title: A Novel Molecular Target in Epidermal Growth Factor Receptor-Mutant Non-Small Cell Lung Cancer treated with a Combination of Osimertinib and Pemetrexed

status: Public on Oct 14 2021

first: Natsuki

last: Takano

address: 1-1-5, Sendagi, Bunkyo-ku

institute: Nippon Medical School

summary:
In this study, we evaluate the therapeutic potential of combining osimertinib with pemetrexed and clarify the underlying molecular mechanisms in order to establish novel therapeutic strategies for EGFR-mutant NSCLC.
We found that the combination of osimertinib and pemetrexed could induce strong apoptotic activity and enhance anti-tumor effects compared to monotherapy in two NSCLC cell lines harboring an EGFR mutation. In addition, we have identified PLK1 as a therapeutic target for combination therapy and as a promising treatment target for overcoming resistance to osimertinib in EGFR-mutated NSCLC patients.

overall_design: Antiproliferative effects of osimertinib+pemetrexed were assessed using PC-9 and H1975 cells harboring EGFR mutations by the MTT assay. GeneChip Human Gene 2.0 Sense Target arrays were used to assess gene expression on exposure to osimertinib in the presence or absence of pemetrexed. Cell lines resistant to osimertinib as well as those resistant to the combination of osimertinib and pemetrexed were established in order to explore mechanisms of resistance.

first: Masahiro

last: Seike


title: Next Generation Sequencing of 786-O-Ctrl and786-O-VHL Transcriptomes

status: Public on Oct 18 2021

city: South Bend

first: XUECHUN

last: WANG

state: Indiana

address: university of notre dame

country: USA

institute: University of Notre Dame

type: Expression profiling by high throughput sequencing

summary: Inactivation of the E3 ubiquitin ligase protein von Hippel-Lindau (VHL) is critical to clear cell renal cell carcinomas (ccRCC) and VHL syndrome. VHL loss leads to stabilization of hypoxia-inducible factor α (HIFα) and other substrate proteins, which may drive various tumor-promoting pathways. This process is likely reversible, because even in the highly aggressive human VHL-deficient ccRCC cell line 786-O, restoring VHL expression almost completely abolishes orthotopic tumor formation in immuno-deficient mice. This result highlights the potential of treating ccRCC by re-expressing VHL with gene therapy. However, there is inadequate understanding of the consequence of VHL restoration at the molecular level. Here, we reinstalled VHL expression in 786-O and performed transcriptome, proteome and ubiquitome profiling to assess the molecular impact.

overall_design: Transcriptomic profiles of 786-O-TR-Ctrl and 786-O-TR-VHL

first: Xuechun

last: Wang


title: Su(H) ChIP-on-chip of Notch-stimulated overgrowing Drosophila melanogaster wing imaginal discs

status: Public on Oct 08 2021

city: Montpellier

first: Alexandre

last: Djiane

address: 208 rue des apothicaires

department: IRCM

country: France

institute: Inserm

type: Genome binding/occupancy profiling by genome tiling array

summary:
Aim: Su(H) chromatin occupancy profiling by ChIP on larval wing imaginal discs of Drosophila melanogaster to study the cooperation between Notch activation and loss of epithelial polarity (scrib mutation) during neoplastic growth.
Results: The combination of Notch activation and scribble mutation (NS) does not lead to a general redeployment of Su(H) binding as compared to individual conditions (Notch only (N), and scrib mutation only (S))

overall_design: Duplicates of pooled dissected 3rd instar larva wing imaginal discs. All dissections at day 6 after egg laying for the following conditions: activated Notch (N), polarity deficient (scrib1 mutant, S), activated Notch and polarity deficient (NS)

first: Sarah

middle: J

last: Bray

first: Rémi

last: Logeay

first: Bettina

last: Fischer


title: The C. burnetii T4SS effector protein AnkG hijacks the 7SK small nuclear riboprotein complex for reprogramming host cell transcription

city: Erlangen

first: Michaela

last: Petter

address: Wassertrumstr. 3-5

department: Mirkobiologisches Institut

country: Germany

institute: Univeritätsklinikum Erlangen

summary: In this study, we analyzed the molecular activity of the anti-apoptotic T4SS effector protein AnkG (CBU0781) to understand how C. burnetii manipulates host cell viability. We demonstrate by RNA-immunoprecipitation that AnkG binds to the host cell 7SK snRNA, an important regulator of the positive transcription elongation factor P-TEFb. Consistent with the documented function of released P-TEFb in RNA Pol II pause release, RNA sequencing experiments confirmed AnkG-mediated transcriptional reprogramming and showed that expression of genes involved in apoptosis, trafficking, and transcription is influenced by AnkG.

overall_design: RNA-Seq of HEK293T cells transfected with either GFP-NLS-AnkG or GFP alone and RIP-Seq of HEK293T cells transfected GFP-NLS-AnkG

first: Arne

last: Cordsmeier

first: Myriam

last: Jeninga

first: Anja

last: Lührmann


title: Transcriptional profiling of beta cell specific CD8 T cells from non-obese diabetic mice

status: Public on Oct 15 2021

city: New York

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: CD8 T cells specific for beta cell antigen islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP) were identified and isolated with NRP-V7 tetramers from the pancreatic draining lymph node and pancreas of non-obese diabetic (NOD) mice and used for single-cell RNA-seq and VDJ-seq.

overall_design: Activated CD8+NRP-V7+ T cells were sorted from the pancreatic lymph node and pancreas of non-obese diabetic mice using hashtags to identify individual mice and feature barcoding antibodies against CD44, CD127, CD62L, CD73, PD1, CD38, and CD39.

first: Doron

last: Betel

first: Paul

last: Zumbo

first: Friederike

last: Duendar

first: Sofia

middle: V

last: Gearty


title: Brahma safeguards canalization of cardiac mesoderm differentiation

status: Public on Oct 26 2021

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens Street

institute: Gladstone Institute of Cardiovascular Disease

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA-Seq of Notch-stimulated overgrowing Drosophila melanogaster wing imaginal discs

status: Public on Oct 07 2021

summary:
Aim: mRNA profile of larval wing imaginal discs of Drosophila melanogaster to study the cooperation between Notch activation and loss of epithelial polarity (scrib mutation) during neoplastic growth.
Results: The combination of Notch activation and scribble mutation (NS) results in mRNA expression changes that, while partly overlapping with Notch only (N), and with scrib mutation only (S), are unique to the combination

overall_design: Triplicates of pooled dissected 3rd instar larva wing imaginal discs (60 discs in each pool). All dissections at day 6 after egg laying for the following conditions: wild type (WT), activated Notch (N), polarity deficient (scrib1 mutant, S), activated Notch and polarity deficient (NS)


title: Changes of gene expression related to cellular senescence in human umbilical cord-derived mesenchymal stem cells

status: Public on Oct 11 2021

city: Seoul

first: Seong-Who

last: Kim

address: 88, Olympic-ro 43-gil

country: South Korea

institute: University of Ulsan

summary: Mesenchymal stem cells (MSCs) are recognized as potential treatments for multiple degenerative and inflammatory disorders as a number of animal and human studies have indicated their therapeutic effects. There are also several approved medicinal products manufactured using these cells. For large-scale manufacturing requirements, the in vitro expansion of harvested MSCs is essential. Multiple subculturing of MSCs, however, provokes cellular senescence process which is known to deteriorate the therapeutic efficacy of the cells.  Strategies to rejuvenate or selectively remove senescent MSCs are therefore highly desirable for fostering future clinical applications of these cells. In this present study, we investigated gene expression changes related to cellular senescence of MSCs derived from umbilical cord blood (hUCB-MSCs) and found that CD26, also known as DPP4, is significantly upregulated upon cellular aging.

overall_design: For differental gene expression analysis between pre-senescent and senescent MSCs, microarray was performed using the Affymetrix GeneChip (Human Gene 2.0 ST Array; DNA Link, Inc, Korea). Total RNA obtained form passage 4 or passage 9 MSCs was extracted and used. two biological replicates of each passage were analyzed.

first: Hyang-Ju

last: Lee

first: Jinyoung

last: Go


title: Systematic analysis of the cancer-stroma interactome of a diverse collection of patient-derived xenografts

city: Tokyo

first: Kuniyo

last: Sueyoshi

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Preventive Medicine, Graduate School of Medicine

country: Japan

institute: The University of Tokyo

summary: Transcriptomes of the cancer (human) and stroma (mouse) of 70 PDX samples consisted of 9 distinctive tumor types were analyzed in this study to investigate to the tumor micro-environment (TME). PDX models recapitulated the features of the original tumors, including tumor-purity, stromal cell composition, and putative signaling. An integrated analysis was conducted to identify the upstream paracrine effectors that govern the stromal transcriptome in KIRC PDXs, which were confirmed by using the complementary cancer transcriptome based on the hypothesis that cancer-derived effectors which play key roles in the formation of the cancer-stroma communication should be upregulated in cancer cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
70 PDX samples consisted of 9 distinctive tumor types were established. Whole transcriptome sequencing of the samples and subsequent read assignment to human/mouse taxonomies yeilded cancer or stroma transcriptome data of each PDX sample.
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Authors state " Unfortunately, I am not allowed to make raw sequencing data (in fastq or BAM formats) to be available publicly due to the restriction of our Institutional Review Board and Ethic Committee because of patient privacy concerns."

first: Daisuke

last: Komura

first: Hiroto

last: Katoh

first: Tsuyoshi

last: Chijiwa

first: Hiroshi

last: Suemizu

first: Masato

last: Nakamura

first: Yohei

last: Miyagi

first: Hiroyuki

last: Aburatani

first: Shumpei

last: Ishikawa


title: Histone modification profiles on Human Umbilical Vein Endothelial Cells (HUVECs) under Vasucular Endothelial Cell Growth Factor (VEGF) stimulation

status: Public on Oct 06 2021

first: Yasuharu

last: Kanki

address: 4-6-1 Komaba, Meguro-ku

summary: Endothelial cells (ECs) are phenotypically heterogeneous mainly due to their dynamic epigenetic status. VEGF, the best-known angiogenic factor, activates calcium-NFAT signalling following acute angiogenic gene transcription. Here, we evaluated the global mapping of VEGF-mediated dynamic transcriptional events with a particular focus on major histone-code profiles using ChIP-seq. Remarkably, the regulatory regions of angiogenic transcription factors exclusively acquired embryonic stem-like bivalent histone marks after the VEGF stimulus. Moreover, the newly discovered NFAT-associated epigenome modifier, PTIP in the COMPASS complex, directed gene transcription via MLL3/4-enrichment which overwhelmed the polycomb-brakes. The non-canonical polycomb1 variant, PRC1.3, specifically bound to and allowed the transactivation of PRC2-enriched bivalent angiogenic genes until conventional PRC1 association and gene silencing. Knockdown of these epigenome modifiers abrogated postnatal aberrant neovessel formation via selective inhibition of acute angiogenic bivalent gene transcription. Collectively, the reported dynamic epigenome landscape in ECs may support the development of advanced therapeutic strategies against various vasculopathies.

