title: Obesity reprograms the pulmonary polyunsaturated fatty acid-derived lipidome prior to injury in a diet-dependent manner

status: Public on Sep 28 2022

city: Chapel Hill

first: Rafia

last: Virk

state: NC

address: 135 Dauer Drive, Michael Hooker Research Center, Room 2204

institute: University of North Carolina at Chapel Hill

summary: Obesity exacerbates inflammation upon lung injury; however, the mechanisms by which obesity primes pulmonary dysregulation prior to injury are not well studied.  Notably, little is known about how obesity dysregulates pulmonary polyunsaturated fatty acid (PUFA) metabolism that is central to inflammation initiation and resolution.  Herein, we first show that a high fat diet (HFD) administered to C57BL/6J mice increases the relative abundance of pulmonary PUFA-containing triglycerides and the concentration of PUFA-derived oxylipins, independent of an increase in total pulmonary PUFAs, prior to onset of pulmonary inflammation. Experiments with a genetic model of obesity did not recapitulate the effects of the HFD on the pulmonary oxylipin signature, revealing a diet-driven effect.  Subsequent pulmonary next-generation RNA sequencing identified complex and unique transcriptional regulation with the HFD.  The HFD increased pathways related to glycerophospholipid metabolism and immunity, including an elevation in B cell differentiation and signaling.  Finally, computational integration of lipidomic with transcriptomic data revealed novel HFD-driven networks between glycerophospholipid metabolism and B cell receptor signaling with specific PUFA-derived oxylipins. Collectively, these data show obesity dysregulates pulmonary PUFA metabolism prior to lung injury, which may be a mechanism by which obesity primes the lungs to respond poorly upon infectious and/or inflammatory challenges.

overall_design: Lung lipidomic and transcriptomic profile of mice fed a high fat diet versus mice fed a lean diet.

first: Nicole

last: Buddenbaum

first: Abrar

last: Al-Shaer

first: Michael

last: Armstrong

first: Jonathan

last: Manke

first: Nichole

last: Reisdorph

first: Selin

last: Sergin

first: Jenifer

last: Fenton

first: E

last: Wallace

first: Brandie

last: Ehrmann

first: Hannah

last: Lovins

first: Kymberly

last: Gowdy

first: M

last: Smith

first: Saame

last: Shaikh


title: Transcriptome (RNA-Seq) of PPN2-overexpressing S. cerevisiae in normal and alkali conditions

status: Public on Aug 31 2022

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

type: Expression profiling by high throughput sequencing

summary: We present RNA-Seq data obtained from CRN and CRN/pMB1_PPN2 Sc yeast strains showing transcriptome alterations in normal and alkali conditions.

overall_design: The RNA-Seq libraries were constructed from poly(A)-selected RNA in two independent biological replicates.

first: Tatiana

last: Kulakovskaya

first: Dmitry

middle: N

last: Lyabin

first: Irina

middle: A

last: Eliseeva


title: Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [ATAC-Seq]

status: Public on Aug 29 2022

city: Palo ALto

first: Yizhou

last: Zhu

state: CA

address: 3165 Porter Dr, Rm 2260

department: Genetics

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Although the 3D genome architecture is essential for long-range gene regulation, the significance of physical chromatin interactions is challenged by recent findings of mutual insensitiveness between contact propensity and gene expression. Here we report hundred basepair-resolution profiling of chromatin conformation in 33 colon tissues tracing the formation and malignant transformation of colorectal polyps. We identified progressive genome-wide decays of chromatin structures such as interaction stripes and loops on all types of cis-regulatory elements, particularly promoters, independent to the alterations of DNA methylation and chromatin accessibility. Instead of linearly correlated with degree of structural decays, transcription levels shifted toward correction of their quantitative mismatching with corresponding promoter contact propensity. These observations suggest increasing sensitivity of transcription to regulatory architecture integrity along with its loss during early cancer development, a mechanism which may provide novel insights to the misregulations of cancer driving genes.

overall_design: bulk ATAC-seq was performed on 23 colon samples samples representing different stages of CRC progression

middle: P

last: Snyder


title: Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [Hi-C]

overall_design: mHi-C was performed on 33 colon samples samples representing different stages of CRC progression


title: Genetic risk of osteoarthritis operates during human skeletogenesis

status: Public on Oct 26 2022

city: Newcastle upon Tyne

first: Sarah

middle: J

last: Rice

state: Tyne and Wear

address: International Centre for Life, Central Parkway

country: United Kingdom

institute: Newcastle University

summary: Osteoarthritis (OA) is a polygenic disease of older people resulting in the breakdown of cartilage within articular joints. Although a leading cause of disability, there are no disease-modifying therapies. Evidence is emerging to support the origins of OA in skeletogenesis. Whilst methylation QTLs (mQTLs) co-localizing with OA GWAS signals have been identified in aged human cartilage and used to identify effector genes and variants, such analyses have never been conducted during human development. Here, for the first time, we have investigated the developmental origins of OA genetic risk at seven well-characterized OA risk loci, comprising 39 OA-mQTL CpGs, in human fetal limb (FL) and cartilage (FC) tissues using a range of molecular genetic techniques. We compared our results to aged cartilage samples (AC) and identified significant OA-mQTLs at 14 CpGs and 29 CpGs in FL and FC tissues, respectively. Differential methylation was observed at 26 sites between fetal and aged cartilage, with the majority becoming actively hypermethylated in old age. Notably, 6/9 OA effector genes showed allelic expression imbalances during fetal development. Finally, we conducted ATAC-sequencing in cartilage from the developing and aged hip and knee to identify accessible chromatin regions, and found enrichment for transcription factor-binding motifs including SOX9 and FOS/JUN. For the first time, we have demonstrated the activity of OA-mQTLs and expression imbalance of OA effector genes during skeletogenesis. We show striking differences in the spatiotemporal function of these loci, contributing to our understanding of OA aetiology, with implications for the timing and strategy of pharmacological interventions.

overall_design: Cartilage tissue was isolated from the ends of the long bones of the proximal femur (hip) or distal femur (knee) in 12pcw human foetuses. Articular cartilage was taken from the hip or knee of osteoarthritis patients undergoing joint replacement surgery. Chondrocytes were isolated by collagenase treatment of both tissue types and the nuclei isolated. ATAC-seq was then carried out.

first: Abby

last: Brumwell

first: Julia

last: Falk

first: Yulia

middle: S

last: Kehayova

first: John

last: Casement

first: Eleanor

last: Parker

first: Ines

middle: M

last: Hofer

first: Colin

last: Shepherd

last: Loughlin


title: Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [RNA-Seq]

overall_design: mRNA-seq was performed on 24 colon samples samples representing different stages of CRC progression

first: Michael


title: Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development

status: Public on Aug 27 2022

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

overall_design: Refer to individual Series


title: Downstream Effects of Mutations in SOD1 and TARDBP Converge on Gene Expression Impairment in Patient-Derived Motor Neurons

status: Public on Aug 17 2022

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

country: Germany

institute: University Medical Center Rostock

type: Non-coding RNA profiling by high throughput sequencing

summary:
We established iPSCs from healthy donors, SOD1-ALS and TDP43-ALS patients. Using our differentiation protocol originally developed by Reinhardt et al.,2013, we diferentiated these iPSCs toward spinal motor neurons (MNs) and reproduce ALS pathology in a dish. To extend our understanding of finding different molecular mechanisms and pathways related to SOD1- and TDP43 mutations in ALS disease, we have performed a comprehensive gene expression profiling study using RNA-Seq of the iPSC-derived MN models from control individuals and carefully compared with those from SOD1-ALS and TDP43-ALS patients.
To generate novel hypotheses of putative underlying molecular mechanisms in ALS, we used human induced pluripotent stem cell (hiPSCs)-derived motor neurons (MNs) from SOD1- and TARDBP (TDP-43 protein)-mutant-ALS patients and healthy controls to perform high-throughput RNA-sequencing (RNA-Seq). An integrated bioinformatics approach was employed to identify differentially expressed genes (DEGs) and key pathways underlying these familial forms of the disease (fALS). In TDP43-ALS, we found dysregulation of transcripts encoding components of the transcriptional machinery and transcripts involved in splicing regulation were particularly affected. In contrast, less is known about the role of SOD1 in RNA metabolism in motor neurons. Here we found that many transcripts relevant for mitochondrial function were specifically altered in SOD1-ALS, indicating transcriptional signatures and expression patterns can vary significantly depending on the causal gene that is mutated. Surprisingly, however, we identified a clear downregulation of genes involved in protein translation in SOD1-ALS suggesting that ALS-causing SOD1 mutations shift cellular RNA abundance profiles to cause neural dysfunction. Altogether, we provided here an extensive profiling of mRNA expression in two ALS models at the cellular level, corroborating the major role of RNA metabolism and protein translation as a common pathomechanism in ALS

overall_design: We isolated total RNA from iPSC-derived MNs (healthy donor: 3 samples, SOD1-ALS: 2 samples, TDP43-ALS: 3 samples. Total 8 samples) for the gene expression RNA-Seqanalysis (Illumina HiSeq 2500). All of the iPSC lines we used were low passage number (less than 20) and analysis were performed at DIV 30. We isolated  total RNA from iPSC-derived MNs (healthy donor: 3 samples, SOD1-ALS: 2 samples, TDP43-ALS: 3 samples. Total 8 samples) and performed small RNA-seq  (Illumina HiSeq 2500). All of the iPSC lines we used were low passage number (less than 20) and analysis were performed at DIV 30-45.

first: Axel

last: Freischmidt

first: Banaja

last: Dash


title: Three-dimensional connectivity and chromatin environment mediate the activation efficiency of mammalian DNA replication origins

status: Public on Aug 24 2022

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: Genome-wide detection of replication origins by sequencing of short nascent strands (SNS) purified from mouse embryonic stem cells (mESCs).

overall_design: Replication origins were mapped in mESCs grown in control and stress conditions induced by aphidicolin or CDC6 overexpression

first: Karolina

last: Jodkowska

first: Ricardo

last: Almeida

last: Graña-Castro

first: José

last: Fernández-Justel

first: Miriam

last: Rubio-Camarillo

first: María

last: Gómez

first: Juan

last: Méndez


title: Protocol for Mapping Protein-DNA Interactions with Directed Methylation with Long-read Sequecing (DiMeLo-seq)

status: Public on Jul 18 2022

city: Berkeley

first: Aaron

last: Streets

address: Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

summary: DiMeLo-seq uses a protein A Hia5 fusion to direct adenine methylation at specific regions of the genome using antibodies for chromatin-bound factors. Adenine and cytosine methylation are then read out by methylation-sensitive long-read sequencing.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: DiMeLo-seq is performed in situ on H3K27ac, H3K27me3, and H3K4me3 in GM12878 cells. DiMeLo-seq is also performed in situ on H3K9me3 in D. melanogaster embryos.

