title: Transcriptome Profiling sequencing analysis of feline ovarian granulosa cell treated with Atractylenolide Ⅰ

status: Public on Aug 01 2021

city: Hohhot

first: Yuli

last: Guo

address: Zhaowuda Road

institute: Inner Mongolia Agricultural University

summary: Through the application of a transcriptome profiling strategy, we were able to ascertain the differentially expressed genes and complicated pathways involved in the interactions between Atractylenolide-I and feline ovarian granulosa cells. Based on the results of our transcriptome profiling study, we found the highest number of DEGs participated in cholesterol metabolism pathways, the activation of which might be a major factor underlying Atractylenolide I promote the luteinization of the feline ovarian granulosa cells.

overall_design: Divided into treatment group and control group,Three biological replicates were designed for the treatment and control experiments

first: Chenggong

last: Liu

first: Jinshan

last: Cao


title: Panoramix SUMOylation at chromatin recruits the heterochromatin machinery to piRNA target loci [ChIP-seq]

status: Public on Aug 22 2021

city: Vienna

first: Julius

middle: Fabian

last: Brennecke

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA-Institute for Molecular Biotechnology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Nuclear Argonaute proteins, guided by small RNAs, mediate sequence-specific heterochromatin formation. The molecular principles that link Argonaute–small RNA complexes, once bound to a nascent target RNA, to general heterochromatin effectors are poorly understood. Here, we uncover the mechanistic basis of how the PIWI interacting RNA (piRNA) pathway engages the heterochromatin machinery in Drosophila. Piwi-mediated recruitment of the corepressor complex SFiNX to chromatin leads to SUMOylation of its Panoramix subunit. SUMOylation, together with a hydrophobic LxxLL motif in the intrinsically disordered repressor domain of Panoramix, are necessary and sufficient to recruit Small ovary (Sov), a multi-zinc finger protein essential for general heterochromatin formation and viability. Structure-guided mutations that abrogate the Panoramix-Sov interaction or that prevent Panoramix SUMOylation uncouple Sov from the piRNA pathway, resulting in viable but sterile flies that exhibit de-repression of Piwi-targeted transposons. Thus, coupling the piRNA-guided recruitment of a corepressor to chromatin with its SUMOylation underlies sequence-specific heterochromatin formation.

overall_design: ChIP-seq of OSCs.

first: Veselin

middle: I

last: Andreev

first: Changwei

last: Yu

first: Juncheng

last: Wang

first: Jakob

last: Schnabl

first: Laszlo

last: Tirian

first: Maja

last: Gehre

first: Dominik

last: Handler

first: Grzegorz

last: Sienski

first: Lisa

last: Baumgartner

first: Peter

last: Duchek

first: Karl

last: Mechtler

first: Dinshaw

middle: J

last: Patel


title: Single-Cell RNA Sequencing Reveals the Immunological Profiles of Renal Allograft Rejection in mice

status: Public on Jul 21 2021

city: Hangzhou

first: QIXIA

last: SHEN

state: Zhejiang

address: Qinchun Rd.79, Hangzhou

country: China

institute: The first affiliated hospital, Hangzhou, China

type: Expression profiling by high throughput sequencing

summary:
Background: Acute T cell-mediated rejection (TCMR) is a common immunological feature  in renal transplantation and is associated with reduced graft survival. However, the full immunological profiling  of acute TCMR remains unknown.
Methods: A fully mismatched acute TCMR model was induced  by transplanting the left kidneys from BALB/c mice into C56BL/6J mice. Allografted kidneys were harvested on day 7 (D7) and sorted for CD45+ leukocytes for single cell RNA sequencing (scRNA-seq) . In addition,  scRNA-seq data of CD45+ immune cells on day 15 (D15) containing GSE157292 dataset (samples GSM4761000 and GSM4761003) were downloaded from Gene Expression Omnibus. All data obtained from  D7 and D15 were integrated and analyzed.
Results: We identified 20 major immune cell types among 10921 immune cells, including macrophages, B cells, T cells, dendritic cells, natural killer cells, neutrophils, and basophils in kidney allografts. Macrophages and CD8 T cells constituted the main immune cell populations on both D7 and D15. In the process towards immune regression, the proportion of CD8 T cells dropped significantly by about 25%, mainly due to decreased proliferation and naïve CD8 T cell infiltration. The proportion of both B cells and neutrophils also decreased  by about 3 folds. On the contrary, the relative proportion of macrophages and DCs increased significantly, especially by  a 4 fold increase in Ly6cloMrc1+ resident macrophages A group of Ly6cloEar2+ macrophages also increased by about 3 folds. Moreover, myeloid cells harbored the richest ligand and receptor (LR) pairs with other cell types, particularly for chemokine ligands such as Cxcl9, Cxcl10, Cxcl16 and Yars. However, macrophages with weak response to  interferon gamma (IFNg) contributed to rejection regression.
Conclusions: There is  a comprehensive single-cell landscape of the kidney allograft immune cells from rejection progression to  regression in acute TCMR. Reduction in CD8 T cells, B cells, and neutrophils while increasing in Ly6clo macrophages, including Ly6cloMrc1+ resident macrophages and Ly6cloEar2+ macrophages, may  contribute significantly to immune rejection regression during acute TCMR.

overall_design: Kidneys from 8 weeks old BALB/c male mice were transplanted into 8 weeks old B6 male recipients. Immune profiles were explored by scRNA-seq.

first: Shen

last: Qixia

first: Chen

last: Jianghua

first: Jiang

last: Hong

first: Lan

last: Huiyao

first: Wang

last: Yucheng


title: Single-cell analyses unravel cell type-specific responses to a vitamin D analogue in prostatic precancerous lesions [RNA-Seq]

status: Public on Aug 04 2021

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

summary: We treated PTENpe-/- mice, in which PTEN is selectively ablated in prostatic epithelial cells, with a Vitamin D analog. We extracted RNA from the prostate of oil (vehicle) and Vitamin D analog-treated mice.

overall_design: Three conditions were investigated: control mice (PtenL2/L2), and Pten(i)pe-/- mice treated for three weeks with either a vehicle or the vitamin D analogue Gemini-72. Two biological replicates of control mice were prepared (n=2 prostates), whereas three biological replicates of each of the other two conditions were prepared (n=3 prostates/condition).

first: Anna-Isavella

last: Rerra

first: Elise

last: Grelet


title: TNFα-producing Macrophages Determine Subtype Identity and Prognosis via AP1 Enhancer Reprogramming in Pancreatic Cancer [ChIP-/ATAC-seq]

status: Public on Jul 09 2021

city: Göttingen

first: Shiv K.

last: Singh

address: Robert-Koch-Str. 40

department: Gastroenterology and Gastrointestinal Oncology

country: Germany

institute: Univeristy Medical Center

summary: In pancreatic cancer, two distinct transcriptomic subtypes were identified with a high prognostic relevance: the classical and basal-like subtype. Therefore, in this study, we wanted to use an unbiased method to investigate the global chromatin accessibility in subtype-defined pancreatic cancer cell lines, as well as define the binding profile of the highly subtype-dependent JUN/AP1 transcription factors JUNB (classical) and cJUN (basal). Hence, we performed ATAC-seq in two classical and basal-like cells, as well as ChIP-seq for JUNB in classical CAPAN1 cells and for cJUN in basal-like PANC1 cells.

overall_design: ChIP-seq was performed for JUNB in CAPAN1 cells, as well as for cJUN in PANC1. Two repeats were used in each group. ATAC-seq was performed in CAPAN1, CAPAN2, PANC1 and MiaPaCa2 cells. Three repeats for CAPAN1, CAPAN2, PANC1; two repeats for MiaPaCa2.

first: Shiv

middle: K

first: Mengyu

last: Tu

first: Lukas

last: Klein


title: Amino acids activate mTORC1 to release roe deer embryos from decelerated proliferation during diapause [Luminal epithelium]

status: Public on Aug 15 2021

city: Berlin

first: Vera

last: van der Weijden

address: Ihnestraße 63-73

department: Department of Genome Regulation

institute: Max Planck Institute for Molecular Genetics

summary: mRNA sequencing of diapausing and embryos that resumed a fast rate of development to identify molecular factors involved in the regulation of embryonic diapause

overall_design: Luminal epithelial mRNA profiles of diapausing and reactivated roe deer embryos

middle: A

first: Jochen

middle: T

last: Bick

first: Stefan

last: Bauersachs

first: Anna

middle: B

last: Rüegg

first: Frank

last: Goeritz

first: Katarina

last: Jewgenow

first: Thomas

last: Hildebrandt

first: Pieter

last: Giesbertz

first: Hannelore

last: Daniel

first: Pascale

last: Chavatte-Palmer

first: Rupert

middle: M

last: Bruckmaier

first: Barbara

last: Drews

first: Susanne

middle: E

last: Ulbrich


title: Raw datas of the transcriptome in testes of Hezuo pigs and Landrace pigs at two different ages

status: Public on Aug 31 2021

city: Lanzhou

first: Bo

last: Zhang

address: No. 1 Yingmen village, Anning District

institute: Gansu Agricultural University

summary: Hezuo pigs are known in China for early sexual maturity. In this study, we obtained transcriptome data from testicular tissues of 30-day-old and 120-day-old Hezuo and Landrace pigs. Through comparative analysis of their differences, we searched for some genes related to the regulation of precocious sexual traits in male cooperating pigs and revealed their molecular regulatory mechanisms, which can then provide references for the diagnosis and treatment of precocious sexual diseases in humans and for accelerating the breeding of high-fertility animals.

overall_design: Testicular tissues of 30 and 120 days old Hezuo and Landrace pigs, 3 biological replicates each, 12 samples in total.

first: Zunqiang

last: Yan

first: Shuangbao

last: Gun


title: TNFα-producing Macrophages Determine Subtype Identity and Prognosis via AP1 Enhancer Reprogramming in Pancreatic Cancer [i4C-seq]

status: Public on Jul 02 2021

first: Shiv K.

last: Singh

summary: According to our previous data, BRD4 controls the inflammatory cJUN transcription factor via enhancer interaction to promote a basal-like phenotype in pancreatic cancer. Therefore, in this study, we wanted to asses BRD4-mediated 3D chromatin interactions at a potential cJUN enhancer locus in pancreatic cancer. Hence, we performed i4C-seq in PANC1 cells in absencece and presence of the BET/BRD4 inhibitor JQ1 for this site.

overall_design: i4C-seq was performed in PANC1 cells treated with JQ1 or DMSO control. A viewpoint around a cJUN enhancer site was used.

first: Shiv

first: Mengyu

last: Tu

first: Lukas

last: Klein


title: TNFα-producing Macrophages Determine Subtype Identity and Prognosis via AP1 Enhancer Reprogramming in Pancreatic Cancer [TNFa-treatment RNA-seq]

summary: In pancreatic cancer, classical and basal-like subtypes are identified as two major PDAC subtypes. Our previous data showed that PDAC tumor cells can switch between the two phenotypes through transcriptional reprogramming particularly in response to inflammatory cues. In this study, we were trying to understand TNFα mediated transcription regulatory network  in pancreatic cancer. Hence, we performed RNA-seq in TNFα treated classical cells as well as aqua dest control.