overall_design: Epigenetic profile (histone modifications and open chromatin regions) of human endothelial cells through VEGF-induced angiogenic signaling

first: Takashi

last: Minami


title: Transcriptional Characterization of Pterygium

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary: Purpose: To characterize the transcriptome of pterygium and to investigate transcriptional regulation of HIF target genes.

overall_design: MACE RNA sequencing of 8 human conjunctival pterygium and 8 healthy conjunctival samples serving as controls.

first: Julian

last: Wolf

first: Claudia

last: Auw-Haedrich


title: Molecular Pathways are influenced by Progranulin in a neuronal cell model

city: Montreal

first: Andrew

last: Bateman

state: Quebec

address: 1001 boul. Décarie

department: Medicine

country: Canada

institute: McGill University

summary:
Gene expression microarrays were used to identify how the mRNA phenotype of NSC-34 cells responds to PGRN expression levels. PGRN expression correlated well with molecular phenotypes that included mRNA pathways associated with the regulation of the cytoskeleton
Gene expression profile was determined using Illumina Mouse Whole-Genome Expression BeadChips (MouseWG-6 v2.0

overall_design: Total RNA obtained from NSC-34 vector control cells, and cells that either stably over-express human PGRN (NSC-34/hPGRN) or under-express murine PGRN (NSC-34/shPGRN) were compared using Illumina Mouse Whole--Genome Expression BeadChips (MouseWG-6 v2).

first: B

middle: P

last: Chitramuthu

first: A


title: Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonising the epidermal stem cell fate

status: Public on Oct 05 2021

city: London

first: Dimitris

last: Katsanos

address: Sir Alexander Fleming building, Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

summary: In this study we adapt targeted DamID (TaDa) for use in C.elegans and employ it to identify targets within the epidermis for the transcription factors LIN-22 and NHR-25 that are key epidermal development regulators.

overall_design: Identification of LIN-22 and NHR-25 genome-wide binding by epidermis-specific expression of TF-Dam fusions in C. elegans.

first: Michalis

last: Barkoulas


title: RNAseq of two mouse LUSC cell lines derived from NTCU-induced model

status: Public on Oct 02 2021

city: Pamplona

first: Luis

middle: M

last: Montuenga

state: Navarra

address: Edificio CIMA. Avda Pio XII 55

department: Solid Tumors Program

country: Spain

institute: Cener for Applied Medical Research (CIMA). University of Navarra

summary:
We report RNAseq data form two independent mouse syngeneic LUSC cell lines UN-SCC679 and UN-SCC680
Carcinogenesis and cell line generation: LUSC tumors were induced by N-nitroso-tris-chloroethylurea (NTCU) (Toronto Research Chemicals) treatment applying 0.04 M NTCU by skin painting twice a week for 20 weeks to 8-week-old A/J mice. Lungs of euthanized mice were excised and tumor cell lines UN-SCC679 and UN-SCC680 were derived and cultured for 25 passes to ensure they were immortalized, subcutaneously injected into 6-week-old female Rag2-/-IL2Rg-/- immunodeficient mice flanks subcutaneously and finally engrafted in syngeneic 8-week-old A/J mice. These cell lines were cultured in RPMI 1640 supplemented with 10% Fetalclone (Thermo Fisher Scientific) and 100 U/mL penicillin-100 µg/mL streptomycin (Thermo Fisher Scientific). All cells were grown in a humidified incubator containing 5% CO2 at 37°C. Cell lines were routinely tested for mycoplasma.

overall_design: Characterization of mouse syngeneic lung Squamous carcinoma (LUSC) cell lines (UN-SCC679 and UN-SCC680) transcriptome

first: Karmele

last: Valencia


title: The gene expression signature of chronic marijuana use

city: Aurora

first: Ellen

middle: L

last: Burnham

state: CO

address: 13001 East 17th Place

department: Division of Pulmonary Sciences and Critical Care Medicine

institute: University of Colorado Anschutz Medical Campus

summary: Alveolar macrophage (AM) gene expression studies in cigarette smokers have identified dysregulated molecular pathways relevant to clinical outcomes. However, parallel studies in cannabis smokers are limited, despite marijuana’s increasing public health relevance. We performed the first genome-wide gene expression analysis from the lungs of marijuana smokers to test the hypothesis that marijuana is associated with changes in AM gene expression that may contribute to altered immune function. AMs from bronchoalveolar lavage from 15 marijuana smokers, 16 cigarette smokers, and 10 non-smokers were isolated for RNA sequencing. We performed differential expression analysis to identify genes that differed on average between smoking groups, with emphasis on genes associated with M1/M2 macrophage polarization and immunity.

overall_design: N = 15 marijuana smokers, N = 16 cigarette smokers, N = 10 non-smoker controls with no major comorbidities (see publication supplement). Marijuana smokers reported daily or near-daily use and smoking equivalent to at least 20 joint-years, <1 pack-year cigarette history,  and no active tobacco use. Tobacco smoking participants reported daily or near-daily cigarette smoking, no active marijuana consumption, and <1 joint-year of marijuana use. Tobacco smoking participants reported daily or near-daily cigarette smoking, no active marijuana consumption, and <1 joint-year of marijuana use. Non-smoking control participants reported no active use of either substance, <1 joint-year marijuana use, and <1 pack-year tobacco use.

first: Sunita

last: Sharma

first: Cuining

last: Liu


title: RNA-seq quantification in EPS15 knockdown and scramble-oligo controls in JEG3 cells

city: Houston

first: Arjun

last: Bhattacharya

state: TX

address: 1155 Pressler Street

department: Epidemiology

institute: University of Texas MD Anderson Cancer Center

summary:
Purpose: The goals of this study are to compare transcriptomic profiles of JEG-3 cells in EPS15 knockdown and control cells.
Methods: EPS15 scramble oligos were used as a negative control, while an siRNA targetting EPS15 was used to generate knockdown cell lines.
Results: Using an optimized data pipeline, we quantified mRNA expression of 37,788 genes and detected differentially-expressed genes across knockdown and control cell lines.
Conclusions: Our results provide some experimental evidence that EPS15 has transcriptomic consequences in human placenta-derived JEG3 cells.

overall_design: mRNA profiles of EPS15 knockdown JEG-3 cells and control cells

first: Hudson

last: Santos


title: Methylation Mediated Silencing of Protein Kinase C Zeta Induces Apoptosis Avoidance through ATM/Chk-2 Inactivation in Dedifferentiated Chondrosarcoma

status: Public on Oct 04 2021

city: Fukuoka

first: Eijiro

last: Shimada

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Orthopaedic Surgery

institute: Kyushu University

type: Methylation profiling by high throughput sequencing

summary: To examine methylation levels of genes, we performed whole-genome bisulfite sequence for 2 cell lines: NDCS-1, which was established from dedifferentiated chondrosarcoma and had a fast-growing phenotype, and OUMS-27, which was established from conventional chondrosarcoma and had a slow-growing phenotype.

overall_design: WGBS in 2 chondrosarcoma cell lines: OUMS-27 and NDCS-1.

first: Yoshihiro

last: Matsumoto

first: Makoto

last: Nakagawa

first: Yosuke

last: Susuki

last: Endo

first: Nokitaka

last: Setsu

first: Toshifumi

last: Fujiwara

first: Keiichiro

last: Iida

first: Akira

last: Nabeshima

first: Kenichiro

last: Yahiro

first: Atsushi

last: Kimura

first: Takeshi

last: Hirose

first: Masaya

last: Kanahori

first: Ryunosuke

last: Oyama

first: Yoshinao

last: Oda

first: Yasuharu

last: Nakashima


title: Chromatin remodelers interact with Eya1 and Six2 to control nephron progenitor cell self-renewal maintenance

status: Public on Oct 01 2021

first: Jun

last: Li

address: 1425 Madsion Ave, 14th Fl, RM 14-02

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Eya1 interacts with Six1/2 to induce nephron fate and promote nephron progenitor self-renewal. Haploinsufficiency for these genes in humans causes kidney agenesis or hypoplasia. However, how the Eya1-centered network operates remains elusive. Here we identify Eya1's interacting factors via mass-spectrometry and show that Eya1 and Six2 interact with Brg1-based SWI/SNF chromatin-remodeling complex in the kidney. Depletion of Brg1 results in lack of metanephric mesenchyme and depletion of nephron progenitor cells, which is linked to loss of Eya1 expression. Transcriptional profiling reveals conspicuous downregulation of the proto-oncogene Pbx1 and the Dchs1/Fat4 signaling but premature upregulation of a large subset of genes for podocyte lineages and aberrant activation of oncogenic factors in Brg1-deficent cell. ChIP-seq identifies Brg1-occupancy to enhancers at Pbx1 to a distal enhancer of Eya1 that drives nephron progenitor-specific expression. We demonstrate Six2-dependent Brg1 enrichment to the proximal-promoter of Mycn and two distal enhancers of Pbx1, all of which govern nephron progenitor-specific expression in response to binding to Six2. Together, our results suggest a possible mechanism through which the functional specificity of Brg1-BAFs and Eya1-Six2 in cell cycle regulation and self-renewal of the nephron progenitors may be in part achieved.

overall_design: Genome-wide Brg1 binding feature was characterized in kidney using ChIP-seq.

first: Aarthi

last: Ramakrishnan

first: Li

last: Shen

first: Pin-Xian

last: Xu


title: Isogenic human pluripotent stem cell disease models reveal actin binding Rho activating protein deficiency underlies the cardiac troponin T DK210 mutation-induced familial dilated cardiomyopathy II

city: Shanghai

first: Bin

address: Dong'an Road

department: Department of Physiology and Pathophysiology

country: China

institute: Fudan University

summary: Different single mutations on the same sarcomeric gene often cause distinct cardiomyopathy phenotypes as dilated (DCM) or hypertrophic cardiomyopathy (HCM). The key factors involved in this disease divergence is unknown and could be key for disease intervention.We generated isogenic familial DCM and HCM disease-specific human embryonic stem cells (hESCs) carrying the cTnT-DK210 and -DE160 mutation, respectively. Whole transcriptomic RNA-sequencing was used to identify the key gene involved in the earliest disease divergence of cTnT-DK210 caused DCM and cTnT-DE160 caused HCM. Results provide insight into the new molecular mechanisms underlying familial dilated cardiomyopathy.

overall_design: Whole transcriptomic analyses of cTnT-DK210 and -DE160 mutant hESCs-derived cardiomyocytes.