first: Annie

last: Maslan

first: Nicola

last: s Altemose


title: Transcriptome and chromatin accessibility landscapes across 25 human brain regions expand the susceptibility gene set for neuropsychiatric disorders [RNA-Seq]

status: Public on Aug 25 2022

city: New York

first: Panos

last: Roussos

state: NY

address: 1470 madison ave

institute: Icahn school of medicine at mount sinai

summary:
Brain region- and cell-specific transcriptome and epigenome molecular features are associated with heritability for neuropsychiatric traits. Here, we provide an atlas of chromatin accessibility and gene expression in neuronal and non-neuronal cells across 25 distinct regions across cortical and subcortical areas of the human brain from 6 neurotypical controls. We identified extensive gene expression and chromatin accessibility differences across brain regions. We further identified variation in alternative promoter-isoform usage and enhancer-promoter interactions across brain regions and found genes with distinct promoter-isoform usage are strongly enriched for neuropsychiatric risk variants.
We identified brain region-specific chromatin co-accessibility and gene-coexpression modules that are robustly associated with genetic risk variants for neuropsychiatric disorders. Using an integrative approach, we identify a novel set of genes that is enriched for neuropsychiatric disorders risk variants but is independent of cell-type specific gene expression and annotated pathways. Our results provide a valuable multi-brain region molecular regulation resource and suggest a  unique contribution of epigenetic modifications from the subcortical areas to neuropsychiatric disorders.

overall_design: RNA-seq profiles in neuronal and non-neuronal nuclei isolated from 25 brain regions covering the forebrain, basal ganglia , midbrain/thalamus, and hindbrain of six control subjects

first: John

middle: F

last: Fullard

first: Pengfei

last: Dong

first: Jaroslav

last: Bendl


title: Rewiring of liver diurnal transcriptome rhythms by triiodothyronine (T3) supplementation

status: Public on Jul 26 2022

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

institute: University of Lübeck

summary: Diurnal (i.e., 24-hour) physiological rhythms depend on transcriptional programs controlled by a set of circadian clock genes/proteins. Systemic factors like humoral and neuronal signals, oscillations in body temperature, and food intake align physiological circadian rhythms with external time. Thyroid hormones (THs) are major regulators of circadian clock target processes such as energy metabolism, but little is known about how fluctuations in TH levels affect the circadian coordination of tissue physiology. In this study, a high triiodothyronine (T3) state was induced in mice by supplementing T3 in the drinking water, which affected body temperature, and oxygen consumption in a time-of-day dependent manner. 24-hour transcriptome profiling of liver tissue identified 37 robustly and time independently T3 associated transcripts as potential TH state markers in the liver. Such genes participated in xenobiotic transport, lipid and xenobiotic metabolism. We also identified 10 – 15 % of the liver transcriptome as rhythmic in control and T3 groups, but only 4 % of the liver transcriptome (1,033 genes) were rhythmic across both conditions – amongst these several core clock genes. In-depth rhythm analyses showed that most changes in transcript rhythms were related to mesor (50%), followed by amplitude (10%), and phase (10%). Gene set enrichment analysis revealed TH state dependent reorganization of metabolic processes such as lipid and glucose metabolism. At high T3 levels, we observed weakening or loss of rhythmicity for transcripts associated with glucose and fatty acid metabolism, suggesting increased hepatic energy turnover. In sum, we provide evidence that tonic changes in T3 levels restructure the diurnal liver metabolic transcriptome independent of local molecular circadian clocks.

overall_design: Two to three months-old male C57BL/6J mice were housed in groups of three under a 12-hour light, 12-hour dark (LD, ~300 lux) cycle at 22 ± 2 °C and a relative humidity of 60 ± 5 % with ad-libitum access to food and water. To render mice hyperthyroid (i.e., high T3 levels) the animals received one week of 0.01 % BSA (Sigma-Aldrich, St. Louis, USA, A7906-50G) in their drinking water, followed by two weeks with water supplemented with T3 (0.5 mg/L, Sigma-Aldrich T6397, in 0.01 % of BSA). Control animals received only 0.01 % BSA in the drinking water over the whole treatment period. Methimazole (MMI) is used for hyperthyroidism treatment. At the end of three weeks, mice were sacrificed, and livers were collected every 4h for 24h. RNA was isolated and processed for microarray analysis.

first: Lisbeth

last: Harder

first: Henrik

last: Oster


title: Transcriptome and chromatin accessibility landscapes across 25 human brain regions expand the susceptibility gene set for neuropsychiatric disorders


title: Evaluation of mouse laryngeal inflammation upon low and high dose cigarette smoke exposures via NanoString analysis

status: Public on Jul 13 2022

city: Stanford

first: Meena

last: Easwaran

state: California

address: 240 Pasteur Dr, BMI 1400

summary: Cigarette smoking is a major risk factor for laryngeal diseases. Despite well-documented cigarette smoke (CS) induced laryngeal histopathological changes in animal models and humans, the underlying immunopathological mechanisms remain largely unexplored. The goal of this study was to evaluate inflammatory and immune cell responses in a CS-exposed larynx. Specifically, we investigated these responses in the mouse larynx after a 4-week subacute low (LD) and high-dose (HD) whole-body mainstream CS exposure.

overall_design: Adult C57BL/6 male mice were assigned to air-exposed control ( n = 10) , low dose (LD; n = 12) and high dose (HD; n = 12) cigarette smoke (CS) exposure groups. LD and HD mice were exposed 1h/day and 4h/day to CS respectively for a total of 4 weeks, M-F only. Laryngeal tissues were harvested 24h after the final exposure, for mRNA expression using a NanoString inflammation panel ( n = 6) and neutrophil/macrophage/T-cell immunohistochemistry (IHC) (n = 6).  Out of the 6 samples assigned for NanoString analyses, only 4 per group had stable RIN values and these were subjected to NanoString analysis.

first: Joshua

middle: D

last: Martinez

first: Juyong

middle: B

last: Kim

first: Elizabeth

last: Erickson-DiRenzo


title: Spatiotemporal single-cell regulatory atlas reveals neural crest lineage diversification and cellular function during tooth morphogenesis

status: Public on Jul 14 2022

city: Los Angeles

first: Junjun

last: Jing

address: 2250 Alcazar Street

institute: Center for Craniofacial Molecular Biology, University of Southern California

summary: In this study, using the mouse molar as a model, we took advantage of single-cell transcriptome profiling, lineage tracing and transgenic mouse models to interrogate the cellular heterogeneity and gene regulatory networks (GRNs) of postmigratory CNCCs.In this study, we have put together a dynamic spatiotemporal single-cell regulatory atlas and revealed the landscape of transcriptional heterogeneity and defined the cellular domains during the progression of cranial neural crest cell (CNCC)-derived dental lineage diversification. Importantly, we identified cell type-specific gene regulatory networks (GRNs) during CNCC-derived dental lineage development.

overall_design: Single-cell transcriptomes were obtained from the digestion of the tooth and its surrounding tissue at E13.5, E14.5, E16.5, P3.5 and P7.5


title: An atlas of healthy and injured cell states and niches in the human kidney [Slide-seq2]

status: Public on Oct 10 2022

city: La Jolla

first: Kun

last: Zhang

address: 9500 Gilman Drive

institute: UCSD

summary: Understanding kidney disease relies upon defining the complexity of cell types and states, their associated molecular profiles, and interactions within tissue neighborhoods. We applied multiple single-cell or -nucleus assays (>400,000 nuclei/cells) and spatial imaging technologies to a broad spectrum of healthy reference (45 donors) and diseased (48 patients) kidneys. This has provided a high resolution cellular atlas of 51 main cell types that include rare and novel cell populations. The multi-omic approach provides detailed transcriptomic profiles, epigenomic regulatory factors, and spatial localizations spanning the entire kidney. We further define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive or maladaptive repair, transitioning and degenerative states. Molecular signatures permitted localization of these states within injury neighborhoods using spatial transcriptomics, while large-scale 3D imaging analysis (~1.2 million neighborhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents the most comprehensive benchmark of cellular states, neighborhoods, outcome-associated signatures, and publicly available interactive visualizations.

overall_design:
Slide-Seq2 was performed on kidney (cortex and medulla) tissue pucks from six healthy reference (Ref) individuals. This data was produced as part of the Human BioMolecular Atlas Program (HuBMAP - in the labs of Fei Chen and Evan Macosko) and Kidney Precision Medicine Project (KPMP - in the labs of Fei Chen and Anna Greka).

>>> Submitter declares that the raw data are deposited in HuBMAP due to patient privacy concerns. <<<

first: Blue

last: Lake

first: Kian

last: Kalhor

first: Evan

last: Murray

first: Amanda

last: Knoten

first: Diane

last: Salamon

first: Joseph

last: Gaut

first: Jamie

middle: L

last: Marshall

first: Teia

last: Noel

first: Anna

last: Greka

first: Fei

last: Chen

middle: Z

last: Macosko

first: Sanjay

last: Jain


title: A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys [RNA-seq]

status: Public on Jun 27 2022

city: Nanjing

first: Dijun

state: Jiangsu

address: Xianlin

department: Life Sciences

country: China

institute: Nanjing University

summary: Non-human primates (NHP) are attractive laboratory animal models that accurately reflect both developmental and pathological features of humans. Here we present a compendium of cell types from the cynomolgus monkey Macaca fascicularis (denoted as ‘Monkey Atlas’) using both single-cell chromatin accessibility (scATAC-seq) and RNA sequencing (scRNA-seq) data at the organism-wide level. The integrated cell map enables in-depth dissection and comparison of molecular dynamics, cell-type composition and cellular heterogeneity across multiple tissues and organs. Using single-cell transcriptomic data, we inferred pseudotime cell trajectories and cell-cell communications to uncover key molecular signatures underlying their cellular processes. Furthermore, we identified various cell-specific cis-regulatory elements and constructed organ-specific gene regulatory networks at the single-cell level. Finally, we performed a comparative analysis of single-cell landscapes among mouse, cynomolgus monkey and human, and we showed that cynomolgus monkey has significantly higher degree of cell-type similarity to human than mouse. Taken together, our study provides a valuable resource for NHP cell biology.

