Authors state the following "Raw data with reads from our samples need controlled access, since they derive from human tumors."
----------------------------------------------
Clarification for columns “cell type”, “cell line” and “treatment”.
The column “cell type” defines the type of samples
LM: liver metastasis
PR: primary (from colon)
The column “cell line” defines the origin of samples
H: patients
X: xenografts
O: organoids
The column “treatment” describes the experiments done with cetuximab
cetuxi: treated samples (72h (written as h) or 6w for xenografts)
NT: non-treated control
The word “basale” indicates xenografts or organoids grown in normal conditions. They are not the non-treated control of the cetuximab experiments.

first: Elena

last: Grassi

first: Simonetta

last: Leto

first: Martina

last: Ferri

first: Marco

last: Viviani

first: Eugenia

last: Zanella

first: Francesca

last: Cottino

first: Valentina

last: Vurchio

first: Claudio

last: Isella

first: Enzo

last: Medico

first: Andrea

last: Bertotti


title: Gene regulatory dynamics during craniofacial development in a carnivorous marsupial

city: Berkeley

first: Laura

middle: E

last: Cook

state: California

address: 1 Cyclotron Road

department: Biosciences

institute: Lawrence Berkeley National Laboratory

summary: Marsupials and placental mammals exhibit significant differences in reproductive and life history strategies. Marsupials are born highly underdeveloped after an extremely short period of gestation, leading to prioritization of the development of structures critical for post-birth survival in the pouch. Critically, they must undergo accelerated development of the oro-facial region compared to placentals. Previously we described the accelerated development of the oro-facial region in the carnivorous Australian marsupial, the fat-tailed dunnart Sminthopsis crassicaudata that has one of the shortest gestations of any mammal. By combining genome comparisons of the mouse and dunnart with functional data for the enhancer-associated chromatin modifications, H3K4me3 and H3K27ac, we investigated divergence of craniofacial regulatory landscapes between these species. While genes involved in regulating facial development were largely conserved in mouse and dunnart, the regulatory landscape varied significantly. Additionally, a subset of dunnart-specific enhancers were associated with genes highly expressed only in dunnart relating to cranial neural crest proliferation, embryonic myogenesis and epidermis development. Comparative RNA-seq analyses of facial tissue revealed dunnart-specific expression of genes involved in the development of the mechanosensory system. Accelerated development of the dunnart sensory system likely relates to the sensory cues received by the nasal-oral region during the postnatal journey to the pouch. Together these data suggest that accelerated development in the dunnart can be driven by dunnart-specific enhancer activity. Our study highlights the power of marsupial-placental comparative genomics for understanding the role of enhancers in driving temporal shifts in development.

overall_design: Examination of 2 different histone modifications and gene expression in craniofacial tissue from newborn fat-tailed dunnart pouch young.

first: Irene

last: Gallego Romero

first: Andrew

middle: J

last: Pask


title: Dissecting and Targeting Noncanonical Functions of EZH2 in Multiple Myeloma via an EZH2 Degrader [RNA-seq]

status: Public on Jan 25 2023

city: Nanjing

first: jun

last: wang

state: Jiangsu

address: No. 163 Xianlin Avenue, Qixia District

department: IMB

institute: Nanjing University

summary: Multiple myeloma (MM) is the second most common hematological malignancy with poor prognosis. Enhancer of zeste homolog 2 (EZH2) is the enzymatic subunit of polycomb repressive complex 2 (PRC2), which catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) for transcriptional repression. EZH2 have been implicated in numerous hematological malignancies, including MM. However, noncanonical functions of EZH2 in MM tumorigenesis are not well understood. Here, we uncovered a noncanonical function of EZH2 in MM malignancy. In addition to the PRC2-mediated and H3K27me3-dependent canonical function, EZH2 interacts with cMyc and co-localizes with gene activation markers, promoting MM tumorigenesis in a PRC2- and H3K27me3-independent manner. Both canonical EZH2-PRC2 and noncanonical EZH2-cMyc complexes can be effectively depleted in MM cells by MS177, an EZH2 degrader we reported previously, leading to profound activation of EZH2-PRC2-associated genes and suppression of EZH2-cMyc oncogenic nodes. The MS177-induced degradation of both canonical EZH2-PRC2 and noncanonical EZH2-cMyc complexes also reactivated immune response genes in MM cells. Phenotypically, targeting of EZH2’s both canonical and noncanonical functions by MS177 effectively suppressed the proliferation of MM cells both in vitro and in vivo. Collectively, this study uncovers a new noncanonical function of EZH2 in MM tumorigenesis and provides a novel therapeutic strategy, pharmacological degradation of EZH2, for treating EZH2-dependent MM.

overall_design: We used RNA-seq to examine transcriptomic profiles of MM1.S cells after the treatment with either MS177, C24 or MS177N1, compared DMSO.