overall_design: RNA-seq was performed in aqua dest treated CAPAN1 control samples, as well as 18 h TNFα treated CAPAN1 cells (10 ng/ul). Three biological repeats were used in each group.


title: TNFα-producing Macrophages Determine Subtype Identity and Prognosis via AP1 Enhancer Reprogramming in Pancreatic Cancer

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

overall_design: Refer to individual Series


title: TNFα-producing Macrophages Determine Subtype Identity and Prognosis via AP1 Enhancer Reprogramming in Pancreatic Cancer [cJUN-OE RNA-seq]

summary: According to our previous data, it shows that cJUN plays an important role in regulating inflammation and basal-like phenotype in pancreatic cancer. Therefore, in this study, we wanted to use an unbiased method to investigate the global effect of cJUN in pancreatic cancer. Hence, we performed RNA-seq in GCDX62-EV cells, as well as GCDX62-cJUN cells

overall_design: RNA-seq was performed in pMSCV empty vector transduced GCDX62 cells, as well as cJUN stable overexpression cells (transduced with pMSCV-cJUN plasmid). Three technical repeats were used in each group.


title: A reservoir of stem-like CD8+ T cells in the tumor-draining lymph node preserves the ongoing anti-tumor immune response

status: Public on Aug 27 2021

city: New Haven

first: Kelli

last: Connolly

state: CT

address: 300 Cedar St.

department: Immunobiology

country: USA

institute: Yale University

summary:
“Stem-like” TCF1+ CD8+ T cells (TSL) are necessary for long-term maintenance of T cell responses and the efficacy of immunotherapy but, as tumors contain signals that should drive T-cell terminal-differentiation, how these cells are maintained in tumors remains unclear. In this study, we found that a small number of TCF1+ tumor-specific CD8+ T cells were present in lung tumors throughout their development. Yet, most intratumoral T cells differentiated as tumors progressed, corresponding with an immunologic shift in the tumor microenvironment (TME) from “hot” (T cell-inflamed) to “cold” (non-T cell-inflamed). By contrast, most tumor-specific CD8+ T cells in tumor-draining lymph nodes (dLNs) had functions and gene expression signatures similar to TSL from chronic LCMV infection, and this population was stable over time, despite the changes in the TME. dLN T cells were the developmental precursors of, and were clonally related to, their more-differentiated intratumoral counterparts. Our data support the hypothesis that dLN T cells are the developmental precursors of the TCF1+ T cells in tumors which are maintained by continuous migration. Finally, CD8+ T cells similar to TSL were also present in LNs from lung adenocarcinoma patients, suggesting a similar model may be relevant in human disease. Thus, we propose that the dLN TSL reservoir has a critical function in sustaining antitumor T cells during tumor development and protecting them from the terminal differentiation that occurs in the TME.
Methods:  We analyzed single-cell RNA-sequencing to assess the differentiation state and trajectory of the cell subsets present after FACs sorting on endogenous GP33-specific CD8+ T cells from tumors and draining lymph nodes of tumor-bearing KP-NINJA mice, comparing them to GP33-specific CD8+ T cells from spleens of mice infected with acute or chronic LCMV. In order to determine the clonal relationship of these cells from tumors and draining lymph nodes, we analyzed paired single-cell TCR sequencing.

overall_design: GP33-loaded MHC I tetramer+ CD8+ T cells were FACS sorted from tumor-draining lymph nodes and tumors of n=3 KP-NINJA mice and pooled for RNA- and TCR- sequencing at two different time points (8 weeks and 17 weeks after tumor induction). GP33-loaded MHC I tetramer+ CD8+ T cells were FACS sorted from the spleens of C57BL/6 mice 28 days after infection with either LCMV Armstrong (acute) or LCMV Clone 13 (chronic) and used as a reference for T cell differentiation states.

first: Manik

last: Kuchroo

first: Aarthi

last: Venkat

first: Achia

last: Khatun

first: Jiawei

last: Wang

first: Ivana

last: William

first: Noah

last: Hornick

first: Brittany

last: Fitzgerald

first: Martina

last: Damo

first: Moujtaba

middle: Y

last: Kasmani

first: Can

last: Cui

first: Eric

last: Fagerberg

first: Isabel

last: Monroy

first: Amanda

last: Hutchins

first: Julie

middle: F

last: Cheung

first: Gena

middle: G

last: Foster

first: Dylan

middle: L

last: Mariuzza

first: Mursal

last: Nader

first: Hongyu

last: Zhao

first: Weiguo

first: Smita

last: Krishnaswamy

first: Nikhil

middle: S

last: Joshi


title: A comprehensive transcriptome profiling in inclusion body myositis [RNA-Seq]

status: Public on Jul 01 2021

city: Helsinki

first: Mridul

last: Johari

state: Uusimaa

address: Haartmaninkatu 8, Biomedicum

country: Finland

institute: Folkhälsan Research Center

summary: Gene expression profile of coding and non-coding RNA in IBM muscles.

overall_design:
Comparison of transcriptome profile of muscle biopsies of patients with Inclusion body Myositis and controls with Tibial Muscular dystrophy and amputees with histopathologically normal muscle.

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Bjarne

last: Udd


title: A single-cell and spatially resolved atlas of human breast cancers

status: Public on Jun 24 2021

city: Darlinghurst

first: Alexander

last: Swarbrick

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: This study presents a single cell and spatially resolved transcriptomics analysis of human breast cancers. We develop a single cell method of intrinsic subtype classification (scSubtype) to reveal recurrent neoplastic cell heterogeneity. Immunophenotyping using CITE-Seq provides high-resolution immune profiles, including novel PD-L1/PD-L2+ macrophage populations associated with clinical outcome. Mesenchymal cells displayed diverse functions and cell surface protein expression through differentiation within 3 major lineages. Stromal-immune niches were spatially organized in tumors, offering insights into anti-tumor immune regulation. Using single cell signatures, we deconvoluted large breast cancer cohorts to stratify them into nine clusters, termed ‘ecotypes’, with unique cellular compositions and clinical outcomes. This study provides a comprehensive transcriptional atlas of the cellular architecture of breast cancer.

overall_design:
We performed scRNA-Seq (Chromium, 10X Genomics) on 26 primary tumors from three major clinical subtypes of breast cancer, including 11 ER+, 5 HER2+ and 10 TNBC. We also performed bulk RNA-Seq on a total of 24 of these matched samples.
***Raw Data Disclaimer: Raw human data files are deposited to the EGA (EGAS00001005173) to adhere to ethics.***

first: Sunny

last: Wu

first: Ghamdan

last: Al-Eryani

first: Daniel

last: Roden


title: A comprehensive transcriptomic profiling in inclusion body myositis

type: Non-coding RNA profiling by high throughput sequencing


title: Dissecting OCT4 defines the role of nucleosome binding in pluripotency maintenance

city: Edinburgh

first: Abdenour

last: Soufi

address: 5 Little France Drive

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

summary: The aim of this study is to dissect the transcription factor OCT4 and reveal which parts of the protein are essential for interaction with nucleosomes and access to closed chromatin. We revealed that the DNA-binding domain mediates the interaction of OCT4 with nucleosomes. Remarkably, nucleosome-binding can be uncoupled from DNA-binding, diminishing the ability of OCT4 to access to closed chromatin, thus losing the pioneer function. We show that the pioneer function of OCT4 is not only essential during reprogramming differentiated cells to pluripotency but also during pluripotency maintenance of embryonic stem cells. Overall, this study shows how pioneer transcription factors interact with nucleosomes to engage the genome and control cellular identity, highlighting that nucleosomes are not always barriers to genome accessibility.

overall_design: Measuring Chromatin accessibility (ATAC-seq) during stem cell self-renewal, when endogenous OCT4 is knocked down and replaced with OCT4 wild-type or mutant.


title: Epigenetic therapies in ovarian cancer alter repetitive element expression in a TP53-dependent manner: OC Line RNAseq

status: Public on Aug 17 2021

city: Washington

first: James

last: McDonald

state: DC

address: 800 22nd St, NW, Suite 8960

institute: The George Washington University

summary:
Abstract: Epithelial ovarian carcinomas (OC) are particularly deadly due to intratumoral heterogeneity, resistance to standard-of-care therapies, and poor response to alternative treatments such as immunotherapy. Targeting the OC epigenome with DNA methyltransferase inhibitors (DNMTi) or histone deacetylase inhibitors (HDACi) increases immune signaling and recruits CD8+ T cells and NK cells to fight OC in murine models. This increased immune activity is caused by increased transcription of repetitive elements (RE) that form double-stranded RNA (dsRNA) and trigger an interferon response. To understand which REs are affected by epigenetic therapies in OC, we assessed the effect of DNMTi and HDACi on OC cell lines and patient samples. Subfamily-level (TEtranscripts) and individual locus-level (Telescope) analysis of REs showed that DNMTi treatment upregulated more REs than HDACi treatment. Upregulated REs were predominantly LTR and SINE subfamilies, and SINEs exhibited the greatest loss of DNA methylation upon DNMTi treatment. Cell lines with TP53 mutations exhibited significantly fewer upregulated REs with epigenetic therapy than wild type TP53 cell lines. This observation was validated using isogenic cell lines; the TP53 mutant cell line had significantly higher baseline expression of REs but upregulated fewer upon epigenetic treatment. In addition, p53 activation increased expression of REs in wild type but not mutant cell lines. These data give a comprehensive, genome-wide picture of RE chromatin and transcription-related changes in OC after epigenetic treatment and implicate p53 in RE transcriptional regulation.
The data in this data series represent the analysis of RNAseq libraries generated from the A2780, Hey, Kuramochi, and TykNu ovarian carcinoma cell lines. Each cell line was treated with ITF-2357 (HDACi), 5-azacytidine (DNMTi), or a combination of both. RNA-seq libraries were sequenced, trimmed, aligned, and analyzed with TEtranscripts and Telescope software.

overall_design: Single replicates of RNA-seq were performed in A2780, Hey, Kuramochi, and TykNu cell lines given mock, ITF-2357, 5-azacytidine, or ITF-2357/5-azacytidine combined.

first: Noor

last: Diab

first: Elisa

last: Arthofer

first: Melissa

last: Hadley

first: Tomas

last: Kanholm

first: Uzma

last: Rentia

first: Stephanie

last: Gomez

first: Angela

last: Yu

first: Erin

last: Grundy

first: Olivia

last: Cox

first: Michael

last: Topper

first: Xiaoyun

last: Xing

first: Pamela

last: Strissel

first: Reiner

last: Strick

first: Ting

last: Wang

first: Stephen

last: Baylin

first: Katherine

last: Chiappinelli


title: Bulk RNA sequencing in minor salivary glands of Brazilian patients with primary Sjögren’s syndrome (SS) and healthy volunteers

status: Public on Jun 16 2021

city: Bethesda

first: Thomas

middle: John

last: Pranzatelli

state: MD

address: 10 Center Dr

department: Molecular Physiology and Therapeutics Branch

institute: National Institute of Dental and Craniofacial Research

summary: We aimed to study the difference of gene expression profile in minor salivary glands between SS patients and healthy volunteers, as well as the difference among different subgroups of SS patients.

overall_design: Total mRNA was extracted from minor salivary glands of 43 SS patients and 7 healthy volunteers.