overall_design: The cynomolgus monkey project included 20 RNA samples

first: Yang

last: Sun

first: Yicheng

last: Xie

first: Jiao

last: Qu

first: Fa

last: Yang

first: Tao

last: Zhu


title: A pilot study of the Bruton's tyrosine kinase inhibitor ibrutinib in combination with nivolumab in patients with metastatic solid tumors

status: Public on Jun 24 2022

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

summary:
Background: Preclinical work has demonstrated that ibrutinib inhibits the generation, migration and immunosuppressive function of myeloid-derived suppressor cells (MDSC). A pilot study tested the combination of ibrutinib and nivolumab in patients with metastatic solid tumors.
Methods: Sixteen patients with metastatic solid malignancies were treated with ibrutinib (420 mg) daily and nivolumab (240 mg) IV on days 1 and 15 of 28 day cycles.  Ibrutinib dosing started 7 days before cycle 1 of nivolumab and was given until cycle 1, day 8 of nivolumab. The effect of ibrutinib alone and in combination with nivolumab on circulating MDSC and immune subsets and cytokine/chemokine levels were measured. Single-cell RNA and TCR sequencing was also performed.
Results: The most common treatment-related AEs were fatigue (31%) and anorexia (31%). Five patients had a clinical response (4 partial, 1 complete). Four patients had stable disease at 3 months. Median progression-free survival was 3.5 months and median overall survival 10.8 months. MDSC levels increased following 7 days of single-agent ibrutinib compared to baseline (21.91% vs. 27.67%). There was increased T cell proliferation in response (33.9% vs. 40.06%, p<0.01) to the combination regimen. Plasma levels of CCL2, CCL3, CCL4, CCL13, IL- 8, and VEGF-α decreased with ibrutinib treatment. Ibrutinib treatment altered the transcriptional state of the myeloid cell compartment and led to increased cancer-associated TCR clonotypes.
Conclusion: The combination of ibrutinib and nivolumab was well tolerated and ibrutinib significantly impacted MDSC and T cell function in patients with solid metastatic tumors.

overall_design: 16 patients with metastatic solid tumors were treated with a combination of ibrutinib and nivolumab.  Samples were collected before administration of ibrutinib on day minus 7 and before administration of nivolumab on day plus 1.  Samples are therefore reflective of "baseline" and "on ibrutinib" conditions.  28 paired and 2 unpaired (30 total) samples were obtained for single cell RNA sequencing.

middle: W

first: William

middle: E

last: Carson


title: The natural compound atraric acid suppresses androgen-regulated neo-angiogenesis of castration‑resistant prostate cancer through angiopoietin 2

status: Public on Jun 23 2022

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

summary: Castration‑resistant prostate cancer (CRPC) is an aggressive lethal form of prostate cancer (PCa), which presents a major therapeutic challenge. Here, we show that the natural compound, atraric acid (AA), inhibits not only the androgen receptor (AR) but also targets those AR-mutants that confer therapy resistance to other clinically used AR-antagonists indicating a different mode of AR-antagonism. AA induces cellular senescence in CRPC and inhibits CRPC tumour growth in vivo xenograft model. The secretome of CRPC cells induces androgen-dependent angiogenesis, which is counteracted by AA regulated senescence-associated secretory phenotype (SASP) in two in vitro models using primary human endothelial cells. In line with this, in tumours, vessel number is decreased in the mouse group treated with AA suggesting the repression of intratumoural neo-angiogenesis by AA. Transcriptome sequencing and mass spec analysis of the secretome revealed upregulated angiogenic pathways by androgen, however, being VEGF-independent and pointing to the secretion of the pro-angiogenic factor angiopoietin 2 (ANGPT2) induced by androgens and repressed by AA as a key driver of neo-angiogenesis. In agreement with this, AA treatment of native patient-derived PCa tumour samples ex vivo inhibits ANGPT2 expression. Mechanistically, besides AA, immune-depletion of ANGPT2 or blocking ANGPT2-receptors inhibits androgen-induced angiogenesis. Taken together, we reveal a VEGF-independent ANGPT2 pathway targeted by AA to inhibit androgen-regulated neo-angiogenesis.

overall_design: Transcriptional profile of C4-2 cells treated with androgen receptor ligands

first: Marzieh

last: Ehsani

first: Seyed

first: Lisa

last: Adam

first: Francesco

last: Neri

first: Aria

last: Baniahmad


title: Effect of glucocorticoid receptor deletion on gene expression of cardiomyocytes at neonatal and early postnatal stages

status: Public on May 16 2022

city: Bologna

first: Gabriele

last: D'Uva

address: via Massarenti 9

country: Italy

institute: University of Bologna


title: Neurons and astrocytes elicit brain region specific transcriptional responses to prion disease in the murine CA1 and thalamus

status: Public on Apr 28 2022

city: Winnipeg

first: Jessy

middle: Andrew

last: Slota

state: Manitoba

address: 1015 Arlington St.

department: One Health Division

country: Canada

institute: National Microbiology Laboratory; Public Health Agency of Canada

summary: Progressive dysfunction and loss of neurons ultimately culminates in the symptoms and eventual fatality of prion disease, yet the pathways and mechanisms that lead to neuronal degeneration remain elusive. Here, we used RNAseq to profile transcriptional changes in microdissected CA1 and thalamus brain tissues from prion infected mice. Numerous transcripts were altered during clinical disease, whereas very few transcripts were reliably altered at pre-clinical time points. Prion altered transcripts were assigned to broadly defined brain cell types and we noted a strong transcriptional signature that was affiliated with reactive microglia and astrocytes. While very few neuronal transcripts were common between the CA1 and thalamus, we described transcriptional changes in both regions that were related to synaptic dysfunction. Using transcriptional profiling to compare how different neuronal populations respond during prion disease may help decipher mechanisms that lead to neuronal demise and should be investigated with greater detail.

overall_design: comparitive transcriptional profiling of RNAseq data from the hippocampal CA1 region and thalamus of mice that were intraperitoneally inoculated with RML mouse adapted scrapie, or mock infected

first: Sarah

last: Medina

first: Kathy

last: Frost

first: Stephanie

last: Booth


title: RNA-Seq of Mytilus galloprovincialis's hepatopancreas

status: Public on May 15 2022

city: San Giuliano Terme

first: Paolo

last: Aretini

state: Pisa

address: Via Ferruccio Giovannini 13

institute: Fondazione Pisana per la Scienza

summary: Contaminants of Emerging Concern (CECs) are a class of chemicals that can spread throughout the environment causing adverse biological and ecological effects. Through the different classes of CECs, the occurrence of pharmaceutical drugs such as natural and synthetic estrogens, is well documented in the aquatic environment. In this study mussels (Mytilus galloprovincialis), chosen as model organism, were exposed to the synthetic hormone 17 α-Ethinylestradiol (EE2), the primary component in contraceptive pills. Mussels were exposed to a single concentration of EE2 ( 5 ng/L) of EE2 in a semi-static and time-dependent experiment. The total period of exposure was 28 days and the mussels were analysed 14 days (T14) and 28 days (T28) after treatment. RNA-Seq analysis showed signs of stress with significant differential expression at 99 genes (T14 compared to controls), 73 genes (T28 compared to controls) and 103 DEGs after two weeks of exposure. EE2 treatment resulted in up-regulation of 3 gene/proteins for lipid transport/metabolism and 7 gene/proteins upregulated encoding immune and antibacterial function.

overall_design: Two set of individuals exposed at 5 ng/l of EE2 for 14 and 28 days

first: Mariella

last: Baratti

first: Carlo

last: Pretti


title: Gene expression profile at single cell level yeast cells under stress

status: Public on Apr 26 2022

city: Stockton

first: Yangqi

last: Su

address: 4142 E Morada Ln, Apt 6303

department: Bioinformatics

institute: UNC Charlotte

summary: To understand transcriptomic changes in baker’s yeast S. cerevisiae cells under stress conditions, we sequenced 117 yeast cells under three stress treatments (hypotonic condition, glucose starvation and amino acid starvation) using a full-length based single-cell RNA-Seq method. We found that though single cells from the same treatment showed varying degrees of uniformity, technical noise and batch effects can confound results significantly. However, upon careful selection of samples to reduce technical artifacts and account for batch-effects, we were able to capture distinct transcriptomic signatures for different stress conditions. Our results show that a full single cell based transcriptomic analysis of the yeast may help paint a clearer picture of how the model organism responds to stress than do bulk cell population-based methods.

overall_design: Yeast single cells were subject to three different stress treatments (hypotonic condition, glucose starvation and amino acid starvation) and sequenced using a full-length single cell RNAseq protocol

first: Chen

last: Xu

first: Jonathan

last: Shea

first: Darla

last: DeStephanis

first: Zhengchang


title: Gene expression profile of yeast cells under stress [bulk RNA-seq]


title: Gene expression profile of yeast cells under stress

overall_design:
Refer to individual Series

The file at the foot of this records contains the TPM values for all samples in this SuperSeries.


title: RNA-seq analysis of BAP1 mutant and wild-type uveal melanoma cell lines

status: Public on Apr 25 2022

city: Philadelphia

first: Andrew

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

summary: Inactivating mutations of BAP1 are associated with an increased risk of developing metastasis in uveal melanoma (UM), but the roles of BAP1 in UM progression is unclear. To characterize BAP1’s functions in UM, we performed RNA sequencing on BAP1 wild-type and mutant UM cell lines. Differential analysis revealed that BAP1 loss is associated with an upregulated gene expression profile of multiple cell adhesion molecules (CAMs), including E-cadherin (CDH1), cell adhesion molecule 1 (CADM1), and syndecan-2 (SDC2).

overall_design: RNA was isolated from BAP1 wild-type (92.1) and mutant (WM3618F and MM28) UM cell lines.

first: Usman

last: Baqai

first: Timothy

last: Purwin

first: Anna

last: Han


title: Brominated carbazole's antibiotic adjuvant effects in MRSA 43300

status: Public on Apr 14 2022

city: High Point

first: Heather

middle: Bennett

last: Miller

address: One University Parkway

department: Chemistry

institute: High Point University

summary: Methicillin-resistant Staphylococcus aureus (MRSA) is a major threat to human health, as the US mortality rate outweighs those from HIV, tuberculosis, and viral hepatitis combined. In the wake of the COVID-19 pandemic, antibiotic resistant bacterial infections acquired during hospital stays have increased. Instead of designing and deploying new antibiotics which MRSA would quickly develop resistance to, adjuvants are a key strategy to combatting these bacteria. We have evaluated several small molecule adjuvants that have strong potentiation with β-lactam antibiotics and have now investigated at the molecular level how the lead adjuvant exerts its effects. We hypothesized that the expression levels of key resistance genes would decrease once cotreated with a β-lactam antibiotic (oxacillin) and the adjuvant (compound 8). Furthermore, bioinformatic analyses would reveal biochemical pathways enriched in differentially expressed genes. RNA-seq analysis showed 176 and 233 genes significantly up and downregulated, respectively, upon cotreatment with oxacillin and compound 8. We identified four subclusters of genes that were regulated in similar patterns in response to drug treatment. Many of these genes displayed a similar pattern of expression where they were unaffected by compound 8 treatment alone, upregulated upon antibiotic challenge, and downregulated again upon cotreatment. GO categories that were significantly enriched among downregulated genes involved carbohydrate utilization and/or transport. Most of the biochemical pathways enriched with significantly downregulated genes involved carbohydrate utilization, such as the citric acid cycle (p=6.4x10-6) and the phosphotransferase system (p=1.8x10-5). The most populated pathway was S. aureus infection (p=3.0x10-3). Creating a network of affected gene products helped uncover potential master regulators for further investigation. This study revealed a dramatic impact of our lead adjuvant on the transcriptome that is consistent with a pleiotropic effect. These results point to this adjuvant as having potential broad therapeutic use in combatting MRSA infections.