first: Jun

last: Wang

first: Xufen

last: Yu

first: Greg

first: Jian

last: Jin


title: Dissecting and Targeting Noncanonical Functions of EZH2 in Multiple Myeloma via an EZH2 Degrader

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

overall_design: Refer to individual Series


title: Sexual Dimorphism of Circadian Liver Transcriptome

city: Cleveland

first: Roman

last: Kondratov

address: 2121 Euclid Ave

department: BGES

institute: Cleveland State University

summary:
Purpose: To conduct a transcriptomic study of gene oscillations in mouse liver by RNA sequencing of total RNA samples from 6 different time points across the day. Specific interest is to see whether sex is a factor in large scale gene oscillations under ad-libitum control conditions and in response to caloric restriction diet, since caloric restriction was previously reported to affect gene oscillation
Methods: Total RNA was isolated from 20 mg mouse liver tissue using mini spin column QIAGEN RNeasy Mini Kit (Ref #74104, Lot#163035346, Hilden, Germany) according to the manufacturer’s protocol. Sample purity was checked on Nano Drop 2000 (Thermo Fisher Scientific, Waltham, MA, USA) with 260/280 ratio ≥ 2.0 and 260/230 ratio  ≥ 2.0  for every sample. Each sample used for the analysis had RNA integrity number > 7. The RNA sequencing was performed by Novogene Corporation Inc (Sacramento, CA, USA). After sample quality control, non-directional – polyA enrichment library was prepared using NEBNext Ultra™ II RNA Library Prep Kit for Illumina, and 50M reads (150bp, paired end) per sample were generated on Illumina NovaSeq 6000 platform. RNA-seq reads were mapped to the mouse protein coding genes (Ensembl: Mus_musculus; GRCm38) using Bowtie allowing up to 2-mismatches. The gene expected read counts and Transcripts Per Million (TPM) were estimated by RSEM (v1.2.3). The TPMs were further normalized by EBSeq R package to correct potential batch effect.
Results: We have performed RNA sequencing analysis of mouse livers on Ad-libitum and timed Caloric Restriction diet across 6 time points in 24h. The results of subsequent compareRhythms analysis (R package) revealed that circadian rhythms in total RNA liver transcriptome are different between sexes of mice in both the number of oscillating genes and phase under ad-libitum diet. Caloric restriction increased the number of oscillating genes in both sexes and resulted in a larger overlap of rhythmic transcriptome between sexes, but did not eliminate the difference completely. The response of transcriptome to caloric restriction in terms of gain or loss of rhythm in gene expression profiles was also different between sexes. Additionally, we have shown that the lack of data stratification by sex might result in the failure to detect rhythmic changes in expression of some genes.
Conclusions: Our study represents the first systematic analysis of the effect of sex on circadian rhythms of liver transcriptome under ad libitum and caloric restriction diets. We have shown that sex based differences exist in rhythmic transcriptome, as well as in the response of rhythmic transcriptome to diet. We are providing the data useful for both circadian and metabolic researchers and point out the gene candidates which may not be identified as rhythmic, if the data is not stratified by sex. With the help of GO analysis we have concluded that sex also influences the preference towards different processes to be regulated in rhythmic manner on transcriptional level - fatty acid metabolism and protein transport in males vs nucleic acid metabolism and RNA processing in females on ad-libitum diet. On calorie-restricted diet nucleic acid metabolism and RNA processing were enriched in males vs protein transport and signal transduction in females on calorie-restricted diet. These findings highlight a complex interaction of sex and diet in their effect on circadian rhythms in liver gene expression.
All of the data from sequenced RNA samples from MALE liver were previously uploaded with the GSE211975 dataset.
The current dataset only contains RNA-seq samples from FEMALE liver.

overall_design: Liver mRNA profiles of 5 mo old mice on ad-libitum and 30% caloric-restriction diets across 6 time points in 24 hours

first: Artem

last: Astafev

first: Volha

last: Mezhnina

first: Allan

last: Poe

first: Peng

last: Jiang

middle: V


title: Alpha kinase 3 signaling at the M-band maintains sarcomere integrity and proteostasis in striated muscle

status: Public on Jan 10 2023

city: Melbourne

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

summary: Muscle contraction is driven by the molecular machinery of the sarcomere. While the constituent components of the sarcomere are well characterized, it is less clear how the activity and turnover of sarcomeric proteins is regulated. In particular, phosphorylation is critical regulator of muscle function. Thus, identification of regulatory kinases is key to understanding the sarcomere function. Pathogenic variants in alpha kinase 3 (ALPK3) cause cardiomyopathy and musculoskeletal disease, but little is known about this atypical kinase. Here we show that ALPK3 localizes to the M-Band of the sarcomere and define the ALPK3-dependent phosphoproteome. ALPK3 deficiency disrupted sarcomeric organization and calcium kinetics in hPSC-derived cardiomyocytes and reduced force generation in cardiac organoids. Phosphoproteomic profiling identified ALPK3-dependant phospho-peptides that were enriched for sarcomeric components of the M-band and the ubiquitin-binding protein SQSTM1. Analysis of the ALPK3 interactome confirmed binding to M-band proteins including SQSTM1. Importantly, in hPSC-derived cardiomyocytes modeling ALPK3 deficiency and cardiomyopathic ALPK3 mutations, sarcomeric organization and M-band localization of SQSTM1 were abnormal. These data suggest ALPK3 has an integral role in maintaining sarcomere integrity and proteostasis in striated muscle. We propose this mechanism may underly disease pathogenesis in patients with ALPK3 variants.

