city: Debrecen

first: Attila

middle: Gábor

last: Szöllősi

address: Egyetem tér 1.

department: Department of Immunology

country: Hungary

institute: University of Debrecen

overall_design: Transcriptomic profiling of control and CBD treated monocyte-derived dendritic cells in three or four biological replicates.

first: Zsófia

last: Pénzes


title: Neutrophil metalloproteinase driven spleen architecture breakdown hampers plasma cell generation and infection control of trypanosomiasis.

status: Public on Aug 10 2023

city: Incheon

first: Hien

middle: Thi Thu

last: Pham

address: Songdomunhwa-ro 119

country: South Korea

institute: Ghent University Global Campus

type: Expression profiling by high throughput sequencing

summary: Recent blood transcriptomic analysis of rhodesiense sleeping sickness patients has revealed that neutrophil signature genes and activation markers constitute the top indicators of trypanosomiasis-associated inflammation. Here, we used single cell RNA sequencing (scRNA-seq) to analyze the diversity of neutrophils in the spleen. We show that Trypanosoma brucei infection results in expansion and differentiation of four splenic neutrophil subpopulations, including Mki67+Birc5+Gfi1+Cebpe+ proliferation-competent precursors, two intermediate immature subpopulations and Cebpb+Spi1+Irf7+Mcl1+Csf3r+ inflammation reprogrammed mature neutrophils.  Transcriptomic scRNA-seq profiling identified the largest immature subpopulation by Mmp8/9 positive tertiary granule markers.

overall_design: Spleen were isolated from mice non-infected and 14 day post infected by T. brucei. brucei Antat1.1E, homogenized, then red blool cells lysis and analyzed using scRNAseq. The Naive dataset included in this repository was generated from an experiment that was specifically designed to be paired and performed alongside the T.b.brucei 14 dpi infected sample. The aim of this paired experiment was to study the response of the immune system, to the infection caused by T.b.brucei)

first: Magdalena

last: Radwanska

first: Stefan

last: Magez


title: Targeting an RNA polymerase II-associated PHF5A transcriptional subcomplex with a KMT2A-WDR5 inhibitor impairs self-renewal and tumorigenicity of pancreatic cancer stem cells

city: Oxford

first: Siwei

last: Deng

address: Old Rd, Headington

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Refined read-out: hUHRF1‑tandem Tudor prefers histone H3 containing K9me2/3 and K4me1

status: Public on Aug 11 2023

city: Stuttgart

first: Albert

last: Jeltsch

address: Allmandring 31

department: Institute of Biochemistry and Technical Biochemistry

country: Germany

institute: University Stuttgart

summary: Histone post-translational modifications (PTMs) are an important part of chromatin signaling mechanisms. Among them, histone H3 has a prominent role, and combinations of multiple PTMs are common. We investigated binding of multiple marks on the same H3 histone by the human UHRF1-TTD (Uniprot Q96T88, residues 126-280), known to bind H3K9me2/3 histones. We verified binding to H3K9me2/3 and demonstrated stronger binding to synthetic H3 peptides containing K4me1 and K9me2/3 as well as native HepG2 mononucleosomes bearing both H3K9me2/3 and H3K4me1.

overall_design: CIDOP (ChIP-like) pulldown of HepG2 native mononucleosomes with hUHRF1-TTD (GST-tagged).

first: Michel

last: Choudalakis

first: Pavel

last: Bashtrykov


title: Targeting an RNA polymerase II-associated PHF5A transcriptional subcomplex with a KMT2A-WDR5 inhibitor impairs self-renewal and tumorigenicity of pancreatic cancer stem cells I

summary: Pancreatic cancer remains one of the most aggressive and lethal cancers in humans. It is undeniably known for its notorious resistance to conventional chemotherapeutics which are often associated with a transient response to treatment but rapidly followed by drug resistance and tumor recurrence. Increasing evidence suggests that therapy failure in pancreatic cancer is largely ascribed to the residual subpopulation of undifferentiated cells, known as cancer stem cells (CSCs), which are evolutionary 'fitter' than other tumor cells to evade the cytotoxic effects of chemotherapy. Those cells are outstandingly critical for tumor relapse as they possess unique 'stem cell-like' features of self-renewal and differentiation which render them capable of regenerating the original tumor. Through the identification of key epigenetic regulators of CSCs phenotypes and functions, this project seeks to gain insight into the molecular mechanisms underlying tumor recurrence and identify novel therapeutic candidates for eliminating CSCs and achieving long-term clinical responses in pancreatic cancer patients.

overall_design: Chromatin immunoprecipitation DNA-sequencing (chIP-seq) for KMT2A, PHF14 and PHF5A in ABCG2+ L3.6pl tumorspheres

first: Mai

last: Abdel Mouti

first: Jessica

last: Malzahn

first: Stefania

last: Militi

first: Reshma

last: Nibani

first: Aniko

last: Rendek

first: Udo

last: Oppermann

first: Zahir

last: Soonawalla

first: Chang-il

last: Hwang

first: Siim

last: Pauklin


title: Targeting an RNA polymerase II-associated PHF5A transcriptional subcomplex with a KMT2A-WDR5 inhibitor impairs self-renewal and tumorigenicity of pancreatic cancer stem cells III

overall_design: RNA samples for RNA-sequencing (RNA-seq) of ABCG2+ L3.6pl tumorspheres treated with DMSO, Gemcitabine, and MM-102.


title: Targeting an RNA polymerase II-associated PHF5A transcriptional subcomplex with a KMT2A-WDR5 inhibitor impairs self-renewal, pluripotency and tumorigenicity of pancreatic cancer stem cells II

overall_design: Chromatin immunoprecipitation DNA-sequencing (chIP-seq) for PHF5A and PHF14 in ABCG2+ L3.6pl tumorspheres treated with DMSO (control) and 50 µM MM-102


title: Effect of depletion of GPR30 on gene expression in female C57BL/6J mice

city: xi'an

first: Xin-shang

last: Wang

state: China

address: Changle road No.169

country: China

institute: Fourth Military Medical University

summary: To test the cell-specific function of GPR30 in learning and memory, we generated global GPR30 knockout (KO) mice (Δ3102), astrocyte-specific GPR30 KO (AG-KO)  mice and neuron-specific GPR30 KO (NG-KO)  mice. We found that GPR30 in astrocytes but not neurons is required to maintain normal learning and memory. To further elucidate the signaling pathway by which GPR30 plays a role in astrocyte function, high-throughput RNA sequencing of hippocampal tissues from Δ3102, AG-KO, and NG-KO mice was performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT, Δ3102, AG-KO, and NG-KO mice

first: Shui-bing

last: Liu


title: Effect of depletion of transcription factors Sp1 and Sp3 on gene expression of primary MLECs (mouse endothelial lung cells)

city: Jinan

first: Hanlin

last: Lu

address: No. 107, Wen Hua Xi Rd, Jinan, Shandong, China

institute: Qilu Hospital of Shandong University

summary:
To investigate the function of transcription factors Sp1 and Sp3 in the regulation of endothelial functions, we established tamoxifen-induced endothelial Sp1/Sp3 knockout mice and isolated the MLECs
We then performed gene expression profiling analysis using data obtained from RNA-seq of MLECs from endothelial Sp1/Sp3 knockout mice and their control mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MLECs from endothelial Sp1/Sp3 knockout mice and their control mice

first: Wencheng

last: Zhang


title: Comparative study of 3D vs. 2D cell culture transcriptional changes of murine embryonic stem cells, stromal cells and lung cancer cells

city: Zhunan, Miaoli County

first: Chia-Chi

last: Chang

address: 35 Keyan Road

department: Institute of Cellular and System Medicine

country: Taiwan

institute: National Health Research Institutes

summary: Transcriptional profiling of 3D and 2D condition on mouse embryonic stem cells, stromal cells (M210B4) and Lewis lung cancer cells (LLC).

overall_design: Two-condition experiment: 3D vs. 2D cell culture of mESCs, M210B4, and LLC. RNA samples were collected at 72 h for each condition.

first: Shih-Sheng

last: Jiang

first: B. Linju Yen

last: Yen


title: Single-Cell Profiling of Murine Bladder Cancer Identifies Sex Specific Transcriptional Signatures with Prognostic Relevance

status: Public on Aug 09 2023

city: Los Angeles

first: Saravana Kumar

last: Kailasam Mani

address: 8700 Beverly Blvd

country: USA

institute: Cedars Sinai Medical Center

summary: Bladder cancer (BLCA) is more common in men but more aggressive in women. A common model used to study sex-based differences in cancer biology is murine BLCA generated by N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN). While tumors in this model have been profiled, these profiles provided limited information on the tumor microenvironment. Hence, we applied single-cell RNA sequencing to characterize cell type specific transcriptional differences between male and female BBN induced tumors and then studied their human relevance. We found proportion and gene expression differences in the epithelial and non-epithelial subpopulations between male and female tumors. Of translational importance, expression of several genes was found to predict sex specific survival in several human BLCA datasets. We also noted a male biased CD8 T cell exhaustion program in this model that correlates highly with androgen receptor activity. Our study identified novel and clinically relevant sex specific transcriptional signatures and validates the relevance of the BBN model for studying sex differences in human BLCA. This work highlights the importance of considering sex as a biological variable in cancer marker development.

overall_design: Single cell RNA-sequencing of mouse bladder tissue following BBN treatment for 6 months (n=20) pooled into 10 samples

first: Hany

middle: A

last: Abdel-Hafiz

first: Saravana

middle: K

last: Mani

first: Simon

middle: R

last: Knott

first: Dan

last: Theodorescu


title: Gene expression profiles in the hearts of WT and Bcl-xL S14A KI mice after TAC or Sham

city: Newark

first: Michinari

last: Nakamura

state: NJ

address: 185 South Orange Ave, Medical Science Building G609

department: Cell Biology and Molecular Medicine

institute: Rutgers New Jersey Medical School

summary: Acute increase of blood pressure by transverse aortic constriction (TAC), pressure overload, stimulates hypertrophic signaling in the heart, which is suppressed in Bcl-xL Ser14Ala knock-in mice.

overall_design: Hearts were harvested from Bcl-xL Ser14Ala knock-in or wild-type control mice 9 hours after TAC or Sham surgery. Each n=3.

first: Junichi

last: Sadoshima


title: NAD(H) homeostasis is essential for host protection mediated by glycolytic myeloid cells in tuberculosis

city: Birmingham

first: Hayden

last: Pacl

state: AL

address: 845 19th St S, BBRB 308

department: Microbiology

institute: University of Alabama at Birmingham

summary:
To investigate the role of LDHA in myeloid cells in the response to pulmonary infection with Mycobacterium tuberculosis, we infected  LDHAfl/fl:LysM+/- mice with Mtb-H37Rv via the aerosol route.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the lungs of these animals at 4 and 30 weeks post infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the lung tissue of LDHAfl/fl:LysM+/- (WT) and LDHAfl/fl:LysM+/- (KO) mice infected with Mycobacterium tuberculosis for 4 or 30 weeks.

