title: RB-loss determines selective resistance and novel vulnerabilities in breast cancer modelsRB loss

city: Buffalo

first: Jianxin

last: Wang

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

summary: The retinoblastoma tumor suppressor (RB1) plays a critical role in coordinating multiple pathways that impact on tumor initiation, disease progression, and therapeutic responses.   Here we interrogated the effect of cIAP inhibitor, birinapant in two different isogenic ER+ breast cancer models. Using  MCF7-WT and MCF7-RB-del cell lines we investigated the differential gene expression pattern that link the effect of CIAP inhibition and RB dependency .

overall_design: MCF7-WT and MCF7-RB-del cells were treated with birinapant at a concentration of 500 nM for 48 hours. RNA was extracted using Quiagen Rneasy plus kit.


title: Effects of loss of LSD1  activity on small cell lung cancer cell lines via pharmacological inhibition

status: Public on Jun 13 2022

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial SLoan-Kettering Cancer Center

type: Expression profiling by high throughput sequencing

summary:
To investigate the effects of loss of LSD1 (KDM1A) on differential gene expression, we treated two cell lines of small cell lung cancer with 1𝝁M LSD1 inhibitor ORY-1001 or vehicle control for 10 days.
We then performed gene expression profiling analysis on treated and control cells for each of the two cell lines.

overall_design: Comparative gene expression profiling for SCLC cell lines with or without treatment with LSD1 inhibitor.

first: Evelyn

middle: M

last: Nguyen

first: Andrew

last: Chow

first: Charles

last: Rudin


title: Donor T-cell DNMT3a regulates alloreactivity in murine models of hematopoietic stem cell transplantation [WGBS]

city: Baltimore

first: Yiouli

last: Ktena

state: MD

address: 1800 Orleans Street

department: SOM Onc Pediatric Oncology

institute: JHU; School of Medicine

summary: Donor T-cell methylation state has an effect on alloreactivity. We applied WGBS and the InformME analysis pipeline to investigate the role of DNA methylation in mice receiving transplantation from T-cell conditional DNMT3a KO donors.

overall_design: WGBS was carried out on DNA from purified donor splenic T-cells post-transplantation from WT or DNMT3a KO donors in models of GVHD. The InformME analytic pipeline was applied to these data.

first: Michael

middle: I

last: Barbato

middle: A

last: Koldobskiy

middle: P


title: Comprehensive Benchmarking of CITE-seq versus DOGMA-seq Single Cell Multimodal Omics

city: Pittsburgh

first: Wei

last: Chen

address: 4401 Penn Ave, Rangos Research Building 9125

institute: UPMC Children's Hospital of Pittsburgh

summary: The recently developed transcription, epitopes, and chromatin accessibility by sequencing (TEA-seq) and similar DOGMA-seq single-cell trimodal omics assays provide unprecedented opportunities for understanding cell biology, but independent optimization, benchmarking and evaluation are lacking. We explored the utility, pros and cons of DOGMA-seq compared to the bimodal cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) assay in activated and stimulated human peripheral blood T cells. We identified an optimal incubation time and concentration of digitonin (DIG) for cell permeabilization and found that single-cell trimodal omics measurements after DIG permeabilization were generally better than after an alternative “low-loss lysis” (LLL) permeabilization condition. Next, we found that DOGMA-seq with optimized DIG permeabilization and its ATAC library provides more information, even though its mRNA and cell surface protein antibody-derived tag (ADT) libraries have slightly inferior quality, compared to CITE-seq. Finally, we recognized the additional value of DOGMA-seq for studying lineage-specific T helper cells.

overall_design: For comparison between DIG and LLL conditions, eight aliquots of T cells were activated and stimulated separately. After labeled by hashtags, two groups of four aliquots of T cells were pooled together, stained by antibody cocktail, and permeabilized with DIG or LLL. For comparison between CITE-seq and DOGMA-seq, sixteen aliquots of T cells were activated and stimulated separately. After labeled by hashtags, two groups of eight aliquots of T cells were pooled together, stained by antibody cocktail, and subjected to CITE-seq or DOGMA-seq.

first: Zhongli

last: Xu

first: Elisa

last: Heidrich-O’Hare

first: Richard

middle: H

last: Duerr


title: N6-methyladenosine mRNA Modification Is Essential for Human Pancreatic Lineage Specification [m6A-Seq]

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

country: China

institute: Zhejiang University

type: Methylation profiling by high throughput sequencing

summary: Recent advances in pancreatic differentiation from human pluripotent stem cells (hPSCs) hold great potentials for disease modeling and regenerative medicine, and more precise control over the dynamic differentiation process is critical. N6-methyladenosine (m6A) is the most prevalent internal messenger RNA (mRNA) modification, while the roles of m6A mark in pancreatic differentiation and development remain elusive. In addition, ALKBH5 is a major mRNA m6A demethylase and its role in pancreatic differentiation has not been reported. Here, we firstly studied mRNA m6A dynamics during pancreatic differentiation from hPSCs. Next, using the CRISPR-based genome editing tool, we generated ALKBH5 knockout hPSC lines and found that ALKBH5 plays important roles in pancreatic specification. After that, we conducted a series of functional and mechanistic studies, and demonstrated that ALKBH5 modulated many important genes involved in pancreatic differentiation. Collectively, our findings identified ALKBH5 as an essential regulator of human pancreatic differentiation and highlighted that m6A modification presents a new layer of regulation at epitranscriptome levels during cell-fate specification.