first: John

last: Chiorini

first: Ying-Qian

last: Mo

first: Drew

last: Michael

first: Youngmi

last: Ji

first: Eduardo

last: Rocha


title: Single-cell analyses unravel cell type-specific responses to a vitamin D analogue in prostatic precancerous lesions [scRNA-Seq]

first: Gilles

last: Laverny

summary: Epidemiological data have linked vitamin D deficiency to the onset of various cancers, including prostate cancer, and although in-vitro studies have demonstrated anti-cancer activities for the vitamin, clinical trials provided conflicting results. To determine the impact of vitamin D signaling on prostatic precancerous lesions, we treated genetically-engineered mice harboring prostatic intraepithelial neoplasia (PIN) with Gemini-72, a vitamin D analogue with reported anti-cancer activities, and comprehensively analyzed its effects on various cell types in such lesions. We show that this analogue induces apoptosis in senescent PINs and normalizes extracellular matrix remodeling by stromal fibroblasts in an epithelial VDR-dependent manner. Furthermore, it reduces the prostatic infiltration of immunosuppressive myeloid-derived suppressor cells in an epithelial VDR-independent manner. Moreover, single-cell RNA-sequencing analysis demonstrates that while a subset of luminal epithelial cells, expressing Krt4 and Tacstd2 (termed luminal-C) with enhanced interferon signature, is lost by such a treatment, anti-apoptotic pathways are induced in persistent luminal-C cells. Therefore, our findings delineate the distinct responses of prostatic precancerous lesions and the microenvironment to the vitamin D analogue, and shed light on mechanisms that limit treatment’s efficacy.

overall_design: 2 samples were analyzed, and prepared from dissociated prostates of vehicle- and Gemini-72-treated Pten(i)pe-/- mice.

first: Daniel

last: Metzger

first: Mohamed

last: Abu el Maaty


title: Gingival transcriptomics phases of periodontitis lesions in nonhuman primate model

status: Public on Jul 22 2021

city: Lexington

first: kuey

middle: Chu

last: Chen

state: KENTUCKY

address: 800 Rose Street, UK Med Ctr

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

summary:
We used a nonhuman primate (NHP) model of ligature-induced periodontitis to identify gingival transcriptome changes associated with aging during the phases of periodontitis lesions (initiation, progression, and resolution).
Four age groups of nonhuman primate were studied: Young (<3 years of age); Adolescent (3 to 7 years), Adult (12 to 15 years), and Aged (17-23 years)

overall_design: Gingival tissues from healthy nonhuman primates were obtained at baseline (BL) before ligation, 2 weeks and 1 month (initiation), 3 months (progression) after placing ligatures, as well as two months after removing the ligatures (5M-resolution) for RNA extraction and hybridization on Affymetrix microarrays.

first: Octavio

last: Gonzalez

first: Jeffrey

last: Ebersole


title: Integrative Analysis of miRNA and gene Expression Profiles of Early-Onset Preeclampsia

status: Public on Jun 12 2021

city: shanghai

first: Tao

last: Duan

address: NO.2699, West Gao ke Road, Pudong New District

department: obstetrics

institute: shanghai first maternity and infant hospital , tongji university school of medicine

summary: To investigate the differentially expressed mRNAs and microRNAs in human placenta between early-onset preeclampsia (EO-PE) and preterm birth controls (PTB), next generation sequencing was performed in 5 paired EO-PE and PTB placentas.

overall_design: The rapid development of gene microarray and next generation sequencing has expedited the understanding of the genetic landscape of PE. While substantial evidence supports differential placental gene expression in PE, few studies were reported to systematically study miRNA and gene expression profiles in PE which should provide new insights into the miRNA-gene regulatory networks during the pathological process of PE. To address this paucity of data, we investigated global placental miRNA and gene expression using high-throughput RNA sequencing and quantitative real-time (qRT)-polymerase chain reaction (PCR) methodologies among 5 EO-PE cases and 5 normotensive preterm control subjects to identify miRNA-gene interaction networks and PE-associated biological pathways.

first: Xiaobo

last: Zhao

first: Gang

last: Zou

first: Donghai

last: Zhang


title: Amino acids activate mTORC1 to release roe deer embryos from decelerated proliferation during diapause

first: Vera

last: van der Weijden


title: Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia

status: Public on Jun 10 2021

city: Grand Rapids

first: Derek

middle: H

last: Janssens

state: MI

address: 333 Bostwick Ave. NE

department: Epigenetics

institute: Van Andel Institute

summary: Acute myeloid and lymphoid leukemias often harbor chromosomal translocations involving the Mixed Lineage Leukemia-1 gene, which encodes the KMT2A lysine methyltransferase. The most common translocations produce in-frame fusions of KMT2A to trans-activation domains of chromatin regulatory proteins. Here we develop a strategy to map the genome-wide occupancy of oncogenic KMT2A fusion proteins in primary patient samples regardless of fusion partner. By modifying the versatile CUT&Tag method for full automation we identify common and tumor-specific patterns of aberrant chromatin regulation induced by different KMT2A fusion proteins. Integration of automated and single-cell CUT&Tag uncovers lineage heterogeneity within patient samples and provides an attractive avenue for future diagnostics.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.

first: Michael

middle: P

last: Meers

first: Steven

last: Wu

first: Ekaterina

last: Babaeva

first: Soheil

last: Meshinchi

first: Jay

last: Sarthy

first: Kami

last: Ahmad

last: Henikoff


title: Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation

status: Public on Jun 03 2021

city: Baltimore

first: Joshua

last: Popp

state: Maryland

address: 3100 Wyman Park Drive South Wing, Room S249

department: Biomedical Engineering

institute: Johns Hopkins University

summary: The impact of genetic regulatory elements on gene expression can vary across cell states. During dynamic processes such as cellular differentiation, cells transition through multiple cell states, and may differentiate toward multiple terminal cell types. We collected time-series single-cell RNA-sequencing data from 19 human cell lines, capturing 7 time points along a 16-day differentiation from induced pluripotent stem cells to cardiomyocytes. We used unsupervised clustering, marker gene expression patterns, and pseudotime inference methods to map individual cells to a position along one of two bifurcating differentiation trajectories that were inferred from the data. We then identified genetic effects on gene regulation with varying effects across these trajectories. We identified hundreds of dynamic eQTLs that change significantly across pseudotime, including many variants whose effects are specific to one of the two lineages. We then re-analyzed previously collected bulk data, and used cell state information to infer cell type interaction eQTLs in bulk, assigning previously identified dynamic eQTLs to one of the newly characterized cellular trajectories.

overall_design: We obtained droplet-based single-cell RNA-seq data for 19 Yoruba individuals at 7 time points each during the differentiation from iPSC to cardiomyocyte. There are a total of 57 collections, each containing cells pooled from 3 human cell lines.

first: Reem

last: Elorbany

first: Katherine

last: Rhodes

first: Benjamin

last: Strober

first: Kenneth

last: Barr

first: Guanghao

last: Qi

first: Yoav

last: Gilad

first: Alexis

last: Battle


title: Targeting cancer stem cells with differentiation agents as an alternative to genotoxic chemotherapy for the treatment of malignant testicular germ cell tumors

status: Public on Apr 23 2021

city: Ithaca

first: Amanda

middle: R

last: Loehr

state: NY

address: 618 Tower Rd

department: Biomedical Sciences

institute: Cornell University

summary: Testicular germ cell tumors (TGCTs) are exceptionally sensitive to genotoxic chemotherapy, resulting in a high cure rate for the young men presenting with these malignancies. However, this treatment is associated with significant toxicity, and a subset of malignant TGCTs demonstrate chemoresistance. Mixed non-seminomas often contain pluripotent embryonal carcinoma (EC) cells, the cancer stem cells (CSCs) of these tumors. We hypothesized that differentiation therapy, a treatment strategy which aims to induce differentiation of tumor-propagating CSCs to slow tumor growth, could effectively treat mixed non-seminomas without significant toxicity. The FDA-approved anti-psychotic thioridazine and the agricultural antibiotic salinomycin are two drugs previously found to selectively target CSCs, and here we report that these agents differentiate EC cells in vitro and greatly reduce their tumorigenic potential in vivo. Using a novel transformed induced pluripotent stem cell allograft model and a human xenograft model, we show that thioridazine extends the survival of tumor-bearing mice and can reduce the number of pluripotent EC cells within tumors. These results suggest that thioridazine could be repurposed as an alternative TGCT treatment that avoids the toxicity of conventional chemotherapeutics.

overall_design: Gene expression profiles were generated for two independent murine embryonal carcinoma cell lines and thioridazine-differentiated derivatives of those cell lines, each with 3 biological replicates.

first: Robert

last: Weiss


title: Cargo receptor-assisted endoplasmic reticulum export of pathogenic α1-antitrypsin polymers

status: Public on Jun 02 2021

city: Cambridge

first: Adriana

last: Ordonez

address: Cambridge Biomedical Campus Keith Peters Building, Hills Rd

department: Clinical Biochemistry

institute: University of Cambridge

summary: Background: Circulating polymers of alpha1-antitrypsin (α1AT) are chemo-attractant for neutrophils and contribute to inflammation in pulmonary, vascular and adipose tissues. Cellular factors affecting the intracellular itinerary of mutant polymerogenic α1AT remain obscure. Methods: Here, we report on an unbiased genome-wide CRISPR/Cas9 screen for regulators of trafficking of the polymerogenic α1AT-H334D variant. Single guide RNAs targeting genes whose inactivation enhanced accumulation of polymeric α1AT were enriched by iterative construction of CRISPR libraries based on genomic DNA from fixed cells selected for high polymer content by fluorescence-activated cell sorting. This approach bypassed the limitation to conventional enrichment schemes imposed by cell fixation. Results: Our screen identified 121 genes involved in polymer retention at false discovery rate < 0.1. From that set of genes, the pathway ‘cargo loading into COPII-coated vesicles’ was overrepresented with 16 significant genes, including two transmembrane cargo receptors, LMAN1 (ERGIG-53) and SURF4. LMAN1 and SURF4-disrupted cells displayed a secretion defect extended beyond α1AT monomers to polymers, whose low-level secretion was especially dependent on SURF4 and correlated with SURF4-α1AT-H334D physical interaction and with enhanced co-localisation of polymeric α1AT-H334D with the endoplasmic reticulum (ER). Conclusions: These findings suggest that ER cargo receptors co-ordinate intracellular progression of α1AT out of the ER and modulate the accumulation of polymeric α1AT not only by controlling the concentration of precursor monomers but also through a previously-unrecognised role in secretion of the polymers themselves.