overall_design: Differential gene expression was examined between MRSA cultures either untreated, treated with oxacillin only, treated with an antibiotic adjuvant (compound 8), or cotreated with oxacillin and compound 8. Each of the four treatments was performed with biological triplicates.


title: Transcriptome and chromatin accessibility landscapes across 25 human brain regions expand the susceptibility gene set for neuropsychiatric disorders [ATAC-Seq]

first: Panos

last: Roussos

first: John

last: Fullard

first: Pengfei

last: Dong

first: Jaroslav

last: Bendl


title: Mapping Human Transient Transcriptomes Using Single Nucleotide Resolution 4sU Sequencing (SNU-Seq)

status: Public on Apr 01 2022

city: Oxford

first: Jane

last: Mellor

address: South Parks Road

department: Biochemistry

institute: University of Oxford

summary: Genomes are pervasively transcribed leading to stable and unstable transcripts that define functional regions of genomes and contribute to cellular phenotypes. Defining comprehensive nascent transcriptomes is pivotal to understand gene regulation, disease processes, and the impact of extracellular signals on cells. However, currently employed methods are laborious, technically challenging and costly. We developed single-nucleotide resolution 4sU-sequencing (SNU-Seq), involving pulse labelling, biotinylation and direct isolation of nascent transcripts. Artificial poly-(A)-tailing of the 3’ most nucleotide of nascent transcripts ensures oligo-d(T) primer-based library preparation and sequencing using commercial 3’ RNA-Seq kits. We show that SNU-Seq is a cost-effective new method generating even read profiles across transcription units. We used SNU-Seq to identify transcription elongation parameters, to map usage of polyadenylation (PAS) sites and novel enhancers. Remarkably, 4sU labelled nascent RNA accumulates short ~100nt transcripts that map to the 5’ end of genes. We show that isolation of these short nascent RNA and sequencing the 5’ and 3’ ends using size-selected SNU-Seq (ssSNU-Seq) provides highly sensitive annotations of mapped and novel TSSs, promoter-proximal pause/termination sites. Thus, SNU-seq and ssSNU-seq combined yield comprehensive transcriptomics data at low cost with high spatial and temporal resolution.

overall_design:
To develop SNU-Seq and size-selected SNU-Seq for measuring nascent transcription at high resolution.
There are 3 different sample types reported here; SNU-seq, size-selected SNU-seq, and TT-seq. There are 11 different samples. All samples are from HEK293 cell and are spike-in controlled with 3 thiolablled 1kb long fragments from yeast with a 42% GC content. TT-seq samples are a time series - 10,15, 20 mins labelling with 4sU with 1 reapeat (samples 4 to 9) or cells untreated or treated with alpha amanitin during a 5 min pulse label with 4sU (samples 10 and 11). For samples 4 to 11 libraries were prepared using the NEBNext II Ultra Directional RNA library and sequenced on the Illumina NextSeq 500 platform using the High-Output Nextseq 500 kit. For each sample 4 to 9 there are 4 processed files (two repeats (A and B) and reads on the forward (F) and reverse (R) strand) and 16 raw samples per time point with R1 and R2 series representing the paired-ends. For samples 10 and 11 there is one repeat, 2 processed files and 8 raw files per sample with R1 and R2 representing the paired ends. SNU-seq samples were thiolabelled for 10 minutes with 4sU and after adding a polyA track to the 3' end, sequenced from the 3' polyA tail using the Quant-Seq Lexogen 3' mRNA kit on the Ion Proton platform. There are two raw data files representing two repeats (17 and 18). There are six processed files representing the merged data on each strand for the full SNU-seq read out primed from the artifical polyA tail, the 3 prime read on each strand (SNU-seq readout) and the 3 prime read after removal of internal polyA tracks >8nts. Size-selected SNU-seq samples (ssSNU-seq) were labelled as for the SNU-seq but the polyadenylation step was omitted. Instead 50-100bp thiolabelled RNA fragments were selected from the nascent thiolabelled RNA using a gel, adaptors ligated to the 5' or 3' ends and sequenced using an NEBNext Small RNA library kit on the Illumina platform.There are 4 raw data files and four processed files, two for the 5' ends and two for the 3' ends on each strand. In summary there are 24 processed files and 70 raw data files.

first: Philipp

last: Lorenz

last: Lamstaes

first: Shidong

last: Xi

first: Struan

last: Murray


title: Temporal Dynamics of HCMV Gene Expression in Lytic and Latent Infections

status: Public on Mar 29 2022

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Primary infection with Human cytomegalovirus (HCMV) results in a persistent lifelong infection due to its ability to establish latent infection. During productive HCMV infection, viral genes are expressed in a coordinated cascade that is characteristic of all herpesviruses and traditionally relies on the dependencies of viral genes on protein synthesis and viral DNA replication. In contrast, the transcriptional landscape associated with HCMV latency is still disputed and poorly understood. Here, we examine viral transcriptomic dynamics during the establishment of both productive and latent HCMV infections. These temporal measurements reveal that viral gene expression dynamics along productive infection and their dependencies on protein synthesis and viral DNA replication, do not fully align. This illustrates that the regulation of herpesvirus genes does not represent a simple sequential transcriptional cascade and surprisingly many viral genes are regulated by multiple independent modules. Using our improved classification of viral gene expression kinetics in conjunction with transcriptome-wide measurements of the effects of a wide array of chromatin modifiers, we unbiasedly show that a defining characteristic of latent cells is the unique repression of immediate early (IE) genes. In particular, we demonstrate that IE1 (a central IE protein) expression is the principal barrier for achieving a full productive cycle. Altogether, our findings provide an unbiased and elaborate definition of HCMV gene expression in lytic and latent infection states.

sample_organism:
Homo sapiens
Human betaherpesvirus 5

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: For the time course analysis fibroblasts and CD14+ monocytes were infected with the same stock of HCMV strain TB40E-GFP at a multiplicity of infection (MOI) of 1 and 10, respectively. For all other experiments CD14+ monocytes or THP1 cells were infected with HCMV strain TB40E-GFP at an MOI of 5. Cells were incubated with the virus for 2h, washed, and supplemented with fresh medium. CHX was added to infected fibroblasts and CD14+ monocytes immediately after infection at a final concentration of 100 ug/ml and 200 ug/ml or at 100 ug/ml, respectively. PFA was added to fibroblasts and CD14+ monocytes immediately after infection at a final concentration of 400 ug/ml. for epigenetic drug treatments - 48 hpi, TB40-infected CD14+ monocytes were divided into 1.2 ml tubes containing ~100,000 cells per tube and inhibitors or DMSO for negative control were added to a final concentration of 1uM for 24 hours

first: Batsheva

last: Rozman

first: Aharon

last: Nachshon

first: Michal

last: Schwartz


title: RNA-Seq analysis of CD115- monocytes and CD115+ monocytes from naïve and tumor-bearing mice

status: Public on Mar 22 2022

city: Seoul

first: Yunyun

last: Zou

address: 103 Daehak-ro, Jongno-gu,

country: South Korea

institute: Seoul National Universiry

summary:
Purpose: The goals of this study are to compare CD115- monocytes to CD115+ monocytes from naïve and tumor-bearing mice (EL4) with high-throughput data analysis.
Methods: CD115- monocytes and CD115+ monocytes were sorted by flow cytomentry separatly. Total RNA was extracted from cells using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) and residual DNA was removed with a DNA-free Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions. Samples were loaded onto a 1% agarose gel before electrophoresis. DNA-free conditions were confirmed by SYBR Gold staining (Invitrogen). The quantity and the quality of RNA was evaluated by Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific) and bioanalyzer (Agilent 2100; Agilent Technologies, Santa Clara, CA, USA). RNA-Seq libraries were prepared with 1 μg of total RNA from two biological replicates of each group using TruSeq Stranded mRNA LT Sample Prep Kit and analyzed by Illumina Sequencer (both from Illumina, San Diego, CA, USA).
Results: We found 1,723 differetially expressed genes (DEGs) between CD115- monocytes and CD115+ monocytes (cutoff value was set at 2-fold). DEGs of interest are invoved in granulocyte,  transcription factors, mononuclear phagocytes, and angiogenesis.
Conclusions: Our study represents the first detailed DEGs analysis of CD115- monocytes and CD115+ monocytes from naïve and tumor-bearing mice. Our results show that CD115- monocytes may have a closer relationship with neutrophils or PMN-MDSCs than the CD115+ monocytes. Also, our overall transcriptomic analysis further suggests that CD115- M-MDSCs and monocytes are separate subsets of monocytic cells.

overall_design: Examination of CD115- monocytes and CD115+ monocytes from naïve and tumor-bearing mice

first: Sang-Uk

last: Seo


title: TGFβ reprograms TNF stimulation of macrophages towards osteoclastogenesis [RNA-seq]

status: Public on Mar 24 2022

city: NEW YORK

first: Kazuki

last: Inoue

state: New York

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

summary: TNF plays a key role in inflammation and bone resorption. However, the mechanisms regulating TNF-mediated osteoclastogenesis remain largely unclear because its direct osteoclastogenic ability is weak. Here, we found that TGFβ priming enables TNF to effectively induce osteoclastogenesis from macrophages, independently of the osteoclastogenic action of RANKL. Lack of TGFβ signaling in macrophages suppresses inflammatory, but not physiological, osteoclastogenesis and bone resorption in vivo. Mechanistically, TGFβ priming reprograms macrophage response to TNF towards osteoclastogenesis by remodeling chromatin accessibility and histone modification. TGFβ and TNF induce an unconventional osteoclastogenic program, which includes the suppression of the TNF-induced IRF1-IFNβ-IFN stimulated gene (ISG) axis, promotion of IRF8 degradation and B-Myb induction. These mechanisms are present in RA, in which TGFβ level is elevated and correlated with osteoclast activity. Our findings identify a function and mechanism of action for TGFβ in TNF-mediated inflammatory osteoclastogenesis, and open avenues for selective treatment of inflammatory bone loss.

overall_design: Analysis of transcriptional changes in human macrophages with or without TGFb priming in the presence of TNF

first: Baohong

last: Zhao

first: Yuhan

last: Xia


title: TGFβ reprograms TNF stimulation of macrophages towards osteoclastogenesis [ATAC-seq]

overall_design: Analysis of chromatin accessibility changes in human macrophages with or without TGFb priming in the presence of TNF


title: TGFβ reprograms TNF stimulation of macrophages towards osteoclastogenesis

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

overall_design: Refer to individual Series


title: RNA Sequencing Analysis of the gonadal adipose tissue and liver from PEP Wild Type, heterozygotes and knock out mice.