first: Ning

last: Sun

first: Yongkun

last: Zhan

first: Qianqian

last: Liang


title: Isogenic human pluripotent stem cell disease models reveal actin binding Rho activating protein deficiency underlies the cardiac troponin T DK210 mutation-induced familial dilated cardiomyopathy I

summary: The cTnT-DK210 DCM mice  showed ABRA protein deficiency, sarcomeric disruption, and compromised heart contractility. Heart-specific expression of ABRA in cTnT-DK210 mice restored sarcomeric structures, reversed the disease progress, and rescued the DCM phenotypes. ABRA deficiency and compromised downstream serum response factor-regulated muscle gene expression play a key role in familial DCM caused by the cTnT-DK210 mutation. ABRA is a good therapeutic gene for cTnT-DK210-induced DCM and could be translated to other cTnT mutations-induced familial DCM.

overall_design: Whole transcriptomic analyses of wild type, control AAV9-Luciferase and AAV9-ABRA treated cTnT-DK210 mice hearts.


title: BMP4 promotes development and patterning of the tracheal cartilage and trachealis muscle downstream of epithelial-induced Wnt signaling

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

summary: By differentially regulating expression of direct Wnt/b-catenin target genes, Bmp4 modulates levels of Wnt signaling necessary to promote cartilaginous identity and progress tracheal chondrogenesis.

overall_design:
E13.5, Wls flox/flox, ShhCre+ trachea and e13.5 control  tracheas were isolated from mouse embryos and submitted for RNA sequencing. Resulting data was combined with previously generated data to determine gene changes.
E13.5, Chondroblasts  were isolated by FACS negative selection from, Bmp4flox/flox, ?SMAeGFP and  Bmp4flox/flox, Foxg1Cre+, ?SMAeGFP mouse trachea using APC-Epcam and GFP to remove epithelial and muscle cells respectively.

first: Natalia

last: Bottasso-Arias

first: Debora

last: Sinner


title: Massively parallel phenotyping of coding variants in cancer with Perturb-seq

city: Boston

first: Oana

last: Ursu

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Genome sequencing studies have identified millions of somatic variants in cancer, but it remains challenging to predict the phenotypic impact of most. Experimental approaches to distinguish impactful variants often use phenotypic assays that report on predefined gene-specific functional effects in bulk cell populations. Here, we develop an approach to functionally assess variant impact in single cells by pooled Perturb-seq. We measured the impact of 200 TP53 and KRAS variants on RNA profiles in over 300,000 single lung cancer cells, and used the profiles to categorize variants into phenotypic subsets to distinguish gain-of-function, loss-of-function and dominant negative variants, which we validated by comparison with orthogonal assays. We discovered that KRAS variants did not merely fit into discrete functional categories, but spanned a continuum of gain-of-function phenotypes, and that their functional impact could not have been predicted solely by their frequency in patient cohorts. Our work provides a scalable, gene-agnostic method for coding variant impact phenotyping, with potential applications in multiple disease settings.

overall_design:
To map variant impact, we profiled A549 cells (ATCC CCL-185) with 64 channels of 10X Chromium Single Cell 3 RNA-seq v2 (10X Genomics #120237), expressing a pool of barcoded variant sequences The 64 channels were equally split into two experiments: 32 channels for TP53 variants and 32 channels for KRAS variants. We loaded 7,000 cells per channel for each cDNA library to obtain a total of 224,000 cells per experiment (448,000 cells total across the TP53 and KRAS experiments). For each experiment, paired-end libraries were sequenced over 32 lanes on an Illumina Hiseq 2500 per sequencing parameters recommended by 10X Genomics: cell barcode read length 26 bp, index read length 8 bp and transcript read length 98 bp. No dial-out PCR was done, in contrast to typical Perturb-seq (Dixit et al. 2016; Jaitin et al. 2016; Adamson et al. 2016). Variants were assigned to cells based on reads from the RNA-seq data.
Detailed information about the supplementary file formats in this work (raw and processed data) is provided in the supplementary file SCEVIP.README.pdf.

first: James

middle: T

last: Neal

first: Emily

last: Shea

first: Pratiksha

middle: I

last: Thakore

first: Livnat

last: Jerby-Arnon

first: Lan

last: Nguyen

first: Danielle

last: Dionne

first: Celeste

last: Diaz

first: Julia

last: Bauman

first: Mariam

last: Mosaad

first: Christian

last: Fagre

first: April

last: Lo

first: Maria

last: McSharry

first: Andrew

middle: O

last: Giacomelli

first: Seav

middle: H

last: Ly

first: Orit

last: Rozenblatt-Rosen

first: William

middle: C

last: Hahn

last: Aguirre

first: Alice

last: Berger

first: Aviv

last: Regev

first: Jesse

middle: S

last: Boehm


title: Activation of a cGAS-STING-mediated immune response predicts response to neoadjuvant chemotherapy in early breast cancer

status: Public on Sep 30 2021

city: Belfast

first: Stuart

last: McIntosh

address: 97 Lisburn Road

institute: Queen's University Belfast

summary: We report the ability of a gene expression signature to predict response to neoadjuvant chemotherapy in early breast cancer, and also describe transcriptomic changes during treatment

overall_design: Total RNA sequencing from 46 patients with early breast cancer receiving standard of care noeadjuvant chemotherapy; serial tumour biopsies taken at baseline, mid and end of treatment

first: Kienan

last: Savage

first: Richard

last: Kennedy


title: Array data from neoDDRD clinical trial

summary:
Baseline array profiling data from 46 early breast cancer patients
All patients were treated with neoadjuvant anthracycline/anthracycline-taxane regimens

overall_design: We carried out baseline array profiling to determine DDIR assay scores to predict response to neoadjuvant chemotherapy


title: Advances in lentil production through heterosis: evaluating generations and breeding systems

status: Public on Sep 29 2021

city: Melbourne

first: Gurpreet Kaur

last: Suri

state: Victoria

address: 5Ring Road, Bundoora

country: Australia

institute: AgriBio

summary: Purpose: calculate genetic diversity in lentil

overall_design: mRNA profiles of 4 weeks old 47 lentil genotypes

first: Gurpreet

middle: K

first: Shivraj

last: Braich

first: Dianne

last: Noy

first: Garry

last: Rosewarne

first: Noel

last: Cogan

first: Sukhjiwan

last: Kaur


title: Transcriptome profiling of the normal breast of women at either high- or average risk for breast cancer [methyl-capture]

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

institute: Indiana University School of Medicine

summary: Epigenetic mechanisms such as DNA methylation are important regulators of gene expression and are frequently dysregulated early in breast carcinogenesis. The relationship between DNA methylation aberrations in normal breast tissue and breast cancer risk remains unclear. Disease-free breast tissue cores donated by  high-risk (Tyrer-Cuzick lifetime risk ≥20%) and 78 average-risk women were obtained from the Susan G. Komen Tissue Bank and processed for whole methylome and whole transcriptome profiling. We identified 1355 CpGs that were differentially methylated between high- and average-risk breast tissues (ΔZ>0.5, FDR<0.05). Hypomethylated CpGs were overrepresented in high-risk tissue and were found predominantly (68%) in non-coding regions. Hypermethylated CpG sites were found equally in the gene body and non-coding regions. Transcriptomic analysis identified 67 differentially expressed genes (fold change≥2, FDR<0.05, 17 down 50 up), involved in chemokines signaling, metabolism and estrogen biosynthesis. Methylation-expression correlations revealed 6 epigenetically regulated genes in high-risk breast. This is the first gene expression/DNA methylation analysis of normal breasts from women at either high or average risk of breast cancer. Our discovery of epigenetically regulated genes associated with breast cancer risk using a unique resource of normal breast samples opens the doors to a deeper understanding of the process of cancer initiation and provides an opportunity to mechanistically dissect breast cancer susceptibility and risk-associated molecular alterations.

overall_design: The study cohorts includes 165  women at either  average or high risk for breast cancer according to the Tyrer Cuzick risk assessment score.  Fresh frozen breast tssue cores were processed for  RNA/DNA extraction. Methyl-capture was then employed to obtain the methylome profiling, while RNAseq was used to obtain the transcriptome profing of each sample

first: Rana

last: German

first: Ram

last: Podicheti

first: Douglas

middle: B

last: Rush

first: Jun

last: Liu

first: Jie

last: Huang

first: Harikrishna

last: Nakshatri

first: Sha

last: Cao

first: Ashley

last: Vode

first: Anna

last: Storniolo


title: Transcriptome profiling of the normal breast of women at either high- or average risk for breast cancer

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

overall_design: Refer to individual Series


title: Liver single-cell RNA sequencing reveals the transcriptomic landscape and gene regulation of hepatocytes and non-parenchymal cells in healthy and NAFLD mouse liver

city: tarrytown

first: Xiping

last: Cheng

state: new york

address: 777 old saw mill river rd

institute: Regeneron

summary: This study identified unanticipated aspects of the cellular and molecular basis of mouse NAFLD at the single-cell level and advanced our understanding of cellular heterogeneity in NAFLD livers.

overall_design: In order to capture the progression of NAFLD pathogenesis, mice were fed a chow diet, a HFHFD diet for 15 weeks, and a HFHFD diet for 30 weeks. Consistent with previous studies, HFHFD-induced liver injury observed by 15 weeks, from hereon referred to as NAFL mice, and severe fibrosis and inflammation by 30 weeks, from hereon referred to as NASH mice.

first: Qi

last: Su

first: Sun

middle: Y

last: Kim

first: Funmi

last: Adewale

first: Ye

last: Zhou

first: Christina

last: Aldler

first: Min

last: Ni

first: Yi

last: Wei

first: Mickey

last: Atwal

first: Mark

middle: W

last: Sleeman

first: Andrew

last: Murphy

first: Yurong

last: Xin


title: Methylation-dependent and -independent roles of EZH2 coordinately contribute to CDCA8 activation in prostate cancer

first: Yanqiang

last: Li

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Cell division cycle associated 8 (CDCA8) is a component of chromosomal passenger complex (CPC) that participates in mitotic regulation. Although cancer-related CDCA8 hyperactivation has been widely observed, its molecular mechanism remains elusive. Here, we report that CDCA8 overexpression maintains tumorigenicity and is associated with poor clinical outcome in patients with prostate cancer (PCa). Notably, enhancer of zeste homologue 2 (EZH2) is identified to be responsible for CDCA8 activation in PCa. Genome-wide assays revealed that EZH2-induced H3K27 trimethylation represses let-7b expression and thus protects the let-7b-targeting CDCA8 transcripts. More importantly, EZH2 facilitates the self-activation of E2F1 by recruiting E2F1 to its own promoter region in a methylation-independent manner. The high level of E2F1 further promotes transcription of CDCA8 along with the other CPC subunits. Taken together, our study suggests that EZH2-mediated cell cycle regulation in PCa relies on both its methyltransferase and non-methyltransferase activities.

overall_design: Examination of transcription analysis with RNA-seq with 2 replicates at shCTRL and shCDCA8. miRNA expression levels were detected with 2 replicates at shCTRL and shEZH2.