overall_design: Transcriptional analysis of lactate purified cardiomyocytes derived from wild-type and ALPK3 mutant human pluripotent stem cells at 14 and 30 days post differentiation.

first: James

last: McNamara

first: Neda

last: Mehdiabadi

first: David

last: Elliott


title: Multiomic neuropathology improves diagnostic accuracy in pediatric neuro-oncology

status: Public on Jan 30 2023

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

type: Methylation profiling by genome tiling array

summary: To assess their utility in routine neuropathology, we prospectively integrated DNA methylation-based CNS tumor classification and targeted gene panel sequencing of tumor and constitutional DNA with blinded neuropathological reference diagnostics for a population-based cohort of > 1,200 newly-diagnosed pediatric patients.

overall_design: CNS tumor samples from 1,124 patients ≤21 years were profiled using the Illumina Infinium HumanMethylation450 (n = 187) and MethylationEPIC (n = 937) BeadChip arrays at the time of primary diagnosis.

first: Dominik

last: Sturm

last: Capper

first: Felipe

last: Andreiuolo

first: Marco

last: Gessi

first: Christian

last: Koelsche

first: Annekathrin

last: Reinhardt

first: Philipp

last: Sievers

first: Annika

middle: K

last: Wefers

first: Azadeh

last: Ebrahimi

first: Abigail

last: Suwala

first: Gerrit

last: Gielen

first: Daniel

last: Schrimpf

first: Damian

last: Stichel

first: Volker

last: Hovestadt

first: Bjarne

last: Daenekas

first: Agata

last: Rode

first: Stefan

last: Hamelmann

first: Christopher

last: Previti

first: Natalie

last: Jäger

first: Ivo

last: Buchhalter

first: Mirjam

last: Blattner-Johnson

first: Barbara

last: Jones

first: Monika

last: Warmuth-Metz

first: Brigitte

last: Bison

last: Hasselblatt

first: Ulrich

last: Schüller

first: Kerstin

last: Grund

last: Sutter

first: Steffen

last: Hirsch

first: Nicola

last: Dikow

first: Nicolas

middle: U

last: Gerber

first: Christine

last: White

first: Molly

last: Buntine

first: Kathryn

last: Kinross

first: Elizabeth

last: Algar

first: Jordan

last: Hansford

first: Nicholas

last: Gottardo

first: Pablo

last: Hernáiz Driever

first: Astrid

last: Gnekow

first: Olaf

last: Witt


title: Dissecting intracellular receptors regulated transcription networks governing human osteoblast identities

city: Houston

first: Mo-Fan

last: Huang

address: 6431 Fannin Street

institute: University of Texas Health science center


title: Dissecting and Targeting Noncanonical Functions of EZH2 in Multiple Myeloma via an EZH2 Degrader [CUT&RUN]

first: jun

last: wang

overall_design: Examination of the genome-wide binding of EZH2 and H3K27me3 as well as EZH2, H3K27me3 and AR binding after treatment with MS177 in MM1.S cells.

first: Jun

last: Wang

first: Xufen

last: Yu

first: Greg

first: Jian

last: Jin


title: Microenvironment-related genes expression profile from lymph nodes of breast cancer patients using OSNA samples

status: Public on Jan 06 2023

city: Coimbra

first: Henriqueta

middle: A. M. B. L. Coimbra

last: Silva

address: Azinhaga Santa Comba, Celas

department: Coimbra Institute for Clinical and Biomedical Research - Center of Investigation on Environment, Genetics and Oncobiology (iCBR-CIMAGO)

country: Portugal

institute: Faculty of Medicine, University of Coimbra

summary: The One Step Nucleic Acid Amplification (OSNA) assay is used to identify occult metastases in the axillary Sentinel Lymph Nodes (SLNs) of early stage breast cancer patients by quantification of the expression of cytokeratin19 (CK19) gene. The discarded samples of OSNA assay were explored  as a source of information of SLN microenvironment response in patients with early stage Luminal A breast cancer using an RNAseq panel. Funding: project “GenomePT—National Laboratory for Genome Sequencing and Analysis” (POCI-01-0145-FEDER-022184), and project “Central Region Training Project for Personalized/Precision Medicine, with a genomic basis”, financed by the program CENTRO2020 [CENTRO-08-5864-FSE-000039 (PEP IN1194) 07-2021].