overall_design: CHO-K1 Tet-on_α1AT-H334D_Cas9 cells were initially transduced with a genome-wide CRISPR/Cas9 knockout library (Lib0, also called L0) comprising 125,030 single guide RNAs. α1AT-H334D expression was then induced with doxycycline followed, 24 hrs later by fixation, permeabilisation and staining with the polymer-specific monoclonal antibody 2C1 (Mab2C1). Cells were FACS sorted into 3 bins based on Mab2C1-dependent fluorescence intensity: ‘brightest, B’, ‘medium-bright, M’ and ‘dull, D’. Cell fixation precluded conventional enrichment schemes through successive rounds of phenotypic selection and expansion of the pooled cells. To circumvent this impasse, we implemented an approach based on recovery of sgRNA sequences from phenotypically-selected cell populations. Genomic DNA from the ‘brightest’-sorted cells was extracted and fragments covering integrated sgRNA sequences were PCR-amplified and used to generate a derivative CRISPR library. The derivative library (Lib1, also called L1), enriched in viral particles bearing phenotype-linked sgRNA sequences, was transduced into parental CHO-K1 Tet-on_α1AT-H334D_Cas9 cells followed by further phenotypic selection and generation of a second, enriched derivative library (Lib2, also called L2). Genomic DNA, pooled from sorted cells in the different bins at different stages of the phenotypic enrichment process and from unsorted control cells, was subjected to high-throughput sequencing and MAGeCK bioinformatics analysis (Li et al., 2014) to determine sgRNA sequence enrichment and the corresponding gene ranking list.

first: Heather

last: Harding

first: Stefan

last: Marciniak

first: David

last: Ron


title: A comprehensive transcriptome profiling in inclusion body myositis [miRNA-Seq]

first: Mridul

last: Johari

summary: Profiling of miRNA RNA in IBM muscles.

first: Bjarne

last: Udd


title: Profile of micro-RNA in ginger-derived nanoparticles

status: Public on May 19 2021

city: Louisville

first: Huang-Ge

last: Zhang

state: KY

address: 505 S Hancock Street

department: James Graham Brown Cancer Center

institute: University of Louisville

summary: Comparative analysis of micro-RNA (miRNA) in ginger-derived nanoparticles and ginger donor tissue using next-generation sequencing (NGS). The ginger-derived nanoparticles were prepared by differential ultracentrifuges. We mapped about 30 to 50 million sequence reads to the plant miRNA database and identified total of 2228 miRNAs including 532 miRNAs higher in nanoparticles and 1,280 miRNAs higner in tissue.

overall_design: High-throughput profiling of miRNA in ginger-derived nanoparticles and tissue.

first: Yun

last: Teng


title: BMH-21 inhibits RNA polymerase I transcription cycle and rDNA occupancy

status: Public on May 26 2021

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

summary: The objective of this study was to determine the effect of a small-molecule Pol I inhibitor, BMH-21, on rRNA synthesis in vivo. NET-seq was performed to determine the Pol I occupancy after BMH-21 treatment, as compared to vehicle-treatment (phosphate buffer control). Our findings suggest that BMH-21 treatment reduces Pol I occupancy on the rDNA template. Additionally, BMH-21 induces repositioning of Pol I in AT-rich rDNA regions that are directly upstream from GC-rich regions. This study suggests that BMH-21 is a powerful inhibitor of transcription by Pol I, and gives a potential mechanism of action for this inhibitor in vivo.

overall_design: In vivo NET-seq was performed to determine the effect of BMH-21 treatment on Pol I occupancy in biological triplicate.

first: Ruth

middle: Q

last: Jacobs

last: Schneider


title: Single-cell RNA sequencing of human femoral head in vivo

status: Public on Mar 24 2021

city: Changsha

first: Xiang

last: Qiu

state: Hunan

address: 172 Tongzipo Road, Yuelu District

department: School of Basic Medical Science

institute: Central South University

summary: The homeostasis of bone metabolism depends on the coupling and precise regulation of various types of cells in bone tissue. However, the communication and interaction between bone tissue cells at the single-cell level remains poorly understood. Thus, we performed single-cell RNA sequencing (scRNA-seq) on the primary human femoral head tissue cells (FHTCs). Nine cell types were identified in 26,574 primary human (FHTCs), including granulocytes, T cells, monocytes, B cells, red blood cells, osteoblastic lineage cells, endothelial cells, endothelial progenitor cells (EPCs) and plasmacytoid dendritic cells. We identified serine protease 23 (PRSS23) and matrix remodeling associated protein 8 (MXRA8) as novel bone metabolism-related genes. Additionally, we found that several subtypes of monocytes, T cells and B cells were related to bone metabolism. Cell-cell communication analysis showed that collagen, chemokine, transforming growth factor and their ligands have significant roles in the crosstalks between FHTCs. In particular, EPCs communicated with osteoblastic lineage cells closely via the "COL2A1-ITGB1" pair. Collectively, this study provided an initial characterization of the cellular composition of the human FHTCs and the complex crosstalks between them at the single-cell level. It is a unique starting resource for in-depth insights into bone metabolism.

overall_design: Applied scRNA-seq technology to characterize cellular heterogeneity at single-cell level in freshly isolated human femoral head tissue cells.

first: Hong-Wen

last: Deng


title: RNA sequencing of suprachiasmic nucleus (SCN) of mice with rev-erb𝛂/𝛃 knockout in GABAergic neuron

city: Houston

first: Zheng

last: Sun

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We compared differentially expressed genes (DEGs) in isolated SCN of female wild-type and GABAergic neuron rev-erb𝛂/𝛃 knockout (KO) mice at ZT12-14. 29 genes are significantly upregulated and 14 genes are statistically downregulated in SCN of KO mice. Aside from the circadian rhythm as an expected top-enriched functional entity, DEGs were enriched with cell surface proteins and associated modulators. Many of these genes are related to neurotransmission or neurological diseases.

overall_design: SCN were isolated at ZT12-14. Equal amount of RNA from 2 SCN were pooled for each sample. Three samples were analyzed for each genotype.

first: Xin

last: Li


title: Extracellular vesicle-enriched miRNA profiles across pregnancy in the MADRES cohort

status: Public on Apr 27 2021

city: Los Angeles

first: Helen

middle: Bermudez

last: Foley

email: hfoley@usc.edu, helenbfoley@gmail.com

state: CA

address: 1441 Eastlake

department: Preventive Medicine

institute: University of Southern California

summary: We describe changes in miRNA in early and late pregnancy from the MADRES cohort of primarily low-income Hispanic women based in Los Angeles, CA. miRNA derived from extracellular-vesicles (EVs) were isolated from maternal blood plasma samples collected in early and late pregnancy. In this study, we identified 64 of 130 detectable miRNA which significantly increased with the gestational age (GA), and 26 which decreased with GA. Possible fetal sex-specific associations were observed for 30 of these 90 significant miRNA. Predicted gene targets for miRNA significantly associated with GA were identified using MirDIP and were found to be enriched for Gene Ontology categories that included energetic and metabolic processes but were underrepresented in immune-related categories.  Circulating EV-associated miRNA during pregnancy are likely important for maternal-fetal communication, and may play roles in supporting and maintaining a healthy pregnancy, given the changing needs of the fetus.

overall_design:
Profiling of miRNA in early and late pregnancy from the MADRES cohort of primarily low-income Hispanic women based in Los Angeles, CA. miRNA derived from extracellular-vesicles (EVs) were isolated from maternal blood plasma samples collected in early and late pregnancy.
sample-specific positive and negative controls included in RCC files. 6 duplicated samples.

first: Caitlin

last: Howe

first: Sandrah

last: Eckel

first: Thomas

last: Chavez

first: Lili

last: Gevorkian

first: Eileen

last: Reyes

first: Bethany

last: Kapanke

first: Danilo

last: Martinez

first: Shanyan

last: Xue

first: Shakira

last: Suglia

first: Theresa

last: Bastain

first: Carmen

last: Marsit

first: Carrie

middle: V

last: Breton


title: HEPACAM2 expression is specific to small cell cancers and regulates cell-matrix interactions

status: Public on Apr 01 2021

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

summary: HEPACAM2 is a member of the immunoglobulin-like superfamily about which little is known. We initially discovered specific high expression of this gene in small cell lung cancer (SCLC) relative to non-small cell lung cancer (NSCLC), similar to several neuroendocrine genes. Further examination of RNA-seq data from the Cancer Cell Line Encyclopedia and the Cancer Genome Atlas revealed that HEPACAM2 was highly expressed only in SCLC relative to all other cancers. HEPACAM2 expression was greater in SCLC compared with matching normal tissue; and also compared with pulmonary carcinoids. Although endogenous HEPACAM2 could not be detected by western blotting SCLC cells, stable over-expression of FLAG-tagged HEPACAM2 in NSCLC cells allowed detection of a ~70 kDa protein that was reduced to ~50 kDa by tunicamycin treatment, indicating its modification by glycosylation. Biotin labelling experiments further demonstrated that HEPACAM2 was present on the cell surface. Interestingly, in vitro experiments showed that HEPACAM2 over-expressing cells demonstrated more rapid cell attachment and slower wound healing relative to parental controls. This result was supported by RNA-seq analyses that revealed significant changes in gene expression related to cell adhesion and migration pathways in HEPACAM2 over-expressing cells, however validation assays demonstrated increased, not decreased, MMP2 and MMP9 expression. Remarkably, stable CRISPR knockdown of endogenous HEPACAM2 had no significant effects by pathway analysis. Nevertheless, specific and high expression of HEPACAM2 in SCLC suggests that it plays a unique and important role in SCLC biology and whose cell surface location may provide an attractive therapeutic target for this cancer.

overall_design: RNA-seq was performed on two HEPACAM2 overexpressing cell lines and two HEPACAM2 knockdown cell lines. Three independent biological replicates were used in each group.

first: Karen

last: McColl

first: Gary

last: Wildey

first: Afshin

last: Dowlati


title: Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas [RNA-Seq]

status: Public on Mar 04 2021

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University of Freiburg Medical Center

summary: Intratumoral microglia and MΦ constitute up to 70% of the tumor mass of high-grade gliomas (HGG) with profound impact on hallmarks of malignancy such as angiogenesis and immunosuppression. The dynamics and functional states of intratumoral myeloid cells during tumor progression and the molecular mechanisms controlling them are poorly understood. Here we define homeostatic and antigen-presenting myeloid cellular states in experimental and human HGG by longitudinal single-cell RNA-sequencing and combined transcriptome and proteome profiling. During glioma progression, myeloid cells gradually shift from a homeostatic to a tumor-associated effector state. We show that these dynamics are under strict control by early changes in resident microglia and the tumor genotype: In gliomas with mutations in isocitrate dehydrogenase (IDH), a disease-defining driver mutation, differentiation of invaded myeloid cells was blocked resulting in an immature, immunosuppressive phenotype. In late-stage IDH-mutant gliomas, monocyte-derived MΦ drive a tolerogenic remodeling of the glioma microenvironment thus preventing T-cell response. We define the molecular mechanism responsible for the tumor genotype-dependent education of infiltrating MΦ to be causally related to an enzymatically enhanced tryptophan catabolism via TDO2, resulting in the production of kynurenine, an endogenous ligand of the aryl hydrocarbon receptor (AHR). TDO2 activation further induces an amino acid starvation response triggering the import of exogenous tryptophan by intratumoral MΦ via LAT1-CD98. We here provide evidence that paracrine R-2-HG and tryptophan are critically involved in the differentiation and activation of monocyte-derived MΦ and that the previously observed altered amino acid metabolism in IDHmut gliomas is also responsible for shaping an immunosuppressive tumor microenvironment through maintenance of this complex metabolic axis. We further show that this regulatory metabolic network is particularly active in infiltrating MΦ because of their distinct expression profile that constitutes an immune subset-specific metabolic vulnerability. Consequently, the immunosuppressive phenotype in IDH-mutant glioma models was reversed by pharmacological inhibition of LAT1-CD98 or AHR. Thus, we provide evidence for a tumor genotype-dependent, dynamic network of resident and recruited intratumoral myeloid cells that shape the immune microenvironment of IDH-mutant HGG through pleiotropic interaction with the tumor metabolome and identify tryptophan metabolism as a viable therapeutic target for the immunotherapy of IDH-mutant tumors.