overall_design: m6A-seq of cells at defined developmental stages from stem cells to human islet organoid-like cells. m6A-seq of PP-WT and PP-A5-KO cells.

first: Xiaojie

last: Ma

first: Jie

last: Cao

first: Ziyu

last: Zhou

first: Jianzhao

last: Liu

first: Saiyong

last: Zhu


title: Gene expression profile at single cell level of cells derived from the arcuate nucleus of the hypothalamus (ARC) of mice fed with standard chow (SC) or high-fat high-sugar (HFHS) diet

status: Public on Jun 10 2022

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

summary: Hypercaloric diet affects hypothalamic cells at different levels. However, the time-dependent transcriptional changes of hypothalamic cells, and more particularly ARC cells, following the exposure to a HFHS diet are largely unknown. We used single cell RNA sequencing (scRNA-Seq) to analyze the impact of HFHS diet feeding on the transcriptional profile of ARC cells at different timepoints, with a special focus on astrocytes. The timepoints analyzed consist in 5 and 15 days of HFHS diet exposure, at which mice gain a not significant or a significant body weight respectively.

overall_design: ARC tissue derived from C57BL/6JRj mice fed with SC diet (control), 5 days of HFHS (58%) diet, and 15 days of HFHS (58%) diet was dissociated by enzymatic digestion into single cells, which were then analyzed by scRNA-Seq. Per each experimental group, the ARCs from 6 animals were pulled into one sample.

first: Luiza

last: Lutomska

first: Viktorian

last: Miok

first: Natalie

last: Krahmer

first: Ismael

middle: G

last: García

first: Tim

last: Gruber

first: Ophélia

last: Le Thuc

first: Cahuê

last: De Bernardis Murat

first: Beata

last: Legutko

last: Sterr

first: Gesine

last: Saher

first: Heiko

last: Lickert

first: Timo

middle: D

last: Müller

first: Siegfried

last: Ussar

first: Matthias

last: Tschöp

first: Cristina

last: García-Cáceres


title: Donor T-cell DNMT3a regulates alloreactivity in murine models of hematopoietic stem cell transplantation [RNA-seq]

first: Yiouli

last: Ktena

summary: Donor T-cell RNA expression state has an effect on alloreactivity. We applied RNA-Seq and the Deseq2 analysis pipeline to investigate the role of gene expression in mice receiving transplantation from T-cell conditional DNMT3a KO donors.

overall_design: RNA-Seq was carried out on RNA from purified donor splenic T-cells post-transplantation from WT or DNMT3a KO donors in models of GVHD. The Deseq2 analytic pipeline was applied to these data.

first: Michael

last: Barbato

last: Koldobskiy


title: Integrated analysis of immune parameters, miRNA-mRNA interaction, and immune genes expression in the liver of rainbow trout following infectious hematopoietic necrosis virus infection.

status: Public on Jun 12 2022

city: Lanzhou City

first: lu

last: zhao

state: Gansu Province

address: Yintan Road Street

institute: Gansu Agricultural University

summary: Rainbow trout (Oncorhynchus mykiss) is an important economical cold-water fish worldwide. However, infection with infectious hematopoietic necrosis virus (IHNV) has severely restricted the development of aquaculture and caused huge economic losses. Currently, little is known about the immune defense mechanisms of rainbow trout against IHNV. In this study, we detected the changes of immune parameters over different post-infection periods (6-, 12-, 24-, 48-, 72-, 96-, 120-, and 144 hours post-infection (hpi)), mRNA and miRNA expression profiles under 48 hpi (T48L) compared to control (C48L), and key immune-related genes expression patterns in rainbow trout liver following IHNV challenge through biochemical methods, RNA-seq, and qRT-PCR, and the function of miR-330-y was verified by overexpression and silencing in vitro and in vivo. The results revealed that AKP, ALT, CAT, and T-SOD activities, and LZM content showed significant peaks at 48 hpi (P < 0.05), whereas MAD content and AST activity decreased continuously during infection (P < 0.05), and ACP activity varied slightly. From RNA-seq, a total of 6844 genes and 86 miRNAs were differentially expressed, and numerous immune-related differentially expressed genes (DEGs) involved in RIG-I-like receptor signaling pathway, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, cytokine-cytokine receptor interaction, and antigen processing and presentation were significantly upregulated in T48Lm group, including IFIH1, DHX58, MAVS, TRAF3, IRF3, IRF7, MX1, TLR3, TLR8, MYD88, NOD1, NOD2, IL-8, CXCR1, CD209, CD83, and TAP1. Integrated analysis identified seven miRNAs (miR-425-x, miR-185-x, miR-338-x, miR-330-y, miR-361-x, miR-505-y, and miR-191-x) that target at least three key immune-related DEGs. Expression analysis showed that IFIH1, DHX58, IRF3, IRF7, MX1, TLR3, TLR8, and MYD88 showed a marked increase after 24 hpi during infection. Further research confirmed TAP1 as one of the targets of miR-330-y, overexpression of miR-330-y with mimics or agomir significantly reduced the expression levels of TAP1, IRF3, and IFN, and the opposite effects were obtained by inhibitor. These results facilitate in-depth understanding of the immune mechanisms in rainbow trout against IHNV and will provide valuable information for disease resistance breeding.