middle: T

first: Krishna

middle: C

last: Chinta

first: Vineel

middle: P

last: Reddy

first: Sajid

last: Nadeem

first: Ritesh

last: Sevalkar

first: Kievershan

last: Nargan

first: Kapongo

last: Lumamba

first: Threnesan

last: Naidoo

first: Joel

middle: N

last: Glasgow

first: Anupam

last: Agarwal

first: Adrie

middle: J

last: Steyn


title: HD2B and HD2C interact with Argonaute 4 to promote tolerance and heterochromatin stabilization during heat stress [ncRNA-Seq]

status: Public on Aug 12 2023

city: Wuhan

first: Xiangsong

last: Chen

state: Hubei

address: Bayi Road

institute: Wuhan university

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we show that HD2B/C work with AGO4 to promote heat tolerance

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and hd2b/c plants under normal and heat-treated conditions,whole-genome bisulfite sequencing in WT and hd2b/c under both normal and heat conditions,high-throughput small RNA sequencing in WT and hd2b/c

first: Yingnan

last: Sun

first: Fangfang

last: Yang


title: Platelets and inflammation: insights from platelet non-coding RNA content and release in the Bruneck Study

city: London

first: Konstantinos

last: Theofilatos

address: 125 Coldharbour Lane

institute: King's CollegeLondon

summary: Platelets contain non-coding RNAs (ncRNAs), and their measurement may complement aggregometry. In the community-based Bruneck Study (N = 338), we conducted over 2,700 aggregometry measurements and over 65,000 RT-qPCR measurements in platelet releasates, platelet-poor plasma and isolated platelets. We show agonist-specific, dose-dependent platelet ncRNA release that is inhibited by aspirin. Collagen induces the strongest release for most ncRNAs, while miR-150 is hyperresponsive to ADP and miR-21 is hyperresponsive to arachidonic acid. Inflammation and high leukocyte-derived RNA content in platelets correlate inversely with platelet aggregation and platelet ncRNA release after stimulation. This inverse correlation is not observed in aspirin users. Finally, we reveal that platelet-derived microRNAs and YRNAs are carried by proteins and readily released, while circular RNAs, long non-coding RNAs and messenger RNAs are carried by vesicles and preferentially retained. Our findings provide evidence that inflammation leads to platelet pre-activation in vivo resulting in platelet exhaustion ex vivo.

overall_design: To identify lncRNA candidates, we conducted an additional RNA-Seq experiment in platelets collected from 4 healthy volunteers. RNA-seq results were validated by RT-qPCR measurements in platelet poor plasma, platelet-rich plasma (PRP) and platelets, and selected lncRNA candidates based on abundance (14 lncRNAs) as well as lncRNAs with the gene ontology term platelet.

first: Clemens

last: Gutmann

first: Temo

last: Brwari

first: Christian

last: Schulte

first: Bhawana

last: Singh

first: Kaloyan

last: Takov

first: Gonca

last: Suna

first: Melissa

last: Chan

first: Paul

last: Armstrong

last: Cassel

first: Peter

last: Santer

last: Willeit

last: Hengstenberg

first: Stefan

last: Kiechl

first: Johann

first: Timothy

last: Warner

first: Manuel

last: Mayr


title: RNA sequencing on pulmonary fibrosis mice.

city: Hangzhou

first: Tianyuan

last: Zhang

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

summary: To investigate the differential genes associated with mitochondria in pulmonary fibrosis mice, we established pulmonary fibrosis mice and applied mitochondrial replenishment therapy.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of pulmonary fibrosis mice, Fe-hMSC treated pulmonary fibrosis mice, Pg-Fe-hMSC treated pulmonary fibrosis mice.

first: Jianqing

last: Gao

first: Ting

last: Huang


title: Activation of GPCR-GNAS-PKA signaling in melanoma cells impairs T cell infiltration to dampen antitumor immunity

city: Beijing

first: Yazhong

last: Cui

address: 7 Science Park Road ZGC Life Science Park, Beijing

institute: National institute of biological sciences, Beijing

summary:
To investigate the machanism by which MC1R represses the expression of a subset of IFNg reponsvie genes.
We then performed ATAC seq and H3K27ac ChIP-seq to identify promoter and enhancer of MC1R-repressed IFNg reponsive genes.

overall_design: We designed B16F10 ATAC seq under 4 different conditions and B16F10 H3K27ac ChIP-seq under 2 different conditions.

last: Han


title: Inhibition of PPARg by BZ26, a GW9662 derivate, attenuated obesity-related breast cancer progression by inhibiting the reprogramming of mature adipocytes into to cancer associate adipocyte-like cells

first: Xiujing

last: Feng

address: School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China

institute: Shandong First Medical University

summary: Obesity has been associated with the development of 13 different types of cancers, including breast cancer. Evidence has indicated that cancer-associated adipocytes (CAAs) promote the proliferation, invasion, and metastasis of cancer. However, the mechanisms that link CAAs to the progression of obesity-related cancer are still unknown. Here, we found the mature adipocytes in the visceral fat of HFD-fed mice have a CAAs phenotype but the stromal vascular fraction (SVF) of the visceral fat has not. Importantly, we found the derivate of the potent PPARg antagonist GW9662, BZ26 inhibited the reprogramming of mature adipocytes in the visceral fat of HFD-fed mice into CAA-like cells and inhibited the proliferation and invasion of obesity-related breast cancer. Further study found that it mediated the browning of visceral, subcutaneous and perirenal fat and attenuated inflammation of adipose tissue and metabolic disorders. For the mechanism, we found that higher PPARg expression was associated with poorer overall survival of breast cancer patients, and further study showed that BZ26 bound and inhibited PPAR by acting as a new modulator. Therefore, BZ26 serves as a novel modulator of PPARg activity that is capable of inhibiting obesity-related breast cancer progression by inhibiting of CAA-like cell formation, suggesting that inhibiting the reprogramming of mature adipocytes into CAAs or CAA-like cells may be a potential therapeutic strategy for obesity-related cancer treatment.

overall_design: To investigate whether CAAs or CAAs-like cells are present in adipose tissue of obese mice to establish a clearer link between obesity and cancer, we  isolated the visceral (epididymis) fat from ND-fed and HFD-fed mice and subjected the AT to RNA-Seq.

first: Liangge

last: Li

first: Jiafeng

last: Geng


title: Chromatin remodeling of prostaglandin signaling in smooth muscle enables mouse embryo passage through the female reproductive tract

city: Bethesda

first: qiliang

last: Xin

state: MD

address: 50 South Dr

department: NIDDK

institute: NIH


title: Affymetrix SNP array data for mice with or without the whorled phenotype

city: MINNEAPOLIS

first: Maureen

last: Cetera

state: MN

address: 515 Delaware St SE, Moos room 5-143

institute: University of Minnesota-Twin Cities

summary: The goal of this study was to narrow down a region of interest that contains the causative mutation that  results in the whorled fur phenotype of the rosette fancy mouse.

overall_design:
DNA was extracted from ear punches or tail clips using the Qiagen DNeasy Blood and Tissue kit. We sent high molecular weight DNA to FisherScientific for genotyping array service using the Affymetrix Mouse Diversity Array.
The data set includes the original whorled founder male and a sibling along with ancestors from outcrossing to the C57BL/6 background. The whorled phenotype was treated as a binary trait and 91 mice were categorized as whorled (1) or non-whorled (0)


title: Chromatin remodeling of prostaglandin signaling in smooth muscle enables mouse embryo passage through the female reproductive tract [RNA-seq]

summary: After fertilization, early mammalian development takes place as the embryo transits the oviduct prior to implantation on the wall of the uterus. This transport is precisely orchestrated by secreted oviduct fluid, unidirectional beating of epithelial cilia and smooth muscle contractions. Using multiple gene-edited mice to affect the female reproductive tract, we document that conditional disruption of Pbrm1, a component of the SWI/SNF chromatin remodeling complex, prevents embryo transport. Loss of Pbrm1 in epithelial cells lining the oviduct had no effect, but ablation in smooth muscle phenocopied the transport defect without perturbing embryogenesis. Analysis with RNA-seq, ATAC-seq, ChIC-seq and pharmacologic rescue experiments implicated prostaglandin signaling pathways. In comparison to wildtype, gene-edited mice had compromised chromatin accessibility at enhancer/promoters of Ptgs2, Pla2g16, Pla2r1 and Ptger3 (EP3) as well as decreased enhancer-promoter interactive looping critical for Ptgs2 (prostaglandin-endoperoxide synthase 2, aka Cox-2) expression in a SWI/SNF complex dependent manner in smooth muscle. These observations provide mechanistic insight into potential causes of ectopic pregnancy in fallopian tubes that is a significant cause of morbidity and mortality in human pregnancies.

overall_design: RNA-seq was performed using D2 primary oviductal smooth muscle cell between control and Pbrm1 cKO mice in order to identify the differentially expressed genes.

first: Qiliang

first: Guoyun

last: Yu

first: Iris

first: Jurrien

last: Dean


title: Chromatin remodeling of prostaglandin signaling in smooth muscle enables mouse embryo passage through the female reproductive tract [ATAC-seq]

overall_design: ATAC-seq was performed using D2 primary oviductal smooth muscle cell between control and Pbrm1 cKO mice in order to identify the differentially chromatin accessibility.


title: Chromatin remodeling of prostaglandin signaling in smooth muscle enables mouse embryo passage through the female reproductive tract [CHIC-seq Pbrm1 & Brg1]

overall_design: CHIC-seq was performed using D2 WT primary oviductal smooth muscle cell  in order to identify the directly binding sites.


title: A simplified platform to generate and purify human primordial germ cells in vitro provides new insights into germline specification [RNA-Seq]

city: Stanford

first: Sivakamasundari

last: Vijayakumar

state: CA

address: 265 Campus Drive, Lokey Stem Cell Building, Rm G3105

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: Generating primordial germ cells (PGCs) from human pluripotent stem cells (hPSCs) advances studies of human reproduction and development of infertility treatments, but currently entails complex 3D aggregates. Here we develop a simplified, monolayer method to differentiate hPSCs into PGCs within 3.5 days, with higher efficiencies and improved consistency across multiple hPSC lines. We used our simplified differentiation platform, bulk RNA-seq and single-cell RNA-sequencing to uncover new insights into PGC specification. Transient WNT activation for 12 hours followed by WNT inhibition specified PGCs; by contrast, sustained WNT instead induced primitive streak. Thus, somatic (primitive streak) and PGCs are related—yet distinct—lineages segregated by temporally-dynamic signaling. Pluripotency factors are continuously expressed during the transition from pluripotency to posterior epiblast to PGCs, thus bridging pluripotent and germline states. Finally, hPSC-derived PGCs can be easily purified by virtue of their CXCR4+PDGFRA-GARP- surface-marker profile and single-cell RNA-sequencing reveals that they harbor strong transcriptional similarities with fetal PGCs. We report single-cell RNA-sequencing data of in vitro differentiated hPSCs (H9) cells into human Primordial germ cell-like cells (PGCLCs), profiled at different time-points of differentiation - Day 0 (H9), D0.5, D3.5 (sorted) and D3.5 unsorted population and a negative control of hPSCs differentiated into definitive endoderm (DE) (using the protocol described in (Loh et al., 2014, Cell Stem Cell 14, 237-252)). The data comprises of 5 single-cell RNA-sequencing libraries (H9, D0.5, D3.5S, D3.5U and DE) generated using 10xChromium Single cell RNA-expression platform and 10xGenomics Chromium version 2 chemistry with a targeted capture of ~6000 cells each. Single cell libraries were sequenced on Illumina HiSeq4000 platform as paired-end 150bp reads. Bulk RNA seq libraries were sequnced as paired-end reads.