overall_design: GL261 glioma cell lines were episomally expressing wildtype or R132H-mutated Isocitrate Dehydrogenase 1. RNA expression was compared between both conditions.

first: Mirco

last: Friedrich

first: Lukas

last: Bunse

first: Marco

last: Prinz

first: Michael

last: Platten


title: Dissecting OCT4 defines the role of nucleosome binding in reprogramming

first: Abdenour

last: Soufi

summary: The aim of this study is to dissect the transcription factor OCT4 and reveal which parts of the protein are essential for interaction with nucleosomes and access to closed chromatin. We revealed that the DNA-binding domain mediates the interaction of OCT4 with nucleosomes. Remarkably, nucleosome-binding can be uncoupled from DNA-binding, diminishing the ability of OCT4 to access to closed chromatin, thus losing the pioneer function. We show that the pioneer function of OCT4 is not only essential during reprogramming differentiated cells to pluripotency but also during pluripotency maintenance of embryonic stem cells. Overall, this study shows how pioneer transcription factors interact with nucleosomes to engage the genome and control cellular identity, highlighting that nucleosomes are not always barriers to genome accessibility .

overall_design: ChIP-seq of OCT4 WT and mutants during early reprogramming


title: Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Dissecting OCT4 defines the role of nucleosome binding in pluripotency

status: Public on Jun 23 2021


title: whole-transcriptome analysis of Granulosa Cells Between the Healthy and Atresia Follicles in Chinese Buffalo

status: Public on Mar 16 2021

city: Nanning

first: Yu

last: Pan

state: Guangxi

address: No. 100, Daxuedong Road, Xixiangtang District, Nanning, Guangxi

department: College of Animal Science and Technology

institute: Guangxi University

summary: GCs were collected from HFs and AFs , to use second-generation high-throughput sequencing for whole-transcriptome analysis, respectively. In total, 1861 and 1075 mRNAs, 159 and 24 miRNAs, 123 and 100 lncRNAs, and 58 and 54 circRNAs were identified to be differentially expressed (DE) in up-regulated and down-regulated. Enrichment of functions and signaling pathways of the DEgenes showed that most of DEmRNAs and targets of DEmiRNAs, DElncRNAs and DEcricRNAs were annotated to the categories of ‘PI3K-Akt signaling pathway’, ‘ECM-receptor interaction’, ‘Focal adhesion’, ‘mTOR signaling pathway ’ ‘TGF-beta signaling pathway’, ‘Rap1 signaling pathway’, and ‘Estrogen signaling pathway’. The ceRNA (competing endogenous RNA) network was constructed based on ceRNA theory further revealed regulatory roles of these DERNAs in granulosa cells of buffalo atretic follicles. A large number of mRNAs, lncRNAs, circRNAs, and miRNAs in buffalo granulosa were altered in healthy and atretic follicles, which may play crucial roles in atretic of buffalo follicles through the ceRNA regulatory network.

overall_design: In total, 6 samples include: HF groups(n=3) and AF groups(n=3)

first: Deshun

last: Shi

first: Yanfei

last: Deng


title: Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas [CEL-Seq2]

summary: Intratumoral microglia and MΦ constitute up to 70% of the tumor mass of high-grade gliomas (HGG) with profound impact on hallmarks of malignancy such as angiogenesis and immunosuppression. The dynamics and functional states of intratumoral myeloid cells during tumor progression and the molecular mechanisms controlling them are poorly understood. Here we define homeostatic and antigen-presenting myeloid cellular states in experimental and human HGG by longitudinal single-cell RNA-sequencing and combined transcriptome and proteome profiling, respectively. During glioma progression, myeloid cells gradually shift from a homeostatic to a tumor-associated effector state. We show that these dynamics are under strict control by early changes in resident microglia and the tumor genotype: In gliomas with mutations in isocitrate dehydrogenase (IDH), a disease-defining driver mutation, differentiation of invaded myeloid cells was blocked resulting in an immature, immunosuppressive phenotype. In late-stage IDH-mutant gliomas, monocyte-derived MΦ drive a tolerogenic remodeling of the glioma microenvironment thus preventing T-cell response. We define the molecular mechanism responsible for blocking functional differentiation in IDH-mutant gliomas to be causally related to enhanced metabolization of tryptophan to kynurenine, an endogenous ligand of the aryl hydrocarbon receptor (AHR), leading to a time-dependent uptake of extracellular tryptophan via LAT1-CD98 by intratumoral myeloid cells. Consequently, the immunosuppressive phenotype in IDH-mutant glioma models was reversed by pharmacologic inhibition of LAT1-CD98 or AHR. Thus, we provide evidence for a tumor genotype-dependent dynamic network of resident and recruited intratumoral myeloid cells shaping the immune microenvironment of IDH-mutant HGG and identify tryptophan metabolism as a viable therapeutic target for the immunotherapy of IDH-mutant tumors.

overall_design: CD45+ Lin- cells were FACS sorted from cell suspensions of control patients or cases wirh IDHwt or IDHmut glioblastoma multiforme. CEL-Seq2 protocol was used for single cell sequencing (Hashimshony et al. 2016).


title: The microglial transcriptome of a novel murine model of Alzheimer's Disease: FACS-isolated microglia from heterozygous and homozygous App-SAA mice and WT littermate controls.

status: Public on Jan 20 2021

city: South San Francisco

first: Thomas

last: Sandmann

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

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: We created a novel murine model of Alzheimer's Disease using a knock-in strategy to humanize the sequence of the murine App gene and introduced three familial AD (FAD) mutations, Swedish (Swedish  (KM670/671NL), Arctic (E693G)) and Austrian (T712I).  We characterized the effects of these genetic modifications on the transcriptome of FACS-isolated microglia from 8-month-old App-SAA mice. Numerous genes were differentially expressed between cells from homozygous App-SAA animals compared to those from WT littermates. For example, we observed up-regulation of Disease-associated microglia (DAM) genes. In contrast, the transcriptome of microglia from heterozygous App-SAA animals broadly resembles that of their WT counterparts.

overall_design: This experiments examines FACS-isolated microglia from 18 mice from three genetic backgrounds (N = 6 WT, N =6 heterozygous App-SAA and N = 6 homozygous App-SAA animals). Microglia were isolated from the brain (cortex & hippocampus) of each animal using FACS and gene expression changes were analyzed using 3-tag RNA-seq. From each mouse, two (technical) replicate pools of microglia were collected and processed into separate libraries (library_replicate).

first: Dan

last: Xia

first: Steve

last: Lianoglou

first: Chia-Ching

last: Lin

first: Elliot

last: Thomsen

first: Connie

last: Ha

first: Pascal

last: Sanchez


title: Single Cell Profiling Identifies the Histone Demethylase, JMJD3, Modulates Macrophage Phenotype in Abdominal Aortic Aneurysm Formation

status: Public on Feb 13 2021

city: Ann Arbor

first: Lam

last: Tsoi

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: Abdominal aortic aneurysm (AAA) is a life-threatening disease characterized by an inflammatory macrophage phenotype that contributes to pathological vascular remodeling.  Although the mechanisms regulating macrophage-mediated inflammation during AAA development remain undefined, accumulating evidence suggests that epigenetic alterations play a critical role.  Here using single cell RNA-sequencing techniques, we identify that the histone demethylase JMJD3  is elevated in human AAA monocytes/macrophages, resulting in the upregulation of cellular activation and a proinflammatory immune response.

overall_design: scRNA-seq for AAA

first: Frank

last: Davis

middle: C

first: Johann

last: Gudjonsson

first: Katherine

middle: A

last: Gallagher


title: Gene expression profiling of murine BCR-ABL+ CDK6-wt and CDK6-KO cells

status: Public on Nov 24 2020

city: Vienna

first: Markus

last: Zojer

address: Josef-Baumanngasse

department: Institute for Pharmakology and Toxokology

institute: University of Veterinary Medicine

summary: Dertermination of chromatin accessibility in murine BCR-ABL+ CDK6-wt and  CDK6-KO cells

overall_design: RNA-seq:Murine (C57Bl/6J) CDK6wt and CDK6−/− cell lines obtained from single  cell bone marrow suspension were retrovirally transduced with a  pMSCV-BCR-ABLp185-IRES-GFP vector. To test for differences in  transcriptional gene expression RNA from CDK6wt and CDK6−/− cell lines  was analysed by RNA-seq. Thus, total RNA was prepared using the RNeasy  Kit (Qiagen) and processed for sequencing using the TruSeq RNA Sample  Preparation Kit (Illumina Inc, San Diego, CA, USA). Sequencing was  performed using the Illumina HiSeq3000/4000 platform. RNA-seq  experiments were performed in biological triplicates. ATAC-seq: Murine (C57Bl/6J) CDK6wt and CDK6−/− cell lines obtained from single  cell bone marrow suspension were retrovirally transduced with a  pMSCV-BCR-ABLp185-IRES-GFP vector. Chromatin accessibility was assessed  by ATAC-seq. Briefly, cells were washed once in 50 μl PBS and  resuspended in transposase reaction mix (12.5 μl 2 × TD buffer, 2 μl  transposase (Illumina), 10.5 μl nuclease-free water and 0.01% NP-40).  Tagmentation was performed for 30 min at 37 °C. Following library  amplification, fragments larger than 1,200 bp were excluded by SPRI size  selection. Libraries were amplified using custom Nextera primers and  sequenced using the Illumina HiSeq3000/4000 platform.

first: Gerwin

last: Heller

first: Karoline

last: Kollmann

first: Sofie

last: Nebenfuehr

first: Veronika

last: Sexl


title: Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas [scRNA-Seq]

first: Roman

last: Sankowski

overall_design: GL261 glioma cell lines episomally expressing wildtype or R132H-mutated Isocitrate Dehydrogenase 1 were injected intracerebrally into C57Bl6/J mice. After 7 or 28 days mice were sacrificed and cells were FACS-sorted on CD45. Single-cell RNA-Seq libraries were prepared using the 10x Single Cell 3' v2 Kit.

