title: Entinostat decreases immune suppression to promote an anti-tumor response within a HER2+ breast tumor microenvironment.

city: Los Angeles

first: Evanthia

last: Roussos-Torres

address: 1441 Eastlake Ave

institute: USC Keck School of Medicine

summary: Therapeutic combinations to alter solid tumor microenvironments (TME) in immunosuppressive tumors such as breast cancer are essential to improve their responses to immune checkpoint inhibitors (ICIs). Entinostat, an oral histone deacetylase inhibitor (HDACi), has been shown to improve responses to ICIs in various tumor models with immunosuppressive TMEs. The precise and comprehensive alterations to the TME induced by entinostat remain unknown. Here, we employ single-cell RNA-sequencing on HER2 overexpressing breast tumors from mice treated with entinostat and ICIs to characterize for the first time changes across all cell types within the TME. This analysis demonstrates that treatment with entinostat induces a shift from a pro-tumor to an anti-tumor TME signature characterized predominantly by changes in the myeloid cells. We confirm myeloid-derived suppressor cells (MDSCs) within entinostat-treated tumors are associated with a less suppressive G-MDSC phenotype and now demonstrate altered suppressive signaling involves the NFkB and STAT3 pathways. In addition to MDSCs, tumor-associated macrophages are epigenetically reprogrammed toward an anti-tumor M1-like phenotype likely contributing to a more sensitized TME. Overall, our in-depth analysis suggests entinostat-induced changes on multiple myeloid cell types reduce immunosuppression and increase mechanisms of an anti-tumor response that improve sensitivity to ICI. Sensitization of the TME by entinostat could ultimately broaden the population of patients with breast cancer who could derive benefit from ICIs.

overall_design:
Single Cell RNA sequencing of NeuN NT2.5 treated with Entinostat and aCTLA4/aPD1 combination treatments.
Bulk RNAseq of J774M cells treated with Entinostat or DMSO control.

first: Dimitrios

last: Sidiropoulos

first: Elana

last: Fertig

last: Torres


title: Beauvericin (BEA) and enniatin B (ENNB)-induced impairment of mitochondria and lysosomes - potential sources of intracellular reactive iron triggering ferroptosis in Atlantic salmon primary hepatocytes

status: Public on Jan 17 2022

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

type: Expression profiling by high throughput sequencing

summary: Beauvericin (BEA) and enniatin B (ENNB) are emerging mycotoxins frequently detected in plant-based fish feed. With ionophoric properties, they have shown cytotoxic potential in mammalian models. Sensitivity in fish is still largely unknown. Primary hepatocytes isolated from Atlantic salmon (Salmo salar) were used as a model and exposed to BEA and ENNB (0.05 – 10 µM) for 48 hours. Microscopy, evaluation of cell viability, total ATP, total H2O2, total iron content, total Gpx enzyme activity, and RNA sequencing were used to characterize the toxicodynamics of BEA and ENNB. Both mycotoxins became cytotoxic at ≥ 5 µM, causing condensation of the hepatocytes followed by formation of blister-like protrusions on the cell's membrane. RNA sequencing analysis at sub-cytotoxic levels indicated BEA and ENNB exposed hepatocytes to experience increased energy expenditure, elevated oxidative stress, and iron homeostasis disturbances sensitizing the hepatocytes to ferroptosis. The present study provides valuable knowledge disclosing the toxic action of these mycotoxins in Atlantic salmon primary hepatocytes.

overall_design: Primary hepatocytes were extracted from 6 fish. Isolated hepatocyte from each individual fish were exposed to four concentrations of ennb or bea (0µM, 0.05µM, 0.5µM and 2.5 µM) enabeling to investigate the response in hepatocytes from each individual fish, thus removing noise.

middle: K

first: Sofie

last: Søderstrøm

first: Anne-Katrine

last: Lundebye

first: Liv

last: Søfteland


title: scRNA-seq of fin and body zebrafish melanocytes

city: New York

first: Joshua

middle: M

last: Weiss

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre-existing transcriptional programs in the cell of origin. Here, we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet, or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL-driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs, indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes, compared to body melanocytes, revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL-driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults.

overall_design: For this experiment we used our zebrafish transgenic model of Acral melanoma, which was generated by injecting Casper fish with MniCoopR-GFP, mitfa:hsCRKL, mitfa:hsGAB2, mitfa:hsTERT, mitfa:Cas9-mCherry;U6nf1a-gRNA, mitfa:Cas9-mCherry;U6-nf1b-gRNA. Fish were dissected to collect body skin and fins, digested using liberase, and then FACS sorted for GFP+ melanocytes and GFP- microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 months post-fertilization. This led to generation of 4 samples total, GFP+ body cells, GFP- body cells, GFP+ fin cells, GFP- fin cells. Data was then analyzed and pooled together, taking note of their sample origin.

first: Miranda

middle: V

last: Hunter

first: Yilun

last: Ma

first: Tianhao

last: Xu

first: Ronan

last: Chaligné

first: Richard

last: White


title: Bulk RNA-seq of fin and body melanocytes and microenvironments

summary: Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: (1) cell lineage: melanocyte vs bulk microenvironment, (2) anatomic location: fin vs body, (3) genotype: wildtype vs CRKL,GAB2,TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL.

overall_design: For this experiment we used two genetic strains of zebrafish. (1) Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR-eGFP. (2) Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR-eGFP, mitfa:hsCRKL, mitfa:hsGAB2, mitfa:hsTERT, mitfa:Cas9-mCherry;U6-nf1a-gRNA, mitfa:Cas9-mCherry;U6-nf1b-gRNA. Fish were dissected to collect body skin and fins, digested using liberase, and then FACS sorted for GFP+ melanocytes and GFP- microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strains(WT_v_Acral) x 2 anatomic locations(fin_v_body) x 2 sorted conditions(GFP+_v_GFP-) x 3 biological replicates = 24 samples total.


title: NicE-C efficiently reveals open chromatin associated chromosome interactions at high resolution

status: Public on Jan 18 2022

city: HeFei

first: Zhengyu

last: Luo

state: AnHui

address: Huangshan street

country: China

institute: USTC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Enhancer-promoter communication is known to regulate spatiotemporal gene expression. Here, we present NicE-C, a method that leverages nicking enzyme mediated open chromatin profiling and chromosome conformation capture to enable robust and cost-effective detection of chromatin interactions among open chromatin regions (e.g., between enhancers and promoters). Demonstrating its application utility, NicE-C revealed dynamic enhancer-promoter interactions associated with gene expression changes after TNFɑ stimulation in HeLa cells and during aging process in mice kidney.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: NicE-C  are generated for HeLa cells, HeLaS3 cells with or without TNFa stimulation, IMR90 cells, Mice kidney of young and old mice. RNA-seq are generated for HeLa cells, HeLaS3 cells with or without TNFa stimulation and kidney of young and old mice. HiC and  NicE-seq are generated for HeLa cells.

first: Ran

last: Zhang

first: Tengfei

last: Hu

first: Xiaoyuan

last: Song


title: A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci

city: Amsterdam

first: Frank

last: Jacobs

address: Science Park 904

department: Sammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

summary: Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci, but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SVA (Sine-VNTR-Alu) elements, a class of great-ape specific transposable elements with gene-regulatory roles, which represents a major source of structural variability in the human population. We highlight the presence of structurally variable SVAs (SV-SVAs) in neurological disease-associated loci, and further associate SV-SVAs to disease-associated SNPs and differential gene expression using luciferase assays and expression quantitative trait loci data. Finally, we genetically deleted SV-SVAs in the BIN1 and CD2AP Alzheimer-associated risk loci and in the BCKDK Parkinson disease-associated risk locus and assessed multiple aspects of their gene-regulatory influence in a human neuronal context. Together, this study reveals a novel layer of genetic variation in transposable elements that may contribute to identification of the structural variants that are the actual drivers of disease-associations of GWAS loci.

overall_design: RNA and ChIP-seq analysis of CRISPR/Cas9 SVA-KO and wild type hESC-derived cortical organoids.

first: Elisabeth

middle: J

last: van Bree

first: Rita

last: Guimarães

first: Mischa

last: Lundberg

first: Elena

middle: R

last: Blujdea

first: Jimi

middle: L

last: Rosenkrantz

first: Fred

middle: T

first: Josse

last: Poppinga

first: Paula

last: Ferrer Raventos

first: Anne-Fleur

middle: E

last: Schneider

first: Isabella

last: Clayton

first: David

last: Haussler

first: Marcel

last: Reinders

first: Henne

last: Holstege

first: Adam

middle: D

last: Ewing

first: Colette

last: Moses


title: DJ-1 gene and immunoaging

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

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

overall_design: Refer to individual Series


title: Transcription factor-like 5 is a potential DNA/RNA binding protein essential for maintaining male fertility in mice

city: Nanjing

first: Weiya

last: Xu

state: Jiangsu

address: No. 818, Tianyuan East Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

summary: Tissue-specific transcriptional factors often play key roles in the development of specific cell lineages. Transcription factor-like 5 (TCFL5) is a testis-specific protein that contains the basic helix-loop-helix domain but the in vivo functions of TCFL5 remained unknown. Here, we generated CRISPR/Cas9-mediated knockout mice to dissect the function of TCFL5 in mouse testes.The target RNAs of TCFL5 in wild-type mouse testes were analyzed by eCLIP-sequencing.

overall_design: The 21d mouse testes were used to performed eCLIP experiment and the purified RNAs by eCLIP were sequenced on the Illumina NovaSeq platform, in two duplicate samples.

first: Xin

last: Wu


title: Transcription factor-like 5 is a potential DNA/RNA binding protein essential for maintaining male fertility in mice [RNA-seq]

summary: Tissue-specific transcriptional factors often play key roles in the development of specific cell lineages. Transcription factor-like 5 (TCFL5) is a testis-specific protein that contains the basic helix-loop-helix domain but the in vivo functions of TCFL5 remained unknown. Here, we generated CRISPR/Cas9-mediated knockout mice to dissect the function of TCFL5 in mouse testes. mRNA profiles of pachytene spermatocytes from Tcfl5+/+ and Tcfl5+/- mice sere generated by high throughput sequencing. The bound genes of TCFL5 in wild-type mouse testes were analyzed by ChIP-sequencing.

overall_design: Pachytene spermatocytes were isolated from the testis of Tcfl5+/+ and Tcfl5+/-  mice respectively. mRNA profiles of these cells were generated by high throughput sequencing, in two duplicate samples, using BGISEQ-500 platform of BGI Tech. Purified DNA by ChIP was also sequenced on the BGISEQ-500 platform of BGI Tech.