status: Public on Mar 13 2022

city: Cambridge

first: Vanessa

last: Pellegrinelli

address: Metabolic Research Labs (BX289) Addenbrookes Site, Keith Day Road, Institute of Metabolic Science

institute: Wellcome Trust Research Laboratories

summary: Purpose: Peptidase D (PEP) plays a vital role in collagen turnover by degrading proline-containing dipeptides but its specific functional relevance in adipose tissue is unknown. The goal of this study is to compare  transcriptome profiling (RNA-seq) in the gonadal adipose tissue and liver of wild type mice and mice where PEP has been ablated either partially (heterozygotes) or totaly (knock out).

overall_design: We performed RNA-Sequencing of the liver of PEPWT,  HET, and KO mice fed chow, control diet, Alios diet and HFD 45 %. Total liver RNA was extracted and quality checked (RIN >7).  1ug of RNA was used to construct barcoded sequencing libraries . All the libraries were validated  and then multiplexed and sequenced on two lanes of Illumina HiSeq 4000.

first: Sergio

last: Rodriguez-Cuenca

first: Christine

last: Rouault

first: Elizabeth

last: Figueroa-Juarez

first: Hanna

last: Schilbert

first: Samuel

last: Virtue

first: José

last: Moreno-Navarrete

first: Guillaume

last: Bidault

first: María

last: del Carmen Vázquez-Borrego

first: Ana

middle: R

last: Dias

first: Boas

last: Pucker

first: Martin

last: Dale

first: Mark

last: Campbell

first: Stefania

last: Carobbio

first: Yu-Hung

last: Lin

first: Michele

last: Vacca

first: Judith

last: Aron-Wisnewsky

first: Silvia

last: Mora

first: Mauro

last: Masiero

first: Anastasia

last: Emmanouilidou

first: Subhankar

last: Mukhopadhyay

first: Gordon

last: Dougan

first: Marcel

last: den Hoed

first: Ruth

last: Loos

last: Fernández-Real

first: Davide

last: Chiarugi

first: Karine

last: Clément

first: Antonio

last: Vidal-Puig


title: GLI transcriptional repression is inert prior to HH pathway activation

status: Public on Jan 21 2022

city: Austin

first: Steven

middle: A.

last: Vokes

state: Texas

address: 2500 Speedway, STOP A5000

department: Molecular Biosciences

institute: University of Texas at Austin

summary:
Purpose: Most Hedgehog responsive gene expression is mediated through GLI de-repression. Additionally GLI -repression is proposed to play roles in limb pre-patterning before HH pathway activation. This study evaluates if GLI repression is established prior to HH pathway activation.
Methods: To determine if GLI-repression is established prior to pathway activation, we used genomic approaches to study GLI-mediated repression using the mouse developing limb as a model. We identified pre-HH (E9.25, 21-23S) and post-HH (E10.5, 32-25S) GLI3 binding regions using CUT&RUN for endogenous FLAG-tagged GLI3 proteins. Using a combination of ChIP-seq, CUT&RUN, CUT&Tag, ATAC-seq and RNA-seq, we tested whether loss of Gli3 prior to HH signaling was able to de-repress genes and enhancers, as it does after HH signaling.
Results: Prior to HH signaling, GLI3 binds to poised, accessible regions with histone deacetylase (HDAC) proteins, similar to post-HH signaling. Despite GLI3 binding to most regions as it does in the post-HH limb, loss of Gli3 is unable to prematurely active target genes or enhancers. Furthermore, we find that GLI3-dependent chromatin compaction does not occur until roughly 10 hours after HH signaling would have normally been induced. Collectively, these results support that GLI repressor proteins are inert prior to HH pathway activation.

overall_design: ChIP-seq, CUT&RUN, CUT&Tag, ATAC-seq and RNA-seq on pre-HH (E9.25, 21-23S) and post-HH (E10.5, 32-25S) forelimb buds.

first: Rachel

middle: K

last: Lex

first: Weiqiang

last: Zhou

first: Hongkai

last: Ji


title: A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys

first: Dijun

last: Chen


title: D2.0R mouse breast cancer cells cultured on stiff or soft ECM hydrogels

status: Public on Dec 21 2021

city: PADOVA

first: SIRIO

last: DUPONT

state: PD

address: VIA BASSI 58/B

department: Department of Molecular Medicine

institute: University of Padua

summary: Metastatic breast cancer cells disseminate to organs with a soft microenvironment. Whether and how tissue mechanical properties influence their response to treatment remains unclear. Here we found that a soft ECM empowers redox homeostasis. Cells cultured on a soft ECM display increased peri-mitochondrial F-actin promoted by Spire1C and Arp2/3 nucleation factors, and increased DRP1- and MIEF1/2-dependent mitochondrial fission. Changes in mitochondrial dynamics lead to increased mtROS production and activate the NRF2 antioxidant transcriptional response, including increased cystine uptake and glutathione metabolism. This retrograde response endows cells with resistance to oxidative stress and ROS-dependent chemotherapy drugs. This is relevant in a mouse model of metastatic breast cancer cells dormant in the lung soft tissue, where inhibition of DRP1 and NRF2 restored cisplatin sensitivity and prevented disseminated cancer cell awakening. We propose that targeting this mitochondrial dynamics- and redox-based mechanotransduction pathway could open new avenues to prevent metastatic relapse.

overall_design: D2.0R mouse breast cancer cells stably expressing lentiviral pLKO.1 shCONTROL cultured for 24 h on plastics, on Collagen-1-coated stiff (E=50kPa) acrylamide hydrogels, and on soft (E=0,2 kPa) hydrogels. Three independent biological replicates cultured in parallel in a single experiment were sequenced.

first: Sirio

last: Dupont

first: Patrizia

last: Romani

first: Mattia

last: Arboit


title: Expression data of murine T-ALL OT-1 (Tot-1si) with early expression of mature alphabeta TCR

status: Public on Jun 28 2022

city: Columbia

first: Kimberly

middle: G

last: Laffey

state: Missouri

address: 1030 Hitt Street

department: Molecular Microbiology and Immunology

institute: University of Missouri

type:
Expression profiling by array
Third-party reanalysis

summary: In mice and humans, an immature CD4-CD8- double negative (DN) thymocyte subset expresses early, mature αβTCR. These early αβTCR+ DN (EADN) cells are susceptible to leukemogenesis in both species. Using the OT-1 TCR transgenic system to model EADN-stage αβ TCR expression, we found that EADN cells show coreceptor-independent reactivity to MHC, and their TCR:MHC dependent signals can drive T-ALL transformation. We generated gene expression data from OT-1 leukemic cells and assessed their developmental stage by comparing to wild-type thymocyte subsets.

overall_design: CD4-CD8- OT-1 TCR+ leukemic cells (Tot-1si cells) were adapted to in vitro culture from the leukemic spleen of a T-ALL tumor bearing OT-1 mouse. Total RNA was extracted from cultured cells and gene expression profiling was done using Affymetrix Mouse Gene 1.0 ST Array. Tot-1si microarray data were analyzed with data of 30 wild-type thymocyte subsets from ImmGen (GSE15907). All raw datasets were preprocessed together for background correction and RMA normalization.


title: ATF6-Mediated Signaling Contributes to PARP Inhibitor Resistance in Ovarian Cancer

city: Denver

first: Benjamin

last: Bitler

state: CO

department: OB-GYN

institute: The University of Colorado

summary: The overall goal of this study was to link AP-1 signaling and DNA damage repair in the context of PARPi resistance

overall_design: RNA-seq was used to identify genes and pathways deregulated upon shRNA-mediated knockdown of ATF6 in PARPi resistant high grade serous ovarian cancer cell line PEO1-OR

first: Alexandra

last: McMellen

first: Tomomi

last: Yamamoto

first: Lubna

last: Qamar

first: Brooke

last: Sanders

first: Amber

last: Berning

first: Miriam

last: Post

first: Joshua

last: Johnson

first: Kian

last: Behbahkt

first: Elmar

last: Nurmemmedov


title: Opposite response of hTERT expression by androgen dose: Androgen-mediated inhibition of hTERT is mediated by the ING1 and ING2 tumor suppressors in prostate cancer cells

status: Public on Mar 04 2022

first: Seyed Mohammd Mahdi

last: Rasa

summary: The catalytic subunit of the human telomerase (hTERT) is activated during tumorigenesis in many cancers including prostate cancer (PCa). Androgens mediate their effect through the androgen receptor (AR), a key factor controlling PCa growth. hTERT expression is known to be regulated by androgens, however contrarily observed to be inhibited or activated. Here, we reveal that androgens repress or activate hTERT expression in a concentration-dependent manner. Low physiological androgen levels activate while supraphysiological androgen levels (SAL) repress hTERT expression. We confirmed SAL-mediated gene repression of hTERT in native human PCa samples derived from patients treated ex vivo as well as in cancer spheroids derived from androgen-dependent and castration resistant PCa (CRPC) cells. Interestingly, based on chromatin immunoprecipitation (ChIP) data both a positive androgen response element (pARE) at -4kb distal and a negative response element (nARE) at the proximal -0.1kb promoter region were identified. Focusing on the nARE it was narrowed down to -121 to -58 bp in the core promoter region. ChIP experiments confirmed an androgen-dependent recruitment of AR and the tumor suppressors inhibitor of growth 1 and 2 (ING1 and ING2), recently identified as AR co-repressors. Mechanistically, the knockdown of either ING1 or ING2 reduced androgen-mediated repression of hTERT indicating that ING1 and ING2 mediate AR-regulated transrepression on the hTERT expression. Thus, our data suggest a dual, biphasic function of AR to control hTERT expression by transactivation and transrepression. The inhibition of hTERT by androgens by a nARE located in the proximal promoter region is mediated at least in part by the AR co-repressors ING1 and ING2.

overall_design: Transcriptional profile of C-42 and LNCaP cells upon androgen treatment.

first: Sophie

last: Bartsch

first: Kimia

last: Mirzakhani

first: Marzieh

last: Ehsani

first: Seyed

first: Francesco

last: Neri

first: Aria

last: Baniahmad


title: Single-cell RNA sequencing of the rat carotid arteries uncovers mechanisms of in-stent restenosis

status: Public on Dec 29 2021

city: China

first: aiqun

last: chen

address: Changlelu, 68#

institute: Nanjing First Hospital

summary: Maps of heterogeneous cellular landscape in carotid artery were defined by single-cell RNA sequencing and revealed several cell types with their internal relations in the ISR model. This study highlights the crucial role of VSMC phenotype switching in the progression of ISR, and provides the clues of the underlying mechanism of ISR.