overall_design: Bulk RNA-sequencing of hPSCs (H9) cells differentiated into human Primordial germ cell-like cells (PGCLCs) using our simplified monolayer serum-free differentiation protocol was performed for the following time-points: Day 0 (H9), Day 0.5, Day 1, Day 1.5, Day 2.5, Day 3.5, Day 3.5 sorted (NANOG-YFP+CXCR4+), Day 3.5 sorted (NANOG-CXCR4-). Libraries were sequenced on HiSeq4000, 2x150bp paired-end format.

first: Roberta

last: Sala

first: Gugene

last: Kang

first: Angela

last: Chen

first: Abidemi

middle: I

last: Adebayo

first: Andrea

last: Cipriano

first: Jonas

middle: L

last: Fowler

first: Lay

last: Ang

first: Danielle

last: Gomes

first: Michelle

last: Pablo

first: Kyle

middle: M

last: Loh

first: Vittorio

last: Sebastiano


title: Chromatin remodeling of prostaglandin signaling in smooth muscle enables mouse embryo passage through the female reproductive tract [CHIC-seq H3K27ac & H3K4me1]

first: qiliang

last: Feng


title: PD-1 restrains glycolysis for histone acetylation to suppress T-cell lymphoma

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

summary: PDCD1, which encodes for the PD-1 immune checkpoint receptor, is a key tumor suppressor in T cells that is recurrently inactivated in human T cell non-Hodgkin lymphomas (T-NHLs)1-3. The highest frequencies of PDCD1 deletions are detected in advanced disease, predicting inferior prognosis2. Nevertheless, the tumor-suppressive mechanisms of PD-1 signaling remain unknown. Using tractable mouse models of human T-NHL, we demonstrate that PD-1 activity in pre-malignant cells prevents cellular transformation by inhibiting the induction of rate-limiting factors for glucose uptake and conversion upon oncogenic T cell signaling. Furthermore, PD-1 negatively regulates ATP-citrate lyase (ACLY), which generates extramitochondrial acetyl-CoA for histone acetylation. Consequently, inactivation of PD-1 enables oncogene-expressing T cells to switch to glycolysis to metabolically fuel overt malignancy and unleashes ACLY activity to promote de novo histone acetylation to increase chromatin accessibility of oncogenic AP-1 transcription factors. Multimodal molecular and functional analyses of primary human T-NHL samples confirmed enforced glucose metabolism, epigenetic reprogramming, and AP-1 activation upon PDCD1 loss in patients. Thus, our results identified PD-1 as a central metabolic gatekeeper of T cell transformation and lymphoma progression and established a mechanistic link between the PD-1 checkpoint receptor and glucose-dependent histone acetylation. Together, these data uncover novel putative genotype-specific vulnerabilities in T-NHL and present a starting point for the exploration of PD-1 dependent epigenetic reprogramming in T cell biology.

overall_design: H3K27ac ChIPseq in T cells

first: Filippo

first: Tim

last: Wartewig

first: Jürgen

last: Ruland

first: Gunnar

last: Schotta


title: Resolvin D2-GPR18 Enhances Bone Marrow Function and Limits Steatosis and Hepatic Collagen Accumulation in Aging

status: Public on Aug 08 2023

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: Aging is associated with nonresolving inflammation and tissue dysfunction. Resolvin D2 (RvD2) is a proresolving ligand that acts through the G-protein-coupled receptor called GPR18. Unbiased RNA sequencing revealed increased Gpr18 expression in macrophages from old mice, and in livers from elderly humans, which was associated with increased steatosis and fibrosis in middle-aged (MA) and old mice. MA mice that lack GPR18 on myeloid cells had exacerbated steatosis and hepatic fibrosis, which was associated with a decline in Mac2+ macrophages. Treatment of MA mice with RvD2 reduced steatosis and decreased hepatic fibrosis, correlating with increased Mac2+ macrophages, increased monocyte-derived macrophages, and elevated numbers of monocytes in the liver, blood, and bone marrow. RvD2 acted directly on the bone marrow to increase monocyte-macrophage progenitors. A transplantation assay further demonstrated that bone marrow from old mice facilitated hepatic collagen accumulation in young mice, and transient RvD2 treatment to mice transplanted with bone marrow from old mice prevented hepatic collagen accumulation. Together, this study demonstrates that RvD2-GPR18 signaling controls steatosis and fibrosis and provides a mechanistic-based therapy for promoting liver repair in aging.

overall_design: There were 3 mice in each group and RNA from each mouse was sequenced in triplicate

first: Gabrielle

last: Fredman

middle: B

last: Ramos


title: Functionally distinct cancer-associated fibroblast subpopulations establish a tumor-promoting environment in squamous cell carcinoma

city: Heidelberg

first: Manuel

last: Rodríguez-Paredes

address: Im Neuenheimer Feld 280

institute: German Cancer Center (DKFZ)

summary: Cutaneous squamous cell carcinoma (cSCC) is a serious public health problem due to its high incidence and metastatic potential. It may progress from actinic keratosis (AK), a precancerous lesion, or the in situ carcinoma Bowen's disease (BD). During this progression, malignant keratinocytes activate dermal fibroblasts into tumor-promoting cancer-associated fibroblasts (CAFs), whose origin and emergence remain largely unknown. Here, we generate and analyze >115,000 single-cell transcriptomes from healthy skin, BD and cSCC of male donors. Our results reveal immunoregulatory and matrix-remodeling CAF subtypes that might derive from pro-inflammatory and mesenchymal fibroblasts, respectively. These CAF subtypes are largely absent in AK and interact with different cell types to establish a pro-tumorigenic microenvironment. These findings are cSCC-specific and could not be recapitulated in basal cell carcinomas. Our study provides important insights into the functionalities of dermal CAFs that will be highly beneficial for the specific targeting of the cSCC microenvironment.

overall_design: scRNA-seq of three human healthy UVR-exposed skin samples, three human Bowen's disease samples and five human cSCC samples using the Chromium Single Cell Reagent kit (v3.1 chemistry) from 10X Genomics.

first: Sabrina

last: Schütz

first: Llorenç

last: Solé-Boldo

first: Carlota

last: Lucena-Porcel

first: Jochen

last: Hoffmann

first: Alexander

last: Brobeil

first: Anke

middle: S

last: Lonsdorf

first: Frank

last: Lyko


first: Yazhong

last: Cui

summary:
To investigate the function of MC1R in antitumor immunity, we compared the gene expression between B16F10 WT and B16F10 Mc1r knockdown cells at different conditions.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at three treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for B16F10 cells and its KD derivatives (sgMc1r) under different conditions.

first: Ting

last: Han


title: A simplified platform to generate and purify human primordial germ cells in vitro provides new insights into germline specification

first: Sivakamasundari

last: Vijayakumar

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

overall_design: Refer to individual Series


title: Target-directed microRNA degradation broadly regulates microRNA expression and embryonic growth in mammals

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: UT Southwestern

summary: MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. Target-directed miRNA degradation (TDMD), a pathway in which miRNAs that bind to specialized targets with extensive complementarity are rapidly decayed, has emerged as a potent mechanism of controlling miRNA levels. Nevertheless, the biological role and scope of miRNA regulation by TDMD in mammals remains poorly understood. To address these questions, we generated mice with constitutional or conditional deletion of Zswim8, which encodes an essential TDMD factor. Loss of Zswim8 resulted in major developmental defects in heart and lung, growth restriction, and perinatal lethality. Small RNA sequencing of embryonic tissues revealed widespread miRNA regulation by TDMD. Deletion of two miRNAs, miR-322 and miR-503, rescued growth of Zswim8 null embryos, directly implicating the TDMD pathway as a key regulator of mammalian body size. These data reveal the broad landscape and developmental role of TDMD in mammals.

overall_design: To investigate the landscape of target-directed microRNA degradation in mammals, we generated Zswim8 knockout mice using CRISPR/Cas9. We then performed small RNA sequencing on tissues from embryonic day 18.5 tissues. Tissues sequenced include brain, heart, kidney, liver, lung, intestines, skin, and stomach. Three biological replicates were used for both wildtype and Zswim8 knockout.

first: Benjamin

last: Jones

first: Jaeil

first: Asha

last: Acharya

first: He

last: Zhang

first: Robert

middle: E

last: Hammer

first: Bret

last: Evers

first: Dinesh

last: Rakheja


title: Photo-click hydrogels for in situ differentiation of pancreatic progenitors from iPSCs

city: Indianapolis

first: Matthew

last: Arkenberg

state: IN

address: 980 W Walnut St

department: Otolaryngology - Head and Neck Surgery

institute: Indiana University School of Medicine

summary: Induced pluripotent stem cells (iPSC) can be differentiated to cells in all three germ layers, as well as cells in the extraembryonic tissues. Efforts in iPSC differentiation into pancreatic progenitors in vitro have largely been focused on optimizing soluble growth cues in conventional two-dimensional (2D) culture, whereas the impact of three-dimensional (3D) matrix properties on the morphogenesis of iPSC remains elusive. In this work, we employ gelatin-based thiol-norbornene photo-click hydrogels for in situ 3D differentiation of human iPSCs into pancreatic progenitors (PP). Molecular analysis and single cell RNA-sequencing were utilized to elucidate on the distinct identities of subpopulations within the 2D and 3D differentiated cells. We found that, while established soluble cues led to predominately PP cells in 2D culture, differentiation of iPSCs using the same soluble factors led to prominent branching morphogenesis, ductal network formation, and generation of diverse endoderm populations. Through single-cell RNA-sequencing, we found that 3D differentiation resulted in enrichments of pan-endodermal cells and ductal cells. We further noted the emergence of a group of extraembryonic cells in 3D, which was absent in 2D differentiation. The unexpected emergence of extraembryonic cells in 3D was found to be associated with enrichment of Wnt and BMP signaling pathways, which may have contributed to the emergence of diverse cell populations. The expressions of PP signature genes PDX1 and NKX6.1 were restored through inhibition of Wnt signaling at the beginning of the posterior foregut stage. To our knowledge, this work established the first 3D hydrogel system for in situ differentiation of human iPSCs into PPs. Ongoing work focuses on enhancing pancreatic differentiation efficiency through modulating physicochemical properties of the iPSC-laden matrices.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pancreatic progenitors derived from ChiPSC12 cells differentiated in 2D monolayer format and 3D gelatin-based hydrogels.