first: Mirco

last: Friedrich

first: Lukas

last: Bunse

first: Marco

last: Prinz

first: Michael

last: Platten


title: A novel P2X2-dependent purinergic mechanism of enteric gliosis in intestinal inflammation

status: Public on Nov 15 2020

city: Bonn

first: Reiner

last: Schneider

address: Venusberg-Campus 1

department: Surgery Department

institute: University Clinics Bonn


title: A novel CULLIN3-KBTBD4 ligase complex controls the epigenetic marks that mediate human hematopoietic stem cell self-renewal

status: Public on Dec 08 2020

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer


summary: surgery samples of patients at early and late timepoints of a pancreatectomy

overall_design: human surgical specimens collected during a pancreaticoduodenectomy at an early and a late time point of surgery. Samples were provided on ice directly from the operation room and muscularis externa (ME) was separated from the lamina propria mucosae

first: Tim

last: Glowka

first: Sven

last: Wehner


title: A phase separation mechanism underlies development of cancer and aberrant organization of three-dimensional chromatin structure

status: Public on Apr 19 2021

city: Chapel Hill

first: Gang

middle: Greg

last: Wang

state: NC

address: 450 West Drive

department: Dept of Biochemistry and Biophysics

institute: UNC Lineberger Comprehensive Cancer Center


title: UM171 effect in AML1 cells in KBTBD4 null context

status: Public on Mar 09 2021

summary: UM171 and TCP1 effect in AML1 cellsengeneered to express low levels of KBTBD4 and/or RCOR1

overall_design: OCI-AML1 cell line engeneered to expressed either sgRNA AAVS1 (CT) or sgRNA against KBTBD4  and either shRNA luciferase or shRNA against RCOR1 were exposed to DMSO, UM171, UM134 or TCP1 for different time points. RNA were extracted and sequences were obtained with an Illumina NovaSeq 6000 sequencer.

first: Jalila

last: Chagraoui


title: Purinergic signaling in enteric gliosis [Dataset EV1]

summary: Enteric Glia treated with exATP

overall_design: Primary cells treated with exATP to investigate the changes in gene expression.


title: A phase separation mechanism underscores development of cancer and aberrant organization of three-dimensional chromatin structure [Hi-C]

first: Douglas

last: Phanstiel

address: 104 Manning Dr (Thurston Bowles Building), Rm 4019

institute: University of North Carolina at Chapel Hill

summary: Development of cancer is intimately associated with genetic abnormalities that target proteins with intrinsically disordered regions (IDRs).  In human hematological malignancies, recurrent chromosomal translocation of nucleoporin (NUP98 or NUP214) generates an aberrant chimera that invariably retains nucleoporin’s IDR, tandemly dispersed phenylalanine-and-glycine (FG) repeats. However, it remains largely elusive how unstructured IDRs contribute to oncogenesis. We here show that IDR or FG repeats harbored within NUP98-HOXA9, a HOX transcription factor (TF) chimera recurrently detected in acute leukemia patients, is essential for establishing nuclear liquid-liquid phase separation (LLPS) puncta and for inducing leukemic transformation of primary hematopoietic cells in vitro and in vivo. Strikingly, LLPS of NUP98-HOXA9 not only promotes chromatin occupancy of chimera TF oncoproteins but is also required for formation of a broad, ‘super-enhancer’-like binding pattern, typically seen at a battery of leukemia-related loci exemplified by HOX, MEIS and PBX genes, potentiating their transcriptional activation. An artificial HOX chimera, created by replacing NUP98’s FG repeats with an unrelated LLPS-forming IDR of FUS, had similar enhancement effects on chimera’s chromatin binding and target gene activation. Via Hi-C mapping, we further demonstrated that the phase-separated NUP98-HOXA9 protein assembly is able to induce de novo formation of CTCF-independent chromatin looping enriched at leukemic oncogenes. Together, this report describes a proof-of-principle example wherein cancer acquires mutation to establish multi-molecule assemblies of oncogenic TFs via a phase separation mechanism, which simultaneously enhances their chromatin targeting and induces organization of aberrant three-dimensional chromatin structure during tumorous transformation. As a range of LLPS-competent molecules are implicated in various human cancers, this mechanism can potentially be generalized to many malignant and diseased settings.

overall_design: Constructs of a NUP98-HOXA9 fusion with a wild type intrinsically disordered region (NUP_IDR_WT/A9) and a NUP98-HOXA9 fusion with a phenylalanine to serine (F to S) mutant intrinsically disordered region (NUP_IDR_FS/A9) were retrovirally transduced into the HEK293FT cell line to produce stable NUP_IDR_WT/A9 and NUP_IDR_FS/A9 cell lines. In situ Hi-C was performed as described by Rao et al. 2014 (PMID: 25497547) on each cell line in biological duplicate. To retain library complexity, two Hi-C libraries were generated for each biological replicate (2 cell lines x 2 biological replicates x 2 libraries = 8 libraries total).

first: JeongHyun

last: Ahn

first: Eric

last: Davis

first: Hidetaka

last: Uryu

first: Timothy

last: Daugird

first: Ivana

last: Quiroga

first: Jie

last: Li

first: Yi-Hsuan

last: Tsai

first: Joel

last: Parker

first: Deyou

last: Zheng

first: Wesley

last: Legant


title: Estrogen-dependent gene expression in skeletal muscle

status: Public on Nov 05 2020

city: Berlin

first: Georgios

last: Kararigas

address: Hessische Str. 3-4

institute: Charite University Hospital

summary:
Menopause - when estrogen (E2) levels are decreased - is associated with a loss of skeletal muscle mass and strength.
We performed genome-wide expression profiling to identify the underlying mechanisms.

overall_design: Female mice were ovariectomized and treated with E2 (pellets releasing 0.18 mg of E2 over 60 days) or placebo (Plac = control).


title: Chronic IL-1 exposure drives LNCaP cells to evolve androgen and AR independence

status: Public on Nov 01 2020

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

summary: Chronic IL-1 treatment selects for cells that are less sensitive to cytotoxicity associated with serum starvation, loss of AR expression, and inflammatory cytokine signaling.

overall_design: LNCaP cells were treated with 0.5 ng/ml IL-1 alpha (in DMEM + 10% FBS) for 3 months or treated with 0.5 ng/ml IL-1 beta (in DMEM + 10% FBS) for 4 months. IL-1 is cytotoxic, so the viable, proliferating colonies that emerged after 3 months in IL-1a or 4 months in IL-1b were expanded to generate the IL-1a subline (LNas1) and the IL-1b subline (LNbs1).  LNCaP, LNas1, and LNbs1 cells were plated and cultured in DMEM + 10% FBS for 7 days and RNA isolated for RNA sequencing.

first: Haley

last: Dahl

first: Mohammed

last: Kanchwala

first: Shayna

middle: E

last: Thomas-Jardin

first: Amrit

last: Sandhu

first: Preethi

last: Kanumuri

first: Afshan

last: Nawas

first: Chao

last: Xing

first: Chenchu

last: Lin

first: Daniel

last: Frigo


title: Purinergic signaling in enteric gliosis [Dataset EV2]

first: Reiner

last: Schneider

summary: Postoperative ileus mouse model

overall_design: Bl6 mice undergoing intestinal manipulation and are sacrificed after 3 and 24h

first: Sven

last: Wehner


title: Sex-specific Schistosomiasis induced metabolic modulation of the myeloid lineage

city: Salt Lake City

first: Keke

middle: Celeste

last: Fairfax

state: UT

address: 15 N Medical Drive East

department: Pathology

institute: University of Utah

summary: Despite strong evidence that prior helminth infection exerts a protective effect against the development of metabolic disease, a major gap exists in understanding the mechanism(s) underlying this protection. We previously found that Schistosoma mansoni infection induces dramatic transcriptional alterations in hepatic macrophage metabolism, and that this correlates with protection from high fat diet (HFD) induced atherosclerosis and glucose intolerance in male ApoE-/- mice. We sought in the present study to determine the broad effects of S. mansoni exposure on the myeloid lineage using the ApoE-/- HFD model. We uncovered that macrophages derived from the bone marrow of S. mansoni infected male mice have dramatically increased oxygen consumption and mitochondrial mass compared to those from uninfected mice. This shift is accompanied by increased glucose shuttling into TCA cycle intermediates and decreased cholesterol esters. When we examined the role of biological sex in schistosome induced modulation.  We found that S. mansoni infection does not reliably protect ApoE-/- female mice from HFD induced weight gain or glucose intolerance. The sex-dependent effect of infection extends to myeloid precursors, where the metabolic phenotype of bone marrow derived macrophages from infected females are the opposite of those from infected males. Overall, these data present the first evidence that S. mansoni systemically modulates the myeloid compartment in a sex-dependent manner.

overall_design: mRNAseq of BMDM from 4 uninfected male ApoE-/- mice on HFD, 5 schistosoma mansoni infected male ApoE-/- mice on HFD, 4 uninfected female ApoE-/- mice on HFD, 5 Schistosoma mansoni infected. All samples are from 10 week post infection/mock infection ApoE-/- mice on HFD

first: Diana

last: Cortes-Selva


title: The Mechanistic Differences/Similarities of Azacitidine and Decitabine in Models of Mature T-cell Lymphoma

status: Public on Oct 24 2020

city: New York

first: Owen

last: O"Connor

address: 51 West 51st Street

department: enter for Lymphoid Malignancies

institute: Columbia University Medical Center

summary: We perform expression analysis on a panel of three T-cell lymphoma lines exposed to 5-azacytidine and decitabine as single agent.

overall_design: Gene expression profiles of cells exposed and not exposed to 5-azacytidine and decitabine.

last: O'Connor

first: Luigi

last: Scotto


title: The effect of decitabine (DAC) treatment on glioma cells

status: Public on Oct 01 2020

city: Heidelberg

first: Jongwhi

last: Park

address: INF 460

institute: Heidelberg university hospital

summary: The objective of this study is to identify molecular determinants of DAC response in gliomas

overall_design: Two biological replicates were analyzed for each of 6 conditions (four cell lines; DMSO or DAC treatment per each cell line)

first: Sevin

last: Turcan


title: Creation and validation of models to predict response to chemotherapy before treatment in serous ovarian cancer

status: Public on Feb 10 2021

city: Iowa City

first: Jesus

last: Gonzalez Bosquet

state: IA

address: 200 Hawkins Dr

institute: University of Iowa

summary: This is a retrospective case-control study that integrates comprehensive clinical and genomic data from 88 patients with HGSC from a single institution. Responders were those patients with a progression-free survival of at least 6 months after treatment. Only patients with complete clinical information and frozen specimen at surgery were included. Gene, miRNA, exon, and long non-coding RNA (lncRNA) expression, gene copy number, somatic mutations, and fusion-gene determination were extracted from RNA-sequencing data. Initial models included only one variable. Variables were then combined to create complex models. Validation of all models was performed using TCGA HGSC database. By integrating clinical and genomic variables, we achieved prediction performances of over 95% in AUC. Most performances in the validation set did not differ from the training set. Models with DNA methylation or lncRNA underperformed in the validation set.

overall_design: A retrospective case-control study that integrates clinical and biological data to build prediction models of clinical outcomes.

first: Eric

middle: J

last: Devor

last: Gonzalez-Bosquet


title: Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [RNAseq_DAC_celllines]

status: Public on Sep 24 2020

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

summary: Cancer cells display DNA hypermethylation at specific CpG islands in comparison to their normal healthy counterparts, but the mechanism that drives this so-called CpG island methylator phenotype (CIMP) remains poorly understood. Here, we show that CpG island methylation in human T-cell acute lymphoblastic leukemia (T-ALL) mainly occurs at promoters of PRC2 target genes that are not expressed in normal or malignant T-cells and which display a reciprocal association with H3K27me3 binding. In addition, we found that this aberrant methylation profile shows a strong correlation with the epigenetic age of the leukemic T cells and elucidate that a similar CpG island methylation signature is gradually established in aging pre-leukemic thymocytes from CD2-Lmo2 transgenic mice. Finally, we unexpectedly uncover that this age-related CpG island hypermethylation signature is completely resistant to the FDA-approved hypomethylating agent Decitabine. Altogether, our work demonstrates that DNA methylation reflects the epigenetic history of leukemic T cells and suggests that methylation-based subtypes of human T-ALL have followed a different trajectory towards T-cell transformation, possibly mediated by differences in the self-renewing capacity of the putative T-ALL cell-of-origin. Given that the concept of preleukemic thymocytes has only been reported in T-ALL mouse models so far, we here provide, for the first time, conceptual evidence that a pre-leukemic phase might also be involved in the pathogenesis of the human disease.