overall_design: Discarded samples of OSNA assay from 32 patients with Luminal A early stage breast cancer (cT1-T2 N0)  (8th Ed Edition of the AJCC Cancer Staging Manual; 2019 World Health Organization classification of tumours of the breast) were analysed. OSNA assay was performed accoring to Sysmex Corporation  protocol. Based on the calculated number of CK19 mRNA copies/ul, in accordance with the previous cut off level determined by Tsujimoto et al.: > 5000 copies/uL correspond to macrometastasis (pN1), 250 to 5000 copies/uL to micrometastasis (pN1mi), and values <  250 copies/uL are classified as negative (pN0) SLN.  For  RNA sequencing, a NGS panel of 395 genes involved in tumor-immune interactions and inflammatory signalling was used. No replicates were included.

first: Joana

last: Ribeiro

first: João

middle: P

last: Mendes

first: Ana

last: Gomes

first: Inês

last: Gante

first: Maria

middle: F

last: Dias


title: Predicting drivers of proximal tubule cell state through regularized regression analysis of single cell multiomic sequencing

status: Public on Jan 02 2023

city: Saint Louis

first: Nicolas

last: Ledru

state: MO

address: 660. S Euclid Ave., CB 8118

institute: Washington University in St. Louis

summary: In this study, we generated a single nucleus multiomic (snRNA-seq and snATAC-seq) dataset of adult human kidney. We developed a bioinformatic tool to analyze this dataset by identifying key cis-regulatory elements and transcription factors associated with specific cell types and states. We applied this tool to identify transcription factors implicated in proximal tubule cell injury and failed repair states. We demonstrate this tool can be applied to single cell multiomic datasets to derive insight into cell type- and state-specific gene regulatory networks.

overall_design: RNA-seq on primary RPTEC, siRNA

first: Benjamin

last: Humphreys


title: Single-cell RNA sequencing of human peripheral blood mononuclear cells reveals distinct immune response in gout flare and remission

status: Public on Jan 01 2023

city: Jingan district

first: Hanjie

state: Shanghai

institute: Shanghai Tenth People’s Hospital

summary: Gout typically presents as an acute, self-limiting inflammatory monoarthritis. Based on single-cell RNA sequencing (scRNA-seq), we profiled peripheral blood mononuclear cells (PBMCs) from the same patients with gout flare and gout remission We identified the dynamics of cell abundance, gene expression patterns and biological processes underlying the immune dysregulation of each cell compartment. The single-cell landscape of both innate and adaptive immune responses provides new insights into pathogenesis and therapy of gout flare.

overall_design: PBMCs from the same patients with gout flare and gout remission were subjected to scRNA-seq with 10x Genomics and validated by flow cytometry and LC-MS/MS.

first: Wen

last: Xue

first: Ling

first: Ai

last: Peng


title: The effects of ifosfamide and citalopram on developing zebrafish

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

summary: For RNA-seq experiments, 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10-minute window. Exposure groups included ERM, 1 µg/L, and 100 µg/L ifosfamide or 10 and 1000 µg/L citalopram (N=5 beakers per treatment). On 7 days post fertilization (dpf), fish were transferred to a labeled and pre-weighed 1.7 mL tube using a p1000 with the tip cut off, then water was completely removed using a p200. The tube was then immediately flash frozen in liquid nitrogen prior to RNA-seq analysis.

overall_design: Exposure groups included ERM, 1 µg/L, and 100 µg/L ifosfamide or 10 and 1000 µg/L citalopram (N=5 beakers per treatment). Four replicates out of the 5 were ultimately selected for RNA-seq.

first: Cole

last: English

first: Chris

last: Souders

first: Kira

last: Kazi


overall_design: CUT&RUN on primary RPTECs


title: Single nucleus RNA-seq, ATAC-seq, and multiomic sequencing of adult human kidney

overall_design: single nucleus RNA-sequencing (snRNA-seq) on 4 adult human kidney biopsy samples, single nucleus ATAC-sequencing (snATAC-seq) on 3 adult human kidney biopsy samples, and single nucleus multiomic (joint snRNA-seq and snATAC-seq) sequencing on an additional 7 adult human kidney samples.


title: Hyperactivation of the IL-17 axis and IL-36 signaling in Card14-mutant pityriasis rubra pilaris model mice

status: Public on Dec 31 2022

city: Nagoya

first: Takenori

last: Yoshikawa

address: 65 Tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University Hospital

summary: We performed single cell RNA sequencing (scRNA-seq) to further analyze the differentially expressed genes in each cell type from WT and Card14KI mice. As a result of scRNA-seq, changes in gene expression were large in granular layer cells, cells in the outer roof sheath and fibroblasts.