first: Yoshitomo

last: Ueda

first: Eri

last: Hashino

first: Chien-Chi

last: Lin


title: The transcriptional networks governing the spatial regulation of RPE differentiation are regulated by the SWI/SNF complexes

city: Guangzhou

first: Cui

last: Guizhong

state: Guangdong

address: 188 KaiYuan Road, Huangpu District

department: Center of Cell Lineage and Atlas

institute: Guangzhou Laboratory

summary: During embryonic development, tissue-specific transcription factors and chromatin remodelers function together to assure the gradual, coordinated differentiation of multiple lineages. Here, we study this  regulatory interplay in the developing retinal pigmented epithelium (RPE), a neuroectodermal lineage essential for the development, function, and maintenance of the adjacent retina. We present a high-resolution spatial transcriptomic atlas of the developing mouse RPE and the adjacent ocular mesenchyme, obtained by geographic positional sequencing (Geo-Seq) of a single development stage of the eye, encompassing young and more mature ocular progenitors. These transcriptomic data, available through an online web tool, reveal the major transcription factors and their gene regulatory networks that control over 5000 genes during RPE and ocular mesenchyme differentiation. We also present evidence, based on conditional inactivation followed by Geo-seq, that this differentiation program is dependent on the activity of the SWI/SNF complexes. We find that these complexes are required for the expression and activity of the RPE TFs and inhibition of the competing, default neuronal progenitor phenotypes and cell proliferation genes. The persistent expression of proliferation genes, despite onset of neurogenesis upon loss of SWI/SNF supports the tumor suppressive activity of these complexes. Our work reveals that the TFs regulation of a timely, gradual differentiation program, as well as maintenance of cell fate and ensuring exit from the cell cycle, depends on the chromatin terrine defined by the SWI/SNF chromatin remodelers.

overall_design: We used spatial transcriptomic of Geo-Seq analyses of the embryonic  retinal pigmented epithelium (R/PE) and ocular mesenchyme (M/Me). We collected  samples lengths ranging from 180 to 450µm from the PE and Me  by laser capture microscopy (LCM), from 20um cryosections of E14.5 embryonic mouse eyes.  From each tissue (PE or Me) we collected a total of 8 samples: 4 samples were from the dorsal and 4 from the ventral optic cup along the proximal-distal axis.  We used this design to collect samples from 4 control (C) embryos and 3 conditional mutants in the PE, of both Smarcc1 and Smarcc2 (Smarcc1 loxP/loxP; Smarcc2loxP/loxP;DCT-Cre termed FcKO/F). We constructed from the data a high resolution spatial transcriptomic atlas of the developing PE and Me lineages in the control and in the FcKO.

first: Shai

last: Ovadia

first: Guizhong

first: Naihe

last: Jing

first: Ruth

last: Ashery-Padan

first: Ran

last: Elkon


title: Characterization of early transcriptomic changes associated with hepatitis B virus exposure in human and macaque immune cell populations

city: Lyon

first: Xavier

last: Grand

address: 46 allée d'Italie

country: France

institute: INSERM U1052, UCBL1, ENS de Lyon

summary: Chronic hepatitis B virus (HBV) infection affects close to 300 million individuals worldwide, representing one of the major etiological factors for the development of cirrhosis and hepatocellular carcinoma (HCC). At the molecular level, the mechanisms behind chronic HBV infection are based on the persistence of the viral genome as an episomal structure termed covalently closed circular DNA (cccDNA), and the evasion of both innate and adaptive immune responses. Thus, it is considered that HBV cure will be a multi-layered combination approach of anti-viral and immune-boosting strategies. Although the development of potential HBV therapeutics has been hampered by the lack of suitable long-term infection models, the stark contrast between human and non-human primates regarding their immune responses and infection outcomes, represents an opportunity to identify the molecular mechanisms favoring HBV elimination. Therefore, we aimed to characterize the early transcriptomic changes associated with HBV exposure in human and macaque immune cell populations.

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens

overall_design: RNA-Seq profiles from T cells, B cells, myeloid dendritic cells (mDCs) and plasmacytoid dendritic cells (pDCs) with our without HBV exposure (2 h). Experiments were performed for both human and macaque immune cell populations.

first: Armando

last: Roca Suarez

first: Andrea

last: Tamellini

first: Fabrice

last: Porcheray

first: Séverine

last: Planel

first: Céline

last: Couturier

first: Frédéric

last: Reynier

first: Trang

last: Tran

last: Elie

first: Adrien

last: Saliou

first: Chloé

last: Baum


title: Whole transcriptome RNAseq analysis of E13.5, E15.5 and PND 0 Inha WT and KO testes

city: Giessen

first: Daniela

last: Fietz

address: Frankfurter Straße 98

department: Institute for Veterinary Anatomy,  Histology and Embryology

institute: Justus Liebig University Giessen

summary: We performed bulk RNA-Seq on testes from E13.5, E15.5 and PND 0 whole testes from Inha WT and KO mouse (lacking the inhibin a gene).

overall_design: The aim of this experiment was to examine how elevated activin A affects the mouse testes after sex determination upto the time of birth.

first: P

last: Whiley

first: M

last: Luu

first: L

last: O’Donnell

first: D

last: Handelsman

first: K

last: Loveland


title: N-linked glycosylation is essential for anti-tumor activities of KIAA1324 in gastric cancer

status: Public on Aug 07 2023

city: Songpa

first: Junil

last: Kim

state: Seoul

address: 369 Sangdo-Ro

department: Department of Bioinformatics

institute: Soongsil University

summary: KIAA1324 is a transmembrane protein largely reported as a tumor suppressor and favorable prognosis marker in various cancers, including gastric cancer. In this study, we report the role of N-linked glycosylation in KIAA1324 as a functional post-translational modification (PTM). Loss of N-linked glycosylation eliminated the potential of KIAA1324 to suppress cancer cell proliferation and migration. Furthermore, we demonstrated that KIAA1324 undergoes fucosylation, a modification of the N-glycan mediated by fucosyltransferase, and inhibition of fucosylation also significantly suppressed KIAA1324-induced cell growth inhibition and apoptosis of gastric cancer cells. In addition, KIAA1324-mediated apoptosis and tumor regression were inhibited by the loss of N-linked glycosylation. RNA sequencing (RNAseq) analysis revealed that genes most relevant to the apoptosis and cell cycle arrest pathways were modulated by KIAA1324 with the N-linked glycosylation, and Gene Regulatory Network (GRN) analysis suggested novel targets of KIAA1324 for anti-tumor effects in transcription level. The N-linked glycosylation blockade decreased protein stability through rapid proteasomal degradation. The non-glycosylated mutant also showed altered localization and lost apoptotic activity that inhibits the interaction between GRP78 and caspase 7. These data demonstrate that N-linked glycosylation of KIAA1324 is essential for the suppressive role of KIAA1324 protein in gastric cancer progression and indicates that KIAA1324 may have anti-tumor effects by targeting cancer-related genes with N-linked glycosylation. In conclusion, our study suggests the PTM of KIAA1324 including N-linked glycosylation and fucosylation is a necessary factor to consider for cancer prognosis and therapy improvement.

overall_design: We performed RNAseq on total RNA from Luc, KIAA1324 WT-, 3NQ-, and ΔTM-expressing MKN28 cells.


title: Epithelial Plasticity and Innate Immune Activation Promote Lung Tissue Remodeling following Respiratory Viral Infection.

city: Los Angeles

first: Barry

last: Stripp

address: 8700 Beverly Blvd

department: Lung Institute

institute: Cedars Sinai Medical Center

summary: As observed in mice with genetic depletion of stem cells, epithelial plasticity is a critical component of tissue repair in response to injury; however, the physiological relevance of this process and the involved progenitor populations are not well understood. Severe respiratory viral infection and chronic lung disease share pathological features including stem cell loss in the gas-exchange regions, basal cell (BC) hyperplasia in small airways, and innate immune activation. Collectively, these processes contribute to epithelial remodeling and loss of diffusion capacity. Here, we show that small airways harbor a previously undescribed lineage of secretory cells, intralobar serous (IS) cells, that are activated to assume BC fates following influenza virus infection. Nascent BC were distinguished from pre-existing BC by high expression of IL-22Ra1 and a dependency on innate immune activation and local IL-22 production for self-renewal and colonization of injured alveoli. Resolution of virus-elicited inflammation and the associated decline in IL-22 signaling resulted in basal to serous re-differentiation in repopulated alveoli, and increased local expression of antimicrobial factors, but failed to replace normal alveolar epithelium. We define a mechanism whereby epithelial plasticity confers protection against mortality from acute respiratory viral infection but has potential to contribute to progressive lung remodeling and life-threatening declines in lung function among patients with chronic lung disease.

overall_design: Single cell RNAseq was used to assess dynamic changes in gene expression and cell representation at indicated time points following influenza induced acute lung injury (naïve, 3, 5 , 7, 9 , 11, 14, 17, 21, 120, 240). Immune and Epithelial cell were enriched prior to cell capture by FACS.

first: Andrew

last: Beppu


title: Idronoxil inhibition of TBK1 signalling

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary:
Purpose: Analysis of the transcriptional effects of Idronoxil (IDX) on primary bone marrow derived macrophages (BMDMs) from Trex1 mutant mice.
Methods: Primary BMDMs from 3 different mice were treated overnight with Idronoxil at 1.25uM. RNA sequencing was performed with one NextSeq2000 P2 run using 19bp forward read and 101bp reverse reads.
Conclusion: Idronoxil strongly decreased the basal TBK1 driven interferon gene signature in these cells.

overall_design: Trex1-mutant mice have a single-base mutation in Trex1 leading to a premature stop codon (Q98X). Homozygous mutant mice have aberrant accumulation of cytoplasmic DNA, resulting in basal engagement of the cGAS-STING-TBK1 pathway (Ellyard J.I. and Vinuesa C.G., manuscript in preparation). Cells were treated overnight with 1.25uM Idronoxil prior to total RNA purification and RNA sequencing.

first: Michael

last: Gantier

first: Tomalika

last: Ullah

first: Arwaf

last: Alharbi

first: Linden


title: CUT&RUN Profiling in CBF-Glis2 AMLs Identifies the Chromatin Remodeler Brg1 as a Key Dependency

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

summary: Oncogenic fusions involving transcription factors are present in the majority of pediatric leukemias, however, the context-specific mechanisms they employ to drive cancer remain poorly understood. CBFA2T3-GLIS2 (C/G) fusions occur in treatment-refractory acute myeloid leukemias and are restricted to young children. To understand how the C/G fusion drives oncogenesis we applied CUT&RUN chromatin profiling to an umbilical cord blood/endothelial cell (EC) co-culture model of C/G AML that recapitulates the biology of this malignancy. We find C/G fusion binding is mediated by its zinc finger domains. Integration of fusion binding sites in C/G-transduced cells with PRC2 sites in control cord blood cells identifies MYCN, WT1, and GATA2 as C/G targets. Transcriptomic analysis of a pediatric AML cohort shows that these genes are upregulated in C/G patient samples. Single cell RNA-sequencing of umbilical cord blood identifies a population of megakaryocyte precursors that already express many of these genes despite lacking the fusion. By integrating CUT&RUN data with CRISPR dependency screens we identify BRG1/SMARCA4 as a vulnerability in C/G AML. Brg1 profiling in C/G patient-derived cell lines shows that the CBFA2T3 promoter is a binding site, and treatment with clinically-available Brg1 inhibitors reduces fusion levels and downstream C/G targets including N-Myc, killing C/G leukemia cells.