title: Intrinsic IL-2 Production by Effector CD8 T Cells Attenuates IL-2-signalling and Promotes Fate Decisions, Stemness, and Viral Protection

city: Birmingham

first: Allan

last: Zajac

state: AL

address: 845 19th Street South

department: Microbiology

institute: University of Alabama at Birmingham

summary: Interleukin-2 (IL-2) plays pivotal roles in directing the differentiation of effector and memory CD8 T cells; nevertheless, the contributions of IL-2 synthesis by CD8 T cells versus sensitivity to IL-2 signals in shaping their developmental fates and protective efficacy is less clear.  Here we show that, rather than acting in an autocrine manner, the production of IL-2 by CD8 T cells restricts their ability to receive STAT5-dependent IL-2 signals, and the capacity to manufacture IL-2 delineates constituents of the expanded effector pool that display stem-like features, preferentially survive, more rapidly attain memory traits, and control chronic viral challenges.  Despite having distinct properties during the effector phase, IL-2-producing and non-producing CD8 T cells phenotypically coalesce as memory matures to form populations with equal recall abilities.  Therefore, the potential to produce IL-2 during the effector but not memory phase is a consequential cellular feature that dictates the protective capabilities of the response.

overall_design: Naïve P14 CD8 T cells from Ifng.Thy1.1 IL-2.GFP knock in double cytokine reporter mice were transferred into naïve allogenically marked recipient mice one day prior to LCMV-Armstrong infection. Splenocytes from three separate mice were harvested on day 9 (effector) and  from four mice on days 308-309 (memory) post infection. THY1.1+ GFP+ (IFN-γ+IL-2+) and THY1.1+ GFP- (IFN-γ+ IL-2-) subsets were sorted directly into Trizo-LSl.  RNA was then isolated from the sorted fractions using a Direct-Zol RNA isolation kit (Zymo Research, Irvine CA).  RNA samples were then submitted to the UAB Helfin Center for Genomic Science (Birmingham, AL) for quality assessment and RNA sequencing.

first: Shannon

last: Kahan

first: Rakesh

last: Bakshi

first: R

middle: C

last: Hendrickson

first: Elliot

last: Lefkowitz

last: Crossman

first: Laurie

last: Harrington

first: Casey

last: Weaver

first: Jennifer

last: Ingram


title: Transcription factor-like 5 is a potential DNA/RNA binding protein essential for maintaining male fertility in mice [ChIP-seq]


title: Transcriptomic analysis of the developing neocortex of the Australian marsupial fat-tailed dunnart (Sminthopsis crassicaudata)

city: St Lucia

first: Peter

last: Kozulin

state: Queensland

address: Building 79

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

summary: The six-layered neocortex is exclusively present in mammals and mediates sensory-motor and higher-order functions. Key differences in this structure and its connections exist between the main mammalian groups: eutherians and marsupials, however, the molecular changes that underlie these known morphological differences remain unknown. This question is particularly difficult to address because small and transient changes in gene expression during development may be crucial to brain formation, which would not be detectable in adult transcriptomic analyses. To address this question of the developmental origin of changes in the evolution of the mammalian neocortex, we performed transcriptomic analysis on the marsupial fat-tailed dunnart (Sminthopsis crassicaudata) at postnatal ages P12 and P20 corresponding to the generation of infragranular (layers 5/6) and supragranular (layers 2/3) neurons, respectively. We assembled a de novo transcriptome of the neocortex of fat-tailed dunnarts using RNA-seq data from all samples, then differential gene expression analysis performed across the two ages. Additional cross-species analysis was performed against existing mouse neocortical datasets in the NCBI Sequence Read Archive at equivalent developmental ages embryonic (E) day 12.5 (SRR1509162, SRR1509163, SRR1509164) and E16 (SRR5755669, SRR5755670, SRR5755671, SRR5755672). We identified 12,632 protein-coding transcripts orthologous to mouse RNA reference sequences (Refseq) in the dunnart neocortical transciptome. The results also revealed divergences in gene sets known to be enriched in different neuronal populations, revealing a more advanced stage of maturation in the marsupial neocortex at the period of infragranular birth compared to the eutherian mouse.

overall_design: Fat-tailed dunnarts were bred at the Native Wildlife Teaching and Research Facility at The University of Queensland, Queensland, Australia. Specimens at postnatal ages P12 and P20 (N=3 each age) were used. For each specimen both hemispheres of the neocortex were micro-dissected out followed by total RNA extraction, RNA quality analysis on a Bioanalyzer 2100 RNA Nano assay (Agilent), cDNA library preparation using a Truseq Stranded Total RNA kit v4 (Illumina), and sequencing on an Illumina HiSeq 2000 with 125 bp paired-end reads. A de novo transciptome was assembled using the pooled RNA sequence data of all samples using Trinity, then differential gene expression analysis performed across developmental ages (RSEM, edgeR).

first: Rodrigo

last: Suárez

first: Qion-Yi

last: Zhao

first: Annalisa

last: Paolino

first: Linda

last: Richards

first: Laura

last: Fenlon


title: Transcription factor-like 5 is a potential DNA/RNA binding protein essential for maintaining male fertility in mice.

last: Xu


title: Human distal lung maps and lineage hierarchies reveal a bipotent progenitor [human lung organoids]

status: Public on Jan 16 2022

city: Durham

first: Purushothama Rao

last: Tata

email: pt93@duke.edu, tata.lab@yahoo.com

state: NC

address: 303 Research Dr., Alexander Sands Building, Room- 451, BOX 3709

department: Department of Cell Biology

institute: Duke University School of Medicine

summary: We performed single-cell RNA-seq using 10x Genomic Chromium v3.1 on human lung organoid cultures.

overall_design: Single cell RNA-seq on human lung organoids.

first: Preetish

last: Kadur Lakshminarasimha Murthy

first: Vishwaraj

last: Sontake

first: Aleksandra

first: Yoshihiko

last: Kobayashi


title: Differentially expressed genes in head and neck cancer cell line (Sa3), control Sa3 and miR-30e-3p transfected Sa3

city: Chiba city

first: Chikashi

last: MInemura

state: Chiba prefucture

address: 1-8-1 Inohana, chuo-ku

department: Oral science

country: Japan

institute: Chiba University

overall_design: To identify the target genes of miR-30e-3p, microarray analysis was performed on control Sa3 and miR-30e-3p transfected Sa3.

first: Naohiko

last: Seki

last: Minemura


title: 5mC oxidation products in the nucleic acids of the Basidiomycete fungi Laccaria bicolor and Coprinopsis cinerea

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

type: Methylation profiling by high throughput sequencing

summary: We analyzed oxidized 5-methylcytosine derivatives 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in nucleic acids of multicellular fungi Laccaria bicolor and Coprinopsis cinerea which have been used as models to study DNA methylation, developmental processes and symbiotic interactions. All three cytosine derivatives were detected in the genomes of both fungi, and importantly, we discovered 5carC in the RNA fractions, potentially including large non-coding, messenger RNAs and small RNA molecules, indicating gene regulatory functions of 5carC.

sample_organism:
Coprinopsis cinerea
Laccaria bicolor

platform_organism:
Coprinopsis cinerea
Laccaria bicolor

overall_design: 5-hydroxymethylcytosine and 5-formylcytosine analysis in Basidiomycete fungi Laccaria bicolor and Coprinopsis cinerea using hMe-Seal, fC-Seal, hmTOP-seq and foTOP-seq methods. Vitamin C was used to increace amounts of 5-hydroxymethylcytosine and 5-formylcytosine in the hmTOP-seq and foTOP-seq methods for L.bicolor

first: Janina

last: Licyte

first: Audrone

last: Ruksenaite

first: Egle

last: Godliauskaite

first: Povilas

last: Gibas

first: Vita

last: Tomkute

first: Grazina

last: Petraityte

first: Viktoras

last: Masevicius

first: Saulius

last: Klimasauskas

first: Edita

last: Kriukiene


title: Human distal lung maps and lineage hierarchies reveal a bipotent progenitor [Spatial transcriptomics]

first: Purushothama Rao

last: Tata

summary: We performed spatial transcriptomics using 10x Genomic Visium Spatial Gene Expression on human lung.

overall_design: Spatial transcriptomics on normal human lung.


title: Human distal lung maps and lineage hierarchies reveal a bipotent progenitor [single-cell RNA-seq]

summary: We performed single-cell RNA-seq using 10x Genomic Chromium v3.1 on micro-dissected human distal airways.

overall_design: Single cell RNA-seq on normal human distal airways.

first: Preetish

last: Kadur Lakshminarasimha Murthy


title: Pharmacologically enhanced regulatory hematopoietic stem cells (HSC.Regs) reverts experimental autoimmune diabetes (Mouse)

city: San Diego

first: Dave

last: Robbins

state: CA

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

summary:
Ex-vivo pharmacological modulation enhances the immunoregulatory and trafficking properties of HSCs which mitigated autoimmune diabetes and other autoimmune disorders.
We used GeneChip microarrays to compare the whole transcriptomes of vehicle (DMSO) and dmPGE2 (10uM) + Dexamenthasone (uM) modulated NOD mouse Lin- c-Kit+ (LKs) HSPCs.

overall_design: Total RNA was extracted from in vitro modulated (4hr) NOD murine Lin- c-Kit+ (LKs) HSPCs. Each sample was processed with douplicate biological samples and gene expression due to ex vivo modulation was compared.

first: D


title: Antimicrobial production by perifollicular dermal preadipocytes is essential to the pathophysiology of acne

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: Innate immune defense against deep tissue infection by Staphylococcus aureus is orchestrated by fibroblasts that become antimicrobial when triggered to differentiate into adipocytes. However, the role of this process in non-infectious human diseases is unknown. To investigate the potential role of adipogenesis by dermal fibroblasts in acne, a disorder triggered by Cutibacterium acnes (C. acnes), single-cell RNA-sequencing was performed on human acne lesions and mouse skin challenged by C. acnes. A transcriptome consistent with adipogenesis was observed within specific fibroblast subsets from human acne and mouse skin lesions infected with C. acnes. Perifollicular dermal preadipocytes in human acne and mouse skin lesions showed colocalization of PREF1, an early marker of adipogenesis, and cathelicidin (Camp), an antimicrobial peptide. This capacity of C. acnes to trigger production of cathelicidin in preadipocytes was dependent on TLR2. Treatment of wild-type mice with retinoic acid (RA) suppressed the capacity of C. acnes to form acne-like lesions, inhibited adipogenesis and enhanced cathelicidin expression in preadipocytes, but lesions were unresponsive in Camp-/- mice, despite the anti-adipogenic action of RA. Analysis of inflamed skin of acne patients after retinoid treatment also showed enhanced induction of cathelicidin, a previously unknown beneficial effect of retinoids in difficult-to-treat acne. Overall, these data provide evidence that adipogenic fibroblasts are a critical component of the pathogenesis of acne and represent a potential target for future therapy.

overall_design: Single-cell RNA-seq of skin biopsies from mice intradermally infected with C acnes or injected with reinforced clostridial media (RCM) control

first: Alan

last: O'Neill

first: Marc

last: Liggins

first: Richard

last: Gallo


title: RNA-seq of Basidiomycete fungi Laccaria bicolor

first: Kotryna

last: Kvederaviciute

summary: We performed whole transcriptome sequencing of L. bicolor mycelium cultivated under normal and elevated vitamin C conditions.