overall_design: Single cell suspention of whole skin from WT and Card14KI mice were analyzed using scRNAseq.

first: Takuya

last: Takeichi

first: Tetsuya

last: Hirabayashi

first: Yoshinao

last: Muro

first: Yuki

last: Miyasaka

first: Tamio

last: Ohno

first: Masashi

last: Akiyama


title: Transcriptome analysis and 5‘-end mapping of total RNA from Rhodobacter sphaeroides wild type and RNase E (rne) mutant strain, grown under aerobic, microaerobic or phototrophic conditions

status: Public on Dec 28 2022

city: Philadelphia

first: Tobias

last: Friedrich

address: 421 Curie Boulevard

summary: The conserved endoribonuclease RNase E is essential in Rhodobacter sphaeroides and acts as global regulator of the transcriptome. By comparison of an RNase E mutant (showing reduced enzyme activity) with the Rhodobacter sphaeroides wild type, both grown under three different growth conditions, we analysed the impact of RNase E on the adaption of Rhodobacter sphaeroides to different growth conditions.

overall_design: Comparative gene expression profiling analysis of RNAseq data of independent biological triplicates of Rhodobacter sphaeroides wild type and RNase E (rne) mutant strain under three different growth conditions (aerobic, microaerobic or phototrophic).

first: Janek

last: Börner

first: Marek

last: Bartkuhn

first: Gabriele

last: Klug


title: Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing

first: Nicolas

last: Ledru


title: Single cell RNA-seq for brain cerebral cortex transcriptome

city: Uppsala

first: Ying

last: Sun

address: Dag Hammarskjölds väg 20

institute: Uppsala University

summary: By analyzing brain cerebral cortex transcriptome, we provide the gene expression profile from diverse cell types from brain.

overall_design: Brain cerebral cortices  were dissected from the two hemispheres of three animals and pooled. We profiled these samples using droplet based 10X method (10x Genomics Chromium).

first: Ahmed

last: Osman

first: Klas

last: Blomgren


title: E4F1 COORDINATES PYRUVATE METABOLISM AND THE ACTIVITY OF THE ELONGATOR COMPLEX TO ENSURE TRANSLATION FIDELITY DURING BRAIN DEVELOPMENT

status: Public on Dec 20 2022

city: Montpellier

first: Pierre-François

last: Roux

address: 208 rue des Apothicaires

institute: Inserm

summary: Pyruvate metabolism defects lead to severe neuropathies such as the Leigh syndrome (LS) but the molecular mechanisms underlying neuronal cell death remain poorly understood. Here, we unravel a connection between pyruvate metabolism and the regulation of the epitranscriptome that is relevant to LS pathogenesis. We identified the transcription factor E4F1 as a key coordinator of AcetylCoenzyme A (AcCoA) production by the pyruvate dehydrogenase complex (PDC) and its utilization as an essential co-factor by the Elongator complex to acetylate tRNAs at the wobble position uridine 34 (U34). E4F1-mediated direct transcriptional regulation of Dlat and Elp3, two genes encoding key subunits of the PDC and of the Elongator complex, respectively, ensured proper translation fidelity and cell survival in the central nervous system (CNS) during mouse embryonic development. Furthermore, analysis of PDH-deficient cells highlighted a crosstalk linking the PDC to ELP3 expression that is perturbed in LS patients.

overall_design: mRNA profiles of 3 brains of E14.5 wild type (WT) and E4f1 KO (KO) mice.

first: Michela

last: Di Michele

first: Justine

last: Guegan

first: Matthieu

last: Lacroix

first: Laurent

last: Le Cam


title: Malignant Schwann cell precursors mediate intratumoral plasticity in human neuroblastoma [Array]

status: Public on Dec 14 2022

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

summary:
we used single-cell transcriptomics and genotyping arrays to characterize 17 neuroblastoma samples across different risk groups and genetic subsets.Fresh samples, obtained from surgical resections and core biopsies, were used for genome variation profiling.
DNA extraction from neuroblastoma samples was performed using the DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol. DNA quality was assessed using the Tapestation platform (Agilent). SNP microarray analysis was performed using the Cytoscan HD Array (Affymetrix) and data was processed using the Chromosome Analysis Suite version 3.3.0.139.

overall_design: Copy number aberration analysis of Cytoscan HD arrays (Affymetrix) was performed for 17 neuroblastoma samples across different risk groups and genetic subsets

first: Ninib

last: Baryawno


title: miR-29 controls aging-related phenotypes through regulation of the p53 signaling pathway

status: Public on Dec 06 2022

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: We examine the effects of over-expressing miR-29 on phenotypes related to aging

overall_design: RNA-seq of liver tissue from WT young (P60) mice and old (P2yr) mice, young (P60) miR-29 overexpressing mice, and young (P60) miR-29 overexpressing / P53 heterozygous mice.