first: Yang

last: Yi

first: Kaifu

last: Chen


title: Transcriptome profiling of the normal breast of women at either high- or average risk for breast cancer [RNA-Seq]

first: Natascia

last: Marino

first: Rana

last: German

first: Ram

last: Podicheti

first: Douglas

last: Rush

first: Jun

last: Liu

first: Jie

last: Huang

first: Harikrishna

last: Nakshatri

first: Sha

last: Cao

first: Ashley

last: Vode


title: Fasting and feeding hormones differentially impact activity dynamics of transcriptionally distinct lateral hypothalamic glutamate projection neurons

status: Public on Sep 28 2021

city: Chapel Hill

first: Marcus

middle: Luis

last: Basiri

state: NC

address: 115 Mason Farm Road

institute: UNC Chapel Hill

summary: We characterize the transcriptional profiles of LHA glutamatergic projections to the LHb and VTA.

overall_design: High-throughput single-cell RNA sequencing of lateral hypothalamic area (LHA) tissue in mice injected with retrogradely-traffic viral vectors in the lateral habenula (LHb) and ventral tegmental area (VTA).

middle: A

last: Rossi

first: Garret

middle: D

last: Stuber


title: Genome-wide gene expression patterns in reprogramming MEF infected by SeVdp vectors carrying KLF4 WT or L507A mutant

status: Public on Sep 27 2021

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

institute: RIKEN

summary:
To evaluate global gene expression pattern changes between KLF4 L507A and WT during reprogramming, RNA-Seq was performed on the samples collected from reprogramming MEF infected with SeVdp vectors carrying KLF4 WT or L507A mutant. Original MEF and resulting miPSCs (mouse iPSCs) were also used as samples.
RNA-seq library was generated using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) and NEBNext rRNA Delepletion Kit (New England Biolabs) by Lab Droid “Maholo” (Robotic Biology Institute) automatically. Paired-end sequencing of the libraries was performed using Novaseq 6000 SP Sequencing system using SP 100 cycle kit (Illumina). Reads from RNA-seq experiments were mapped to the mouse genome (GRCm38 or mm10) and analyzed for differential gene expression and PCA (principal component analysis) using CLC Genomics Workbench (Qiagen) software.

overall_design: RNA-seq data from each conditions (n=3)


title: The effect of radiotherapy on the transcriptional profile of proliferating human cells

status: Public on Sep 23 2021

city: Parkville

first: Matthew

last: Ritchie

address: 1G Royal Parade

institute: The Walter and Eliza Hall Institute of Medical Research

summary: We have used RNA-sequencing on six different proliferating cell lines consisting of normal human dermal fibroblasts (NHDF), normal human epidermal keratinocytes (NHEK), pericytes (PC), human microvADSCular blood endothelial cells (HMEC), lymphatic endothelial cells (LEC) and adipose derived stem cells (ADSC), subjected to different doses of radiotherapy.

overall_design: RNA-seq was performed on proliferating cell lines in duplicate or triplicate under no treatment (0Gy), 5x 2Gy fractions of radiotherapy or 10Gy single dose radiotherapy. Each replicate  refers to cells that came from different flasks (i.e. grown separately).

first: Stuart

last: Lee

first: Lipi

last: Shukla

first: Ramin

last: Shayan

middle: E

first: Mei

middle: R

last: Du

first: Tara

last: Karnezis


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Stk11-/- Endothelial cell Transcriptomes [LKB1]

status: Public on Sep 26 2021

city: Atlanta

first: Qiang

last: Zhao

state: GA

address: 157 Decatur St SE

institute: Georgia State University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived endothelial cell transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: Methods: Endothelial cell mRNA profiles of 2-months-old wild-type (WT) and endothelial cell specific Serine/Threonine Kinase 11 (Stk11-/-) knock out mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT-PCR validation was performed using TaqMan and SYBR Green assays

first: Ming-hui

last: Zou


title: Early developmental alteration of neurite outgrowth occurs besides late-appearing neurodegenerative processes in Wolfram syndrome

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

summary: Developmental alteration in brain wiring that would make it more susceptible to later pathological processes has been suggested as a basis for the occurrence of neurodegenerative diseases, but mechanisms have remained elusive. A recent series of magnetic resonance imaging studies have demonstrated that, in Wolfram syndrome, neurodegenerative processes appear during childhood and adolescence on top of a clinically silent global defect in brain development. Here, differentiation of induced pluripotent stem cell lines derived from Wolfram syndrome patients’ cells along the neural lineage has revealed phenotypic and molecular correlates of that global brain defect. A proportion of neural cells displayed aberrant neurite outgrowth associated with alterations in the expression of genes involved in axonal guidance. In contrast, an activation of endoplasmic reticulum stress response genes was absent while it is present in late Wolfram syndrome degenerative processes. These results concur to the broader hypothesis that axon guidance genes may play a role in the susceptibility to neurodegenerative diseases.

overall_design: 6 samples (3 wildtype (WT1, WT2, WT3) and 3 wolfram (WS1, WS2, WS)) for NSCs and 6 samples (3 wildtype (WT1, WT2, WT3) and 3 wolfram (WS1, WS2, WS)) for neurons.

first: Sandra

last: Pourtoy

first: Axel

last: Sciauvaud

first: Maria-Gabriela

last: Boza-Moran

first: Michel

last: Cailleret

first: Margot

last: Jarrige

first: Jérôme

last: Polentes

first: Eric

last: Chevet

first: Cécile

last: Martinat

first: Marc

last: Peschanski

first: Laetitia

last: Aubry


title: Next Generation Sequencing Facilitates Quantitative Analysis of endothelial cells transfected with Ptbp1(wt), Ptbp1(T138A) or Ptbp1(T138E) plasmid Transcriptomes

overall_design: Methods: mRNA profiles of  endothelial cells transfected with Ptbp1(wt), Ptbp1(T138A) or Ptbp1(T138E) plasmid were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays


title: Placental exosomes

status: Public on Sep 16 2021

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong


title: Human placental exosomes induce maternal systemic immune tolerance in a monocyte-dependent manner

summary: Maternal immune tolerance toward to the semi-allograft fetus is a prerequisite condition for successful pregnancy. However, the role of maternal monocytes in the induction of systemic immune tolerance is poorly understood. Here we report that placenta facilitates maternal immune tolerance by extruding exosomes. Maternal monocytes were transformed into an immunosuppressive phenotype after taking up exosomes. Mechanistically, PD-L1 was significantly increased in pEXO-educated monocytes via miRNA-29a-3p/PTEN signaling pathway. In addition, pEXO-treated monocytes could increase Treg pool in maternal blood through a direct cell-cell interaction. Moreover, Th1 cytokines, IFNγ and TNF-α, in monocyte-T cell co-culture system were significantly decreased. Together, our results indicated that maternal monocyte is indispensable components in systemic immune tolerance establishment.

overall_design: mRNA profiles of pEXO-treated monocyte (N=4) and Control monocyte (N=4)

first: Philiiip

last: Chiu

first: Bai

last: Kunfeng


title: Placental exosomes polarize human monocyte-derived macrophages to a decidual M2-like macrophage phenotype

summary: Macrophages are abundant in uterine mucosa during the peri-implantation phase and early pregnancy. Decidual macrophages display dynamic changes alone with pregnancy progress: During the peri-implantation phase, macrophages displayed a pro-inflammatory phenotype which facilitates embryo implantation. While, In the late firster trimester and second trimester, decidual macrophages are anti-proinflammatory which are helpful to pregnancy maintenance. Alterations in the ratio of pro-inflammatory/anti-inflammatory decidual macrophages lead to abortion, preeclampsia, and preterm birth. Placenta-derived exosomes (pEXO) are critical in the immune cell modulation such as T cell apoptosis, NK activities, and T regulatory (Treg) differentiation. However, it is unknown whether placenta-derived exosomes contribute to decidual macrophage polarization during early pregnancy. Here we report that exosomes from the placenta explant stimulate M2 macrophage polarization via exosomal miRNA-30d-5p. Mechanistically, miRNA-30d-5p polarized macrophages to M2 phenotype by inhibiting HDAC9 expression. Furthermore, the conditioned medium of pEXO-treated macrophages promoted trophoblast migration and invasion. By contrast, conditioned medium impaired the ability of endothelial cell tube formation. However, pEXO-treated macrophages have no impact on T cell proliferation. Together, we demonstrated that pEXO promoted trophoblast migration and invasion, endothelial cell migration, and attenuation of endothelial cell tube formation by polarizing macrophage to decidua-like macrophage.

overall_design: mRNA profiles of pEXO-treated macrophages (N=2) and Control macrophage (N=2)


title: Longitudinal clinico-genomic data generation, drugable target development and multi-sites validation for drug development enhancement

city: Seoul

first: Tae Won

last: Kim

address: 88 Olympic-ro 43-gil

institute: Asan Medical Center

summary: We report the gene expression profiles of colon cancers before and after cetuximab-based chemotherapy.

overall_design: RNA sequencing of formalin-fixed paraffin-embedded (FFPE) tumor tissue obtained before and after cetuximab treatment

first: Tae


title: IFNalpha-blockade during ART-treated SIV infection lowers tissue vDNA, rescues immune function, and improves overall health

first: Rafick-Pierre

last: Sekaly

address: 1750 Haygood Drive

department: Pathology

institute: Emory University

summary: The induction of type I interferons during acute viral infections drives local and systemic anti-viral responses. However, in chornic virus infection these type I interferon driven responses can be detrimental and can be characterized impaired immune responses (greater T cell exhaustion) and an overall decline in health outcomes. To parse out the role of type I IFN and assess the therapeutic impact of blocking type I IFN, we administered IFN-a blocking antibody to a cohort of SIV-infected ART treated Maccaca mulata. After 9 weeks of treatment (1 injection per week), we observed a significant reduction in the SIV-DNA levels in the lymphnode. This reduced SIV reservoir was seem with a systemic increase in immune cell subset signatures associated with better CD8 T cell function and lower plasma levels of TGF-beta. In addition, upon interruption of ART (16 weeks after ART initiation and after 16 rounds of anti-IFNa infusion), we observed that the non-human primates that underwent type I interferon blockade maintained better overall health and hemoglobin levels.

overall_design: 12 female Rhesus Macaques (4-5 years of age) were intravenously challenged with SIVmac251 after testing negative for simian retrovirus, simian T-lymphotropic virus, hepatitis B, and helminthic infections. At 8 weeks p.i., NHPs commenced an ART treatment regimen of L-612 (RAL, 150 mg PO BID, Merck), emtricitabine (FTC, 30 mg/kg/day, Gilead), tenofovir (PMPA, 20 mg/kg/day, Gilead), and darunavir (DRV, 400 mg PO BID, Tibotec) until ATI at 36 weeks p.i. After 12 weeks of ART (20 weeks p.i.), 6 NHPs received anti-IFN humanized Ab AGS-009 i.v. at 10-11 mg/kg and the other 6 control NHPs received an irrelevant Ab (an anti-hepatitis B antibody, prepared by Keith Reimann) weekly for 16 weeks. AGS-009 and control Ab were administered i.v. in 50 ml saline solution, with an injection rate of 2.5-8 ml/min. Peripheral blood, rectal pinch biopsies, and peripheral lymph node biopsies were sampled to evaluate VL, CD4+ T cell counts, immune phenotype and function, and transcriptional and serological signatures.