overall_design: RNAseq of T-ALL cell lines treated with Decitabine or vehicle control.

first: Morgan

last: Thénoz

first: Pieter

last: Van Vlierberghe


title: Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [EPICarray_PDX]

type: Methylation profiling by genome tiling array

overall_design: Bisulphite converted DNA of T-ALL blasts isolated from patient derived xenografts was hybridized to the Illumina Infinium HumanMethylation850 BeadChip


title: Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [RNAseq_DACPDX]

overall_design: RNAseq of T-ALL patient derived xenografts treated with Decitabine or vehicle control


title: Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [RRBS_mouseTALL]

type: Methylation profiling by high throughput sequencing

overall_design: RRBS of (pre)leukemic cells from the Lck-Cretg/+ Ptenfl/fl and CD2-Lmo2tg/+ mouse T-ALL models


title: Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [EPICarray_109TALL]

overall_design: Bisulphite converted DNA of 109 T-ALL and duplicates of ten subsets of developing thymocytes were hybridized to the Illumina Infinium HumanMethylation850 BeadChip


title: Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [ChIPmentation_TALL]

overall_design: ChIPmentation for histone marks on 6 T-ALL samples with input controls


title: RNA-seq in mouse duodenum

status: Public on Sep 01 2020

first: Gilles

last: Laverny

address: 1 rue Laurent fries

institute: IGBMC

summary: Characterization of duodenal gene expression after vitamin D analogs administration

overall_design: 10 week old male C57Bl6 mice were treated per os for 6h.

last: Metzger

first: Anna-Isavella

last: Rerra

first: Daniela

last: Rovito


title: Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [EPICseq_14TALL]

overall_design: DNA methylation profiling by EPICseq of 14 T-ALL samples and biological duplicates of two thymocyte subsets


title: A novel APP knock-in mouse model reveals profound metabolic perturbations in phagocytic microglia

first: Thomas

last: Sandmann

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

overall_design: Refer to individual Series


title: RNA-Seq Analysis of mouse lung cancer cell lines derived from KP mice and Reprogrammed somatic cells

status: Public on Sep 18 2020

city: London

first: Yaohe

last: Wang

address: John Vane Science Centre,  Charterhouse Square

department: Centre for Molecular Oncology

institute: Barts Cancer Institute

summary: We report the gene expression profile of three murine lung cancer cell lines, and also comparing the similarities of gene expression between KP mice-derived tumor cells and Regrogrammed somatic cells-derived tumor cells.

overall_design: The whole RNA deep sequencing was performed for the three murine lung cancer cell lines. The gene experssion profile was bioinformatically analysed.

first: Zhe

last: Zhang

first: Zhizhong


title: circRNAs at 5 time points during retinal development of mouse

city: wenzhou

first: xue

middle: jiao

last: chen

address: xueyuan road

institute: wenzhou medical university

summary: ciRNAs during retinal development

overall_design: circRNAs expression at E18.5, P1, P7, P14 and P30

first: Xue-Jiao

last: Chen

first: Heng-Qiang

last: Zhao


title: Neuronal diversity and convergence in a visual system developmental atlas (scRNA-seq)

status: Public on Jul 16 2020

city: Kansas City

first: Mehmet Neset

last: Ozel

state: MO

institute: Stowers Institute for Medical Research

summary: Deciphering how neuronal diversity is established and maintained requires a detailed knowledge of neuronal gene expression throughout development. In contrast to mammalian brains, the large neuronal diversity of the Drosophila optic lobes and its connectome are almost completely characterized. However, a molecular characterization of this diversity, particularly during development, has been lacking. We present novel insights into brain development through a nearly exhaustive description of the transcriptomic diversity of the optic lobes. We acquired the transcriptome of 275,000 single-cells at adult and five pupal stages, and developed a machine learning framework to assign them to almost 200 cell-types at all timepoints. We discovered two large neuronal populations that wrap neuropils during development but die just before adulthood, as well as neuronal subtypes that partition dorsal and ventral visual circuits by differential Wnt signaling throughout development. Moreover, we showed that neurons of the same type but produced days apart synchronize their transcriptomes shortly after being produced. We also resolved during synaptogenesis neuronal subtypes that converge to indistinguishable transcriptomic profiles in adults while greatly differing in morphology and connectivity. Our datasets almost completely account for the known neuronal diversity of the optic lobes and serve as a paradigm to understand brain development across species.

overall_design: 38 scRNA-Seq libraries (about 7000 cells each) were generated from adult and pupal (at 5 stages) Drosophila optic lobes using 10X Genomics Chromium™ Single Cell 3’ v2 protocol.

first: Mehmet-Neset

first: Felix

last: Simon


title: scRNAseq of PBMCs from idiopathic multicentric Castleman Disease (iMCD) flare and remission

status: Public on May 20 2020

city: Philadelphia

first: David

last: Fajgenbaum

state: PA

address: 3620 Hamilton Walk

institute: University of Pennsylvania

summary: We performed scRNAseq of PBMCs from three idiopathic multicentric Castleman Disease (iMCD) patients with paired flare and remission samples

overall_design: 6 PBMC samples were analyzed, 3 from flare and three from remission, with two technical replicates. Cryopreserved PBMCs were thawed and immediately loaded on to a GemCode instrument (10X Genomics) to produce single-cell bar-coded droplets using 10X Single Cell 3’ v2 chemistry. Libraries generated were sequenced across at least one lane on the Illumina HiSeq2500 instrument with the HiSeq Rapid SBS kit.

first: Charlly

last: Kao

first: Hakon

last: Hakonarson


title: Expression data from patients with different stages of clear cell renal cell carcinoma

status: Public on May 13 2020

city: Kraków

first: Judyta

last: Górka

address: Gronostajowa 7

department: Department of General Biochemistry

country: Poland

institute: Jagiellonian University

summary: Clear cell renal cell carcinoma is the most common type among kidney cancers, accounting for 80% of all kidney cancer cases and over 30% of patients have metastases at the time disease is diagnosed. The process od epithelial-mesenchymal transition is crucial for the development and progression of cancer, and here we wanted to check the expression of genes on different stages of tumor progression, and find which of them changes significantly with increased grade.

overall_design: Tumor samples from patients were divided into four grades by hospital pathologists. I- grade refers to the first stage of disease, II- grade to second, III-grade to third and IV-grade to fourth. Each patients received unrepetable number. RNA extraction were performed using Eurx kit, and then microarrays were performed using Affymetrix GeneChip WT PLUS Reagent Kit.

first: K

last: Miekus

first: P

last: Marona

first: J

last: Gorka


title: Expression data from livers of wild-type and HLJ1 knockout mice.

status: Public on Apr 08 2020

city: Taipei

first: Kang-Yi

last: Su

address: No.1, Jen-Ai Road

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
HLJ1, also known as DNAJB4, belongs to this family and was first cloned from human liver cDNA in 1998. It is also a tumor suppressor gene and has been shown to be inversely associated with tumor invasive ability in the previous research. In addition, HLJ1 was shown to modulate migration of cancer via interaction with the cell cytoskeleton, especially when under acidic stress. It can significantly reduce cell viability in neuro-progenitor cells. The regulatory mechanism revealed that HLJ1 can be transcriptionally upregulated through enhancer activator protein-1 (AP-1) binding to promoter Yin Yang-1 (YY-1) and  co-activator p300.
We used microarrays to detail the whole-genome transcriptome of gene expression underlying HLJ1 regulation or mediation and identified significant regulatory network involved in physioligical functions.

overall_design: We utilized extracted total RNA from livers of wild-type mice and HLJ1 knockout (by the gene targeting strategy in mouse embryonic stem cells) mice as starting material for microarray assay. Three independent mice from wild-type and HLJ1 knockout mice were used in experiments as biological repeats.


title: Bronchoalveolar lavage of healthy human adults

status: Public on Oct 21 2020

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

summary: Rationale: Airspace macrophages are the most abundant cell in airspaces and are viewed as a homogeneous population during health. Single cell RNA sequencing allows for examination of transcriptional heterogeneity between cells and between individuals. Understanding the conserved repertoire of airspace leukocytes during health is essential to understanding cellular programing during disease.  Objective: We sought to determine the transcriptional heterogeneity of human bronchoalveolar lavage cells in healthy adults. Methods: Ten healthy subjects underwent bronchoscopy. Cells obtained from lavage fluid were subjected to single cell RNA sequencing. Unique cell populations and putative functions were identified. Transcriptional profiles were compared across individuals. Measurements and Main Results:  Based on transcriptional profiling we identify highly conserved macrophage, monocyte-like, lymphocyte, dendritic cell, and cycling cell populations. We define two unique subgroups of resident airspace macrophages - one defined by a pro-inflammatory profile and one by metallothionein gene expression. We identify distinct subsets of monocyte-like cells and directly compared them to peripheral blood mononuclear cells. Finally, we compare global macrophage and monocyte programing between male and female subjects. Conclusions: Healthy human airspaces contain multiple populations of leukocytes that are highly conserved between individuals and between the sexes. Resident macrophages comprise the largest population and include novel subsets defined by inflammatory and metal-binding gene signatures. Monocyte-like cells within the airspaces are transcriptionally distinct from circulating blood cells and include a rare population defined by expression of cell-matrix interaction genes. This study is the first to define airspace immune cell heterogeneity and identifies three previously unrecognized myeloid cell subsets.

overall_design: Fifteen  bronchoalveolar lavage samples from ten healthy adults were included.

first: Kara

last: Mould

middle: M

first: Shannon

last: Hott

first: Alexandra

middle: L

last: McCubbrey

first: Christine

last: Griesmer

first: Peter

last: Henson

first: William

last: Janssen


title: Single cell RNA and TCR sequencing of tumor-infiltrating lymphocytes from human melanoma

status: Public on Apr 07 2020

city: San Francisco

first: Kelly

middle: Maria

last: Mahuron

address: 513 Parnassus Avenue, HSW 1201B

institute: UCSF

summary: The aim of the study is to analyze and compare the transcriptional profiles and clonotypes at a single cell level of tumor-infiltrating lymphocytes from human melanoma.

overall_design: Lymphocytes from 8 samples of PBMCs or tumor-infiltrating lymphocytes from patients with metastatic melanoma were sort-purified and underwent single cell RNA-sequencing with or without single cell TCR sequencing.

first: Joshua

last: Moreau

first: Michael

middle: D

last: Rosenblum


title: Whole transcriptome profiling of Wildtype and EXT1-/- human embryonic stem cells by RNA-Seq

status: Public on Jan 22 2020

city: Cambridge

first: Sayaka

last: Masuko

state: MA

address: 77 Massachusetts Ave.