overall_design: L. bicolor total RNA profiles of control (wild type, S238N-H82) and  vitamin C treated mycelium (two biological replicates per each condition)

first: Janina


title: Effects of yeast species and processing on transcriptomic profile and intestinal health of Atlantic salmon (Salmo salar) fed soybean meal-based diets in seawater

status: Public on Jan 15 2022

city: Ås

first: Jeleel

middle: Opeyemi

last: Agboola

address: Høgskoleveien 3B

department: Animal and Aquacultural Science

institute: Norwegian University of Life Science

summary: The objective of the current study was to examine the effects of yeasts on intestinal health and transcriptomic profile of Atlantic salmon fed SBM-based diets in seawater. Cyberlindnera jadinii (CJ) and Wickerhamomyces anomalus (WA) yeasts were produced in-house and processed by direct heat-inactivation with spray-drying (ICJ and IWA) or autolyzed at 50 ºC for 16 h (ACJ and AWA), followed by spray-drying. Six diets were formulated, one based on fishmeal (FM), a challenging diet with 30% soybean meal (SBM) and four other diets containing 30% SBM and 10% of each of the four yeast fractions (i.e., ICJ, ACJ, IWA and AWA). The results showed that the inclusion of CJ yeasts reduced loss of supranuclear vacuolization, along with reduction in population of CD8α positive cells present in the lamina propria of fish fed the SBM diet. The CJ yeasts controlled the inflammatory profile of fish fed SBM through up-regulation of pathways related to wound healing and taurine metabolism. Additionally, the WA yeasts dampened the inflammatory profile of fish fed SBM through down-regulation of pathways related to toll-like receptor signaling, C-lectin receptor, cytokine receptor and signal transduction. The results suggest that yeasts could be used as protein ingredients with functional properties in diets for Atlantic salmon.

overall_design: Examination of intestinal health of Atlantic salmon fed diets containing four different yeast treatments.

middle: O

first: Dominic

last: Mensah

first: Jon

last: Hansen

first: David

last: Lapeña

first: Liv

last: Mydland

first: Magnus

last: Arntzen

first: Svein

last: Horn

first: Ove

last: Øyas

first: Press

last: McLean

first: Margareth

last: Øverland


title: Transcriptomic profiling of Hnf4a liver knockout mice (AlbCre-Hnf4a fl/fl) vs control (Hnf4a fl/fl) mice.

city: Heraklion

first: Dimitris

last: Kardassis

address: Vassilika Vouton

department: Medical School

country: Greece

institute: University of Crete

summary: Aberrant concentration, structure and functionality of High Density Lipoprotein (HDL) is associated with many prevalent diseases, including cardiovascular disease and non-alcoholic fatty liver disease (NAFLD). Mice with liver-specific ablation of Hnf4α (H4LivKO) present steatosis and dyslipidemia by mechanisms that are not completely understood. The aim of this study was to explore the role of liver Hnf4α in HDL metabolism and the development of steatosis.

overall_design: Liver samples were obtained from 6-weeks old liver knockout mice (AlbCre-Hnf4a fl/fl) and their littermate controls (Hnf4a fl/fl). Total RNA from all mice (4 AlbCre-Hnf4a fl/fl and 4 Hnf4a fl/fl ) was labeled and hybridized to GeneChip™ Mouse Gene 2.0 ST Affymetrix expression arrays. The total of 8 arrays was analyzed by the Affymetrix Transcriptome Analysis Console (TAC) Software Version 4.0.2. Differentially expressed genes were evaluated by specific statistical criteria (p-value <0.05 and absolute fold change ≥1.5).

first: Efstathia

last: Thymiakou


title: Multi-omics reveals mitochondrial metabolism proteins susceptible for drug discovery in AML

city: Omaha

first: Shannon

last: buckley

state: Nebraska

address: 985805 Nebraska Medical Center

department: Genetics, Cell Biology, and Anatomy

institute: Unviversity of Nebraska Med Center

summary: RNA vs protein comparison in mouse AML tumors

overall_design: ckit+ Bone Marrow RNA profiles from e WT mice and spleenic tumor RNA profiles of AML mice with either the Inv16, MLL-ENL, or MLL-AF9 translocation

last: Buckley


title: The Wnt inhibitor sFRP3 protects mitral valve endothelium  from MI-induced EndMT

city: Boston

first: Ali

last: Hashemi Gheinani

address: 300 Longwood

department: Urology

institute: Boston Children's Hospital

summary:
Rational: We previously reported evidence of endothelial to mesenchymal transition (EndMT) and fibrosis in mitral valve (MV) leaflets at two to six months post-myocardial infarction (MI) in sheep. The onset of these changes and the mechanism of their instigation are not known.  Early modulation of EndMT and fibrosis in MV leaflets may limit the development of ischemic mitral regurgitation (IMR) and heart failure. H
Objective: To test the hypothesis that circulating molecules present in plasma within days after MI incite EndMT and fibrotic processes in MV leaflets.
Method and Results: Ovine MVs harvested 8-10 days after inferior MI (IMI) showed an increase in MV thickness by histology and onset of EndMT, shown by increased CD31/α-smooth muscle actin (α-SMA)+ cells in post-MI MV leaflets (10.5±6.9%) versus sham (2.6±4%).  In vitro, post-MI plasma induced EndMT and pro-fibrotic markers and enhanced migration of primary mitral valve endothelial cells (VECs). In contrast, sham plasma did not, despite the presence of TGFβ2 at levels known to induce EndMT in VECs (2 ng/ml). Analysis of sham versus post-MI plasma using a cytokine array revealed a significant drop in the Wnt signaling antagonist secreted frizzled-related protein 3 (sFRP3) in post-MI plasma compared to sham plasma, which was confirmed by ELISA. Addition of recombinant sFRP3 to post-MI plasma reversed its EndMT-inducing effect on mitral VECs, measured by restored VE-cadherin, reduced α-SMA, and reduced TGFβ1-3 expression. Extracellular signal related kinase 1/2 and SMAD2/3 phosphorylation were increased in mitral VEC by post-MI plasma, and both were blocked by supplementing the post-MI plasma with sFRP3. RNA-seq analysis of mitral VECs exposed to post-MI versus sham plasma for 24 hours showed upregulated forkhead box M1 (FOXM1), a transcription factor previously shown to drive fibrosis.  FOXM1 was co-localized with CD31 in MV leaflets obtained from sheep at 8-10 days post-MI, which suggests FOXM1 may be linked to EndMT initiation. Blocking FOXM1 with Siomycin A (Sio A) reduced EndMT and pro-fibrotic transcripts in post-MI plasma treated mitral VECs. Finally, post-MI plasma-induced and TGFβ-induced FOXM1 was downregulated by sFRP3.
Conclusions: Reduced sFRP3 in post-MI plasma appears to facilitate the onset of TGFβ-driven EndMT and fibrosis in mitral VECs by increasing the transcription factor FOXM1. Restoring sFRP3 levels and/or inhibiting FOXM1 may provide new strategies to minimize maladaptive changes that occur in the MV due to MI.

overall_design: Ovine mitral VECs mRNA profiles of 24-hour +ovine post-MI (3 samples) or naive plasma (3 samples)

first: Zahra

last: Alvandi

first: Yasufumi

last: Nagata

first: Livia Silva Araúujo

last: Passos

first: J. Luis

last: Guerrero

first: Dayana Carolina

last: Romero

first: Jill

last: Wylie-Sears

first: Brittan A

last: Morris

first: Suzanne M

last: Sullivan

first: Rosalyn M

last: Adam

first: Elena

last: Aikawa

first: Robert A

last: Levine

first: Joyce

last: Bischoff


title: Gene therapy of Csf2ra-/- deficiency in long-term cultured fetal monocyte precursors restores bona fide alveolar macrophage development and function in mice

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

summary: Tissue-resident macrophage-based immune therapies have been proposed for various diseases. However, generation of sufficient numbers that possess tissue-specific functions remains a major handicap. Here, we show that fetal liver monocytes cultured with GM-CSF (CSF2-cFLiMo) rapidly differentiate into a long-lived, homogeneous alveolar macrophage (AM)-like population in vitro. CSF2-cFLiMo remained the capacity to develop into bona fide AM upon transfer into Csf2ra-/- neonates and prevented development of alveolar proteinosis and accumulation of apoptotic cells for at least 1 year in vivo. CSF2-cFLiMo more efficiently engrafted empty AM niches in the lung and protected mice from severe pathology induced by respiratory viral infection, compared to transplantation of macrophages derived from bone marrow cells cultured with M-CSF (CSF1-cBMM) in the presence or absence of GM-CSF. Harnessing the potential of this approach for gene therapy, we restored a disrupted Csf2ra gene in FLiMo and demonstrated their capacity to develop into AM in vivo. Together, we provide a novel platform for generation of immature AM-like precursors amenable for genetic manipulation, which will be useful to dissect AM development and function and pulmonary transplantation therapy.

first: Fengqi

last: Li

first: Katarzyna

last: Okreglicka

first: Federica

last: Piattini

first: Lea

last: Pohlmeier

first: Christoph

last: Schneider


title: Perturb-map coupled with spatial transcriptomics identifies mutation associated gene signatures in a mouse model of lung adenocarcinoma

city: New York

first: Dana

last: Pe'er

address: 417 E 68th St

department: Computational and Systems Biology

institute: Memorial Sloan Kettering Cancer Center

summary: The cellular architecture of a tumor has a major impact on cancer outcome, and thus there is interest in identifying genes controlling the tumor microenvironment (TME). While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying gene functions operating extracellularly or within a tissue context. To address this, we developed an approach for spatial functional genomics called Perturb-map, which utilizes protein barcodes (Pro-Code) to enable spatial detection of barcoded cells within tissue. We applied Perturb-map to knockout dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Additionally, we paired Perturb-map and spatial transcriptomics for unbiased molecular analysis of Pro-Code/CRISPR lesions. Our studies found in Tgfbr2 knockout lesions, the TME was converted to a fibro-mucinous state and T-cells excluded, concomitant with upregulated TGFb and TGFb-mediated stroma activation, suggesting Tgfbr2 loss on lung cancer cells increased TGFb bioavailability and enhanced its suppressive effects on the TME. These studies establish Perturb-map for functional genomics within a tissue at single cell-resolution with spatial architecture preserved.

overall_design: Male C57BL/6J mice were injected intravenously with KP (Kras G12D, p53 deleted) cells transduced with a Pro-Code/CRISPR library targeting 35 different genes associated with tumor-immune interaction. 10X Visium spatial transcriptomics profiling was performed on 4 separate sections of mouse lung from 3 different mice. Annotations for specific genes targeted in visium spots capturing tumor cells were generated by parallel hyperion imaging on a serial section to identify the linked protein barcode.