first: Louise

last: Swainson

first: Ashish

last: Sharma

first: Peter

last: Wilkinson

first: Khader

last: Ghneim

last: Hunt

first: Joseph

middle: M

last: McCune


title: The Evolutionary Context of an Immune-Mediated Skin response

city: Buffalo

first: Omer

last: Gokcumen

address: 639 Cooke Hall

department: Biological Sciences

institute: University at Buffalo

summary: The skin is vital for protecting the body and perceiving external stimuli in the environment. Ability to adapt between environments is in part based on skin plasticity, indicating evolved homeostasis between skin and environment. This homeostasis reflects the greater relationship between the body and the environment, and disruptions in this balance may lead to accumulation of susceptibility factors for autoimmune disorders like psoriasis. We collected skin tissue biopsies from individuals with psoriasis and compared gene expression in psoriatic plaques to non-plaque psoriatic skin. We then compared these data with non-psoriatic skin transcriptome data from multiple primate species. We found 67 genes showing human-specific skin expression that are also differentially regulated in psoriatic skin; these genes are significantly enriched for skin barrier function, immunity, and neuronal development. We identified 6 gene clusters with differential expression in the context of human evolution and psoriasis, suggesting underlying regulatory mechanisms in these loci. Human and psoriasis-specific enrichment of neuroimmune genes shows the importance of the ongoing evolved homeostatic relationship between skin and external environment. These results have implications for both evolutionary medicine and public health, using transcriptomic data to acknowledge the importance of an individual's surroundings on their overall health.

overall_design: Skin punch biopsies from 3 human individuals with psoriasis, matched samples from lesional and nonlesional psoriatic skin.

first: Izzy

last: Starr


title: Spider mite egg extract modifies Arabidopsis response to future infestations

status: Public on Sep 15 2021

city: POZUELO DE ALARCON

first: M. ESTRELLA

last: SANTAMARIA

state: MADRID

address: Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38

institute: CBGP (UPM-INIA)

summary: Transcriptional plant responses are specially under the scope on herbivore oviposition studies. However, most of the information comes from Lepidopteran models, where egg laying and feeding are separate events, and little is known regarding the plant reaction to those pests where females feed and oviposit simultaneously. The present study unveiled the oviposition-induced transcriptomic response of plants to Tetranychus urticae eggs. Transcriptional evidence indicated that the early events on the plant response to the egg extract involved ATP, Ca2+ and ROS disbalances. The main phytohormones triggered were JA and ET, with which also participated secondary metabolites, volatiles and glucosinolates as defence mechanisms. Many of the regulated genes are also involved during pathogen-defence mechanisms. Negative regulation of defence mechanisms happened at 72 h. Female fertility was significantly reduced when fed on plants pre-exposed to the eggs, while feeding increased on those plants pre-exposed for 72 h.

overall_design: Three-week-old A. thaliana Columbia (Col-0) plants were treated by applying 2 μL of egg extract and 2 μL of water on controls. After 3, 24 and 72 hpt, whole rosettes were sampled simultaneously, introduced in liquid nitrogen and stored at –80°C until used for RNA extraction. Three biological replicates of treated and control tissues were collected for each time point. Each biological replicate consisted of a pool of five whole independent rosettes. Frozen material was thoroughly grinded on liquid nitrogen and total RNA was extracted by means of the RNeasy plant mini kit (Qiagen), and a DNase treatment (Qiagen) following manufacturer´s instructions.

first: Estrella

last: Santamaria

first: Isabel

last: Diaz

first: Dairon

last: Ojeda-Martinez


title: Novel Thyrointegrin αvβ3 antagonist (fp-PMT) with potent affinity in the treatment of cancer

status: Public on Sep 11 2021

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Microarray analysis was carried out on Glioblastoma (GBM 10181360, GBM 021913 and U87 cells), Bladder cancer (JBV253), skin cancer (A375) and  Acute Myelod Leukemia (AML)  (KG1A  and K562  cells) exposed to fb-PMT  at 30 µM concentration. Our genome-wide microarray screens demonstrated that fb-PMT appears to exert its potent anticancer actions on human cancer cells through the molecular interference mechanism with multiple signaling pathways supporting growth and survival of leukemic cells. Notably, fb-PMT had a significant effect on different molecular pathways that contribute to the anticancer activity such as cell cycle control (MYC), survival and maintenance of stem cells (HIF1A; TFAP2C), essential features of the malignant phenotype (TWIST1; SNAI).  Furthermore, the fb-PMT-induced significant transcriptional pathway’s activation includes RB1; IRF9; MAML1; RAP1A; and GATA4 pathways, which known to play an important role in anticancer activity. Finally, Consistent with our previous reports on the crosstalk between integrin αvβ3 and ERα which contributes to the induced proliferation of cancer cells, we found that fb-PMT interference with estrogen signaling. The αvβ3 agonist (thyroid hormone) was associated with increased phosphorylation and nuclear enrichment of estrogen receptor α (ERα).

overall_design: To evaluate biological and molecular functions of genes expression affected  by the treatment of fb-PMT. RNA isolation from two biological replicates of control human cancer cells compared with  cells treated with fb-PMT (30 µM) for 24 h and 48 h.

first: Gennadi

last: Glinsky

first: Kavitha

last: Godugu

first: Thangirala

last: Sudha

first: Bruce

last: Hay

first: Nour

last: Darwish

first: Shaker

last: Mousa

first: Paul

middle: J

last: Davis


title: single-cell analysis of experimental autoimmune orchitis (EAO) in mice

status: Public on Sep 14 2021

city: Nantong

first: Yinchuan

last: Li

state: Jiangsu

address: 16 wenfeng road, Chongchuan

department: Medical School

institute: Nantong University

summary: Adult normal male testes (Nt) of mice and testes insulted with EAO (O50t,50 days after the first immunization) were profiled via scRNA-seq.

overall_design: The induction of EAO were conducted 3 times of immunization with homogenized mouse testis along with Freund’s adjuvant with 14 days interval. Each time was followed by i.p. injection of 100 ng Bordetella pertussis toxin in 100 μl 1X PBS. The normal control group was named as N and its cells digested with trypsin/EDTA was thus named as Nt. The orchitic groups were named as O50 (50 days after the first immunization) and the cells of O50 digested with trypsin/EDTA was named as O50t. 3 unilateral decapsulated testes from 3 mice collected either from the group O50 or N were pooled for digestion.


title: Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [pA-DamID]

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: Cohesin stalling at CTCF binding sites represents one of the main principles of interphase chromosome organization. In the current studies, we dissect the role of cohesin and CTCF, both alone and in combination, in 3D genome organization by depleting these proteins using acute protein degradation techniques. By systematic examination of interactomic, epigenomic and transcriptomic changes using various sequencing techniques, our studies reveal the functions of cohesin and CTCF in mediating the formation of chromatin loops, topologically associating domains, chromosome compartments and nuclear lamina associating domains. Our studies describe fundamental principles of how the architectural proteins contribute to genome folding at multiple genomic scales and transcriptional regulation.

overall_design: Acute depletion of CTCF WAPL and RAD21 using AID-mediated protein depletion, followed by pA-DamID as described (van Schaik et al., 2020).

first: Tom

last: van Schaik

first: Ning

middle: Q

last: Liu


title: Expression data of lncRNAs and mRNAs extracted from serum of tuberculosis patients and healthy individuals

status: Public on Sep 10 2021

city: Zhengzhou

first: Junwei

last: Zhao

state: Henan

address: Jianshe Road

institute: Zhengzhou University

summary:
Efforts to eradicate TB are largely threatened by drug-resistant tuberculosis, particularly, multidrug-resistant tuberculosis (MDR-TB). It is imperative to find one or more specific biomarkers for diagnosing MDR-TB earlier and declining the incidence. Growing evidences have showed lncRNAs are widely expressed and take part in the genesis and development of many diseases, including tuberculosis.
Therefore, to screen the differential lncRNAs among MDR-TB, drug-sensitive tuberculosis(DS-TB) and healthy controls(HCs) is a good strategy to acquire potential biomarkers for MDR-TB diagnosis and partly describe the mechanism of MDR-TB. Here, the present study aimed to investigate the differential expression profile of lncRNAs in serum among patients with MDR-TB ,DS-TB and HCs using lncRNA microarray

overall_design: From Jun 2020 to Feb 2021, hospitalized patients who were diagnosed with MDR-TB and DS-TB were recruited and healthy subjects came from physical examination donors with normal laboratory results and normal computed tomography chest films. Expression profiling studies were performed on the RNA from four independent serum samples in the group of MDR-TB,DS-TB and healthy controls.

first: Shuhui

last: Gao


title: Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [DamID and ChIP]

overall_design: Data files generated to determine CTCF enrichment at the borders of lamina-associated domains (LADs) in mouse neural precursor cells (mNPCs). H3K27me3 ChIP-seq data files from a CTCF depletion time course in mouse embryonic stem cells (mESCs) witih AID-tagged CTCF.

first: Elzo

last: de Wit


title: Analysis of global gene expression in vegetative and reproductive tissues of maize (Zea mays) that differ in accumulation of starch and sucrose

city: IRAPUATO

first: Stewart

last: Gillmor

state: GUANAJUATO

address: CARR. LEON-IRAPUATO

department: UNIDAD DE GENOMICA AVANZADA

country: Mexico

institute: CINVESTAV

summary:
Background. Carbon allocation between vegetative and reproductive tissues impacts cereal grain production. Despite their great agricultural importance, sink-source relationships have not been fully characterized at early reproductive stages in maize. Here we quantify the accumulation of non-structural carbohydrates and patterns of gene expression in the top internode of the stem and the female inflorescence of maize at the onset of grain filling (reproductive stage R1).
Methods. Top internode stem and female inflorescence tissues of the Puma maize inbred line were collected at reproductive stage R1 (without pollination). The accumulation of non-structural carbohydrates was quantified by spectrophotometry. Global gene expression was evaluated in both tissues by RNA sequencing.
Results. At reproductive stage R1, the maize female inflorescence accumulates non-structural carbohydrates, notably starch, at higher levels than the top internode of the stem. Gene expression analysis identified 491 genes to be differentially expressed between the female inflorescence and the stem top internode. Gene ontology classification of differentially expressed genes showed enrichment for sucrose synthesis, the light-dependent reactions of photosynthesis, and transmembrane transporters. Our results suggest that sugar transporters play a key role in sugar partitioning in the maize stem and reveal previously uncharacterized differences between the female inflorescence and the top internode of the stem at early reproductive stages.

overall_design: RNA-seq of two maize tissues by duplicated, the female inflorescence and the top internode section of the stem at reproductive stage before pollination, with differentalstarch and sucrose level

first: Axel

last: Tiessen

first: Cristal

last: Lopez-Gonzalez


title: The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration

status: Public on Sep 07 2021

city: Bethesda

first: Jason

last: Sinclair

state: MD

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

summary: Throughout their lifetime, fish maintain a high capacity for regenerating complex tissues after injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio, which serves as an ideal model of appendage regeneration due to its easy manipulation, relatively simple mixture of cell types, and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema, a mass of dedifferentiated cells capable of replacing lost tissue, a crucial step in all known examples of appendage regeneration. Using this model, we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating after amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA-sequencing on regenerating tails with and without inhibition of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF-β signaling and blocking glucose metabolism largely mimicked inhibition of TGF-β receptors, both resulting in an aberrant blastema. Finally, we showed using genetic ablation of three possible metabolic pathways for glucose, that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration.

overall_design:
Single-cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post-amputation with and without 2-deoxyglucose.