overall_design: Fresh CB samples were processed with red blood cell lysis buffer, enriched for CD34+ cells using CliniMACS CD34 MicroBeads (Miltenyi Biotec, 130-017-501), and frozen down for the future use. On the day of sort, CD34+ cells from multiple pooled CB samples (8 units each) were thawed and stained with the following antibodies: CD45RA-APC-Cyanine7, CD38-PECy7 (Invitrogen), CD34-PerCP, CD90-BV421, EPCR-BV786, Lineage cocktail (CD3, 14, 16,19,20,56)-FITC (BD Biosciences) and DAPI (to exclude dead cells)

first: Jay

last: Sarthy

first: Steve

last: Henikoff


title: Successful secukinumab therapy in plaque psoriasis is associated with altered gut microbiota and related function change I

city: Xi'an

first: Xueshan

last: Du

state: Shannxi Province

address: Xiwu Road, Xi’an, Shaanxi, China

institute: The Second Affiliated Hospital of Xi'an Jiaotong University

summary: The role of gut microbiome dysbiosis in the pathogenesis of psoriasis has gained increasing attention in recent years. Secukinumab, targeting interleukin (IL)-17, has a promising efficacy in psoriasis treatment. However, it remains unclear the gut microbiota alteration and related functional changes caused by successful secukinumab therapy in psoriatic patients. In our study, we compared fecal microbiome profile between psoriatic patients after secukinumab successful treatment (AT) and the other two groups, psoriatic patients without therapy (BT) and healthy people (H), respectively by using next-generation sequencing targeting 16S ribosomal RNA. Then, shotgun metagenomic sequencing was firstly used to characterize bacterial gut microbial communities and related functional change in AT group. We found that the diversity and structure of the microbial community in AT group were significantly changed compared to that of BT group and H group. AT group showed a microbiota profile characterized by increased proportions of the phylum Firmicute, families Ruminococcaceae, and a reduction in the phylum Bacteroidota (elevated F/B ratio). To detect functional alteration, we discovered that secukinumab treatment may construct a more stable homeostasis of gut microbiome with functional alteration. There were different KEGG pathways such as downregulated cardiovascular diseases pathway and upregulated infectious diseases in AT group. By metagenomic analysis, metabolic functional pathway was changed after secukinumab therapy. It seems that gut microbiota investigation during biologic drug treatment is useful for predicting the efficacy and risks of drug treatment in disease.

overall_design: We collected the feces from psoriatic patients without treatment and after secukinumab successful treatment, and feces from healthy people as control. By using the 16S rRNA method and shotgun metagenomic analysis, we detected gut microbiota composition and functional change to investigate the influence of secukinumab successful therapy on gut microbiome in psoriasis.

first: Cong

last: Yan

first: Shuzhen

last: Kong

first: Delu

last: Che

first: Bin

last: Peng

first: Longfei

last: Zhu

first: Songmei

last: Geng

first: Kun

last: Guo


title: ScRNA-seq of Brca2 mammary organoids reveals a subpopulation expansion in response to replication stress

city: CAMBRIDGE

first: Mona

last: Shehata

state: Cambridgeshire

address: Cambridge Biomedical Campus, Hills Road

department: Department of Oncology

institute: Early Cancer Institute

summary: BRCA2 mutation carriers preferentially develop luminal-like breast cancers, but it remains unclear how BRCA2 mutations affect mammary epithelial subpopulations. Here, we report that Brca2mut/WT mammary organoids subjected to replication stress activated a transcriptional response that selectively expands Brca2mut/WT luminal cells lacking hormone receptor expression (HR-). While CyTOF analyses revealed comparable epithelial compositions among wildtype and Brca2mut/WT mammary glands,  Brca2mut/WT HR- luminal cells exhibited greater organoid formation and preferentially survived and expanded under replication stress. ScRNA-seq analysis corroborated the expansion of HR- luminal cells which express elevated levels of Tetraspanin-8 (Tspan8) and Thrsp mRNA, and pathways implicated in replication stress survival including Type I interferon responses. Notably, CRISPR/Cas9-mediated deletion of Tspan8 or Thrsp prevented Brca2mut/WT HR- luminal cell expansion. Our findings indicate that Brca2mut/WT cells have an activate a transcriptional response after replication stress that preferentially favours outgrowth of HR- luminal cells through the expression of interferon-responsive and mammary alveolar genes.

overall_design: In this study we utilised a genetically engineered murine model carrying a monoallelic germline Brca2 truncating mutation, Brca2mut/WT. organoids were generated from Brca2mut/WT and wildtype mammary glands, which were exposed to replication stresses at regular intervals over a two month period. We performed scRNA-seq from early (passage 0) and late (passage 4) organoid culture time points. The data provides xx scRNA-seq profiles using 10X Genomics Chromium platform, compromising a total of 34,200 from 3 independent experiments. This includes the four different conditions (wildtype or Brca2mut/WT with or without HU treatments) and time points (Passage 0 or 4).

first: Maryam

last: Ghaderi Najafabadi

first: Li


title: Successful secukinumab therapy in plaque psoriasis is associated with altered gut microbiota and related function change II


title: Successful secukinumab therapy in plaque psoriasis is associated with altered gut microbiota and related function change


title: TGF-β signaling links early-life endocrine-disrupting chemicals exposure to suppression of nucleotide excision repair in rat myometrial stem cells

city: Chicago

first: Qiwei

last: Yang

state: IL

address: 5821 S Drexel Ave

department: Obstetrics and Gynecology

institute: The University of Chicago

summary:
Environmental exposure to endocrine-disrupting chemicals (EDCs) is associated with uterine fibroids (UFs) development, the most common benign tumors in women of reproductive age. It has been shown that UFs originate from abnormal myometrial stem cells (MMSCs) and there is evidence that defective DNA repair capacity could be involved in the emergence of mutations with implications for tumorigenesis. Moreover, the multifunctional cytokine TGF-β1 has been related to UF progress and some works revealed its connection with certain DNA damage repair pathways. Eker rats develop spontaneous uterine tumors in adulthood, which makes it a useful model for the study of UFs emergence
The purpose of this study was to evaluate the impact of endocrine-disrupting chemicals (EDCs exposure on TGF-β1 pathway and nucleotide excision repair (NER) capacity, on Eker rat myometrial stem cells (MMSCs).

overall_design: MMSCs were isolated using Stro-1 and CD44 surface markers from 5-months old Eker rats exposed neonatally to Diethylstilbestrol (DES, an EDCs) or vehicle (VEH).  After the in vitro treatment of VEH-MMSCs with TGF-β1 or EDC-MMSCs with TGF-β Receptor I inhibitor, we performed RNA-seq to determine global gene expression profiles and identified altered genes and pathways.

first: Ayman

last: Al-Hendy

first: Maria

middle: V

last: Bariani

first: Mohamed

last: Ali


title: Depletion of 16S ribosomal RNA improves single-cell RNA-seq of planarians by DASH

city: ITHACA

first: Carolyn

last: Adler

state: NY

address: 930 Campus road

institute: Cornell University

summary: Single-cell transcriptomics (scRNA-seq) has revolutionized our understanding of cell types and states in various contexts, such as development and disease. Most methodology relies on poly(A) enrichment to selectively capture protein-coding polyadenylated transcripts, intending to exclude ribosomal transcripts that constitute >80% of the transcriptome. However, it is common for ribosomal transcripts to sneak into the library, which can add significant background by flooding libraries with irrelevant sequences. The challenge of amplifying all RNA transcripts from a single cell has motivated the development of new technologies to optimize retrieval of transcripts of interest. This problem is notable in planarians, where we find that 16S ribosomal transcripts were widely enriched (20-80%) across single-cell methods. Therefore, we adapted the Depletion of Abundant Sequences by Hybridization (DASH) to the standard 10X scRNA-seq protocol. We designed single-guide RNAs tiling the 16S sequence for CRISPR-mediated degradation, and subsequently generated untreated and DASH-treated datasets from the same libraries to enable a side-by-side comparison of the effects of DASH. DASH specifically removes 16S sequences without off-target removal of other genes. By assessing the cell barcodes shared by both libraries, DASH-treated cells have consistently higher complexity given the same amount of reads, which allows the detection of a rare cell cluster and more differentially expressed genes. In conclusion, DASH can be easily integrated into existing sequencing protocols and customized to deplete any unwanted transcripts.

overall_design: Planarian stem cells were isolated by Fluorescence-activated cell sorting (FACS) by cell cycle analysis. 10X Chromium was used to generate 3'scRNA-seq, and DASH was used to deplete 16S rRNA. Untreated and DASH-treated sample were sequnced by assessing impact of DASH.

first: Kuang-Tse

last: Wang


title: Regulation of p300 acetyltransferase activity by the TAZ2 domain

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute


title: Regulation of p300 acetyltransferase activity by the TAZ2 domain [ATAC-seq]

summary: The E1A binding protein P300 (EP300, also known as p300, lysine acetyltransferase 3B or KAT3B) and its close paralogue CREB-binding protein (CREBBP, aka CBP or KAT3A) possess intrinsic histone acetyltransferase (HAT) activity that can act on both histone and non-histone proteins. P300 and CBP are composed of multiple conserved protein domains, many of which are in proximity to the HAT domain modulating its catalytic activity.  Here we show that the TAZ2 domain regulates the intrinsic catalytic activity of p300 in vitro and histone acetylation and chromatin accessibility in cells. Our study extends the knowledge of p300 self-regulation and provides new therapeutic stratagies for human cancers with corresponding p300/CBP mutations.

overall_design: Chromatin accessibility profiles after p300 TAZ2 truncation.

first: Longxia

last: Xu

first: Hongwen

last: Xuan


title: RNautophagic regulation of DNMT3a-dependent DNA methylation

city: Hangzhou

first: Liyuan

address: NO.3, Qingchun Road, Shangcheng District

institute: Zhejiang University

summary: Calorie restriction has long been known to extend lifespans and inhibit carcinogenesis in multiple species by slowing age-related epigenetic changes while the underlying mechanisms remain largely unknown. Herein, we found that starvation activated autophagy to remodel DNA methylation profile by inhibiting DNMT3a expression.  Autophagy is impaired in chemoresistance which was associated with differential DNA methylation and could be reversed by DNMT3a inhibition. Autophagy activation decreases the expression of DNMT3a mRNA, accompanied with the downregulation of chemoresistance-related Linc00942. Knockdown of Linc00942 reduces DNMT3a expression and genome-wide DNA methylation while Linc00942 overexpression increased DNMT3a expression and correlated hypermethylation in cancer cells and primary tumor tissues. As a result, inhibition of autophagy increases Linc00942 expression to promote chemoresistance and autophagy activation or hypomethylating agent decitabine restores chemosensitivity by reducing global DNA methylation.

overall_design: The perfect prepared DNA was treated with Bisulfite from 27 samples, followed by whole genome amplification (WGA) and accomplished fragmentation processing. Then the assessment segues into array (or Chip) hybridization with the well-modified probe (> 850,000 sites, more than 95% CpG islands and 99% RefSeq genes coverage).

first: Hongchuan

last: Jin


title: Regulation of p300 acetyltransferase activity by the TAZ2 domain [ChIP-seq]

overall_design: H3K27ac profiles after p300 TAZ2 or HAT truncations.