first: Samuel

middle: A

last: Rose

first: Maxime

last: Dhainaut

first: Brian

last: Brown


title: Human distal lung maps and lineage hierarchies reveal a bipotent progenitor

first: Purushothama Rao

last: Tata

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

overall_design: Refer to individual Series


title: A single factor elicits multilineage reprogramming of astrocytes in the adult mouse striatum

city: Dallas

first: Boxun

state: Texas

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology

institute: University of Texas Southwestern Medical Center

summary: Astrocytes in the adult brain show cellular plasticity; however, whether they have the potential to generate multiple lineages remains unclear. Here, we perform in vivo screens and identify DLX2 as a transcription factor that can unleash the multipotentiality of adult resident astrocytes. Genetic lineage tracing and time-course analyses reveal that DLX2 enables astrocytes to rapidly become ASCL1+ neural progenitor cells, which give rise to neurons, astrocytes, and oligodendrocytes in the adult mouse striatum. Single-cell transcriptomics and pseudotime trajectories further confirm a neural stem cell-like behavior of reprogrammed astrocytes, transitioning from quiescence to activation, proliferation, and neurogenesis. Gene regulatory networks and mouse genetics identify and confirm key nodes mediating DLX2-dependent fate reprogramming. These include activation of endogenous DLX family transcription factors and suppression of Notch signaling. Such reprogramming-induced multipotency of resident glial cells may be exploited for neural regeneration.

overall_design: Comparison of single-cell RNA-seq data between Lenti-DLX2 mice, Lenti-GFP control mice, and two publicly available WT E18.5 mouse brain datasets.

first: Yunjia

last: Zhang

first: Gary

last: Hon

first: Chun-Li


title: Neuronal mitochondria transport Pink1 mRNA via Synaptojanin 2 to support local mitophagy

status: Public on Jan 14 2022

city: Neuherberg

first: Yiming

last: Cheng

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Munich

summary: PTEN-induced kinase 1 (PINK1) is a very short-lived protein that is required for the removal of damaged mitochondria through Parkin translocation and mitophagy. Because the short half-life of PINK1 limits its ability to be trafficked into neurites, local translation is required for this mitophagy pathway to be active far from the soma. The Pink1 transcript is associated with and cotransported with neuronal mitochondria. In concert with translation, the mitochondrial outer membrane protein Synaptojanin 2 Binding Protein (SYNJ2BP) and Synaptojanin 2 (SYNJ2) are required for tethering Pink1 mRNA to mitochondria via an RNA-binding domain in SYNJ2. This neuron-specific adaptation for local translation of PINK1 provides distal mitochondria with a continuous supply of PINK1 for activation of mitophagy.

overall_design: Examination of the impact of SYNJ2BP mutants on the SYNJ2BP binding RNA

first: Angelika

middle: B

last: Harbauer

first: Inmaculada

last: Segura


title: Gene expression profiling of neural stem cells in 3D hydrogels with different stiffness

city: Berkeley

first: Sanjay

last: Kumar

address: 274A Stanley Hall, University of California - Berkeley

institute: UC Berkeley

summary: We report a transcriptome sequencing to identify 3D hydrogel stiffness-dependent genes

overall_design: Identification of stiffness-dependent genes in neural stem cells

first: David

last: Schaffer

first: Jieung

last: Baek

first: Paola

last: Lopez


title: Genome-wide mRNA expression array to identify dysregulated genes between CD26+ and CD26- HT29 cells

city: Pokfulam

first: Lui

last: Ng

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

summary: Affymetrix HG-U133 Plus2 Array was applied to identify differentially expressed genes between FACS sorted CD26+ and CD26- subpopulations of HT29 colorectal cancer cell-line.

overall_design: Gene expression profiles of FACS sorted CD26+ and CD26- subpopulation of HT29 cells were investigated using the Affymetrix human genome U133 Plus 2.0 GeneChip (Affymetrix). Data generated was analyzed using Genespring GX 350 (Affymetrix) and Genomatix Genome Analyzer (Genomatix). Differentially expressed genes between HT29 CD26+ and CD26- cells were identified.

first: Sunny

last: Wong


title: Genome-wide chromatin state in non-failing and dilated cardiomyaphty human left ventricles [PLAC-seq]

city: Cleveland

first: Chia-Feng

last: Liu

state: OH

address: 9500 Euclid Avenue,

department: Cardiovascular & Metabolic Sciences

institute: Cleveland Clinic Lerner Research Institute

summary: We conducted chromatin immunoprecipitation followed by sequencing (ChIP-seq) and proximity ligation-assisted ChIP-seq (PLAC-seq) for enhancers and promoters (E-P) using left ventricular tissues from dilated cardiomyopathy (DCM) patients and non-heart failure (NF) donors. Differential active enhancer H3K27ac and promoter H3K4me3 regions were identified between NF and DCM. While the average read density (ARD) for H3K27ac is similar between NF and DCM, the ARD of H3K4me3 is significantly lower in DCM samples than in NF.Super-enhancer (SE) analysis revealed that 929 and 129 genes linked to NF- and DCM-specific SE, respectively, and three unique SE-associated genes between NF and DCM  were identified.Moreover, the differential E-P interactions were observed in the known heart failure gene loci and are correlated with the gene expression levels. Motif analysis identified known cardiac factors and possible novel players for DCM.  We have established cistrome of four histone modifications and long-range chromatin interaction for enhancers and promoters in NF and DCM tissues. The differential histone modifications and E-P interactions were found in DCM, and these differences were associated with the gene expression level of a subset of disease-associated genes in human heart failure.

overall_design: PLAC-seq experiments for H3K27ac and H3K4me3 were carreid out in human left ventricles tissues from male patients who underwent cardiac transplantation for dilated cardiomyopathy (DCM) and in matched non-failing donors (NF)

first: Armen

last: Abnousi

first: Peter

last: Bazeley

first: Ying

last: Ni

first: Christine

middle: S

last: Moravec

first: Ming

last: Hu

first: W

middle: H

last: Tang


title: Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer [II]

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Standard cancer therapy targets tumor cells while not considering the possible collateral damage on the tumor microenvironment that could impair therapy response. Employing patient-derived tumor organoids and primary stroma cells or a novel murine rectal cancer model, we show that tumor cell-derived IL-1a polarizes cancer-associated fibroblasts (CAFs) towards a pro-inflammatory phenotype causing an elevated oxidative DNA damage mediated by reactive nitrogen species (NOS) and subsequently sensitizing iCAFs to a p53-mediated therapy-induced senescence, which triggers changes in matrisome composition culminating in chemoradiotherapy resistance and disease progression. Consequently, IL-1 inhibition, prevention of iCAF senescence or senolytic therapy sensitizes mice to irradiation. Importantly, rectal cancer patients with poor response to radiotherapy are characterized by an increased number of CAFs, a dominant inflammatory CAF gene signature as well as lower IL-1 receptor antagonist (IL-1RA) serum levels. Low baseline IL1RA gene expression predicts poor outcome while IL-1RA serum levels are associated with a single nucleotide polymorphism (SNP) in IL1RA (rs4251961 T/C). Moreover, conditioned supernatant from patient tumor organoids sensitizes fibroblasts to undergo radiation-induced senescence in an IL-1-dependent manner. Collectively, we unravel a critical role for inflammatory CAFs in cancer therapy and identify IL-1 signaling as an attractive target for stroma-repolarization and prevention of CAF senescence

overall_design: A total of 20 samples, with 4 replicates in 5 groups

first: Shomroni

last: Orr

first: Adele

middle: M

last: Nicolas


title: Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer [I]

overall_design: Two groups each containing four independent samples


title: Chromatin accessibility landscapes of WT (GFP-) and BATF KO (GFP+) ILC3s sorted from lung mature ILC2s

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: Activated type 2 innate lymphoid cells (ILC2s) accumulate and promote inflammatory resolution and tissue repair in host defense against acute respiratory viral infections. However, the heterogeneity of ILC2s in the lung and the mechanisms by which ILC2 cells contribute to tissue repair remain elusive. Using single-cell RNA-sequencing (scRNA-seq), we identified a transcriptionally distinct ILC2 subset that showed enrichment for wound healing signature genes and the transcription factor BATF. Notably, BATF promoted the proliferation and function of ILC2s and restricted their plasticity during infection with influenza virus. In the absence of BATF, ILC2s lost their immune protective properties and obtained pathogenic ILC3-like function, which led to persist neutrophil infiltration, tissue damage and lethality. Mechanistically, BATF directly bound the cis-regulatory elements of wound healing genes, maintained their chromatin accessibility and promoted their expression. Lastly, BATF played an important role in an IL-33-ST2 feed-forward loop that supports ILC2 cell identity and function. Collectively, our findings shed light on a BATF-dependent ILC2 program, thereby providing a potential therapeutic target for terminating detrimental inflammation during acute viral infection.

overall_design: ATACseq, 2 samples (WT and Batf-/- ILC2s), 2 biological replicates per sample, from lung mauter ILC2s cultured in vitro.

first: Xiaopeng

last: Wu


title: RNA-seq analysis of old versus young, male versus female, and naïve versus effector memory CD4+ T cells.

city: Irvine

first: Haik

last: Mkhikian

state: California

address: D440 Medical Sciences I

institute: UC Irvine

summary: Impaired T cell immunity in the elderly increases mortality from infectious disease. The branching of Asparagine-linked glycans is a critical negative regulator of T cell immunity. We found that N-glycan branching increases with age in female > male, naïve > memory and CD4+ > CD8+ T cells, likely contributing to immunosenescence.  To investigate the mechanisms driving these changes, we performed RNA-seq analysis on highly purified young and old naive (CD3+CD4+CD25-CD62L+CD44-) and effector memory (CD3+CD4+CD25-CD62L-CD44+) CD4+ T cells from male and female mice. Comparing young and old CD4+ TN cells, 158 and 192 differentially expressed genes (DEGs) were identified in females and males, respectively. Remarkably, only 44 of these overlapped between the sexes. There were no significant differences in gene expression of N-glycan branching enzymes or other relevant glycosylation genes. Among the 114 DEGs in female but not male CD4+ TN cells, four were within the IL-7 signaling pathway, a pathway previously implicated in regulating N-glycan branching.  This included reduced expression of IL7Rα (CD127) and increased expression of Suppressor of cytokine signaling 1 (Socs1), Socs3, and Janus kinase 3 (Jak3).  Other IL-7 signaling pathway genes were unchanged.

overall_design: Examination of mRNA profiles from naïve (CD3+CD4+CD25-CD62L+CD44-) and effector memory (CD3+CD4+CD25-CD62L-CD44+) CD4+ T cells from young and aged female and male mice. Three biological replicates of each were analyzed for 24 total samples.

first: Ken

last: Hayama

first: Phuong

middle: Q

last: Tran

first: Michael

last: Demetriou


title: Sustained down-regulation of alphaSmooth muscle actin expression in aortas induced by angiotensin II: a new model of vascular memory to hypertension