first: Mohanish

last: Deshmukh

first: Matt

last: Kanke


title: An investigation into the effects of ATV:Trem2 on AD model mice using scRNA-seq

status: Public on Nov 22 2022

city: South San Francisco

first: David

last: Tatarakis

email: tatarakis@dnli.com, genomics@dnli.com

address: 161 Oyster Point Blvd

department: Discovery Genomics

institute: Denali Therapeutics

summary: WT hTfR-KI mice and APP/SAA hTfR-KI mice were treated with one of: Isotype control ATV, naked 4D9 (activating Trem2 Ab), or ATV:4D9. Drugs were delivered IV. After 24 hours, mice were sacrificed, and perfused cortices were processed into single-cell suspensions. The suspensions were FACS sorted for Cd45+/Cd11b+ cells. Single-cell suspensions were labeled with CellPlex CMO per 10X Genomics protocol (CG000391 Rev A.) After each sample was labeled with CMO tags, equal numbers of cells per sample were combined into sample pools for single cell capture on the Chromium using Chromium Next GEM Single Cell 3’ v3.1 kit. After RT and cDNA amplification, each sample pool was separated into one gene expression (GE) library and one CMO tag library via dual-sided SPRI bead purification. Library preparation was performed per manufacturer’s protocol (CG000388 Rev A)

first: Bettina

last: Van Lengerich

first: Dan

last: Xia

first: Thomas

last: Sandmann

first: Kathryn

last: Monroe

first: Connie

last: Ha


title: MYC induces oncogenic stress through RNA decay and ribonucleotide catabolism

status: Public on Jan 22 2023

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

summary: To investigate the transcriptome that might be dysregulated by MYC hyperactivation specifically when DIS3L is downregulated.

overall_design: MYC was induced for 24 hours by adding 60nM 4-OHT with and without DIS3L depletion in human mammary epithelial cells and rRNA-depleted RNA was sequenced. Total RNA (1ug/sample) was used as input for the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB). After rRNA depletion, libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®, quantified using KAPA Library Quantification Kit, and sequenced on the NextSeq 500/550. After demultiplexing, reads were processed using SAMtools (v1.4) and aligned using Hisat2 (v2.0.4) with default parameters. The reference genome sequences (hg38/GRCh38) and gene annotation files were obtained from the UCSC Genome Browser.

first: Jitendra

last: Meena

last: Westbrook

first: Charles

middle: Y

last: Lin

last: Danan


title: Loss of Ahnak is associated with Congenital Anomalies of the Kidney and Urinary Tract

status: Public on Dec 05 2022

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

country: South Korea

institute: Yonsei University

summary:
Various renal abnormalities including hydronephrosis, polycystic and hydroureter had been reported and these symptoms are present in DiGeorge syndrome, polycystic kidney disease, renal dysplasia and acute kidney failure. However, major target genes of renal abnormalities are not elucidated yet. Previous studies have reported that abnormal calcium homeostasis causes renal disease and calcium homeostasis is regulated by calcium channel. In this study, we focus on Ahnak that regulates calcium homeostasis. Ahnak is expressed in intra-cellular locations such as plasma membrane and cytoplasm. Ahnak plays a role in diverse processes as blood-brain barrier formation, cell structure, migration, calcium channel regulation, and tumor metastasis. Ahnak localization was confirmed in developing mouse kidney and ureter. Imbalance of calcium homeostasis and hydronephrosis which is expanded renal pelvis and hydroureter were observed in Ahnak KO mouse. Moreover, peristalsis movement of smooth muscle in ureter has reduced in Ahnak KO. These results indicated that Ahnak plays pivotal roles in kidney and ureter development and maintaining the function of urinary system.
Examination of the gene expression between WT, Ahnak hetero and Ahnak KO kidney and ureter at PN1.

overall_design: Han-Sung,Jung

first: Jong-Min

last: Lee

first: Yun

last: Bae


title: Single-cell transcriptome analysis of aging bone marrow

status: Public on Nov 18 2022

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Single-cell transcriptome analysis of 1-month, 6-month, 20-month mouse bone marrow

overall_design: Examination of mouse bone marrow

first: Changqing

last: Zhang


title: Effect of PGF2α on the transcriptome of the bovine corpus luteum

status: Public on Nov 04 2022

city: Omaha

first: John S

last: Davis

state: NE

address: 983255 Nebraska Medical Cente

department: Departments of Obstetrics and Gynecology and Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

summary: To investigate the rapid effects of PGF2α on the corpus luteum we performed gene expression profiling analysis using data obtained from RNA-seq of controls and treatments at two time points with 4 biological replicates/group .

overall_design: Cows in the mid luteal phase were injected i.m. with saline or PGF2a. Ovaryectomies were performed after 4 and 12 hours after injection.