title: Regulation of p300 acetyltransferase activity by the TAZ2 domain [RNA-seq]

overall_design: RNA profiles after p300 TAZ2 or HAT truncations and HDAC inhibitor treatment


title: Developmental Reprogramming of Myometrial Stem Cells by Endocrine Disruptor Linking to Risk of Uterine Fibroids

address: 909 S. Wolcott Ave

department: Surgery

institute: University of Illinois at Chicago

type: Methylation profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Developmental Reprogramming of Myometrial Stem Cells by Endocrine Disruptor Linking to Risk of Uterine Fibroids [RNA-Seq]

summary: We report that developmental exposure to the endocrine disrupting chemical (EDC) diethylstilbestrol increases the estrogen action in myometrial stem cells (MMSCs), the origin from which UFs originate. The expression of reprogrammed estrogen responsive genes (ERGs) is driven by activated mixed lineage leukemia protein-1 (MLL1) in MMSCs.  Deactivation of MLL1 reverses reprogramming of ERG expression. In addition, upregulation of ERGs occurs via DNA hypomethylation mechanism. Furthermore, the secretome of reprogrammed MMSCs enhances the proliferation of differentiated myometrial cells through activation of β-catenin signaling. This work identifies epigenetic mechanisms of MLL1/DNA methyltransferase- mediated MMSC reprogramming, and EDC exposure epigenetically targets MMSCs and imparts a hormonal imprint on the ERGs resulting in a “hyper-estrogenized” phenotype and increased hormone-dependent risk of UFs.

overall_design: Examine the transcriptome  in MMSCs from 5 month Eker rat myometrium PND 10-12 exposed to DES and VEH

first: Lindsey

last: Treviño

first: Aymara

last: Mas


title: Developmental Reprogramming of Myometrial Stem Cells by Endocrine Disruptor Linking to Risk of Uterine Fibroids [RRBS]

overall_design: Examine the DNA methylome  in MMSCs from 5 month Eker rat myometrium PND 10-12 exposed to DES and VEH


title: ChIP-seq analysis of E2FA, E2FB, E2FC and RBR targets

status: Public on Aug 06 2023

city: Gif Sur Yvette

first: Xiaoning

last: HE

address: 630,Rue Noetzlin

institute: universite-paris-saclay

summary: The goal of the experiment was to identify and compare at the genome-wide level the targets of E2FA, E2FB and E2FC, the three canonical E2Fs, and those of their binding partner RBR.

overall_design: For each protein a transgenic line expressing a GFP fusion of the protein under the control of the native promoter was obtained. One replicate was produced for each experiment

first: Rim

last: Chaouche

last: He

first: David

last: Latrasse

first: Jing

last: An

first: Moussa

last: Benhamed

first: Cécile

last: Raynaud


title: Hepatic T-cell senescence is implicated in the progression of fatty liver disease in patients with type 2 diabetes

status: Public on Aug 05 2023

city: Daejeon

first: BYEONGCHANG

last: SIM

state: 대전

address: Chungnam National University School of Medicine, 282 Munhwa-ro Jung-gu, Daejeon 35015, Korea

institute: Research Center for Endocrine and Metabolic Diseases, Laboratory of Endocrinology and Immune System

summary: Immunosenescence and exhaustion are involved in the development and progression of type 2 diabetes (T2D) and metabolic liver diseases, including fatty liver, fibrosis, and cirrhosis, in humans.  However, the relationships of the senescence and exhaustion of T cells with insulin resistance-associated liver diseases remain incompletely understood. To better define the relationship of T2D with nonalcoholic fatty liver disease, 59 patients with T2D were studied.

overall_design: Metabolic liver disease mice made by feeding the High Fat High Fructose diet (HFrD) for 24 weeks. The liver immune cells were isolated by Percoll gradient method and analyzed using scRNAseq

first: Byeong

last: Sim

first: Yea

last: Kang

first: Sun

last: You

first: Seong

last: Lee

first: Ha

last: Nga

first: Ho

middle: Y

first: Thi

last: Nguyen

first: Ji

last: Moon

first: Jingwen

last: Tian

first: Hyo

last: Jang

first: Jeong

first: Hyon-Seung

last: Yi


title: Developmental Reprogramming of Myometrial Stem Cells by Endocrine Disruptor Linking to Risk of Uterine Fibroids [ChIP-Seq]

first: Qiwei

last: Yang

summary: We report that developmental exposure to the endocrine disrupting chemical (EDC) diethylstilbestrol increases the estrogen action in myometrial stem cells (MMSCs), the origin from which UFs originate. The expression of reprogrammed estrogen responsive genes (ERGs) is driven by activated mixed lineage leukemia protein-1 (MLL1) in MMSCs.  Deactivation of MLL1 reverses reprogramming of ERG expression. In addition, upregulation of ERGs occurs via DNA hypomethylation mechanism. Furthermore, the secretome of reprogrammed MMSCs enhances the proliferation of differentiated myometrial cells through activation of β-catenin signaling. This work identifies epigenetic mechanisms of MLL1/DNA methyltransferase- mediated MMSC reprogramming, and EDC exposure epigenetically targets MMSCs and imparts a hormonal imprint on the ERGs resulting in a "hyper-estrogenized" phenotype and increased hormone-dependent risk of UFs.

overall_design: Examine the epigenome  in MMSCs from 5 month Eker rat myometrium PND 10-12 exposed to DES and VEH

first: Mohamed

last: Ali

first: Lindsey

last: Treviño

first: Aymara

last: Mas

first: Ayman

last: Al-Hendy


title: Post-transcriptional regulation of Ribosome Biogenesis in Larp1-deficient cells

status: Public on Aug 04 2023

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

institute: NIEHS

summary: Ribosome biogenesis is a critical aspect of cell differentiation. Ribosome synthesis has been previously reported to be regulated at the transcriptional and post-transcriptional levels. Poly(A) tail-length processing is a hallmark of post-transcriptional regulation associated with different steps of transcript metabolism. Here we monitor the contribution of the RNA-binding protein Larp1 in shaping the poly(A) tail profile of undifferentiated P19 cells. We found that Larp1 prevents the widespread shortening of poly(A) tails below 30 nucleotides and confers additional protection to transcripts containing a 5' terminal oligopyrimidine (TOP) motif, such as those encoding for ribosomal proteins.

overall_design: To knock down Larp1, undifferentiated P19 cells seeded in 6-well plates were transfected with 50 nanomoles of the Larp1 siRNA (Dharmacon, J-063706-09-0010) using Lipofectamine 3000 (Invitrogen) according to the manufacturer's instructions. A pool of scrambled siRNAs (Dharmacon, D-001810-10-20) with no significant homology to the human, mouse, or rat genome was used as a negative control. After transfection, cells were incubated at 37°C for 24 hours. To study the long-term effect at 48 hours, an additional transfection using the same conditions was performed 24 hours after the initial knock-down. RNA was collected, and Direct RNA seq libraries were prepared in duplicates or triplicates for each timepoint and run on a Nanopore GridIon device. Reads were mapped to the mouse transcriptome, and their poly(A) tail lengths were determined. This information was then used to monitor the impact of Larp1 knock-down on poly(A) tail length.

first: Marine

last: Baptissart

first: Brian

last: Papas


title: Single cell sequencing of bone marrow infiltrating T lymphocytes in mice and humans affected by monoclonal gammopaties

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

country: Italy

institute: "Annunziata" Hospital of Cosenza

summary: Despite the extensive use of immunotherapies in hematological malignancies, the single-cell landscape of tumor infiltrating lymphocytes (TILs) in these patients lags behind what has been accomplished in solid tumors. One such example is multiple myeloma (MM), an incurable plasma cell malignancy for which treatment is being redefined by immunotherapies, while single-cell studies of TILs are scarce  and the phenotype of tumor-reactive T cells remains unknown. Here we aimed at defining the phenotype of tumor-reactive T cells throughout myelomagenesis. To this end, we performed single-cell RNA and TCR sequencing of bone marrow T cells in MM and its precursor states, both in patients and experimental mouse models of spontaneous disease progression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
scRNA-seq + scTCR-seq were performed in 17 bone marrow aspirates from 3 healthy adults, 3 MGUS, 2 SMM, 9 MM patients and 8 bone marrow aspirates from 2 healthy (Ycɣ1), 3 MGUS (BIcɣ1) and 3 MM (BIcɣ1) bearing mice.
NOTE FROM SUBMITTER:  human raw data not uploaded due to the our current privacy concerns regarding the availability of the Fasta/q files derived from healthy cells (DNA fingerprint) of patients with disease (including the possibility to derive sensible information like HLA haplotype)

first: Cristina

last: Perez

first: Bruno

last: Paiva


title: Effect of SARS-CoV-2 infection on gene expression of iPSC derived sensory neurons

city: Cambridge

first: Anthony

last: Flamier

state: MA

address: 455 Main Street

institute: Whitehead Institute

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


title: A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: The six species of lungfish possess both lungs and gills and are the closest extant relatives of tetrapods. Here, we report a single-cell transcriptome atlas of the West African lungfish (Protopterus annectens). This species manifests the most extreme form of terrestrialization, a life history strategy to survive dry periods in five lungfish species that can last for years, characterized by dormancy and reversible adaptive changes of the gills and lungs. Our atlas highlights the cell type diversity of the West African lungfish, including gene expression consistent with phenotype changes of terrestrialization. Comparisons with terrestrial tetrapods and ray-finned fishes revealed broad homology between the swim bladder and lung cell types as well as shared and idiosyncratic changes of the external gills of the West African lungfish and the internal gills of Atlantic salmon. The single-cell atlas presented here provides a valuable resource for further exploring the evolution of the vertebrate respiratory system and the diversity of lungfish terrestrialization.

overall_design: Single cell expression profiling by high throughput sequencing of African lungfish lung and gill under freshwater and terrestrialization condition.

first: Ruihua

last: Zhang

first: Qun

last: Liu

first: Shanshan

last: Pan

first: Guangyi

last: Fan


title: Post-transcriptional regulation of Ribosome Biogenesis upon treatment with MHY1485

summary: Ribosome biogenesis is a critical aspect of cell differentiation. Ribosome synthesis has been previously reported to be regulated at the transcriptional and post-transcriptional levels. Poly(A) tail-length processing is a hallmark of post-transcriptional regulation associated with different steps of transcript metabolism. Here we monitor the contribution of mTOR pathway activation upon treatment with the agonist MHY1485 in shaping the poly(A) tail profile of undifferentiated P19 cells. We found that transcripts with a 5' terminal oligopyrimidine (TOP) motif, including those encoding for ribosomal proteins, specifically accumulate with poly(A) tails ~60 nucleotides long upon mTOR activation.

overall_design: The day after seeding, undifferentiated P19 cells were treated with 10 µM final concentration of MHY1485 (Selleckchem) for 24 hours, or 48 hours with media changed every 24 hours containing fresh MHY1485 solution. Cells exposed to the same amount of DMSO were used as control. RNA was collected, and Direct RNA seq libraries were prepared in duplicates for each timepoint and run on a Nanopore GridIon device. Reads were mapped to the mouse transcriptome, and their poly(A) tail lengths were determined. This information was then used to monitor the impact of mTOR activation on mRNA poly(A) tail lengths.