department: Chemistry

institute: Massachusetts Institute of Technology

summary:
Purpose: The goals of this study are to identify whole transcriptomic changes between undifferentiated wildtype (H9 cell line) and undifferentiated EXT1-/- human embryonic stem cells using RNA-seq.
Total RNA extraction was performed on low passage number wildtype and EXT1-/- human embryonic stem cells that were cultured in E8 media in quadruplicate. Libraries were prepared using TruSeq Stranded Total RNA kit (Illumina). First-strand cDNA was generated using random primers, followed by second-strand cDNA synthesis. Adapter-ligated PCR-enriched products were used to create cDNA libraries. 3' ends were adenylated and adapter ligated, followed by purification and enrichment with PCR to create cDNA libraries, which were sequenced using the Illumina platform. Single-end reads were mapped to the human genome using STAR. Mapped single-end reads were counted using RSEM.
Results: We identified 1986 genes that were significantly differentially expressed [FDR (false discovery rate)-adjusted p < 0.05] between the two cell types. Of those genes, there were 102 upregulated and 195 downregulated transcripts that showed more than a two-fold change in expression. The top 20 upregulated and downregulated genes include those involved in neural development (e.g., POU3F4, ISLR2, FGF9), and transcription factors involved in early development (e.g., GRHL3, GBX2, ONECUT1). We evaluated the global changes in gene expression influenced by EXT1 deficiency compared with wildtype cells using Ingenuity Pathway Analysis. Gene ontology (GO) analysis of transcripts that significantly differ by more than two-fold revealed that the loss of EXT1 led to a significant enrichment for biological processes related to cell-to-cell signaling, development, and cellular functions.
Conclusions: Our findings suggest that genes involved in human embryonic stem cell differentiation are differentially regulated in EXT1-/- cells and that therefore the capacity of the cells to differentiate may be compromised. Taken together, RNA-seq revealed key differences between wildtype and EXT1-/- cells at the transcript level.

overall_design: Quadruplicate samples each of wildtype (H9 human embryonic stem cells) and EXT1-/- cells, with three technical replicates for each sample.

first: Laura

last: Kiessling


title: Octameric nucleosomes are present within the inner kinetochore of human centromeres

status: Public on Apr 02 2020

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

summary: The centromere is a vital locus on each chromosome which seeds the kinetochore, allowing for a physical connection between the chromosome and the mitotic spindle. At the heart of the centromere is the centromere-specific histone H3 variant CENP-A/CENH3. Throughout the cell cycle the constitutive centromere associated network is bound to CENP-A chromatin, but how this protein network modifies CENP-A nucleosome dynamics in vivo is unknown. Here, using a combination of biophysical and biochemical analyses we provide evidence for the existence of two populations of structurally distinct CENP-A nucleosomes that co-exist at human centromeres.  These two populations display unique sedimentation patterns in a glycerol gradient, and CENP-A nucleosomes that are physically associated with the inner kinetochore appear stabilized in an octameric conformation, with restricted access to the nucleosomal DNA by DNase I. In contrast, the bulk population of CENP-A nucleosomes have diminished heights and weakened DNA interactions. These data suggest that, in vivo, a reserve pool of immature CENP-A nucleosomes exist which wrap DNA loosely, whereas an active inner kinetochore complex associates with stabilized CENP-A nucleosomes. Our data have implications for a function for CENP-A that may be independent of its role in mitotis.

overall_design: ChIP-seq

first: Daniel

last: Melters

first: Tatini

last: Rakshit

first: Sergei

last: Grigoryev

first: Yamini

last: Dalal


title: RNAseq of livers of mice fed high fat high sugar diet and either untreated or treated with curcumin liposomes or calcitriol liposomes

city: Brisbane

first: Muralidhara Rao

last: Maradana

state: Queensland

address: 37 Kent St, Woolloongabba

institute: The University of Queensland

summary: Non-alcoholic fatty liver disease (NAFLD) is a common complication of obesity, where insulin resistance and hepatocyte fat deposition may progress to steatohepatitis (NASH) and fibrosis/ cirrhosis. NASH has no approved treatment. Consequent upon hepatic fat deposition, NF-κB activation in hepatic myeloid cells mediates inflammation and NASH progression. We delivered micro-doses of liposome-encapsulated lipophilic NF-κB inhibitors, curcumin or 1,25-dihydroxy-vitamin D3 (calcitriol), to the pro-fibrogenic inflammatory liver macrophages and dendritic cells (DCs) in diet-induced NASH. After i.v. administration, liver was the primary organ targeted. MHC class-II+ hepatic DCs taking up liposomes in mice and human were F4/80+ and CD14+ respectively, were lipid-laden and expressed pro-inflammatory genes. Curcumin or calcitriol liposomes suppressed hepatic inflammation, fibrosis and fat accumulation, and reduced insulin resistance associated with suppression of immune activation, cell cycle and collagen deposition pathways in vivo. Thus, hepatic inflammatory DCs passively targeted with liposomes encapsulating lipophilic NF-κB inhibitors are beneficial in NASH.

overall_design: Female C57BL/6 mice were fed with high fat high sugar diet for 14 weeks to induce nonalcoholic steatohepatitis. Groups of mice were intravenously injected with either curcumin liposomes or calcitriol liposomes at week 12 and week 13. 2 weeks post initial treatment transcriptome profiling was determined on whole livers.

first: Muralidhara

first: Brendan

last: O'Sullivan

first: Ranjeny

last: Thomas


title: NAFLD model


title: Whole blood transcriptome analysis of Septic shock and Cardiogenic shock patients over one week of ICU stay

status: Public on Jan 08 2020

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

summary: Circulatory shock affects approximately one-third of all patients in the Intensive Care Unit (ICU) and it is correlated with high mortality. Septic shock (SS) and cardiogenic shock (CS) are two types of circulatory shock, with a different etiology. We aimed to assess in whole blood of CS and SS patients the transcriptomic alterations occurring over one week after ICU admission in order to identify the pathways that are modulated in circulatory shock irrespective of the etiology. We used Gene Set Enrichment Analysis (GSEA) to identify the biological processes and transcriptional regulators significantly enriched in both types of shock.

overall_design: We analyzed 21 septic shock and 11 cardiogenic shock patients. For each patient, 3 samples were collected at three timepoints: T1, within 16 hours of ICU admission, T2, 48 hours after study enrollment and T3 on day 7 from ICU admission or before discharge from the ICU.

first: Daniele

last: Braga

first: Cristina

last: Barlassina


title: Single-Cell Map of Diverse Immune Phenotypes in the Metastatic Brain Tumor Microenvironment of Non Small Cell Lung Cancer and triple negative breast cancer

status: Public on Jan 11 2020

city: Shanghai

first: Wei-Lin

last: JIN

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: To shed light on the complexity of tumor-infiltrating immune cells in non-small cell lung cancer (NSCLC) patients and triple negative breast cancer (TNBC) patients with a metastatic brain tumor, we performed massively-parallel single-cell RNA sequencing on 12,196 cells,including 2,012 myeloid cells from 3 surgically removed brain lesions of treatment-naïve NSCLC patients, as well as 6,000 cells from brain lesion of one triple negative breast cancer patient. We found a lack of T lymphocyte infiltration and activation, as well as the vast expansion of tumor-associated macrophage (TAM) in the brain lesions of NSCLC and breast cancer patients. We identified a unique alternative activation (M2) gene expression pattern of the TAM in the brain metastasis and a lack of known T cell co-stimulator expression. Accumulation of M2 polarized TAM may, therefore, cause the comprised anti-tumor T cell response in metastatic brain lesions.

overall_design: Performed single cell RNA-seq on tens of thousands of dissociated metastatic brain tissue cells from 3 human non-small cell lung cancer patients and one triple negative breast cancer patient.

first: Liang

last: Wang

first: Jinxiang

last: Dai

first: Runrun

last: Han

first: Weilin

last: Jin


title: RNAseq of liver dendritic cells targeted with empty liposomes or curcumin liposomes

overall_design: Female C57BL/6 mice were fed with methioinine and choline deficient diet for 2 weeks to induce nonalcoholic steatohepatitis. Groups of mice were intravenously injected with either DiI labelled empty liposomes or DiI labelled curcumin liposomes. 24 hours later hepatic dendritic cells (CD11c+MHC class-II+) that are either positive or negative for DiI were FACS sort purified to compare the transcriptome profiling.


title: Transcriptome analysis of C2C12 myoblasts with mutations in LMNA gene

status: Public on Sep 12 2020

city: Saint Petersburg

first: Oksana

last: Ivanova

address: 2 Akkuratova street

department: Institute of Molecular Biology and Genetics

country: Russia

institute: Almazov National Medical Research Centre

summary: Mutations in LMNA gene cause laminopathies in human. Mostly, laminopathies alter skeletal muscle tissue and lead to cardiomathy and lipodystrophy. We investigated the effect of mutations G232E (EDMD2 syndome) and R482L (FPLD2 syndrome) in LMNA gene on skeletal muclse functioning and metabolism using transgenic C2C12 myoblast cell lines and transcriptome analysis. We found abnormalities of nuclear lamina structure in mutant myoblasts, treir pro-myogenic commitment and metabolic disregulation on all stages of transgenic myoblasts differentiation.

overall_design: C2C12 mouse myoblast cell line was transduced with lentivaral constraction with mutant human LMNA gene. We got three transgenic cell lines: WT-hLMNA C2C12, G232E-hLMNA C2C12 and R482L-hLMNA C2C12. These transgenic myoblasts were differentiated in myogenic direction (using differentiation medium with 2% horse serum). We collected RNA samples on day 0 (undifferentiated myoblasts, controls), day 2 and day 4 of differentiation for all cell lines. Samples were in triplicate. In total, there are 9 biological conditions (3 cell lines, 3 differantiation days) and 27 samples. Libraries were prepared with TruSeq Stranded mRNA kit, samples were RNA-sequenced on Illumina HiSeq 2500, read length 50 bp.

first: Alexey

last: Sergushichev

first: Elena

last: Ignatieva

first: Renata

middle: I

last: Dmitrieva


title: RNA-seq analysis of  CRISPR/Cas9 generated human BMPR2 deficient endothelial cell lines harboring mutations characteristic for hereditary pulmonary hypertension (HPAH)

status: Public on Nov 14 2019

city: Berlin

first: Petra

last: Knaus

state: Berlin

address: Thielallee 63

department: Department of  Chemistry and Biochemistry

institute: Freie Universität Berlin

summary: Balanced TGFβ/BMP-signalling is essential for tissue formation and homeostasis. While gain in TGFβ signaling is often found in diseases, the underlying cellular mechanisms remain poorly defined. Here we show, that the receptor BMPR2 serves as a central gatekeeper of this balance, highlighted by its deregulation in diseases such as pulmonary arterial hypertension (PAH). We show that BMPR2-deficient cells express genes indicative for altered biophysical properties including up-regulation of ECM proteins and integrins.

overall_design: Endothelial cells (EAhy926) BMPR2wt  and BMPR2∆E2 and BMPR2KO were grown in a confluent monolayer for 3 days in a serum-rich growth media without media change. RNA was isolated using NucleoSpin® RNA from MACHEREY-NAGEL  and submitted for RNA-Seq.

first: Christian

last: Hiepen

first: Jerome

last: Jatzlau