Please note that the UI_ctrl.cloupe is a single sample from uninjured, untreated embryo tails and the ctrl_cloupe.cloupe is an aggregate file of all non-2DG treated samples (UI_ctrl, 24hpa_ctrl, and 48hpa_ctrl).

first: Shawn

last: Burgess

first: Erica

last: Bresciani

first: Weiwei

last: Wu

first: Abdel

middle: G

last: Elkahloun


title: Simultaneous profiling of multiple chromatin proteins in the same cells

status: Public on Sep 06 2021

city: Worcester

first: Thomas

last: Fazzio

address: 364 Plantation St., LRB 519

department: Department of Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: Methods derived from CUT&RUN and CUT&Tag enable genome-wide mapping of the localization of proteins on chromatin from as few as one cell. These and other mapping approaches focus on one protein at a time, preventing direct measurements of co-localization of different chromatin proteins in the same cells and requiring prioritization of targets where samples are limiting. Here we describe multi-CUT&Tag, an adaptation of CUT&Tag that overcomes these hurdles by using antibody-specific barcodes to simultaneously map multiple proteins in the same cells. Highly specific multi-CUT&Tag maps of histone marks and RNA Polymerase II uncovered sites of co-localization in the same cells, active and repressed genes, and candidate cis-regulatory elements. Single-cell multi-CUT&Tag profiling facilitated identification of distinct cell types from a mixed population and inference of cell type-specific gene expression. In sum, multi-CUT&Tag increases the “per cell” information content of epigenomic maps, facilitating direct analysis of the interplay of different proteins on chromatin.

overall_design:
Single, double and triple Antibody multi-CUT&Tag followed by Illumina sequencing.
Please note that *DualAb_* processed data was generated from both rep1 and rep2 samples, and is linked to the corresponding rep1 sample records.

first: Sneha

last: Gopalan

first: Yuqing

last: Wang

first: Nicholas

last: Harper

first: Manuel

last: Garber


title: Effect of acetate pre-treatment on macrophages stimulated with S. pneumoniae

status: Public on Sep 03 2021

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: The objetive of this study was to evaluate the impact of acetate pre-treatment in alveolar macrophage like cells (MPI) stimulated with Streptococcus pneumoniae.  We observed that acetate induce a high modulation of gene expression. Acetate led to similar numbers of up and down-regulated genes and in a enrichment analysis, acetate was shown to regulate different pathways, such as locomotion, cell proliferation and immune processes.

overall_design: MPI macrophages cultured in complete medium (RPMI 10% FBS 1% Pen/Strep) were treated with sodium acetate 30mM and after one hour of incubation at 37°C 5% CO2 they were stimulated with heat killed Streptococcus pneumoniae serotype 1, MOI of 30. Cells were then incubated for 18h. Later cells were lysed and RNA was extracted for RNA-Seq

first: Marina

last: GOMES MACHADO

first: Fraçois

last: TROTTEIN


title: Long-Term Hepatitis B Virus Infection Induces Cytopathic Effects in Primary Human Hepatocytes, and Can be Partially Reversed by Antiviral Therapy

status: Public on Sep 02 2021

city: SHANGHAI

first: Wenjing

last: Zai

address: Dongan Road

institute: Fudan University

summary: Based on our recently developed 5 chemicals-cultured primary human hepatocytes (5C-PHH) model that supports long-term HBV infection, we performed multiplexed quantitative analysis of temporal changes of host proteome and transcriptome on PHH cells infected by HBV for up to 4 weeks. We showed that metabolic-, complement-, cytoskeleton-, mitochondrial- and oxidation-related pathways were modulated at transcriptional or post-transcriptional levels during long-term HBV infection, which led to cytopathic effects and could be partially rescued by early rather than late nucleot(s)ide analogs (NAs) administration.

overall_design: Mock- and HBV- infected (ayw, MOI 200) 5C-PHH to quantify kinetics of changes mRNA expression by RNA sequencing in triplicate at 2, 7, and 28 dpi;  entecavir (ETV) to treat the cells (at 100 nM) right away following HBV infection, and samples were collected at 7 and 28 dpi for RNA-seq analysis.

first: Kongying

last: Hu

first: Jianyu

last: Ye

first: Jiahui

last: Ding

first: Chao

last: Huang

first: Yaming

last: Li

first: Zhong

last: Fang

first: Min

first: Cong

first: Jieliang

last: Chen

first: Zhenghong

last: Yuan


title: A lymphocyte-microglia-astrocyte axis in chronic active multiple sclerosis

status: Public on Sep 01 2021

first: Martina

last: Absinta

address: 10 Center Drive MSC 1400

department: NINDS

institute: NIH

summary: The failure of multiple sclerosis lesions to resolve in the months after they form leads to smouldering demyelination and axon degeneration (chronic active/slowly expanding lesions). To define mechanisms underlying this disabling, progressive neurodegenerative state, and to foster development of new therapeutics, we used MRI-informed single-nucleus RNA sequencing to profile the edge of demyelinated white matter lesions at various stages of inflammation and compared with healthy control white matter.

overall_design: Human single-nucleus RNA profiles collected from 5 progressive multiple sclerosis autopsy brains (sampling of the lesion core,the edge and the periplaque of chronic active vs inactive MS lesions) and 3 healthy controls autopsy brains via 10X Genomics protocol.

first: Dragan

last: Maric

first: Marjan

last: Gharagozloo

first: Thomas

last: Garton

first: Matthew

last: Smith

first: Jing

last: Jin

first: Kathryn

last: Fitzgerald

first: Anya

last: Song

first: Poching

last: Liu

first: Jing-Ping

last: Lin

first: Tianxia

last: Wu

first: Kory

last: Johnson

first: Dorian

last: McGavern

first: Dorothy

middle: P

last: Schafer

first: Peter

last: Calabresi

first: Daniel

last: Reich


title: Characterization of the coding and noncoding transcriptome in undifferentiated and differentiating of WT and Notch1-deficient mouse embryonic stem cells

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: RNA (poly(A)+ fraction)was isolated from WT and Notch1-deleted mouse embryonic stem cells at the undifferetiated and differentiated (6 days; using the hanging drop model) state. Profiling of the transcritome at these two stages of differentiation using deep RNA sequencing allows identifying modulated coding and noncoding transcripts upon induction of differentiation.

overall_design: RNA profiling of mouse embryonic stem cells at two stages of differentiation, i.e. undifferntiated state and at day 6 after induction of differentiation. Four conditions, three biological replicates per condition.

first: Mohamed

last: Nemir

first: Iole

last: Pezzuto

first: Mark

last: Ibberson

first: Thierry

last: Pedrazzini


title: The effect of microgtavity on the epigenetic modification in C. elegans - JAXA "EPIGENETICS" spaceflight experiment

status: Public on Aug 31 2021

city: Tsukuba

first: Akira

last: Higashibata

department: Department of Space Biology and Microgravity Sciences

institute: Japan Aerospace Exploration Agency

summary:
DNA microarray analyses were performed to determine the gene expression profiles of space-flown worms over four generations.
N2 wild-type, RB756 hda-4 (ok518), and VC199 sir-2.1 (ok434) mutants were used to analyze epigenome alterations by histone deacetylase.

overall_design: We compared the entire gene expression  of wild-type and mutants under µG and artificial 1G conditions. Two indipendent culture samples were analyzed for each condition.

first: Atsushi

last: Higashitani

first: Toko

last: Hashizume


title: NCI-H1688 cells treated with natural compounds(sanguinarine chloride, cepharanthine and evodiamine), or (+)-JQ-1, or panobinostat, or sanguinarine chloride in combination with panobinostat or (+)-JQ-1.

city: Guangzhou

first: Xiaodong

last: Ma

state: Guangdong

address: Rm406,Building 29, South China Normal University

institute: South China Normal University

summary: Purpose: we used next generation sequencing to analyze gene expression profiles of NCI-H1688 treated with different drugs and elaborated the combinatorial effect of sanguinarine chloride and panobinostat or (+)-JQ-1.The goals of this study are to compare the drug effect and find out the resonally synergistic effects in NCI-H1688.

overall_design: Human SCLC cell NCI-H1688 was cultured under standard conditions and treated for 24 hours with either DMSO, or sanguinarine(1 μM), or cepharanthine(3 μM), or evodiamine(3 μM), or (+)-JQ-1(28 μM), or panobinostat(60 nM), or sanguinarine chloride(1 μM) combine with panobinostat(60 nM), or sanguinarine chloride(1 μM) combine with (+)-JQ-1(28 μM). Total RNA was collected from each treatment group and sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA sequence was performed using Nova 6000 Illumina sequencing platform. The reads were mapped to the human reference genome (GRCh38) by STAR software (Version 2.5.1), annotation from GENCODE version vM21 was used. Differential gene expression was performed using DESeq2. qRT–PCR validation was performed using SYBR Green assays.


title: Operational tolerance after hematopoietic stem cell transplantation is characterized by distinct transcriptional, phenotypic, and metabolic signatures

city: Paris

first: David

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

institute: Assistance Publique des Hôpitaux de Paris

summary: Immune tolerance is involved physiologically in pregnancy and disrupted in autoimmunity, organ rejection, and graft-versus-host disease (GvHD). In transplantation setting, operational tolerance has been inferred in patients who develop tolerance without a need for immunosuppressants. However, mechanisms underlying operational tolerance in Humans are poorly understood. Using two cohorts of patients who underwent an allo-HSCT from HLA-identical siblings, we used multi-omics approach to decipher immune landscape associated with tolerance in recipients and their related donors. We analyzed two cohorts of patients, one monocentric from Saint Louis hospital (cohort 1, n=41) and one multicenric from the national Cryostem consortium biological collection (cohort 2, n=69). We proceed to deep immunophenotyping of peripheral blood mononuclear cell using mass cytometry, RNA sequencing analysis and metabolomics profiling of plasma in both recipients and related donors. The aim of this study is to determine the evolution of immune landscape after allogeneic HSCT by comparison with healthy donors, and to identify specific biological mechanism associated with immune tolerance in patients.