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: We developped a new model of vascular injury memory in response to AngII stimulation in mice. We used RNAseq (aortas) to try to understand observed sustained phentoype and identify Acta2 (aSMA) as key in observed phenomenon.

overall_design: 11-week male C57B6 mice were implanted with osmotic minipumps delivering of 2.8mg/kg/day of AngII  for 2 weeks. Mice were sacrificed at the end of the treatment (AngII); and after 2 and 3 weeks of AngII (AngII+2W; Ang+3W, respectively). Age matched littermate served as control.  Aortic mRNA profile was compared: CTRL vs AngII; CTRL vs AngII+2W; and CTRL vs AngII+3W

first: Lucie

last: Pothen

first: Jean

last: Balligand

first: Bertrand

last: Bearzatto


title: Characterization of lung innate lymphoid cells during influenza infection using scRNA-seq

summary: Activated type 2 innate lymphoid cells (ILC2s) accumulate and promote inflammatory resolution and tissue repair in host defense against acute respiratory viral infections. However, whether an ILC2 subset that specializes in wound healing exists, and the mechanisms by which ILC2 cells contribute to tissue repair remain elusive. Using single-cell RNA-sequencing (scRNA-seq), we identified a transcriptionally distinct ILC2 subset that showed enrichment for wound healing signature genes and the transcription factor BATF. Notably, BATF promoted the proliferation and function of ILC2s and restricted their plasticity during infection with influenza virus. In the absence of BATF, ILC2s lost their immune protective properties and obtained pathogenic ILC3-like function, which led to persist neutrophil infiltration, tissue damage and lethality. Mechanistically, BATF directly bound the cis-regulatory elements of wound healing genes, maintained their chromatin accessibility and promoted their expression. Lastly, BATF played an important role in an IL-33-ST2 feed-forward loop that supports ILC2 cell identity and function. Collectively, our findings shed light on a BATF-dependent ILC2 program thereby providing a potential therapeutic target for terminating detrimental inflammation during acute viral infection.

overall_design: Two samples (Day 5 and Day 10 post influenza infection) were prepared using 10x Genomics Chromium platform

first: Yao

last: Chen


title: Bulk RNA sequencing of WT and Batf-/- ILC2s sorted from lungs at day 9 after influenza virus infection

overall_design: Bulk RNA sequencing, 2 samples (WT and Batf-/- ILC2s), 3 biological replicates per sample, from lungs at day 9 after influenza virus infection.


title: ChIP-seq analysis of BATF in ILC2s sorted from lungs at day 9 after influenza virus infection

overall_design: BATF CUT&TAG ChIPseq, 2 samples (anti-BATF and Rabbit normal serum IgG1 was used as a control. ), 2 biological replicates per sample, ILC2s sorted from lungs at day 9 after influenza virus infection.


title: Chromatin accessibility landscapes of WT and Batf-/- ILC2s sorted from lungs at day 9 after influenza virus infection

overall_design: ATACseq, 2 samples (WT and Batf-/- ILC2s), 2 biological replicates per sample, from lungs at day 9 after influenza virus infection.


title: Pleiotropic and Non-redundant Effects of an Auxin Importer in Setaria and Maize

status: Public on Jan 13 2022

city: St. Louis

first: Elizabeth

middle: A.

last: Kellogg

state: MO

address: 975 North Warson Rd.

institute: Donald Danforth Plant Science Center

summary:
Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in Setaria viridis and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility.
However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology.  In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development.  A GFP-tagged construct of SvAUX1 under its native promoter showed that the AUX1 protein localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima.
RNA-seq analysis finds that most gene expression modules are conserved between mutant and wildtype plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using CRISPR-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SvAUX1/SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, leaf, and root development. The AUX1 importers are thus not fully redundant in S. viridis.  Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.

overall_design: Comparison of gene expression over three developmental stages of the inflorescence in Setaria viridis accession A10.1 (wild type) and the sparse panicle1 mutant.


title: Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer


title: Iodoacetic Acid Exposure Alters the Transcriptome in Mouse Ovarian Antral Follicles

city: Urbana

first: Mary

last: Laws

address: 2001 S. Lincoln Ave.

institute: University of Illinois

summary: The process of drinking water disinfection forms compounds known as disinfection byproducts (DBPs). Studies have shown that DBPs can be harmful to human and animal health. Iodoacetic acid (IAA) is a non-regulated DBP that is cytotoxic and genotoxic to mammalian cells. In addition, IAA has been shown to be an ovarian toxicant in vitro and in vivo. However, the mechanisms of action underlying IAA toxicity on ovarian follicles in vivo remain unclear. In this study, we determined whether IAA exposure alters gene expression patterns in ovarian antral follicles in mice. Adult female CD-1 mice were dosed with water or IAA (10 or 500mg/L) in the drinking water for 35-40 days. Antral follicles were dissected from the ovaries based on size (220–400 μm). Sera were collected to measure estradiol levels. RNA-sequencing was applied to uncover the global gene expression of the antral follicles in response to IAA exposure. RNA-sequencing analysis identified 410 and 653 differentially expressed genes (DEGs) in the 10 and 500mg/L IAA treatment groups (FDR < 0.1), respectively, compared to controls. Gene Ontology Enrichment analysis showed that DEGs were involved with RNA processing and regulation of angiogenesis (10mg/L) and the cell cycle, cell division, and mitotic nuclear division (500mg/L). In addition, Pathway Enrichment analysis showed that DEGs were involved in the phosphatidylinositol 3-kinase and protein kinase B (PI3K-Akt) signaling pathway, gonadotropin-releasing hormone (GnRH) signaling pathway, estrogen signaling pathway, and insulin signaling pathway (10mg/L). In the 500mg/L group, Pathway Enrichment analysis showed that DEGs were involved in the oocyte meiosis signaling pathway, GnRH signaling pathway, and oxytocin signaling pathway. In addition, RNA-sequencing analysis identified 809 DEGs when comparing the 10 and 500mg/L IAA groups (FDR < 0.1). DEGs were related to ribosome, translation, mRNA processing, oxidative phosphorylation, chromosome, cell cycle, cell division, protein folding, platelet activation, and the oxytocin signaling pathway. Moreover, IAA exposure significantly decreased estradiol levels (500mg/L) in serum compared to control. This study identified key candidate genes and pathways involved in IAA toxicity that could help to further understand the molecular mechanisms of IAA toxicity in ovarian follicles.

overall_design: Murine mRNA profile of ovarian antral follicles. Adult female mice (40 days old) were dosed with vehicle (deionized, reverse osmosis filtered water) or IAA (10 or 500 mg/L) dissolved in reverse osmosis water for 35 days (n=5 per treatment group) via the drinking water. Two experiments were performed a month apart. In experiment 1, animals were exposed to only water (control) or 500mg/L of IAA in drinking water. In experiment 2, animals were exposed to only water (control) or 10mg/L of IAA in drinking water. Antral follicles were mechanically isolated from 1 individual mouse and submitted for mRNA sequencing as 1 experimenal unit. Global analyses combined control groups from both experiments for comparisons with IAA treated groups.

first: Andressa

last: Gonsioroski

middle: J

first: Vasiliki

last: Mourikes

first: Alison

last: Neff

first: Jenny

last: Drnevich

last: Plewa

first: Jodi

last: Flaws


title: Robust transcriptional profiling and identification of differentially expressed genes with low input RNA sequencing of adult hippocampal neural stem and progenitor populations [in vivo]

city: Columbus

middle: Diana

last: Kirby

address: 1835 Neil Ave, 55 Psycholgy

department: Psychology

institute: The Ohio State University

summary: Multipotent neural stem cells (NSCs) are found in several isolated niches of the adult mammalian brain where they have unique potential to assist in tissue repair. Modern transcriptomics offer high-throughput methods for identifying disease or injury associated gene expression signatures in endogenous adult NSCs, but they require adaptation to accommodate the rarity of NSCs. Bulk RNA sequencing of NSCs requires pooling several mice, which impedes application to labor-intensive injury models. Alternatively, single cell RNA sequencing can profile hundreds to thousands of cells from a single mouse and is increasingly used to study NSCs. However, consequences of the low RNA input from a single NSC on downstream identification of differentially expressed genes (DEGs) remains largely unexplored. Here, to clarify the role that low RNA input plays in DEG identification, we directly compared DEGs in an oxidative stress model of cultured NSCs by bulk and single cell sequencing. While both methods yielded DEGs that were replicable, single cell sequencing DEGs derived from genes with higher relative transcript counts compared to all detected genes and exhibited smaller fold changes than DEGs identified by bulk RNAseq. The loss of high fold-change DEGs in the single cell platform presents an important limitation for identifying disease-relevant genes. To facilitate identification of such genes, we determined an RNA-input threshold that enables transcriptional profiling of NSCs comparable to traditional bulk sequencing and used it to establish a workflow for in vivo profiling of endogenous NSCs. We then applied this workflow to identify DEGs after lateral fluid percussion injury, a labor-intensive animal model of traumatic brain injury. Our work suggests that single cell RNA sequencing may underestimate the diversity of pathologic DEGs but population level transcriptomic analysis can be adapted to capture more of these DEGs with similar efficacy and diversity as traditional bulk sequencing. Together, our data and workflow will be useful for investigators interested in understanding and manipulating adult hippocampal NSC responses to various stimuli.

overall_design: In vivo: Whole DG was dissected from perfused NestinGFP mice and digested in to a single cell suspension. Cells were labeled for O1, O4, CD31, CD45, Cd11b and GLAST. Fluorescence activated cell sroting was then used to isolate neural stem cells (O1-O4-CD31-CD45-Cd11b-GFP+GLAST+) and intermediate neural progenitors (O1-O4-CD31-CD45-Cd11b-GFP+GLAST-). 300 cells were collected directly in to lysis buffer and followed by direct cDNA synthesis and sequencing. In one study, mice received either sham injury or lateral fluid percussion injury 4h before perfusion and dissection of the DG ipsilateral to injury/sham.

first: Jiyeon

middle: K

last: Denninger

first: Logan

last: Walker

first: Xi

first: Altan

last: Turkoglu

first: Alex

last: Pan

first: Zoe

last: Tapp

first: Sakthi

last: Senthilvelan

first: Raina

last: Rindani

first: Olga

last: Kokiko-Cochran

first: Ralph

last: Bundschuh

first: Pearlly

last: Yan


title: Robust transcriptional profiling and identification of differentially expressed genes with low input RNA sequencing of adult hippocampal neural stem and progenitor populations

first: Elizabeth

overall_design: Refer to individual Series


title: Robust transcriptional profiling and identification of differentially expressed genes with low input RNA sequencing of adult hippocampal neural stem and progenitor populations [scRNA-Seq]

overall_design: In vitro data: 6 primary cultures of adult mouse hippocampal neural stem cells were used. 3 were treated with vehicle and 3 with H2O2 for 24h to induce oxidative stress before harvest. After harvest, cell suspensions were divided in to 2 workflows: immediate single cell sequencing via 10X Chromium system or RNA extraction for "bulk" RNAseq. Buk RNA was diluted in to 3 spearate input quantities for cDNA synthesis and Illumina paired-end sequencing (1ng, 100pg and 10pg). Single cell data from vehicle treated single cells is available in GSE138381.