overall_design: control: 2 rats left cartoid arteries; case: the same 2 rats right cartoid arteries

first: Xiao-Fei

last: Gao

first: Ai-Qun

last: Chen

first: Zhi-Mei

last: Wang

first: Jun-Jie

last: Zhang


title: Single-cell analyses of memory and memory-phenotype CD4 T cells

first: Thomas

last: Ciucci

summary: Single-cell analyses of memory CD4 T cells after LCMV Armstrong infection and memory-phenotype CD4 T cells

overall_design: Memory Cd4 T cells were isolated 45 days after LCMV infection and memory-phenotype cells from uninfected animals

first: Takeshi

last: Kawabe

first: Remy

last: Bosselut


title: The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer

status: Public on Dec 12 2021

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

type: Methylation profiling by high throughput sequencing


title: Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [RNA-seq]

summary: Here we investigate the impact of epigenetic therapy with Decitabine in endocrine-resistant ER+ breast cancer by using patient-derived xenograft (PDX) models. Decitabine treatment restrained tumour growth, inhibited cell proliferation and resulted in significant loss of DNA methylation, particularly at enhancers and repetitive elements. Systematic integration of matched in situ Hi-C / PCHi-C, EPIC, RNA-seq and ChIP–seq datasets revealed widespread differences in epigenome regulation and enhancer-promoter communication with Decitabine. We find that loss of DNA methylation with Decitabine strongly affects the open (A) and closed (B) compartment structure and TAD boundary insulation. Our study identified and focused on key DNA methylation-dependent, enhancer ER binding sites that are activated in Decitabine-treated PDX tumours, enabling direct interactions between promoters and multiple distal enhancers, inducing expression of ER target genes and pathways. Overall, we demonstrate that epigenetic therapy inhibits tumour progression through to rewiring of ER-mediated 3D chromatin interactions and transcriptome programs. Our findings suggest that targeting the 3D epigenome with epigenetic therapies represents a promising strategy for anti-cancer treatment in ER+ endocrine resistant breast cancer patients.

overall_design: To understand the Decitabine-induced molecular changes driving tumour regression on a global scale, we used in situ Hi-C to generate genome-wide 3D genome maps of PDX breast tumours treated with Decitabine. At the same time, we examined the genome-wide DNA methylation (EPIC Microarrays), promoter-anchored interactome (Promoter Capture Hi-C (PCHi-C)), transcription factor binding (ER and FOXA1 ChIP-seq) and gene expression (RNA-seq) in the same tumours.


title: Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [methylation HCI-005]


title: Induction of T cell dysfunction and NK-like T cell differentiation in vitro and in patients after CAR T cell treatment [RNA-seq]

status: Public on Dec 06 2021

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Chimeric antigen receptor (CAR) T cell therapy has achieved remarkable success in hematological malignancies but remains largely ineffective in solid tumors. A major factor leading to the reduced efficacy of CAR T cell therapy is T cell dysfunction, and the mechanisms mediating this dysfunction are under investigation. Here we establish a robust in vitro model to study mesothelin-redirected CAR T cell dysfunction in pancreatic cancer. Continuous antigen exposure results in hallmark features of exhaustion including reduced proliferation capacity and cytotoxicity, and severe defects in cytokine production. Here we identified a transcriptional signature at both population and single-cell levels in CAR T cells after chronic antigen exposure. In addition, TCR lineage tracing revealed a CD8+ T-to-NK-like T cell plasticity that results in reduced antigen- dependent tumor cell killing. The transcription factors SOX4 and ID3 are specifically expressed in the dysfunctional CAR NK-like T cells and are predicted to be master regulators of the dysfunction gene expression signature and of the post-thymic acquisition of an NK-like T cell fate. Finally, we identified the emergence of CAR NK-like T cells in a subset of patients after infusion of CAR T cells. The findings gleaned from this study reveal new approaches to improve the efficacy of CAR T cell therapy in solid tumors by preventing or revitalizing CAR T cell dysfunction and shed light on the plasticity of human CAR T cells.

overall_design: Examines expression by paired-end RNA-seq in CD8+ T cells with multiple technical repeats across four biological replicates, with three variables: chimeric antigen receptor (CAR) presence (values: present or absent); antigen exposure (values: control, continuous, other); and time (values: day 0, day 16, day 28). Some samples are re-sequenced and were pooled to add coverage; see Data Processing section for details. Primary analysis considers the difference between control and continuous antigen exposure, between CAR presence or absence, and the differences along the time course.    Replicates are R2, R3, R4, and R5.    R2 has two CAR+ technical repeats for all exposure levels. One CAR- sample each is included for control and continuous. No time-course samples are included for this replicate.    R3 has two CAR+ and two CAR- technical repeats for control and continuous exposure. Two CAR+ technical repeats are included for "other" exposure. No time-course samples are included for this replicate.    R4 has two CAR+ and two CAR- technical repeats for control and continuous exposure. Two CAR+ technical repeats are included for "other" exposure. Two CAR+ technical repeats are included for a day 16 time point.    R5 has two CAR+ and two CAR- technical repeats for control and continuous exposure. Two CAR+ technical repeats are included for "other" exposure. Two CAR+ technical repeats are included for a day 16 time point.

first: Shunichiro

last: Kuramitsu

first: Charly

last: Good

first: Parisa

last: Samareh

first: Greg

first: Kenichi

last: Ishiyama

first: Yujie

last: Ma

first: Nils

last: Wellhausen

first: Lifeng

last: Tian

first: Sangya

last: Agarwal

first: Sonia

last: Guedan

first: M

middle: A

last: Aznar

first: Katherine

last: Alexander

first: Zhen

first: Nathan

last: Singh

first: Max

last: Richardson

first: Keisuke

last: Watanabe

first: Janos

last: Tanyi

first: Mark

middle: H

last: O'Hara

first: Marco

last: Ruella

first: Simon

last: Lacey

first: Edmund

last: Moon

first: Stephen

middle: J

last: Schuster

first: Steven

last: Albelda

first: Lewis

last: Lanier

first: Regina

last: Young

first: Shelley

last: Berger

first: Carl

last: June


title: The role of NLRP3 in intra-amniotic inflammation-induced preterm birth

status: Public on Dec 01 2021

city: Detroit

first: Adi

last: Tarca

state: MI

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

summary: Macrophages and neutrophils were sorted from the decidua and uterus of Nlrp3+/+ and Nlrp3-/- mice injected with lipopolysaccharide (LPS) or PBS and analyzed using pair-end RNA-sequencing (RNA-seq) to evaluate the effect of Nlrp3 deficiency on the transcriptomes of these innate immune cells in preterm birth.

overall_design:
The study included Nlrp3+/+ and Nlrp3-/- dams intra-amniotically injected with lipopolysaccharide (LPS) or PBS. Decidual and uterine macrophages and neutrophils were sorted by fluorescence-activated cell sorting. The number of samples analyzed were as follows: Macrophages, n = 3 per group; Neutrophils, n = 2 per group.
Please note that C57BL/6 and B6.129S6-Nlrp3tm1Bhk/J strains were used for the study

first: Nardhy

last: Gomez-Lopez

first: Roberto

last: Romero

first: Bogdan

last: Done


title: Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [ChIP-seq]

first: Joanna

last: Achinger-Kawecka


title: Multiplexed scRNA-seq reveals the cellular and genetic correlates of systemic lupus erythematosus

city: San Francisco

first: Yang

last: Sun

state: CA

address: 513 Parnassus Ave

department: Rheumatology

institute: UCSF

summary: Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and cell states associated with SLE remains incomplete. We profiled over 1.2 million PBMCs (162 cases, 99 controls) with multiplexed single-cell RNA-seq (mux-seq). Cases exhibited prominent expression of type-1 interferon-stimulated genes (ISG) in monocytes, reduction of naïve CD4+ T cells that correlated with monocyte ISG expression, and expansion of repertoire-restricted cytotoxic GZMH+ CD8+ T cells. Cell-type-specific expression features accurately predicted case-control status and stratified patients into two molecular subtypes. We integrated dense genotyping data, mapping cell-type-specific cis-eQTLs and linked known and novel SLE-associated variants to cell-type-specific gene expression. These results demonstrate mux-seq as a systematic approach to characterize cellular composition, identify transcriptional signatures, and annotate genetic variants associated with SLE.

overall_design:
Examination of 1.2 million PBMCs in 162 SLE donors and 99 healthy individuals to find cellular and genetic correlates of SLE.

**The raw data and processed data will be made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) through controlled access due to patient privacy concerns**

first: Richard

last: Perez

first: M

last: Gordon

first: Meena

last: Subramaniam

first: Min

middle: C

last: Kim

first: George

last: Hartoularos

first: Sasha

last: Targ

first: Anton

last: Ogorodnikov

first: Raymund

last: Bueno

first: Andrew

last: Lu

first: Mike

last: Thompson

first: Nadav

last: Rappoport

last: Dahl

first: Cristina

middle: M

last: Lanata

first: Mehrdad

last: Matloubian

first: Lenka

last: Maliskova

first: Serena

middle: S

last: Kwek

first: Tony

last: Li

first: Michal

last: Slyper

first: Orit

last: Rozenblatt-Rosen

first: Lawrence

last: Fong

first: Maria

last: Dall’era

first: Brunilda

last: Balliu

first: Aviv

last: Regev

first: Jinoos

last: Yazdany

first: Lindsey

last: Criswell

first: Noah

last: Zaitlen

first: Chun

last: Ye


title: Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [methylation GAR15-13]

first: Joanna

last: Achinger-Kawecka


title: Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [HiC]


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [Amplicon III]

status: Public on Nov 25 2021

first: Alexander

last: Marson

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

summary: Complex gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression within these networks is sufficiently perturbed it can lead to disease. To understand how gene expression disruptions percolate through a network, we must first map the connections between regulatory genes and their downstream targets. However, it has been challenging to identify the upstream regulators for genes of interest. Here we develop a system for systematic discovery of upstream regulators of critical immune factors – IL2RA, IL-2, and CTLA4 – in primary human T cells. Then, CRISPR perturbations coupled with RNA-Seq, and ATAC-Seq, allowed us to map the full network of these regulators’ target genes and enhancers. These regulators form highly interconnected networks with extensive feedback loops. Furthermore, this network is highly enriched for autoimmune-associated disease variants and genes. These results provide insight into how autoimmune associated disease genes are regulated in T cells as well as broader principles about the structure of human gene regulatory networks.

overall_design: Amplicon sequencing to detect insertion/deletions at CRISPR guide RNA target sites.