overall_design: PBMC total RNAseq analysis of recipients and their relative donors from patients eligible for hematopoietic stem cell transplantation from an HLA-identical sibling donor. Two cohorts:  one monocentric discovery cohort (41 complete couples) and one multicentric confirmation cohort (69 complete couples). Two time-point: 15 days before transplantation for donor and 1 to 2 years after transplantation for recipients. Among patients included in this study, RNA seq data were available in 32 paired donors and recipients from cohort 1, and 62 paired donors and recipients from cohort 2.

first: Laetitia

last: Dubouchet


title: Genome-wide analysis of circular RNAs in cerebral palsy

city: Xi'an City

first: Xuzhao

last: Bian

state: Shaanxi Province

address: No.28 Xianning West Road, Beilin District

department: School of Public Health

institute: Xi’an Jiaotong University

summary: Cerebral palsy (CP) is a spectrum of non-progressive motor disorders caused by brain injury during fetal or postnatal periods. Current diagnosis of CP mainly relies on neuroimaging and motor assessment, and we aimed to explore novel biomarkers for CP diagnosis in the present study. Blood plasma from five CP children and their healthy twin brothers/sisters was analyzed by gene microarray to screen out differential expressed circular RNAs (circRNAs).

overall_design: Five CP children and their healthy twins were selected in our study to exclude interfering factors (Average age: 3.3 ± 1.5, average birth weight: 2.9 ± 0.4 kg). Additional 30 pairs of CP children and healthy controls were recruited for subsequent validation of differential expressed circRNAs (Age: 4.2 ± 1.6; average birth weight: 3.1 ± 0.6 kg). Inclusive criteria: ①undergo no drug therapy; ② with complete clinical information; Exclusive criteria: ① acute/chronic infectious diseases, connective tissue diseases or malignant tumor; ② recent use of immunosuppressant; ③ injury of liver and kidney function.


title: Functional impairment of HIV-specific CD8+ T cells precedes aborted control of viremia

status: Public on Aug 30 2021

city: Cambridge

first: Jonathan

middle: Morris

last: Urbach

state: Massachusetts

address: 400 Technology Sq Rm 851

institute: Ragon Institute of MGH, MIT and Harvard

summary: Spontaneous control of HIV infection has been repeatedly linked to antiviral CD8+ T cells but is not always permanent. To address mechanisms of durable and aborted control of viremia, we evaluated immunologic and virologic parameters in longitudinal samples from 34 subjects with differential outcomes. Despite sustained recognition of autologous virus, aborted control was preceded by impairment of HIV-specific proliferative and cytolytic T cell effector functions without evidence of canonical T cell exhaustion. During aborted control, HIV-specific CD8+ T cells infiltrated lymphoid follicles but exhibited poor functionality relative to durable control. Longitudinal transcriptomic profiling of HIV-specific CD8+ T cells revealed altered expression of genes related to T cell activation, cytokine-mediated signaling and cell cycle regulation preceding aborted control, including increased expression of the antiproliferative transcription factor KLF2. Our results identify prognostic indicators of aborted HIV control and elucidate functional requirements for durable immune control, which may guide development of new therapies

overall_design: Longitudinal RNA-seq of replicate HIV-specific CD8+ T cells preceding aborted or durable control (5 subjects each)

last: Collins

first: Bruce

last: Walker


title: Ontogeny and function of the circadian clock in intestinal organoids

city: Cincinnati

first: Andrew

last: Rosselot

address: 231, Albert Sabin way

department: Department of Pharmacology and Systems Biology

institute: University of Cincinnati, College of Medicine

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

overall_design: Refer to individual Series


title: micro-RNA deregulation in cancer-associated fibroblasts in oral squamous cell carcinoma

status: Public on Aug 27 2021

city: Bergen

first: Saroj

last: Rajthala

state: Hordaland

address: Jonas Lies vei 87

department: Department of Clinical Medicine

country: Norway

institute: University of Bergen

summary: micro-RNA in cancer-associated fibroblasts in oral squamous cell carcinoma vs. dysplasia-associated fibroblasts from dysplastic oral lesions vs. normal fibroblasts from normal oral mucosa from healthy individual.

overall_design: Total RNA from fibroblasts cultured in 3D collagen I matrix was isolated, enriched for small RNA and subjected to microRNA profiling using Illumina microarray v2 panel. There are no replicates for the samples.


title: Single cell RNA sequencing of maize root

first: Li

middle: Xu

last: Hui

address: #10 Shiliugang

institute: Guangdong Academy of Science

summary: The root system is fundamental for maize growth and yield. The primary root system is the most important structure of maize seedlings and is the first organ that emerges at germination, providing water and nutrients for the growing seedlings. However, it is difficult to characterize them at single cell level, due to their complex and heterogeneous cell types. In this study, we profiled the transcriptomes of more than 7000 cells derived from maize root tips of seedlings grown on media with (nitrate+) or without nitrate (nitrate-).

overall_design: Single cell and bulk RNA sequencing of two sample of maize root tips

first: Xuhui

last: Li

first: Xiangbo

last: Zhang

first: Shuai

last: Gao

first: Fangqing

last: Cui

first: Lina

last: Fan

first: Yongwen

last: Qi


title: Bruton’s tyrosine kinase (BTK) and indoleamine 2,3-dioxygenase (IDO) block differentiation of inflammatory dendritic cells in tumors [scRNA-seq]

status: Public on Aug 25 2021

city: Augusta

first: Huidong

last: Shi

department: Georgia Cancer Center

institute: Augusta University

summary: Dendritic cells (DCs) are pivotal drivers of anti-tumor immunity, but many of the DCs in tumors appear dysfunctional or immunosuppressive.  Using mouse models, we found that robustly immunogenic DCs can arise by differentiation from immature myeloid precursor cells during inflammation.  In tumors, however, differentiation of these inflammatory DCs was blocked by a cell-intrinsic signaling pathway created by Bruton’s Tyrosine Kinase (BTK) and the tryptophan-degrading enzyme indoleamine 2,3-dioxygenase (IDO).

overall_design: B16F10 tumors were treated with cyclophosphamide (CTX)/ibrutinib/indoximod, and cells isolated from TDLNs 48 hrs after the dose of CTX.  Separate libraries were contructed for the two biological replicate mice in each treatment group, then pooled for scRNA-seq.

last: Munn

first: Chang-Sheng

last: Chang


title: Gene expression profile of Oryza longistaminata ramet pair roots in response to different nitrogen conditions

status: Public on Aug 23 2021

city: Nagoya

first: Hitoshi

last: Sakakibara

address: Chikusa

institute: Nagoya University

summary: Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We analyzed the transcriptomic response of ramet pairs to heterogeneous nitrogen availability by using a split hydroponic system that allowed each ramet root to be exposed to different conditions.

overall_design: The roots of O. longistaminata ramet pair, connected by rhizomes, were incubated in two separate pots for 24 h. One of the roots was treated with the nutrient solution containing 2.5 mM NH4Cl (plus N split), and the other was treated with 0 mM NH4Cl (minus N split). For comparison, both roots were treated with 2.5 mM NH4Cl (plus N) or 0 mM NH4Cl (minus N).

first: Misato

last: Kawai

first: Ryo

last: Tabata

first: Takehiro

last: Kamiya


title: Bruton’s tyrosine kinase (BTK) and indoleamine 2,3-dioxygenase (IDO) block differentiation of inflammatory dendritic cells in tumors


title: Intergenerational inheritance of trained immunity and heterologous resistance to infections

city: Bonn

first: Branko

last: Cirovic

address: Carl-Troll Str 31

institute: LIMES


title: Intergenerational inheritance of trained immunity and heterologous resistance to infections (RNA-seq)

summary: Intergenerational inheritance (Inter-I) of phenotypic characteristics has been demonstrated in plants and invertebrates, with epigenetic modifications playing a role in the inheritance of a variety of features such as appearance1, adaptation to stress, or resistance to infections. Here we provide evidence of Inter-I of transcriptional and epigenetic signatures of trained immunity to the progeny of mice that survived a sublethal systemic Candida albicans infection. Intergenerational trained mice (F1) presented with significant cellular, developmental, transcriptional, and epigenetic changes within the bone marrow resident myeloid effector and progenitor cell compartment. These alterations led to an enhanced responsiveness to in vivo endotoxin challenge and Escherichia coli infection, providing the offspring with protection against heterologous infections. These results argue for the contribution of Lamarckian evolutionary processes to protect against infections in vertebrates.

overall_design:
Male mice were infected with subletal dose of C. albicans. One month after clearance of the infection, ‘resting’ (mock-infected with PBS, F0R) and the ‘trained’ (C. albicans-infected and recovered, F0T) mice were mated with healthy non-infected females. FACS-enriched granulocyte macrophage progenitors (GMP), common monocyte progenitors (cMoPs) and Ly6chigh monocytes (Ly6Ch) from the bone marrow of the offspring (F1T and F1R, respecively) were subjected to transcriptomic analysis by RNA-seq.