title: Gpr18 agonist dampens inflammation, enhances myogenesis, and restores muscle function in models of Duchenne muscular dystrophy

city: Montréal

first: Nicolas

middle: A

last: Dumont

state: QC

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Saint-Justine

summary: Muscle wasting in Duchenne Muscular Dystrophy is caused by myofiber fragility and poor regeneration that leads to chronic inflammation and muscle replacement by fibrofatty tissue. Our recent findings demonstrated that Resolvins, a class bioactive lipids derived from omega-3 fatty acids, have the capacity to dampen inflammation and stimulate muscle regeneration to alleviate disease progression. This therapeutic avenue has many advantages compared to glucocorticoids, the current gold-standard treatment for Duchenne Muscular Dystrophy. However, the use of bioactive lipids as therapeutic drugs also faces many technical challenges such as their short-half life. Here, we explored the potential of synthetic agonist of bioactive lipid receptor, namely the Gpr18 agonist PSB-KD107, as a therapeutic alternative for Duchenne Muscular Dystrophy. We showed that PSB-KD107 can stimulate the myogenic capacity of human iPSC-derived myoblasts in vitro. RNAseq analysis revealed an enrichment in biological processes related to lipid metabolism, small molecule biosynthesis, and steroid-related processes in PSB-KD107-treated cells, as well as pathways related to fatty acid signaling such as Peroxisome proliferator-activated receptors, AMP-activated protein kinase, and sphingolipid signaling pathways. In vivo, the treatment of dystrophic mdx mice with PSB-KD107 resulted in reduced inflammation, enhanced myogenesis, and improved muscle function compared to vehicle-treated mice. Overall, our findings identified a novel therapeutic target for the treatment of Duchenne Muscular Dystrophy.

overall_design: Transcriptome profiling of untreated mdx muscle stem cells (n=3) as control,  and PSB-KD107-treated mdx muscle stem cells (n=3)

first: Junio

last: Dort

first: Zakaria

last: Orfi

first: Philippe

last: Campeau

first: Melissa

last: Fiscaletti


title: IQGAP1 mediates the communication between the nucleus and the mitochondria via NDUFS4 alternative splicing

city: Barcelona

first: Malgorzata

middle: Ewa

last: Rogaska

address: C/ del Dr. Aiguader, 88

country: Spain

institute: CRG

summary: A constant communication between mitochondria and nucleus ensures cellular homeostasis and adaptation to mitochondrial stress. Anterograde regulatory pathways involving a large number of nuclear-encoded proteins control mitochondrial biogenesis and functions. Such functions are deregulated in cancer, resulting in proliferative advantages for cancer cells, aggressive disease and therapeutic resistance. Transcriptional networks controlling the nuclear-encoded mitochondrial genes are known, however alternative splicing (AS) regulation has not been implicated in this communication. Here, we show that IQGAP1, a scaffold protein that regulates AS of distinct gene subsets in gastric cancer cells, participates in AS regulation that strongly affects mitochondrial respiration. Combined proteomic and RNA-seq analyses of IQGAP1KO and parental cells show that IQGAP1KO alters a specific AS event of the mitochondrial respiratory chain complex I (CI) subunit NDUFS4 and downregulates a subset of CI subunits. In IQGAP1KO cells, CI intermediates accumulate resembling assembly deficiencies observed in patients with Leigh syndrome bearing NDUFS4 mutations. Mitochondrial CI activity is significantly lower in KO compared to parental cells, while exogenous expression of IQGAP1 reverses mitochondrial defects of IQGAP1KO cells. Our work sheds light to a novel facet of IQGAP1 in mitochondrial quality control that involves fine-tuning of CI activity through AS regulation in gastric cancer.

overall_design: 2 cell lines; parental line NDUFS4 and IQGAP1 KO

first: Panagiota

last: Kafasla

last: Rogalska


title: Effect of SARS-CoV-2 infection on gene expression of iPSC derived sensory neurons [scRNAseq]

summary: To investigate the impact of SARS-CoV-2 on the peripheral nervous system, we generated human sensory neurons from induced pluripotent stem cells (iPSC) that we further infected with the SARS-CoV-2 strain WA1/2020 for 48 hours.

overall_design: In this experiment, we co-cultured HEK293T cells and sensory neurons for 3 days, infected the cultures with SARS-CoV-2 for 48h, and analyzed using scRNAseq.

first: Flamier

last: Anthony

first: Jaenisch

last: Rudolf


title: Genome-wide maps of GFPyTBP (ChIP-seq) in yeast kap114-KO SC1005 strains

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

institute: National Yang Ming Chiao Tung University

summary: Multiple nuclear transport receptors, collectively termed karyopherins in yeast, deliver TATA-binding protein (TBP) to the nucleus, facilitating promoter recognition and transcriptional preinitiation complex formation. Among these karyopherins, Kap114p exhibits a sub-nanomolar affinity for yeast TBP (yTBP), four orders of magnitude greater than its counterparts. We hypothesize that the strong binding affinity of Kap114p toward yTBP going beyond what is required for nuclear import facilitates additional functions. Here we employ ChIP-seq assays to profile genome-wide maps of yTBP (through an GFP tag) in yeast kap114-knockout SC1005 strains rescued without or with kap114 wildtype or Δ(899–956) mutant. Our results showed that Kap114p serves as a yTBP suppressor in the transcriptional regulatory network. Importantly, the Kap114p-dependent sequestration prevents a collapse of yTBP dynamics, required for yeast respondding to environmental stresses (e.g. salt stress).

overall_design: Genome-wide binding/occupancy profiling of GFPyTBP by ChIP-seq in yeast kap114-KO SC1005 strains (rescued without or with Kap114 wildtype or Δ(899–956) mutant)


title: Post-transcriptional regulation of Ribosome Biogenesis during differentiation [SLAM-seq]

first: Marcos

last: Morgan

summary: The regulation of ribosome biogenesis is a critical component of cell differentiation. Although ribosome biogenesis is well known to be regulated at the transcriptional level, its post-transcriptional regulation is less well understood. A key component of RNA post-transcriptional regulation is transcript decay rate which, together with the rate of synthesis, defines the abundance of the transcripts. Here we measured the stability of the whole transcriptome of P19 cells before differentiation (D0) and six days after the onset of differentiation (D6). We found that while global decay rates dropped during differentiation, the stability of transcripts encoding for ribosomal proteins remains significantly high throughout the differentiation process. These results indicate a strong and specific post-transcriptional regulation of ribosome biogenesis transcripts that is sustained during cell differentiation.

overall_design: We prepared SLAM-seq catabolic and anabolic libraries for P19 undifferentiated and differentiated cells (4 experiments total). For each experiment, we collected biological duplicates or triplicates at time points 0, 3, 6, and 9 hrs after the removal of 4sU (catabolic experiment) or addition of the 4sU (anabolic experiment), and for each sample, we prepared an RNA seq library. Reads were mapped to the transcriptome, and uracil to cytosine conversions were quantified using the SLAMdunk software. The change in the U to C conversion from 0 to 9 hrs was used to calculate the decay or synthesis half-life of each transcript.

first: Marine

last: Baptissart

first: Brain

last: Papas


title: Multicolor spectral flow cytometry evaluation of peripheral blood mononuclear cells from NSCLC patients

status: Public on Aug 03 2023

city: Sacramento

first: Tianhong

last: Li

address: 2700 Stockton Blvd

institute: UC Davis Health

summary:
To investigate a non-invasive strategy for immune monitoring the peripheral blood by flow cytometry, to address the critical need to itdentify predictive immunological biomarkers that correlate with treatment response
Peripheral blood mononuclear cells (PBMCs) from 19 non–small-cell lung cancer (NSCLC) patients before and after ICI treatment and four healthy human donors were evaluated, utilizing spectral flow to monitor 24 immune cell markers simultaneously over the course of treatment.
We performed immune cell profiling analysis using data obtained from RNA-seq of 19 different patients before and after immunotherapy, to validate the multi-color flow based immune profiling

overall_design: Comparative immune cell profiling through gene expression analysis of RNA-seq data of human PBMCs from NSCLC patients

first: Weijie

last: Ma

first: Sixi

last: Wei

first: Eddie

last: Tian

first: Bridget

last: McLaughlin

first: Maria

last: Jaimes

first: Dennis

last: Montoya

first: Varun

middle: R

last: Viswanath

first: Jeremy

last: Chien

first: Qianjun

last: Zhang

first: Jonathan

last: Van Dyke

first: Shuai


title: Differential ribosome engagement profiling between undifferentiated and neuron-differentiated P19 cells

summary: Translation is tightly regulated during differentiation. To gain insights into the mechanism regulating translational activity at the transcript level, we performed Ribosome Profiling of undifferentiated and neuron-differentiated P19 cells. Relative changes in translational activity between the undifferentiated and differentiated cells show an increase in the translational activity of the transcripts encoding for ribosomal proteins compared to the rest of the transcriptome. Thus, in this differentiation system, the biogenesis of the translational machinery is tightly controlled at the translational level.

overall_design: P19 cells were differentiated into neuronal cells and then lyzed for material collection. Four biological replicates were collected before differentiation (D0), and four biological replicates were collected after six days of differentiation (D6). An RNA-seq library and a Ribosome Protected Fragment (RPF) library were generated for each sample. To estimate the change in ribosome engagement for each transcript between conditions, we compared the ratio of RFP reads to RNA-seq reads per transcript at D6 and D0.

first: Ru-Pin

last: Chi

first: Brian


title: Zika virus targets human trophoblast stem cells and prevents syncytialization in placental trophoblast organoids

city: Suzhou

first: Hang-Yu

last: Zhou

state: Jiangsu

address: 100 Chongwen Road

institute: Institute of Systems Medicine, Chinese Academy of Systems Medicine

summary: Zika virus (ZIKV) infection during pregnancy results in an increased risk of spontaneous abortion and vertical transmission across placenta results in severe congenital defects in newborns. While the infectivity and pathological effects of ZIKV on the placental trophoblast progenitor cells in early human embryos remains largely unknown. Here, using the human trophoblast stem cells (hTSCs) isolated from human blastocyst, we showed that hTSCs were permissive to ZIKV infection, while resistance to ZIKV increased with differentiation. Combined CRISPR/Cas9-mediated gene knockout and RNA-seq assays, we demonstrated that the intrinsic expression of AXL and TIM-1, as well as the absence of potent interferon (IFN)-stimulated genes (ISGs), contributed to the high sensitivity of hTSCs to ZIKV. Furthermore, using our newly developed hTSC-derived 3 dimensional (3D) placental trophoblast organoid model, we demonstrated that ZIKV infection completely disrupted the structure of mature hTSC-organoids and inhibited syncytialization. Overall, our results clearly demonstrated that hTSCs represented the major target cells of ZIKV, and a possible reduced syncytialization may result from ZIKV infection of early developing placenta. These findings deepened our understanding of the characteristics and consequences of ZIKV infection of trophoblast stem cells in early human embryo.

overall_design: The single cells from hTSC-organoids and hTSC-organoids infected with ZIKV at MOI 1 and 10 for scRNA-seq

first: Hao

last: Wu

first: Xing-Yao

last: Huang


title: Effect of SARS-CoV-2 infection on gene expression of iPSC derived sensory neurons [bulkRNAseq]

first: Anthony

last: Flamier

summary:
To investigate the impact of SARS-CoV-2 on the peripheral nervous system, we generated human sensory neurons from induced pluripotent stem cells (iPSC) that we further infected with the SARS-CoV-2 strain WA1/2020 for 48 hours.
We then performed gene expression profiling analysis using data obtained from RNA-seq of mock treated cells compared to SARS-CoV-2 infected cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mock treated cells compared to SARS-CoV-2 infected cells.

first: Flamier

last: Anthony

first: Jaenisch

last: Rudolf


title: Uterine transcriptomic profiles of Nr2f2 deficiency in Pgr-expressing cells at gestation day 3.5