last: Chen


title: AZD5153, a bivalent BRD4 inhibitor, inhibits hepatocellular cancer growth by modulating the HCC transcriptome through repression of critical oncogenes through dissociation of BRD4 from the enhancer/promoter regions of critical genes [RNA-Seq]

first: Kalpana

last: Ghoshal

address: 420 W 12th Ave

summary: Hepatocellular carcinoma (HCC) is the fifth leading cause of cancer-related death worldwide because of late stage detection when curative therapy is not available. The bromodomain and extraterminal (BET) protein BRD4 activates gene expression by interacting with histone H3K27-acetylated (H3K27Ac) chromatin. AZD5153 is an orally bioavailable, potent, bivalent BRD4 inhibitor, currently undergoing clinical trials in lymphoma and ovarian cancer patients. Here, we studied therapeutic potential of AZD5153 against HCC and elucidated the underlying mechanism. In conclusion, our results in preclinical models indicate that the combined effect of AZD5153 could be a novel targeted therapy for HCC and provides rationale for clinical trials of an AZD5153-FK866 combination as an effective and attractive strategy to treat this deadly disease.

overall_design: HCCLM3 cells were treated with AZD5153 (10µM) or DMSO for 24 hours

first: Cho-Hao

last: Lin

first: Chun-Tien

last: Kuo

first: Ding

last: Li


title: Robust transcriptional profiling and identification of differentially expressed genes with low input RNA sequencing of adult hippocampal neural stem and progenitor populations [in vitro dilutions]

overall_design: In vitro data: 6 primary cultures of adult mouse hippocampal neural stem cells were used. 3 were treated with vehicle and 3 with H2O2 for 24h to induce oxidative stress before harvest. After harvest, cell suspensions were divided in to 2 workflows: immediate single cell sequencing via 10X Chromium system or RNA extraction for "bulk" RNAseq. Bulk RNA was diluted in to 3 separate input quantities for cDNA synthesis and Illumina paired-end sequencing (1ng, 100pg and 10pg). Single cell data from vehicle treated single cells is available in GSE138381.


title: AZD5153, a bivalent BRD4 inhibitor, inhibits hepatocellular cancer growth by modulating the HCC transcriptome through repression of critical oncogenes through dissociation of BRD4 from the enhancer/promoter regions of critical genes

overall_design: Identifying chromosomal targets of BDR4 and H3K27Ac that are disrupted by the AZD5153 treatment


title: Oxidized 5mC modifications in fungi

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

institute: Vilnius University


title: HITI junction characterization

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: Mouse retinas and livers were injected with AAV2/8 vectors encoding for SpCas9 under control of tissue-specific promoters, as well as a donor DNA and gRNA used to perform targeted integration in the two target loci (rhodopsin for the retina and albumin for the liver) via non-homologous end joining. Retinas and livers were harvested one month after injection and DNA was extracted. PCR products comprising the 5' and 3' junctions between the endogenous loci and the inserted donor DNA were amplified and used for library generation. NGS analysis allowed characterization of the kinds and relative frequency of insertions and deletions generated at the junction points in order to better understand the precision of integration achieved by this gene editing approach.

overall_design: 5' and 3' junctions were amplified as PCR products from the DNA extracted from one retina (rhodopsin) and one liver (albumin). PCR products were not amplified in negative control samples of retina and liver injected with SpCas9 and donor DNA but without a non-targeting scramble gRNA. Sequences obtained by NGS were aligned to a reference sequence of the expected genome editing outcome, which was constructed using the mouse genome and the sequence of the donor DNA. An ad-hoc algorithm was developed and used to identify insertions and deletions and calculate their relative frequency and position.

first: Patrizia

last: Tornabene

first: Manel

last: Llado-Santaeularia

first: Lucio

last: Di Filippo


title: Therapeutic homology-independent targeted integration in retina and liver

summary: We report the integration of AAV using CRISPr techonology within Mus musculus targeting RHO and ALB genes.

overall_design: Examination of target and off-target integration of AAV

first: Francesco

last: Musacchia


title: Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses

city: East Lasing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Rd.

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: Camelina is an annual oilseed plant that is gaining momentum as a biofuel winter cover crop.  Understanding gene regulatory networks (GRNs) is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. Also, we performed RNA-seq assays of Camelina's seed at 5, 8, and 11 days post-anthesis (DPA) to improve the transcriptomic resolution of the early stages of the Camelina seed development.  We identified ~350 TFs highly co-expressed with lipid-related genes (LRGs). After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16/22 TF using DNA affinity purification sequencing (DAP-seq). Enrichment analyses supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes and aspects unique to Camelina. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confident and shortlist of Camelina TFs involved in controlling lipid metabolism during seed development.

overall_design: Examination of gene expression (RNA-seq) during three-time point during early stages of seed development as well as the evaluation of DNA-binding profiles (DAP-seq ) for 22 TF in Camelina sativa. RNA-seq and DAP-seq experiments were performed in triplicate and duplicate. Processed data is not included for Csa17g034220_deM and  Csa19g036630_deM samples due to their high correlation with the Halo control.

first: Danny

last: Schnell

first: Fabio

last: Gomez-Cano

first: Yi-Hsuan

last: Chu


title: Detection of revertant mosaicism in epidermolysis bullosa through Cas9-targeted long read sequencing

city: Sapporo

first: Yoshikazu

last: Furuta

state: Hokkaido

address: North 20 West 10, Kita-ku

department: International Institute for Zoonosis Control

institute: Hokkaido University

summary: Revertant mosaicism (RM) is a phenomenon in which inherited mutations are spontaneously corrected in somatic cells. RM occurs in some congenital skin diseases, although genetic validation of RM in clinically revertant skin has been challenging, especially when homologous recombination (HR) is responsible for RM. We introduced Nanopore Cas9-targeted sequencing (nCATS) for identifying HR in clinically revertant skin.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: Genomic region of COL7A1 which is about 8 kb long was enriched by PCR or nCATS, then applied for MinION sequencing to detect the allele at two loci c.5932C and c.8029G.

first: Ken

last: Natsuga

first: Shota

last: Takashima

first: Takuma

last: Nohara

first: Hideyuki

last: Kosumi

first: Yosuke

last: Mai

first: Hideaki

last: Higashi

last: Ujiie


title: Skeletal muscle stem cell ciliary pathways

city: Stanford

first: Peter

last: Jackson

address: 279 Campus Dr., CCSR 3230

institute: Stanford University

summary: To identify signaling pathways related to primary cilia in muscle stem cells.

overall_design: Muscle stem cells isolated from  2-4 mo Pax7-CreERT2;IFT88 f/f (IFTKO) or control mice, or from 24 mo wt C57BL6 mice by alpha7+/CD34+ sorting. MuSCs from 24 mo mice were cultured on hydrogels for 24 hours. RNA was collected from 5,000-10,000 total cells.

first: Adelaida

last: Palla

first: Janos

last: Demeter

first: Helen

last: Blau


title: Glial profiling of human tauopathy brain demonstrates enrichment of astrocytic transcripts in tau-related frontotemporal degeneration

status: Public on Jan 12 2022

city: Atlanta

first: Ashlyn

middle: G

last: Johnson

state: GA

address: 615 Michael Street NE

department: Neurology

institute: Emory University

summary: To understand how glia may be altered in frontotemporal degeneration with tau pathology (FTD-tau), we used a NanoString glial profiling panel to measure 770 transcripts related to glial biology in human control (n = 8), Alzheimer’s disease (AD) (n = 8), and FTD-tau (n = 8) dorsolateral prefrontal cortex. Compared to control, 43 genes were upregulated and 86 genes were downregulated in the FTD-tau samples. Only 3 genes were upregulated and 2 were downregulated in AD. Pathway analysis revealed many astrocyte-, microglia-, and oligodendrocyte-related pathway scores increased in FTD-tau, while neuron-related pathway scores decreased. We compared these results to a previously published proteomic dataset containing many of the same samples and found that the targeted panel approach obtained measurements for genes whose proteins were not measured in the proteomics. Our results point to the utility of multi-omic approaches and marked dysregulation of glia in FTD-tau.

overall_design: We analyzed a total of 24 samples of human dorsolateral prefrontal cortex: control (n = 8), Alzheimer’s disease (AD) (n = 8), and FTD-tau (n = 8).  Code used in the analysis can be found here: https://github.com/ashlyngjohnson/JohnsonEtAl_GlialProfilingManuscript.

first: James

last: Webster

first: Chadwick

last: Hales


title: Skeletal muscle stem cell changes between young and aged

address: 269 Campus Dr.

summary: To identify signaling pathways differencees between young and aged muscle stem cells

overall_design: Muscle stem cells isolated from 2-4 month old mice or 24 month old mice by alpha7+/CD34+ sorting. Cells were cultured on hydrogels for 24 hours. RNA was collected from 5,000-10,000 total cells.


title: LincRNA-EPS negatively regulates host antiviral immunity by antagonizing viral RNA interacting with PKR

city: Jiangsu suzhou

first: Jingfei

last: Zhu

state: CN

address: Chongwen Road 215123

institute: ISM

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


title: Fli1 drives the terminal differentiation of a memory precursor-like NK cell during viral infection

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Natural killer (NK) cells are innate lymphocytes that possess traits of adaptive immunity, such as clonal expansion, contraction, and generation of long-lived memory cells following viral infection. However, the molecular mechanisms by which clonally expanded effector NK (NKeff) cells persist to form memory cells is not well understood. Utilizing single cell RNA sequencing, we identify two Ly49H+ NKeff cell populations following mouse cytomegalovirus (MCMV) infection defined by the cell surface protein Ly6C. Ly6C– NKeff cells displayed enhanced survival during the contraction phase in a BCL2-dependent manner. Ly6C– NKeff cells displayed distinct transcriptional and epigenetic signatures compared to Ly6C+ NKeff cells, with a core epigenetic signature shared with memory precursor (MP) CD8+ T cells enriched in ETS1 and Fli1 DNA-binding motifs. Fli1 regulated memory NK cell fate by promoting terminal maturation and decreased persistence of contracting NK cells. Our results suggest that memory NK cells, similar to memory T cells, are generated by a subset of epigenetically distinct MP cell states that preferentially survive during the contraction phase of the response to viral infection.

overall_design: bulk RNA-seq, ATAC-seq and scRNA-seq on Ly6C+ and Ly6C- NK cells.