first: Jacob

last: Freimer

first: Oren

last: Shaked

first: Sahin

last: Naqvi

first: Nasa

last: Sinnott-Armstrong

first: Arwa

last: Kathiria

first: Amy

middle: F

last: Chen

first: Jessica

middle: T

last: Cortez

first: William

last: Greenleaf

first: Jonathan

last: Pritchard


title: RNA sequencing to identify differentially-expressed genes in HER3-depleted KatoII MET-amplified cancer cells

status: Public on Nov 23 2021

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

summary: Receptor tyrosine kinases (RTKs) are recognized as targets of precision medicine in human cancer upon their gene amplification or constitutive activation, resulting in increased downstream signal complexity including heterotypic crosstalk with other RTKs. The Met hepatocyte growth factor RTK exhibits such reciprocal crosstalk with several members of the human EGFR (HER) family of RTKs when amplified in cancer cells. We observed that Met signaling converges on HER3 tyrosine phosphorylation across a panel of seven MET-amplified cancer cell lines and that HER3 is required for cancer cell expansion and oncogenic capacity in vitro and in vivo. In order to identify genes required for cancer cell proliferation in the MET-amplified setting whose expression, we stably transduced KatoII MET-amplified cells with shRNA targeting ERBB3, the gene encoding HER3. Stably-transduced cells were selected with puromycin, assayed for proliferative phenotype, and lysed for RNA extraction. Pooled libraries of total RNA were then sequenced using the Illumina HiSeq4000 platform, and differentially-expressed genes were identified from read counts normalized across samples. Differentially-expressed genes were further assayed for dependence on HER3 in other MET-amplified cell lines to identify genes recurrently dependent on HER3 in the MET-amplified setting.

overall_design: MET-amplified KatoII cells were lentivirally transduced with shRNA targeting the human ERBB3 gene. Stably-transduced cells were selected with puromycin, assayed for proliferation phenotype and lysed in parallel. RNA sequencing of total RNA reads were mapped to genes, normalized across samples and assessed for differential gene expression.

first: Yaakov

last: Stern

first: Benoit

last: Fiset

first: Logan

last: Walsh

first: Morag

last: Park


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [Amplicon II]


title: Single-nucleus RNA-seq of NASH HCC liver tissue

city: Los Angeles

first: Marcus

last: Alvarez

address: 695 Charles E Young Dr South, Gonda 6335

department: Human Genetics

institute: UCLA

summary: Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related death world-wide. The prevalence of non-alcoholic fatty liver disease (NAFLD) has been rising, along with an increase in NAFLD-related HCC.  To investigate cell-type composition in NAFLD and HCC, we performed single-nucleus RNA-seq (snRNA-seq) of patients with fatty liver disease in order to transcriptionally characterize cell-types in an unbiased manner. Out data reveal a large amount of heterogeneity in hepatocyte populations, as well as recovering all expected liver cell-types.

overall_design:
Snap-frozen archived liver biopsies from tumor and adjacent non-tumor resections were processed from 3 patients with fatty liver disease and HCC (n=3 paired; n=6 total). Nuclei were isolated into a suspension and immediately processed with the 10X Chromium platform following the Single Cell 3' v3 protocol for library preparation. Libraries were then sequenced on an Illumina novaSeq 6000.
***Please note that raw data is not provided due to human subject privacy concerns***

first: Alvarez

last: Marcus


title: A Functional Role of OLIG2 in Tumor Heterogeneity of MYC-amplified Medulloblastoma

status: Public on Nov 16 2021

city: Washington

first: Zhenhua

last: Xu

state: District of Columbia

address: 111 Michigan Ave NW

institute: Children's National Hospital

summary: The goal of this study was to compare gene expression profiles of MYC-amplified medulloblastoma tumors under three distinct conditions: primary tumors prior to radiation treatment, tumors derived from implanted radio-resistant tumor cells, and spontaneously recurring tumors several weeks post-irradiation.  The purpose of this experiment was to identify the moleular pathways that are impacted during radiation and those which contribute to tumor recurrence.  Unsupervised hierarchical cluster analysis revealed that the tumors which spontaneously recurred in vivo closely resembled the primary tumors.  Tumors from implanted post-radiation neurospheres, however, had markedly different profiles.  We identified 44 upregulated and 23 downregulated genes in the spontaneously recurred tumors compared to untreated primary tumors.  Furthermore, we identified 817 upregulated and 509 downregulated genes in tumors derived from implanted post-radiation neurospheres compared to untreated primary tumors.  Among these genes, 756 (57%) genes were also differentially expressed between tumors derived from implanted post-radiation neurospheres and spontaneously recurrent tumors.  The downregulated pathways in tumors derived from implanted post-radiation neurospheres were associated with p53, cell cycle, DNA replication, and DNA damage, and the upregulated genes are involved in metabolic pathways.  This study demonstrates that radiation resistant tumor cells exhibit differential gene expression post-irradiation and during tumor recurrence and provides a framework for the study of genetic pathways leading to tumor recurrence post-irradiation.

overall_design: Bulk RNA-seq and transcriptomic analysis of patient-derived MYC-amplified medulloblastoma tumors derived from radioresistant tumor cells post-transplantation, spontaneously relapsed tumors, and primary tumors

first: Samuel

last: Rivero-Hinojosa


title: TGFβ reprograms TNF stimulation of macrophages towards osteoclastogenesis [CUT&RUN]

first: Kazuki

last: Inoue

summary: TNF plays a key role in inflammation and bone resorption. However, the mechanisms regulating TNF-mediated osteoclastogenesis remain largely unclear because its direct osteoclastogenic ability is weak. Here, we found that TGFβ priming enables TNF to effectively induce osteoclastogenesis from macrophages, independently of the osteoclastogenic action of RANKL. Lack of TGFβ signaling in macrophages suppresses inflammatory, but not physiological, osteoclastogenesis and bone resorption in vivo. Mechanistically, TGFβ priming reprograms macrophage response to TNF towards osteoclastogenesis by remodeling chromatin accessibility and histone modification. TGFβ and TNF induce an unconventional osteoclastogenic program, which includes the suppression of the TNF-induced IRF1-IFNβ-IFN stimulated gene (ISG) axis, promotion of IRF8 degradation and B-Myb induction. These mechanisms are present in RA, in which TGFβ level is elevated and correlated with osteoclast activity. Our findings identify a function and mechanism of action for TGFβ in TNF-mediated inflammatory osteoclastogenesis, and open avenues for selective treatment of inflammatory bone loss.

overall_design: Analysis of transcriptional changes in human macrophages with or without TGFb priming in the presence of TNF

first: Baohong

last: Zhao

first: Yuhan

last: Xia


title: Dopamine receptor D2 antagonization normalizes the profibrotic macrophage-endothelial crosstalk in the liver

status: Public on Nov 01 2021

city: chengdu

first: ren

last: yafeng

address: NO.17，3th Section,Renmin South Road

institute: sichuan university

summary: Fibrosis in the liver is a main histological determinant of non-alcoholic steatohepatitis (NASH), a disease paralleling a worldwide surge in metabolic syndrome. Our study demonstrates that myeloid-specific YAP deficiency attenuates liver fibrosis after chronic liver injury via boosting type I interferon. Dopamine receptor D2 (DRD2) antagonization selectively blocks YAP in macrophages and thwarts liver fibrosis in both rodent and large animal models.

overall_design: liver nonparenchymal cells  scRNA sequence of fibrosis model wild type (WT) and yap1flox/floxlyz2cre mice

first: Qing

last: Jie

first: Ren

last: Yafeng


title: Maternal-Fetal Immune Responses in Pregnant Women Infected with SARS-CoV-2

status: Public on Nov 11 2021

first: Adi

last: Tarca

summary: Peripheral and cord blood samples from SARS-CoV-2 positive or control pregnant women were profiled using paired-end DNBseq to evaluate transcriptomic changes associated with SARS-CoV-2 infection during pregnancy.

overall_design: Cross-sectional study analyzing the transcriptome profiles of peripheral and cord blood from SARS-CoV-2-positive or control pregnant women.

first: Nardhy

last: Gomez-Lopez

first: Roberto

last: Romero

middle: L

first: Roger

last: Pique-Regi

first: Bogdan

last: Done


title: Mesenchymal Stromal Cells Equipped by IFNα Empower T Cells with Potent Anti-tumor Immunity

status: Public on Oct 31 2021

city: Boston

first: Tao

last: Zhang

state: MA

address: 450 Brookline Avenue

department: Medical oncology

institute: Dana-Farber Cancer Institute

summary: Cancer treatments have been revolutionized by the emergence of immune checkpoint blockade therapies. However, only a minority of patients with various tumor types have benefited from such treatments. New strategies focusing on the immune contexture of the tumor tissue microenvironment hold great promises. Here, we created IFNα-overexpressing mesenchymal stromal cells (IFNα-MSCs). Upon direct injection into tumors, we found that these cells are powerful in eliminating several types of tumors. Interestingly, the intra-tumoral injection of IFNα-MSCs could also induce specific anti-tumor effects on distant tumors. These IFNα-MSCs promoted tumor cells to produce CXCL10, which in turn potentiates the infiltration of CD8+ T cells in the tumor site. Furthermore, IFNα-MSCs enhanced the expression of granzyme B (GZMB) in CD8+ T cells and invigorated their cytotoxicity in a Stat3-dependent manner. Genetic ablation of Stat3 in CD8+ T cells impaired the effect of IFNα-MSCs on GZMB expression. Importantly, combination of IFNα-MSCs and PD-L1 blockade induced an even stronger anti-tumor immunity. Therefore, IFNα-MSCs represent a novel tumor immunotherapy strategy, especially when combined with PD-L1 blockade.

overall_design: There are four samples,  control group (C1 and C2) and IFNα-treated group (a1 and a2).

first: Yufang

last: Shi

first: Ying

last: Wang


title: Interaction of Male Specific Lethal complex and genomic imbalance on global gene expression in Drosophila

status: Public on Oct 13 2021

city: Beijing

first: Lin

last: Sun

address: Xinjiekouwai Street

institute: Beijing Normal University

summary: Here, in order to investigate the regulation mechanism of the MSL complex in unbalanced genomes and its further functions involved in sexual dimorphism, we over-expressed MSL2 in autosomal aneuploidy (XX, AAA) and sex chromosome aneuploidy (XXX, AA), and analyzed the different transcriptomes.

overall_design: Compare the global expression of trisomy and MSL2-trisomy Drosophila.

first: Shuai


title: IL-33-induced metabolic reprogramming controls the differentiation of alternatively activated macrophages and the resolution of inflammation (scRNA-seq)

status: Public on Oct 06 2021

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

country: Switzerland

institute: University of Bern

summary: Alternatively activated macrophages (AAMs) contribute to the resolution of inflammation and tissue repair. However, molecular pathways that govern their differentiation upon tissue damage have remained incompletely understood. Here, we show that the transcription factor GATA3 specifically controls the IL-4-independent differentiation of pro-resolving and reparative AAMs in response to injury and the necrotic cell-derived alarmin IL-33. In macrophages, IL-33 sequentially triggered an early expression of pro-inflammatory genes as well as a subsequent differentiation into AAMs.  Global analysis of involved signaling events identified an IL-33-induced GATA-3 transcriptional module that specifically orchestrated AAM differentiation. IL-4-induced AAM differentiation, in contrast, was independent of GATA-3. Conditional deletion of GATA-3 in mononuclear phagocytes accordingly abrogated IL-33-induced differentiation of AAMs in vitro and diminished macrophage-mediated tissue repair in vivo. Our data thus identify an IL-33-GATA3 signaling axis that controls plasticity of macrophages in response to injury and fosters resolution of inflammation.