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

summary: Endometrial epithelia and stroma communicate via progesterone and estrogen signaling to prepare a receptive uterus for embryo implantation in early pregnancy. The present study determines, in early pregnancy at the prereceptive stage, the uterine gene signature of the NR2F2 transcription factor that is crucial for mediating the progesterone dependent anti-proliferative actions in the epithelia.

overall_design: Adult mouse uterine tissues from PRCre/+; Nr2f2flox/flox (mutant) and Nr2f2flox/flox (control) at gestation day 3.5 (GD3.5) were subject to RNA-seq analysis.

first: Yeongseok

last: Oh

first: Tianyuan

last: Wang

first: Francesco

last: DeMayo

first: San-Pin


title: Post-transcriptional regulation of Ribosome Biogenesis

first: Marcos

last: Morgan

overall_design: Refer to individual Series


title: Nr2f2 deficiency in Pgr-expressing cells; NR2F2 genome occupancy and the H3K4me1 histone mark; uterus at gestation day 3.5


title: The interplay between dietary fatty acids and gut microbiota influences host metabolism and hepatic steatosis

city: Toulouse

first: Sandrine

last: Ellero-Simatos

address: 180 chemin de Tournefeuille

institute: INRAe

summary: Dietary lipids can affect metabolic health through gut microbiota-mediated mechanisms, but the influence of lipid-microbiota interaction on liver steatosis is unknown. We investigated the effect of dietary lipid composition on human microbiota in an observational study and combined diet experiments with microbiota transplants to study lipid-microbiota interactions and liver status in mice. In humans, low intake of saturated fatty acids (SFA) was associated with increased microbial diversity independent of fiber intake. In mice, cecum levels of SFA correlated negatively with microbial diversity and were associated with a shift in butyrate and propionate producers. Mice fed poorly absorbed SFA had improved metabolism and liver status. These features were transmitted by microbial transfer. Diets enriched in n-6- and/or n-3-polyunsaturated fatty acids were protective against steatosis but had minor influence on the microbiota.  In summary, we find that unabsorbed SFA correlate with microbiota features that may be targeted to decrease liver steatosis.

overall_design: C57Bl/6 8 weeks old male mice were maintained under standard specific-pathogen-free (SPF) conditions. Mice were fed irradiated isocaloric diets differing only in their composition of fat for 9 weeks: Envigo TD.180343 (diet A), TD.180344 (diet B), TD.180345 (diet C), TD.180346 (diet D), TD.180347 (diet E), TD.180348 (diet F), TD.180349 (diet G); 42% kcal fat, 0.2% weight total cholesterol. A milk fat containing diet (Envigo TD.180342) that has previously been shown to induce steatosis served as reference (Ref) diet.

first: Robert

last: Caesar

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Pooled CRISPR screens in human macrophages

city: Washington

first: Xiaolong

last: Cheng

state: DC

address: 7144 13th Place NW

institute: Children's National

summary: To identify the possible genes influencing macrophage pro-inflammatory activation, we designed CRISPR screens using a human metabolic sgRNA library containing metabolism-related transcription factors, small molecule transporters, and metabolic enzymes in a Cas9-expressing lentiviral vector.

overall_design: THP-1 cells or iPSCs were transduced with a viral library for 24 h. After puromycin selection for seven days, the transduced cells were differentiated into macrophages, then stimulated by LPS  plus IFN-γ  for 24 h. The stimulated cells were harvested and stained with anti-human CD80-FITC  for 15 min at room temperature. The CD80-high and CD80-low cells were separated by flow cytometry sorting.

first: Xudong

first: Siyu

last: Su

first: Jin

last: Zhang


title: Effect of depletion of KEAP1 on gene expression after LPS and IFN-γ stimulation of THP-1 derived macrophages

summary:
To investigate the function of KEAP1  in the regulation of macrophage pro-inflammatory polarization, we established a KEAP1 deletion cell line using CRISPR Cas9 technology.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 10 different samples at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for macrophages-derived from WT THP-1 cells and KEAP1-deletion THP-1 cells with or without  LPS and IFN-γ stimulation.


title: Decoding the endometrial niche of Asherman's syndrome at single-cell resolution [organoids]

city: Paterna

first: Raul

last: Pérez-Moraga

state: Valencia

address: Rda. de Narcís Monturiol, 11, Bloque C

institute: Carlos Simon Foundation, INCLIVA Health Research Institute

summary: Asherman’s Syndrome is characterized by intrauterine adhesions or scarring, which cause infertility, menstrual abnormalities, and recurrent pregnancy loss. The pathophysiology of this syndrome remains unknown, with treatment restricted to recurrent surgical removal of intrauterine scarring, which has limited success. Here, we decode the Asherman’s Syndrome endometrial cell niche by analyzing data from over 200,000 cells with single-cell RNA-sequencing in patients with this condition and through in vitro analyses of Asherman’s Syndrome patient-derived endometrial organoids. Our endometrial atlas highlights the loss of the endometrial epithelium, alterations to epithelial differentiation signaling pathways such as Wnt and Notch, and the appearance of characteristic epithelium expressing secretory leukocyte protease inhibitor during the window of implantation. We describe syndrome-associated alterations in cell-to-cell communication and gene expression profiles that support a dysfunctional pro-fibrotic, pro-inflammatory, and anti-angiogenic environment.

overall_design:
Epithelial cells derived organoids from endometrial biopsies from Asherman syndrome pre-treatment and controls

**Submitter declares that the raw data will be deposited in dbGaP, as the data involves living donors under GDPR restrictions related to clinical trials (https://www.clinicaltrialsregister.eu/ctr-search/trial/2016-003975-23/ES) with signed informed consent**

first: Xavier

last: Santamaria

first: Beatriz

last: Roson

last: Perez-Moraga

first: Nandakumar

last: Venkatesan

first: Maria

last: Pardo-Figuerez

first: Javier

last: Gonzalez-Fernandez

first: Jaime

last: Gonzales-Fernandez

first: Estefania

last: Fernández

first: Inmaculada

last: Moreno

first: Andres

last: Salumets

first: Hugo

last: Vankelecom

first: Felipe

last: Vilella

first: Carlos

last: Simon


title: Post-transcriptional regulation of Ribosome Biogenesis during differentiation [dRNA-seq]

first: Marcos

last: Morgan

summary: Ribosome biogenesis is a critical component of cell differentiation. Ribosome synthesis has been previously reported to be highly regulated at the transcriptional level, but less is known about its post-transcriptional regulation. Poly(A) tail length regulation is a hallmark of post-transcriptional regulation associated with transcript stability. Here we monitor poly(A) tail length changes at a transcriptome level during P19 differentiation. We found that poly(A) tail shortening occurs during cell differentiation only for transcript encoding for ribosomal proteins. These findings suggest a strong post-transcriptional regulation of ribosome biogenesis during differentiation.

overall_design: P19 cells were differentiated for 6 days into neuron-like cells. RNA was collected before differentiation (D0) and two (D2), four (D4), and six (D6) days after the initiation of differentiation. Direct RNA seq libraries were prepared in triplicates for each timepoint and run on a Nanopore Minion device. Reads were mapped to the mouse transcriptome, and their poly(A) tail length was determined. This information was then used to monitor the changes in transcript abundance and poly(A) tail length during differentiation.

first: Marine

last: Baptissart

first: Brian

last: Papas


title: NR2F2 genome occupancy and the H3K4me1 histone mark profile in the mouse uterus at gestation day 3.5

first: Franco

last: Demayo

summary: NR2F2 genome occupancy and H3K4me1 histone mark profiles in the prereceptive stage of the pregnant mouse uterine specimens were documented by ChIP-seq to investigate downstream targets of the NR2F2 and candidate partner transcription regulators.

overall_design: Pools of uterine tissues  from gestation day 3.5 wild type mice were subject to the ChIP-seq assay.

first: Yeongseok

last: Oh

first: Tianyuan

last: Wang

first: Francesco

last: DeMayo

first: San-Pin

last: Wu


title: Decoding the endometrial niche of Asherman's syndrome at single-cell resolution

first: Raul

last: Pérez-Moraga

overall_design:
We have samples from Asherman patients in pre-treatment and WOI control samples.
***Submitter declares that the raw data files will be raw data will be deposited in  dbGaP as information involves living donors under GDPR restrictions related to clinical trials (https://www.clinicaltrialsregister.eu/ctr-search/trial/2016-003975-23/ES) with signed informed consent. ***

first: Xavier

last: Santamaria

first: Beatriz

last: Roson

last: Perez-Moraga

first: Nandakumar

last: Venkatesan

first: Maria

last: Pardo-Figuerez

last: Llera-Oyola


title: Metabolic Reprogramming via targeting the ACOD1/KEAP1/NRF2 axis promotes polarization and anti-tumor activity of human CAR-iMACs in solid tumors

first: Xiaolong

last: Cheng

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


title: PD-L1 positive astrocytes attenuate inflammatory functions of PD 1 positive microglia in models of autoimmune neuroinflammation [RNA-seq: IFNb]

status: Public on Aug 02 2023

city: Erlangen

first: Mathias

last: Linnerbauer

address: Schwabachanlage 6

department: Neurology

institute: University Hospital Erlangen

summary: Multiple Sclerosis (MS) is a chronic autoimmune inflammatory disorder of the central nervous system (CNS). Current therapies mainly target inflammatory processes during acute stages, but effective treatments for progressive MS are limited. In this context, astrocytes have gained increasing attention as they have the capacity to drive, but also suppress tissue-degeneration. Here we show that astrocytes upregulate the immunomodulatory checkpoint molecule PD-L1 during acute autoimmune CNS inflammation in response to aryl hydrocarbon receptor and interferon signaling. Using CRISPR-Cas9 genetic perturbation in combination with small-molecule and antibody-mediated inhibition of PD-L1 and PD-1 both in vivo and in vitro, we demonstrate that astrocytic PD-L1 and its interaction with microglial PD-1 is required for the attenuation of autoimmune CNS inflammation in acute and progressive stages in a mouse model of MS. Our findings suggest the glial PD-L1 / PD-1 axis as a new therapeutic target for both acute and progressive MS stages.

overall_design: Bulk RNA Sequencing of astrocytes treated with interferon-beta or vehicle .

first: Tobias

last: Beyer

first: Rupert

last: Öllinger

first: Thomas

last: Engleitner

first: Veit

last: Rothhammer


title: PD-L1 positive astrocytes attenuate inflammatory functions of PD 1 positive microglia in models of autoimmune neuroinflammation [RNA-seq: BMS202]

overall_design: Bulk RNA Sequencing of FACS-sorted astrocytes and microglia during experimental autoimmune encephalomyelitis (EAE) in NOD mice. The animals were treated with BMS202 or vehicle .


title: Gene expression of B cell and T cell of IKZF3 mutant mice

city: Yokohama

first: CHANG

last: JINGJIE

state: -- Choose State --

address: 横滨市鹤见区1Chome suehirocho

country: Japan

institute: RIKEN

summary: To identify genes dysregulated by Aiolos N159S variant, splenic B cell and T cell populations of Ikzf3 +/+, Ikzf3 +/N159S and Ikzf3 N159S/N159S mice were subjected to RNA-seq analyses.

overall_design: Investigation of feature genes expressed by target cell populations (splenic B cells and T cells), and comparative gene expression profiling analysis of RNA-seq data for indicated genotypes.

first: Jingjie

last: Chang

first: Motoi

last: Yamashita

first: Ichiro

last: Taniuchi