first: John

first: Andrea

last: Cupp

first: Emilia

last: Przygrodzka

first: Michele

last: Plewes

first: Corrine

last: Monaco


title: Single cell gene expression profile of GVHD-maintaining CD4 T cells isolated from spleen, colon, skin, and small intestine

status: Public on Jan 04 2023

city: Pittsburgh

first: Warren

last: Shlomchik

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh

summary: We used single cell RNA sequencing (scRNAseq) to analyze the transcriptional profiles of GVHD maintaining T cells in various GVHD target tissues

overall_design:
TS1 Tg CD4 cells were isolated from spleen, colon, skin, and small intestines (lamina propria and intraepithelial lymphocytes) of GVHD mice 4 weeks post-transplantation using fluorescence-activated cell sorting. After sorting, cells from each tissue were labelled with a unique TotalSeq-A hashing antibody and analyzed using scRNAseq
HTO ID for Replicate 1:
ACCCACCAGTAAGAC: Spleen_1
GGTCGAGAGCATTCA: Skin_1
CTTGCCGCATGTCAT: Colon_1
AAAGCATTCTTCACG: IEL_1
CTTTGTCTTTGTGAG: LP_1
HTO ID for Replicate 2:
TATGCTGCCACGGTA: Spleen_2
GAGTCTGCCAGTATC: Skin_2
TATAGAACGCCAGGC: Colon_2
TGCCTATGAAACAAG: IEL_2
CCGATTGTAACAGAC: LP_2


title: RNA-seq of wild-type iNKT1 cells from thymus, liver and spleen

status: Public on Oct 15 2022

city: Chicago

first: Barbara

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

summary: The goal of this study was to compare the gene expression program of iNKT1 cells in the thymus, liver and spleen. To identify iNKT1 cells we created Tbx21Cre bacterial artifical chromosome transgenic mice with a Rosa26-floxed-stop-YFP reporter.  We examined gene expression by RNA-sequencing in sorted iNKT1 cells (CD1d-Tet-PBS57+ YFP+) from the thymus, liver and spleen.  Reads were aligned to the mm10 reference genome using Tophat v 2.1.0.  Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78.   Differential expression was calculated across 3 independent replicates by EdgeR.  We found that iNKT1 cells from all tissues had very similar gene expression programs but that there were subtle difference in each tissue that may have relevance for survival and function in these tissues.

overall_design: Expression profiling analysis of RNA from  iNKT1 cells isolated from Ctrl (Tbx21Cre; Rosa26-YFP+) mice by RNA-sequencing. 3 independent replicates for each sample.

first: Roxroy

middle: C

last: Morgan

first: Cameron

last: Frank

first: Mikael

last: Sigvardsson

first: Elizabeth

last: Bartom


title: Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis

status: Public on Nov 21 2022

city: Berlin

first: Irene

last: Mota-Gomez

address: Hannoversche strasse 28

institute: Max Delbruck Center

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

overall_design: Refer to individual Series

first: Juan

middle: A

last: Rodriguez

first: Shannon

last: Dupont

first: Alicia

last: Hurtado

first: Vanessa

last: Cadenas

first: Oscar

last: Lao

first: Johanna

last: Jedamzick

first: Ralf

last: Kuhn

first: Scott

last: Lacadie

first: Sara

last: Garcia-Moreno

first: Miguel

last: Torres

first: Francisca

last: Real

first: Rafael

middle: D

last: Acemel

first: Blanche

last: Capel

first: Marc

last: Marti-Renom

first: Dario

last: Lupiañez


title: RNA-seq of Tgfbr2-deficient thymic iNKT1 cells

status: Public on Oct 13 2022

first: Barbara

middle: L

last: Kee

summary: The goal of this study was to identify genes that are regulated by TGF-b-signaling in thymic iNKT1 cells. To specifically target Tgfbr2 deletion to iNKT1 cells we created Tbx21Cre bacterial artifical chromosome transgenic mice with a Rosa26-floxed-stop-YFP reporter and floxed alleles of Tgfbr2 .  We examined gene expression by RNA-sequencing in sorted iNKT1 cells (CD1d-Tet-PBS57+ YFP+) from Ctrl (Tbx21Cre; Rosa26-YFP+) and cKO (Tbx21Cre; Rosa26-YFP+; Tgfbr2F/F) mice.  Reads were aligned to the mm10 reference genome using STAR v2.5.2.  Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78.   Differential expression was calculated across 3 independent replicates by EdgeR.  We found that TGF-b was required for normal numbers of iNKT1 cells and induced a classic TGF-b gene program in thymic iNKT1 cells but did not regulate expression of Tbx21 (T-bet).

overall_design: Expression profiling analysis of RNA from  iNKT1 cells isolated from Ctrl (Tbx21Cre; Rosa26-YFP+) and cKO (Tbx21Cre; Rosa26-YFP+; Tgfbr2F/F) mice by RNA-sequencing. 3 independent replicates for each sample.