first: Luke

last: Riggan

first: Matteo

last: Pellegrini

first: Timothy

middle: E

last: O’Sullivan


title: Identification and targeting of the developmental blockade in extranodal natural killer/T cell lymphoma [RNA-seq]

first: Christopher

last: OAKES

address: 400 W. 12th Avenue, Wiseman Hall, Suite 455

summary: Extranodal natural killer/T cell lymphoma (ENKTL) is an aggressive, rare lymphoma of natural killer (NK) cell origin with very poor clinical outcomes and no effective targeted therapies. Improved understanding of the underlying biology of the disease is critical to design more effective treatment. Here we used phenotypic and molecular profiling including epigenetic analyses to investigate how ENKTL ontogeny relates to normal NK cell development. We demonstrate that neoplastic NK cells are stably but reversibly arrested at earlier stages of NK cell maturation. Genes downregulated in the tumors that demonstrated the most epigenetic immaturity were associated with polycomb silencing along with genomic gain and overexpression of EZH2. ENKTL cells exhibited a remarkable degree of genome-wide DNA hypermethylation. Tumor-specific DNA methylation gains were associated with polycomb-marked regions, involved the silencing of hundreds of genes (many involved in NK cell development), and loss of transcription factor binding. To investigate therapeutic targeting of the epigenetic developmental blockade, we treated novel PDX models of ENKTL with the DNA hypomethylating agent, 5-azacytidine. Treatment led to reduction of DNA methylation, re-expression of NK cell developmental genes, phenotypic NK cell differentiation, and prolongation of survival. These studies lay the foundation for epigenetic-directed therapy targeting the developmental blockade in ENKTL.

overall_design: RNA-sequencing was performed on 20 ENKTL tumor samples from derived from FFPE blocks.  Fresh/frozen ENKTL and normal NK samples were analyzed including 21 samples from NK developmental stages, 3 ENKTL, and 18 ENKTL samples derived from PDX mice.

last: Oakes


title: Targeting refractory mantle cell lymphoma for imaging and therapy using C-X-C chemokine receptor type 4 radioligands

city: Vancouver BC

first: Christian

last: Steidl

state: British Columbia

address: 675, West 10th Ave

department: Department of Lymphoid Cancer Research

country: Canada

institute: BC Cancer

summary: CXCR4 is widely expressed in hematological malignancies, including MCL  The Cancer Cell Line Encyclopedia (CCLE) showed relatively high levels of CXCR4 mRNA in hematological malignancies but had no MCL cell lines within its collection. To better assess the suitability of targeting CXCR4 in MCL, we screened 11 MCL cell lines for CXCR4 mRNA expression (Cancer Research Centre, CRC). For comparison, we profiled other lymphoma subtypes, including Burkitt (n=3), activated B cell-like (ABC) diffuse large B-cell lymphoma (DLBCL) (n=6), and germinal center B cell-like (GBC) DLBCL (n=14). On average, all lymphoma cell lines had high mRNA expression of CXCR4, though MCL cell lines had a higher expression of CXCR4 compared to GBC DLBCL (p<0.05). Hematological malignancy cell lines in both CRC and CCLE collections showed a significant increase in CXCR4 mRNA expression compared to a randomly selected sample of other cell lines in the CCLE (Supplementary Figure 6). The CXCR4 expression levels of the DLBCL and Burkitt lymphoma cell lines in the CCLE were in good agreement with our cell line RNA sequencing data when adjusted for batch effects.

overall_design: RNASeq analysis of 34 cell lines derived from lymphoma samples.

first: Daniel

last: Kwon

first: Lauren

last: Chong

first: Katsuyoshi

last: Takata

first: Francois

last: Bernard


title: Expression data from 2-week and 2-month-old mouse testes extracted from wild-type (WT), Sf1:Cre,Prkar1afl/fl (prKO), Amh:Cre,Prkar1afl/fl (srKO), Cyp11a1:Cre,Prkar1afl/fl (lrKO).

city: Clermont-Ferrand

first: Antoine

last: Martinez

address: Faculté de Médecine, CRBC, 28 place Henri Dunant

department: GReD

country: France

institute: CNRS, INSERM, Université Clermont Auvergne

summary:
Prkar1a encodes the regulatory subunit R1a of the proteine kinase A. Prkar1a ablation in the testis results in profound alterations of tissue homeostasis leading to tumor development and infertility.
We used microarrays to analyze gene expression in response to Prkar1a gene ablation in testicular somatic cells (derived from SF1+ cells) (prKO model), in Sertoli cells (sKO model) or in Leydig cells (lrKO model) in 2-week and 2-month-old mouse testes.

overall_design: Testes were dissected from prKO (3-4), srKO (4), lrKO (4) and wild-type littermate (8) mice at 2 weeks and 2 months.

first: Cyril

last: Djari

first: Anne-Marie

last: Lefrançois-Martinez

first: Isabelle

last: Sahut-Barnola

first: Pierre

last: Val


title: PRMT7 regulated chromatin accesibility in myeloid cells [ATAC-Seq]

city: München

first: Thomas

last: Conlon

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

summary: Under inflammatory conditions the extravasation of monocytes into tissues through trans-endothelial migration is a fundamental immunological process underlying innate inflammatory responses across multiple organ systems contributing to tissue injury and the progression of autoimmunity, cardiovascular disease and particularly chronic lung disease. Methylation of protein arginine residues via protein arginine methyltransferases (PRMTs) is a post-translational epigenetic modification implicated in inflammatory responses. How PRMTs, particularly PRMT7, epigenetically regulates monocyte-driven inflammatory response in disease remains unclear. Here, we perform ATAC-seq analysis on an MHS macrophage cell line in which PRMT7 has been disrupted by CRISPR/Cas9 to examine chromatin accessibility regulated by PRMT7.

overall_design: ATAC-Seq analysis of MHS WT and PRMT7null cells.

first: Gizem

last: Günes Günsel

first: Aicha

last: Jeridi

first: Ali

middle: Ö

last: Yildirim


title: 3D collagen-based scaffolds for biophysical tumour microenvironment studies

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

country: United Kingdom

institute: Cardiff University

summary: 3D scaffolds collagen I-based were crosslinked with different percentages of 1, 4-butanediol diglycidyl ether (BDDGE) to mimic native tissue and tumour tissue. Normal fibroblasts (NFs) or cancer-associated fibroblasts (CAFs) were added to the system to assess how mechanical features influence stromal compartment in native or tumour-like systems.

overall_design: Total RNA was obtained from normal fibroblasts (NFs) or cancer-associated fibroblasts (CAFs) cultured for 7 days on stiff collagen scaffolds (St - 1% BDDGE) or soft scaffold (So - 0.01% BDDGE). 2D NFs or CAFs were used as controls.

first: Francesca

last: Paradiso


title: Next Generation Sequencing Facilitates Quantitative Analysis of sevoflurane-treated and sevoflurane-untreated U251 cells Transcriptomes

status: Public on Jan 11 2022

city: Guangzhou

first: Xiaoping

last: Liu

address: No. 9 Jinsui Road, Tianhe District, Guangzhou, Guangdong, China

institute: Guangzhou Women and Children’s Medical Center

summary: To explore the possible mechanisms of Sev inducing ferroptosis in glioma cells, we performed RNA sequencing to screening differential expressed genes between sevoflurane-treated andsevoflurane-treated U251 cells.

overall_design: Examination of U251 cell transcriptome profile after treated with sevoflurane.

first: Yingyi

last: Xu

last: Zhang


title: Modeling androgen deprivation therapy-induced prostate cancer dormancy and its clinical implications

city: Vancouver

first: Yuzhuo

last: Wang

state: BC

address: 2660 Oak Street

department: Vancouver Prostate Centre

institute: University of British Columbia

summary: Purpose: Treatment-induced tumor dormancy is a state in cancer progression where residual disease is present but remains asymptomatic. Dormant cancer cells are treatment-resistant and responsible for cancer recurrence and metastasis. Prostate cancer (PCa) treated with androgen-deprivation therapy (ADT) often enters a dormant state. ADT-induced PCa dormancy remains poorly understood due to the challenge in acquiring clinical dormant PCa cells and the lack of representative models. We, therefore, aimed to develop clinically relevant models that can be used for studying ADT-induced PCa dormancy. Experimental design: Dormant PCa models were established by castrating mice bearing PCa patient-derived xenografts (PDXs) of hormonal naïve or sensitive PCa. Dormancy status and tumor relapse were monitored and evaluated. Paired pre- and post-castration (dormant) PDX tissues were subjected to morphological and transcriptome profiling analyses. Results: We established eleven ADT-induced dormant PCa models that closely mimicked the clinical courses of ADT-treated PCa. We identified two ADT-induced dormancy subtypes that differed in morphology, gene expression, and relapse rates. We discovered transcriptomic differences in pre-castration PDXs that predisposed the dormancy response to ADT. We further developed a dormancy subtype-based, predisposed gene signature that was significantly associated with ADT response in hormonal naïve PCa and clinical outcome in castration-resistant PCa treated with ADT or androgen-receptor pathway inhibitors.

overall_design: Mice bearing patient-derived prostate cancer xenografts were surgically castrated. Tissues for microarray profiling and analyses were harvested at pre-castration and post-castration 12 week timepoints, respectively.

first: Xin

last: Dong

first: Hui

last: Xue

first: Fan

last: Mo

first: Yen-yi

last: Lin

first: Dong

first: Nelson

last: Wong

first: Yingqiang

last: Sun

first: Scott

last: Wilkinson

first: Anson

middle: T

last: Ku

first: Jun

last: Hao

first: Xinpei

last: Ci

first: Rebecca

last: Wu

first: Anne

last: Haegert

last: Silver

first: Mary-Ellen

last: Taplin

first: Steven

last: Balk

first: Joshi

last: Alumkal

first: Adam

last: Sowalsky

first: Martin

last: Gleave

first: Colin

last: Collins


title: Germline Variant in Ctcf Links Mental Retardation to Wilms Tumor Predisposition

city: Valencia

first: Jaime

last: Font de Mora Sain

state: Valencia

address: Avenida Fernando Abril Martorell, 106

department: Oncology

country: Spain

institute: Instituto de Investigación Sanitaria La Fe

type: Genome variation profiling by high throughput sequencing

summary: SNP arrays was combined with next generation sequencing (NGS) to identify an LOH in 16q together with an unreported CTCF missense variant in its zinc finger domain. CTCF is within 16q LOH. We found that germline heterozygous variant I446K became homozygous in the tumor due to a loss of heterozygosity rearrangement affecting the whole q arm on chromosome 16. Based on CTCF role in regulating the epigenetic architechture of the genome, our findings reveal CTCF variant I446K as a link between MRD21 and Wilms tumor predisposition.