overall_design: Examination of macrophages in the inflammed muscle of 2 mouse strains using single cell RNA sequencing

first: Gerhard

last: Kroenke

first: Maria

last: Faas

first: Natacha

last: Ipseiz

first: Stephan

last: Culemann

first: Arif

middle: B

last: Ekici


title: IFNγ induces a dynamic and complex transcriptional, chromatin and enhancer landscape

status: Public on Oct 12 2021

city: SEVENOAKS

first: Anna

middle: Rita

last: Lamstaes

state: Kent

address: 99 Solefields Road

department: Department of Biochemistry

institute: University of Oxford

summary: Aims and methods: To analyze how IFNγ induces coding and non-coding nascent transcriptional changes, SNU-seq is used to measure genome-wide changes in nascent transcription in untreated, 0.5hr, 2hr and 24hr IFNγ treated Hep3B cells. SNU-seq identifies the last transcribed nucleotide at near single-nucleotide resolution. 3'-end RNA-seq is used to examine RNA levels. ChIPmentation and ATAC-seq are used to assess the differential chromatin landscape upon IFNγ treatments, measuring H3K27ac, H3K4me3 and CTCF genome-wide changes as well as DNA accessibility in untreated, 0.5hr, 2hr and 24hr IFNγ treated Hep3B cells. Higher-order chromatin structure is investigated upon IFNγ treatments using Capture-C to measure promoter interactions of three gene promoters; IRF1, STAT1, and CD274. Results:  3'-end RNA-seq reveals IFNγ stimulated genes. SNU-seq identifies dynamic transcription at genes and non-coding intergenic regions and is used to demonstrate differential APA upon IFNγ treatments. By measuring transcription at nucleosome depleted regions, differential enhancer activity was demonstrated. IFNγ induces hundreds of methylation changes and thousands of acetylation changes over 24hrs. Unlike H3K4me3 which is deposited at late timepoints, H3K27ac is dynamically deposited. This acetylation is sometimes sustained throughout 24hrs but is often transiently deposited. CTCF shows very few binding changes throughout the timecourse. IFNγ induces significant changes in promoter:enhancer interactions at IRF1 and STAT1. The CD274 promoter loops to the nearest gene promoter; PLGRKT.

overall_design: SNU-seq, 3'-end RNA-seq and ATAC-seq were performed in triplicate in untreated, 0.5hr, 2hr and 24hr treated Hep3B cells. ChIPmentation was performed in duplicate in untreated, 0.5hr, 2hr and 24hr treated Hep3B cells. Capture-C was performed in duplicate in untreated, 0.5hr, 2hr and 24hr treated Hep3B cells, capturing the IRF1, STAT1 and CD274 promoter.

first: Phil

last: Lorenz

first: Jane

last: Mellor


title: Acrylamide modulates the mouse epididymal proteome to drive alterations to the sperm epigenome and dysregulate embryo development

status: Public on Oct 04 2021

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

summary: Paternal exposure to environmental stressors elicits distinct changes to the sperm sncRNA profile; modifications that have significant post-fertilization consequences. Despite this knowledge, there remains limited mechanistic understanding of how paternal exposures modify the sperm sncRNA landscape. Here, we report the acute sensitivity of the sperm sncRNA profile to the reproductive toxicant, acrylamide. Further, we traced the differential accumulation of acrylamide-responsive sncRNAs to coincide with sperm transit of the proximal (caput) segment of the epididymis, wherein acrylamide exposure altered the abundance of several transcription factors implicated in the expression of acrylamide-sensitive sncRNAs. We also identified extracellular vesicles secreted from the caput epithelium in relaying altered sncRNA profiles to maturing spermatozoa, and dysregulated gene expression during early embryonic development following fertilisation by acrylamide-exposed spermatozoa. These data provide mechanistic links to account for how environmental insults can alter the sperm epigenome and compromise the transcriptomic profile of early embryos.

overall_design:
Examination of the small non-protein coding RNA profile in mature sperm from control and acrylamide exposed mice using next generation sequencing in duplicate.
Examination of the transcriptome of 2-cell embryos that developed from zygotes fertilised by three different populations of spermatozoa (control, epididymal acrylamide exposure and spermatocyte acrylamide exposure) in triplicate.

first: David

last: Skerrett-Byrne

first: Miguel

last: Xavier

first: Wei

last: Zhou

first: Amanda

last: Anderson

first: Simone

last: Stanger

first: Aimee

last: Katen

first: Geoffry

middle: N

last: DeIuliis

first: Matthew

middle: D

last: Dun

first: Shaun

last: Roman

first: Andrew

last: Eamens

first: Brett

last: Nixon


title: IL-33-induced metabolic reprogramming controls the differentiation of alternatively activated macrophages and the resolution of inflammation (bulk RNA-seq)

first: Philipp

last: Kirchner

overall_design: Bulk RNA-Seq analysis of differences in gene expression for control, IL-33 or IL-4 stimulated macrophages from three genetic backgrounds

first: Gerhard

last: Kroenke

first: Maria

last: Faas

first: Natacha

last: Ipseiz

first: Stephan

last: Culemann


title: IL-33-induced metabolic reprogramming controls the differentiation of alternatively activated macrophages and the resolution of inflammation

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

overall_design: Refer to individual Series


title: Whole-genome integration of DNA methylomics and transcriptomics in Salmonella enterica sero. Typhimurium (14028s)

first: Jeffrey

last: Bourgeois

address: 136 Harrison Ave

institute: Tufts University

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: The amniotic fluid cell-free transcriptome in spontaneous preterm labor

status: Public on Oct 01 2021

first: Adi

last: Tarca

summary: The amniotic fluid (AF) cell-free (cf) RNA was shown to reflect physiological and pathological processes in pregnancy, but its value in prediction of spontaneous preterm delivery is unknown. Here we profiled cfRNA in AF samples collected from women who underwent transabdominal amniocentesis after an episode of spontaneous preterm labor and subsequently delivered within 24h (n=10) or later (n=28) in gestation. Expression of known placental single cell (sc) RNA-Seq signatures were quantified in AF cfRNA and compared between groups. Random forest models were applied to predict time to delivery after amniocentesis. There were 2385 genes differentially expressed in AF samples of women who delivered within 24 hours of amniocentesis compared to gestational age-matched samples from women who delivered after 24 hours of amniocentesis.Genes with cfRNA changes were associated with immune and inflammatory processes related to the onset of labor, and expression of placental scRNA-Seq signatures of immune cells were increased with imminent delivery. AF transcriptomic prediction models captured these effects and predicted delivery within 24 hours of amniocentesis (AUROC =0.81). These results may inform development of biomarkers for spontaneous preterm birth.

overall_design: We profiled cfRNA in AF samples collected from women who underwent transabdominal amniocentesis after an episode of spontaneous preterm labor and subsequently delivered within 24h (n=10) or later (n=28) in gestation.

first: Roberto

last: Romero

first: Gaurav

last: Bhatti


title: Comparison of the root tip transcriptome of 2 pearl millet lines with contrasted root soil aggregation

status: Public on Oct 09 2021

city: Montpellier

first: Laurent

last: Laplaze

address: 911 avenue Agropolis

department: DIADE

country: France

institute: IRD

summary: We analyzed global gene expression in the crown tip of 2 pearl millet (Pennisetum glaucum) inbred lines with high (line 249) and low (line 220) root soil aggregation using RNAseq. The obtective was to identify genes potentially associated with changes in rhizosheath formation.

overall_design: Two pearl millet lines with contrasted root soil aggregation were grown in hydropony for 15 days. 3 biological replicates were produced per line. RNA was extracted from the crown root tip (2 cm apex). RNA-seq was performed by the Montpellier GenomiX Platform (MGX, https://www.mgx.cnrs.fr/). Sequencing was performed on an Illumina HiSeq 2500.

first: Marilyne

last: Debieu

first: Alexandre

last: Grondin


title: Transcriptomes of human myometrium in labor  reveals the increased molecular associated with inflammation under hypoxia stress

status: Public on Sep 23 2021

city: Guangzhou

first: Kaiyuan

last: Ji

address: No.9 Jinsui Road, Guangzhou, China

department: Guangzhou Women and Children’s Medical Center

institute: Guangzhou Medical University

summary: Labor involves a variety of coordinated events across physiological and biochemical aspects, the molecular mechanism responsible for the transition of the myometrium from the quiescent to a contractile state remains indistinct.The global transcriptome in human non-labor and in labor myometrium was investigated through RNA sequencing (RNA-seq) to explore biological processes and pathways alterations during labor. The transcriptomic bioinformatics results showed that the up-regulated mRNAs increased inflammation under hypoxia stress in laboring myometrium.

overall_design: mRNA, lncRNA profiles of human myometrium in labor and non-labor

first: Lina

last: Chen

first: Huishu

last: Liu

first: Yihong

last: Luo


title: Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [PCHiC]

first: Joanna

last: Achinger-Kawecka

address: AHMS Building, North Terrace

institute: South Australian Immunogenomics Cancer Institute

summary: Here we investigate the impact of epigenetic therapy with Decitabine in endocrine-resistant ER+ breast cancer by using patient-derived xenograft (PDX) models. Decitabine treatment restrained tumour growth, inhibited cell proliferation and resulted in significant loss of DNA methylation, particularly at enhancers and repetitive elements. Systematic integration of matched in situ Hi-C / PCHi-C, EPIC, RNA-seq and ChIP–seq datasets revealed widespread differences in epigenome regulation and enhancer-promoter communication with Decitabine. We find that loss of DNA methylation with Decitabine strongly affects the open (A) and closed (B) compartment structure and TAD boundary insulation. Our study identified and focused on key DNA methylation-dependent, enhancer ER binding sites that are activated in Decitabine-treated PDX tumours, enabling direct interactions between promoters and multiple distal enhancers, inducing expression of ER target genes and pathways. Overall, we demonstrate that epigenetic therapy inhibits tumour progression through to rewiring of ER-mediated 3D chromatin interactions and transcriptome programs. Our findings suggest that targeting the 3D epigenome with epigenetic therapies represents a promising strategy for anti-cancer treatment in ER+ endocrine resistant breast cancer patients.

overall_design: To understand the Decitabine-induced molecular changes driving tumour regression on a global scale, we used in situ Hi-C to generate genome-wide 3D genome maps of PDX breast tumours treated with Decitabine. At the same time, we examined the genome-wide DNA methylation (EPIC Microarrays), promoter-anchored interactome (Promoter Capture Hi-C (PCHi-C)), transcription factor binding (ER and FOXA1 ChIP-seq) and gene expression (RNA-seq) in the same tumours.


title: Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle

status: Public on Sep 29 2021

city: Ithaca

first: Lauren

last: Walter

state: NY

address: 161 Weill Hall

department: Biomedical Engineering

institute: Cornell University

summary: We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform.

overall_design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.

first: Benjamin

last: Cosgrove

first: David

middle: W

last: McKellar