first: Roxroy

last: Morgan

first: Cameron

last: Frank

first: Mikael

last: Sigvardsson

first: Elizabeth

last: Bartom


title: Differential gene expression during placentation in pregnancies conceived with different fertility treatments compared with spontaneous pregnancies

status: Public on Oct 18 2022

city: Los Angeles

first: Margareta

last: Pisarska

state: CA

address: 8635 West Third Street Suite 160

department: Obstetrics and Gynecology

institute: Cedars-Sinai Medical Center

summary: This SMAART cohort study uses bulk total RNA-sequencing to assses the impact of mode of conception on first trimester human placenta gene expression [PMID: 30611556]. Pregnancies were singleton, gestational age 10-14 weeks, normal karyotype, fetal race Caucasian or biracial Caucasian/Asian, and conceived either with fertility treatments (IVF=in vitro fertilization, NIFT=non-IVF fertility treatment) or without fertility treatments (spontaneous, also called unassisted). Pregnancies were balanced for fetal sex. Chorionic villi tissue leftover after clinical genetic testing was collected for research with informed consent and stored in RNAlater RNA Stabilization Reagent (QIAGEN) at -80C until RNA isolation with the AllPrep DNA/RNA Mini Kit (QIAGEN). RNA-seq libraries of >200 nt were constructed with Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits (Illumina) and depleted of cytoplasmic and mitochondrial ribosomal RNAs. After quality check with FastQC, transcript abundances were quantified against the human reference genome (Ensembl build GRCh38) using Kallisto. Differential expression analysis with DESeq2 was performed to compare mode of conception, adjusted for fetal sex and RNA-seq dataset. The dataset adjustment corrected for batch effects from RNA isolation and/or sequencing runs. There were N=141 subjects total, including 74 spontaneous, 33 non-IVF (NIFT), and 34 IVF pregnancies. The subject columns at the end of the DESeq2 files are counts normalized for sequencing depth.

overall_design: Total RNA-seq differential gene expression analysis comparing different modes of conception: infertility treatments (IVF and NIFT together) vs spontaneous, NIFT vs spontaneous, IVF vs spontaneous, and IVF vs NIFT. Analysis was adjusted for fetal sex and RNA-seq dataset in the DESeq2 model.

first: Bora

last: Lee

first: Alex

last: Koeppel

first: Erica

last: Wang

first: Tania

last: Gonzalez

first: Tianyanxin

last: Sun

first: Lindsay

last: Kroener

first: Yayu

last: Lin

first: Nikhil

last: Joshi

first: Tejal

last: Ghadiali

first: Stephen

last: Turner

last: Rich

first: Charles

middle: R

last: Farber

first: Jerome

middle: I

last: Rotter

first: Yii-Der

last: Chen

first: Mark

middle: O

last: Goodarzi

first: Seth

last: Guller

first: Bryna

last: Harwood

middle: B

last: Serna

first: John

last: Williams III


title: In vivo CRISPR screens identify a dual function of MEN1 in regulating tumor-microenvironment interactions [A549 RNA-seq]

status: Public on Nov 03 2022

first: Yin

last: Liu

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

summary:
In this study, we used a targeted CRISPR/Cas9 screen to identify genes that determine growth of A549 cells in vivo and in vitro.
Functional genomic screens in 2D cell culture are of limited use for identifying therapeutic targets that modulate tumor cell-microenvironment cell interactions. By comparing targeted CRISPR-Cas9 screens in 2D culture of A549 lung cancer cells versus xenografts derived from the same cell line, we identified MEN1 as the top hit that confers differential effects in vitro and in vivo. Knockout of MEN1 in multiple solid cancer types does not impact cell proliferation in vitro, but significantly promotes or inhibits tumor growth in immunodeficient or immunocompetent mice, respectively. Mechanistically, knockout of MEN1 leads to increased chromatin interaction of its interaction partner MLL1 (KMT2A), a histone methyltransferase, to repetitive genomic regions, where it activates expression of double-stranded RNA. This results in MARV and cGAS-STING dependent activation of viral mimicry response, which induces infiltration of neutrophils and CD8+ T cells in immunodeficient and immunocompetent mice respectively. Consistently, multiple immune cell infiltrations are negatively correlated with MEN1 abundance and positively correlated with that of MLL1 in patient tumors of a broad range of cancer types. Pharmacological inhibition of MEN1-MLL interaction reduces tumor growth in CD8+ T cell dependent manner, with enhanced activity in combination with anti-PD-1 treatment. These findings reveal tumor microenvironment dependent oncogenic and tumor suppressive functions of MEN1 and provide rationale for therapeutic targeting of MEN1 alone or in combination with immunotherapy in multiple solid cancer types.

overall_design: mRNA profiling of wild-type(WT) and MEN1 knockout A549 cells

first: Peiran

last: Su

first: Housheng

middle: H

last: He

first: Ming-Sound

last: Tsao

first: Tianyi