***Please note that the sample records have been updated on Feb 9, 2022, as some of the raw files were not correctly matched to the correct samples.

first: Natalie

last: Katzmarski

first: Jorge

last: Domínguez-Andrés

first: Kristian

last: Händler

first: Joachim

middle: L

last: Schultze

first: Evangelos

last: Giamarellos-Bourboulis

first: Andreas

last: Schlitzer

first: Mihai

last: Netea


title: A test of the pioneer factor hypothesis using ectopic liver gene activation [RNAseq]

status: Public on Aug 18 2021

city: St. Louis

first: Barak

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

summary: The Pioneer Factor Hypothesis (PFH) states that pioneer factors (PFs) are a subclass of transcription factors (TFs) that bind to and open inaccessible sites and then recruit non-pioneer factors (nonPFs) that activate batteries of silent genes. We tested the PFH by expressing the endodermal PF FoxA1 and nonPF Hnf4a in K562 lymphoblast cells. While co-expression of FoxA1 and Hnf4a activated a burst of endoderm-specific gene expression, we found no evidence for functional distinction between these two TFs. When expressed independently, both TFs bound and opened inaccessible sites, activated endodermal genes, and “pioneered” for each other, although FoxA1 required fewer copies of its motif to bind at inaccessible sites. A subset of targets required both TFs, but the mode of action at these targets did not conform to the sequential activity predicted by the PFH. From these results we propose an alternative to the PFH where “pioneer activity” depends not on the existence of discrete TF subclasses, but on TF binding affinity and genomic context.

overall_design: To measure expression, we treated clonally derived K562 cell lines that were previously transduced with lentiviral vectors carrying doxycycline-inducible FoxA1, Hnf4a, or both FoxA1-Hnf4a with +/- 0.5µg/ml doxycycline for 24 hours in triplicate. We extracted RNA from 1e6 cells/sample with the PureLink RNA Mini column extraction kit (Invitrogen #12183020) and then treated with on-column DNA digestion with PureLink DNase (Invitrogen #12185010). We then prepared libraries with the NEBNext Ultra II Directional RNA Library Prep Kit, size selected the libraries with AmpureXP beads, and then sequenced them on an Illumina NextSeq 500 using 2x75 paired-end reads.

first: Jeffrey

last: Hansen

first: Kaiser

last: Loell


title: Bruton’s tyrosine kinase (BTK) and indoleamine 2,3-dioxygenase (IDO) block differentiation of inflammatory dendritic cells in tumors [Bulk RNA-seq]

first: Huidong

last: Shi

overall_design: The immature (CD11cNEG Ly6c+c-kit+) cells were sorted from TDLNs of untreated B16F10 tumors, and analyzed by RNA-seq. Three identical replicate experiments were performed (labeled .1, .2, .3).  Results were compared against analysis of publically-available datasets for conventional cDC1 cells.

first: David

last: Munn


title: A test of the pioneer factor hypothesis using ectopic liver gene activation


title: Bruton’s tyrosine kinase (BTK) and indoleamine 2,3-dioxygenase (IDO) block differentiation of inflammatory dendritic cells in tumors [ATAC-seq]

overall_design: To determine if Ly6c+c kit+ precursor cells were epigenetically primed for expression of mature DC genes, immature (CD11cNEG Ly6c+c-kit+) cells were sorted from TDLNs of untreated B16F10 tumors, and chromatin accessibility measured by ATAC-seq.  Results were compared against analysis of publically-available datasets for mature cDC1  and “pre-cDC1” precursors from bone-marrow.    Three identical experiments were performed (labeled rep1, rep2, rep3)


title: lncRNA-CR11538 functions as a decoy of Dif/Dorsal to negatively regulate Drosophila Toll immune responses

status: Public on Aug 13 2021

city: Nanjing

first: Hongjian

last: Zhou

address: No.1 Wenyuan Road, Xianlin University Town, Nanjing

institute: Nanjing Normal University

summary: The maintenance of innate immune homeostasis is critical for animal survival to combat pathogens. Although many positive or negative protein factors have been identified, little is known about the long non-coding RNA that regulates the Toll pathway. Herein, we have discovered a novel lncRNA-CR11538 highly activated during the Drosophila response to gram+ bacterial infection. The transient overexpression of CR11538 inhibited the expression of antimicrobial peptides (Drosomycin and Metchnikowin) in vivo to suppress Toll signaling pathway. Remarkably, core enrichment genes based on RNAseq, subcellular localization and RIP suggest that CR11538 can interact with the transcription factor Dif/Dorsal in nucleus. ChIP-qPCR and dual luciferase report experiments show that CR11538 can sequester Dif/Dorsal away from the promoter thus suppressing the transcription of antimicrobial peptides. In summary, we discovered a novel lncRNA-CR11538 that negatively regulate the Drosophila Toll pathway. It broadens our understanding of the regulatory mechanism of Toll pathway involving lncRNA and provides insights for the research on innate immune system of insects and mammals.

overall_design: the infected M. luteus male adult CR11538-overexpressing and control flies were collected at 12 h post-infection for subsequently RNA-seq

first: Shengjie

last: Li

first: Fei

last: Ma

first: Ping

last: Jin


title: The Protein Complex Ragulator is the Substrate-specific Scaffold for mTORC1 to Regulate Transcription Factor EB

status: Public on Aug 08 2021

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway is activated by nutrition sufficiency signals and extracellular growth signals. mTORC1 acts the hub that integrates these inputs to orchestrate number of cellular responses such as translation, nucleotide synthesis, lipid synthesis, and lysosome biogenesis. However, the scaffold protein which specifically regulates any single downstream signaling molecule has not been identified to date. Here we show the heteropentamer protein complex Ragulator is critically required to regulate nuclear translocation of transcription factor EB (TFEB). We established a unique RAW264.7 clone that lacks Ragulator but maintained total mTORC1 activity. The clone showed a markedly enhanced nuclear translocation of TFEB even in nutrition-sufficient state, despite the full mTORC1 activity. As a cellular phenotype, the number of lysosomes were increased by 10 times in the Ragulator-deficient clone. These findings suggest that mTORC1 essentially requires the scaffold Ragulator to regulate the subcellular location of TFEB. Our finding implicates that mTORC1 has other scaffold proteins that regulate downstream molecules specifically.

overall_design: To investigate the transcriptional activity of TFEB in ΔRagulator cells, we analyzed the transcriptome between ΔRagulator cells in comparison with control cells.

first: Tetsuya

last: Kimura


title: A test of the pioneer factor hypothesis using ectopic liver gene activation [CUTTag]

overall_design: To measure binding, we treated clonally derived K562 cell lines that were previously transduced with lentiviral vectors carrying doxycycline-inducible FoxA1, Hnf4a, or both FoxA1-Hnf4a with +/- 0.5µg/ml doxycycline for 24 hours in duplicate. We then split each uninduced and induced samples and treated with +/- primary antibody followed by a species-specific secondary antibody. Then, we isolated 1e5 cells/sample and followed the CUTANA Direct-to-PCR CUT&Tag protocol from Epicypher. Due to extremely low background in both the uninduced and negative antibody samples and based on recommendation from the lab that developed the technology (Kaya-Okur 2020), we only sequenced +doxycycline +antibody samples. We size selected the libraries with AmpureXP beads and sequenced them on an Illumina NextSeq 500 using 2x150 paired-end reads.


title: A test of the pioneer factor hypothesis using ectopic liver gene activation [ATACseq]

overall_design: To measure accessibility, we treated clonally derived K562 cell lines that were previously transduced with lentiviral vectors carrying doxycycline-inducible FoxA1, Hnf4a, or both FoxA1-Hnf4a with +/- 0.5µg/ml doxycycline for 24 hours in duplicate. We input 2e5 cells/sample into the OMNI-ATAC protocol (Corces et al. 2017) and isolate 5e4 nuclei/sample for tagmentation and library preparation. We size selected the libraries with AmpureXP beads and then sequenced them libraries on an Illumina NextSeq 500 using 2x75 paired-end reads.


title: Inactivation of the response regulator AgrA has a pleiotropic effect on biofilm formation, pathogenesis and stress response in Staphylococcus lugdunensis

status: Public on Aug 16 2021

city: Caen

first: Francois

last: Gravey

state: Normandy

address: Esplanade de la paix

department: Microbiology

institute: Normandy Université

summary: Exploration of the the transcriptomic consequences of the complete deletion of agrA gene in Staphylococcus lugdunensis. Overall, the ΔagrA deletion significantly affected the expression of 400 genes. Among them, 149 were upregulated and 251 were downregulated.

overall_design: Comparison of gene expression between Wild Type and complete agrA deleted gene S. lugdunensis strains.

first: Marion

last: Aubourg

first: Marine

last: Pottier

first: Albertine

last: Léon

first: Benoit

last: Bernay

first: Anne

last: Dhalluin

first: Margherita

last: Cacaci

first: Riccardo

last: Torelli

first: Pierre

last: Ledormand

first: Cecilia

last: Martini

first: Maurizzio

last: Sanginetti

first: Michel

last: Auzou

first: François

first: Jean-Christophe

last: Giard


title: Clonally expanded, GPR15-expressing pathogenic effector Th2 cells are associated with eosinophilic esophagitis

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

institute: MIT

summary: Eosinophilic esophagitis (EoE) is an allergic disorder characterized by the recruitment of eosinophils to the esophagus, resulting in chronic inflammation. We sought to understand the cellular populations present in the esophageal biopsies of patients with EoE and to determine how these populations are altered between active disease and remission. To this end, we analyzed cells from the esophageal biopsies, duodenal biopsies, and peripheral blood of EoE patients in active disease or remission using single-cell RNA and TCR sequencing. We identified gene modules regulated by transcription factors from the NF-κB family that characterize activated eosinophils in patients with active disease. Pathogenic effector Th2 (peTh2) cells present in the esophageal biopsies of patients with active disease expressed unique gene signatures associated with the synthesis of eicosanoids that are predicted to directly promote activation of tissue-resident eosinophils. The tissue-resident peTh2 population also exhibited clonal expansion, suggesting antigen-specific activation. Peripheral CRTH2+CD161- and CRTH2+CD161+ memory CD4+ T cells were enriched for either a conventional Th2 phenotype or a peTh2 phenotype, respectively. These cells also exhibited significant clonal expansion and convergence of TCR sequences, indicating that these cells are expanded in response to a defined set of antigens. The esophagus-homing receptor GPR15 was upregulated by peripheral peTh2 clonotypes that were also detected in the esophagus. Lastly, peTh2 cells and GPR15+ cells were enriched among milk-reactive CD4+ T cells in patients with milk-triggered disease, suggesting that peTh2 cells in EoE are an expanded, food antigen-specific population with enhanced esophagus homing potential.

overall_design:
Analysis of cells from esophageal biopsy, duodenal biopsy, and peripheral blood from patients with eosinophilic esophagitis.

>>> Submitter declares that raw data cannot be published due to patient privacy concerns. <<<

first: D

first: B

last: Ruiter

first: N

last: Smith

first: A

last: Tu

last: Monian

last: Stone

last: Virk-Hundal

first: Q

last: Yuan

first: W

last: Shreffler

first: J

middle: C

last: Love


title: MUC1-C DICTATES NEUROENDOCRINE LINEAGE SPECIFICATION   IN PANCREATIC DUCTAL ADENOCARCINOMAS

city: Boston

first: Yoshihiro

last: Morimoto

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: MUC1-C drives neuroendocrine lineage plasticity in pancreatic adenocarcinomas

overall_design: RNA-seq in PDAC cell lines


title: Discovery of novel hyperthermophilic DNA modifying enzymes using a functional genomics screen

city: Ipswich

first: Paul

last: Caffrey

address: 240 County Road

department: Molecular Enzymology

institute: New England Biolabs

summary: We used RNA-seq to determine expression of Thermococcus kodakarensis genes expressed from fosmids in E. coli

overall_design: Pooled 384 well fosmid plate and determined Thermococcus kodadkarensis transcript levels by RNA-seq.

first: Andrew

middle: F

last: Gardner


title: A novel lncRNA XLOC_032768 rescues cisplatin-induced apoptosis of renal tubular cells and acute kidney injury by repressing TNF-α expression in trans-manner

status: Public on Jul 27 2021

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

overall_design: Refer to individual Series