overall_design: We compared SNP array data with sequences from Wilms tumor and germline (blood-derived) DNA

last: Font de Mora

first: Pablo

last: Gargallo


title: Orthogonally induced differentiation of stem cells for the pattering of vascularized organoids and bioprinted tissues

city: Boston

first: Songlei

last: Liu

state: MA

address: 77 Avenue Louis Pasteur

country: USA

institute: Harvard University

overall_design: Refer to individual Series


title: Germline Variant in *Ctcf* Links Mental Retardation to Wilms Tumor Predisposition

type: Genome variation profiling by genome tiling array


title: Targeting Pancreatic Cancer by TAK-981, a SUMOylation Inhibitor that Activates the Immune System and Blocks Cancer Cell Cycle Progression in a Preclinical Model

city: Leiden

first: Sumit

last: Kumar

address: Einthovenweg 20

department: CCB

institute: Leids Universitair Medisch Centrum  (LUMC)

summary: Pancreatic ductal adenocarcinoma (PDAC) has the characteristics of high-density desmoplastic stroma, a distinctive immunosuppressive microenvironment and is profoundly resistant to all forms of chemo and immunotherapy, leading to a 5-year survival rate of 9%. Our study aims to add novel small molecule therapeutics for the treatment of PDAC. We have studied whether TAK-981, a novel highly selective and potent small molecule inhibitor of the SUMO activating enzyme E1 (SAE) could be used to treat a preclinical syngeneic PDAC mouse model. We found that SUMOylation, a reversible post-translational modification required for cell cycle progression, is increased in PDAC patient samples compared to normal pancreatic tissue. TAK-981 decreased SUMOylation in PDAC cells at the nanomolar range, thereby causing a G2/M cell cycle arrest, mitotic failure and chromosomal segregation defects. TAK-981 efficiently limited tumor burden in the KPC3 syngeneic mouse model without evidence of systemic toxicity. In vivo treatment with TAK-981 enhanced the proportions of activated CD8 T cells and NK cells but transiently decreased B cell numbers in peripheral blood, spleen and lymph nodes. ScRNA sequencing revealed activation of the interferon response upon TAK-981 treatment in lymphocytes including T, B and NK cells. TAK-981 treatment of CD8 T cells ex vivo induced activation of STAT1 and interferon target genes.  Our findings indicate that pharmacological inhibition of the SUMO pathway represents a potential strategy to target PDAC via a dual mechanism: inhibiting cancer cell cycle progression and activating anti-tumor immunity by inducing interferon signaling.

overall_design: Identify genes in response to SUMO inhibition in lymph nodes and spleen

first: Mark

last: Schoonderwoerd

first: Jessie

last: Kroonen

first: Ilona

last: de Graaf

first: Marjolein

last: Sluijter

first: Dina

last: Ruano

first: Román

last: González-Prieto

first: Matty

last: Verlaan–de Vries

first: Jasper

last: Rip

first: Ramon

last: Arens

first: Noel

middle: F

last: de Miranda

first: Lukas

last: Hawinkels

first: Thorbald

last: van Hall

first: Alfred

middle: C

last: Vertegaal


title: RNA sequencing of inguinal white adipose tissue from seipin-deficient mice and appropriate controls

city: Nantes

first: Xavier

last: Prieur

address: 8 quai Moncousu

institute: INSERM

summary: We generated Bscl2lox/lox mice X ERT2-Adipoq-CRE mice, allowing inducible seipin deletion in adipocytes upon tamoxifen addition (iATSKO).  Indeed, a 5-day tamoxifen treatment led to a dramatic decrease in Bscl2 mRNA in the adipose tissue. To study the effects of seipin deficiency in vivo on adipose tissue homeostasis in an unbiased manner, we used 3’-signal recognition particle (SRP) RNA sequencing.

overall_design: This experiment compare the gene expression of 4 groups of mice (Bscl2lox/lox; Bscl2lox/lox -ERT2-Adipoq-CRE; Bscl2lox/lox+ tamoxifen; Bscl2lox/lox -ERT2-Adipoq-CRE + Tamoxifen that we call iATSKO. We are folowing gene expression over time : 15 days, 30 days, and 90 days after the initiation of tamoxifen injection.

first: Yoann

last: Combot

first: Abdelahlim

last: Larlhimi

first: Audrey

last: Bihouée

first: Raluca

last: Teusan


title: SNP array data for Wilms Tumor harboring de novo germline mutation in CTCF

first: Jaime

last: Font de Mora Sain

summary: SNP array was combined with next generation sequencing (NGS) to identify a unique de novo germline mutation in CTCF that became homozygous in the tumor. SNP array shows an LOH through chr16q where CTCF is located.

overall_design: CytoScan HD arrays (Affymetrix) were performed according to the manufacturer's directions on DNA extracted from Wilms tumor sample.

last: Font de Mora

first: Pablo

last: Gargallo


title: Orthogonally induced differentiation of stem cells for the pattering of vascularized organoids and bioprinted tissues [bulkRNA-seq]

first: Songlei

last: Liu

summary: Simultaneous differentiation of human induced pluripotent stem cells (hiPSCs) into divergent cell types offers a pathway to achieving tailorable cellular complexity, patterned architecture, and function in engineered human organoids and tissues. Recent transcription factor (TF) overexpression protocols typically produce a single cell type of interest rather than the multitude of cell types and structural organization found in native human tissues. Here, we report an orthogonal induced differentiation platform, wherein pluripotent cells are simultaneously co-differentiated into distinct cell types to generate organoids and bioprinted tissues with controlled composition and organization. To demonstrate this platform, we differentiated endothelial cells and neurons from hiPSCs in a one-pot system containing either neural or endothelial stem cell-specifying media. By aggregating inducible-TF and wild type hiPSCs into pooled and multicore-shell embryoid bodies, we produced vascularized and patterned cortical organoids within days. Using multimaterial 3D bioprinting, we patterned 3D neural tissues from densely cellular, matrix-free stem cell inks that underwent orthogonal induced differentiation to generate distinct layered regions composed of neural stem cells, endothelium, and neurons, respectively. Given the high proliferative capacity and patient-specificity of hiPSCs, our platform provides a facile route for programming cells and multicellular tissues for drug screening and therapeutic applications.

overall_design: To study the effect of co-differentiation on OID-derived endothelium, a mixture of  iEndo-mKate2 PGP1 cells with either  iEndo-mKate2 PGP1,  WT-PGP1, or  iNeuron PGP1 cells were seeded onto Matrigel-coated plate. To study the effect of co-differentiation on OID-derived endothelium, a mixture of iNeuron-sfGFP PGP1 cells with either iNeuron-sfGFP PGP1, WT-PGP1, or iEndo PGP1 cells were seeded onto Matrigel-coated plates. 5d after seeding, cells were dissociated in 0.05% trypsin-EDTA and single cell-filtered. Flow Cytometry sorting of mKate2+ ETV2 cells and, separately, SFGFP+ iNeuron cells was performed on BD FACS Aria II at the Harvard Bauer Core.

first: Jeremy

last: Huang


title: Orthogonally induced differentiation of stem cells for the pattering of vascularized organoids and bioprinted tissues [scRNA-seq]

overall_design: WT hiPSC, randomly pooled, and multicore-shell cortical organoids were cultured using the methods described in the paper until day 25. Technical duplicates with two batches were created for each of 3 conditions comprising 12 total sequenced organoids. Mixed and Multicore-shell organoids were comprised of WT PGP1s, iEndo PGP1s, and iNeuron PGP1s in different seeding schema.


title: Multi-omics approaches reveal TNF-mediated inhibition of tissue reparative macrophages is via a gene-selective transcriptional mechanism (ATAC-Seq)

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

summary: Anti-TNF therapies are a core anti-inflammatory approach for chronic diseases such as rheumatoid arthritis and Crohn’s Disease. Previously, we and others found that TNF blocks the emergence and function of alternatively-activated or M2 macrophages involved in wound healing and tissue-reparative functions. Conceivably, anti-TNF drugs could mediate their protective effects in part by an altered balanced of macrophage activity. To understand the mechanistic basis of how TNF regulates tissue-reparative macrophages we used RNAseq, scRNAseq, ATACseq, time-resolved phospho-proteomics, gene-specific approaches, metabolic analysis and signaling pathway deconvolution. Our findings reveal that TNF controls tissue-reparative macrophage gene expression in a highly gene-specific way dependent on JNK signaling. We uncover principles of the selectively inhibition by TNF via the type 1 TNF receptor on specific populations of alternative activated macrophages.

overall_design: Chromatin accessibility profiles of wild-type BMDMs stimulated with  IL4/IL13 or IL4/IL13 + TNF  for 24h from 3 separate mice.

first: Stefanie

last: Dichtl

first: David

last: Sanin

first: Edward

last: Pearce

first: Peter

last: Murray


title: Massively parallel reporter perturbation assay uncovers temporal regulatory architecture during neural differentiation

city: Piscataway

first: Anat

last: Kreimer

state: NJ

address: 679 Hoes Ln W

department: CABM

institute: Rutgers University

summary: Gene regulatory elements play a key role in orchestrating gene expression during cellular differentiation, but what determines their function over time remains largely unknown. Here, we performed perturbation-based massively parallel reporter assays at seven early time points of neural differentiation to systematically characterize how regulatory elements and motifs within them guide cellular differentiation. By perturbing over 2,000 putative DNA binding motifs in active regulatory regions, we delineated four categories of functional elements, and observed that activity direction is mostly determined by the sequence itself, while the magnitude of effect depends on the cellular environment. We also find that fine-tuning transcription rates is often achieved by a combined activity of adjacent activating and repressing elements. Our work provides a blueprint for the sequence components needed to induce different transcriptional patterns in general and specifically during neural differentiation.

overall_design: The function of ~10,000 selected sequences was analyzed using massively parallel reporter assays at human embryonic stem cells (hESCs) at seven early neural differentiation time points (0-72 hours) in 3 replicates. Overall, the effect of 255 transcription factor binding motifs was tested across 591 endogenous genomic regions.

first: Tal

last: Ashuach

first: Fumitaka

last: Inoue

first: Alex

last: Khodaverdian

first: Nir

last: Yosef

first: Nadav

last: Ahituv


title: Cerebrospinal fluid regulates skull bone marrow niches via direct access through dural channels

city: Saint Louis

first: Jonathan

last: Kipnis

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: We have previously shown that skull bone marrow derived myeloid cells are different from their blood derived counterparts. Whether or not cues from the CNS microenvironment differentially shape the skull bone marrow niche relative to peripheral bone marrow niches is unknown. To test this, we performed scRNAseq of skull and peripheral bone marrow niches.

overall_design: Tibias and skulls were harvested from WT 8 week old male C57BL/6J mice and the surrounding flesh was removed. For skulls the dura was peeled and removed with fine forceps. Both the tibia and skull were then cut into small pieces using sterile scissors and mechanically dissociated in FACS buffer with a pestle, followed by a filtration step through a 70-μm cell strainer. Samples were centrifuged for 5 minutes at 420 x g, and red blood cell lysis performed with ACK lysis buffer. Samples were washed in fluorescence-activated cell sorting (FACS) buffer (PBS with 2% bovine serum albumin and 1 mM EDTA), stained with DAPI, and Viable (DAPI-) single cells were sorted on a BD FACSAria II (BD Biosciences) then sent for single-cell RNA sequencing.

first: Jose

last: Perez

first: Leon

last: Smyth

first: Taitea

last: Dykstra