overall_design: In this study, both biochemical methods and RNA-seq were performed to analyze the changes of immune parameters and miRNA-mRNA expression profiles in the rainbow trout liver against IHNV infection.

first: Jinqiang

last: Huang

first: Shenji

last: Wu


title: Ezetimibe Ameliorates Ankylosing Spondylitis by Suppressing Th17 Differentiation

status: Public on Jun 11 2022

city: Seoul

first: Seon-Yeong

last: Lee

address: 222 banpo-daero, seocho-gu

department: Rheumatism research center

country: South Korea

institute: the catholic university

summary: Oxidized low-density lipoprotein influences the Th17/Treg balance. A high serum concentration of oxidized low-density lipoprotein is negatively correlated with the number of Treg cells and positively correlated with the number of Th17 cells. Therefore, we expected that the reduction of blood lipid levels using ezetimibe and statin would ameliorate AS disease by reducing the number of Th17 cells.

overall_design:
total 16 samples
Samples of Th0 condition: 4
Samples of Th17 condition: 4
Samples of Ezetimibe with Th17 condition: 4
Samples of Rosuvastatin with Th17 condition: 4

first: Jeong-Hyeon

last: Moon


title: Nucleome programming is required for the foundation of totipotency in mammalian germline development [Hi-C]

status: Public on Jun 15 2022

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in-depth nucleome analysis of mouse germ-cell development in vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome-wide DNA de-methylation, creates broadly open chromatin with abundant enhancer-like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re-methylation, the PGCs-to-spermatogonia/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina-associated domains, generating spermatogonia/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres—an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency.

overall_design: Nucleome profiling of various cell types along murine germ-cell development using Hi-C

first: Masahiro

last: Nagano

first: Bo

last: Hu

first: Shihori

last: Yokobayashi

first: Akitoshi

last: Yamamura

first: Fumiya

last: Umemura

first: Mariel

last: Coradin

first: Hiroshi

last: Ohta

first: Yukiko

last: Ishikura

first: Ikuhiro

last: Okamoto

first: Hiroki

last: Ikeda

first: Naofumi

last: Kawahira

first: Yoshiaki

last: Nosaka

first: Sakura

last: Shimizu

first: Yoji

last: Kojima

first: Ken

last: Mizuta

first: Tomoko

last: Kasahara

first: Yusuke

last: Imoto

first: Killian

last: Meehan

first: Roman

last: Stocsits

first: Gordana

last: Wutz

first: Yasuaki

last: Hiraoka

first: Yasuhiro

last: Murakawa

first: Takuya

last: Yamamoto

first: Kikue

last: Tachibana

first: Jan-Michel

last: Peters

first: Leonid

last: Mirny

first: Benjamin

last: Garcia

first: Jacek

last: Majewski

first: Mitinori

last: Saitou


title: Rif1 functions in complex with PRC1.6 to regulate mouse embryonic stem cells fate potential [RNA-seq]

city: Leiden

first: Jiale

last: Chen

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

summary:
To investigate the cooperative function Rif1 and PRC1.6 complex in the regulation of embryonic development and cell differentiation, we selected embryonic stem cells in which each target gene has been knocked down by shRNA or knocked out  conditionally.
We then performed gene expression profiling analysis using data obtained from RNA-seq of different samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for embryonic stem cells and its KD or KO derivatives (Rif1 CKO, shMax, shPcgf6, shRNF2).

first: Lu

last: Li

first: Pishun

first: Kai

last: Yuan


title: Plasma in patients with acute myeloid leukemia (AML) with acute graft versus host disease (aGVHD) after allogeneic hematopoietic stem cell transplantation vs Plasma in patients with AML without aGVHD

city: Ulsan

first: Sook-Kyoung

last: Heo

address: 877 Bangeojinsunhwan-doro

department: Biomedical Research Center

institute: University of Ulsan College of Medicine

summary:
Comparing between plasma cytokine proteins on AML patients with or without aGVHD
Comparing between plasma cytokine proteins on AML patients with or without aGVHD after allogeneic hematopoietic stem cell transplantation, Day+14

overall_design: one-condition experiment, Comparing between plasma cytokine proteins on AML patients with aGVHD vs without aGVHD. Biological replicates: 1.

first: Sook

middle: K

first: Eui

last: Noh


title: Rif1 functions in complex with PRC1.6 to regulate mouse embryonic stem cells fate potential [ChIP-seq]

summary: To investigate if Rif1 depletion compromised the accurate genomic targeting of the PRC1.6 complex, we performed ChIP-seq analyses of Rif1, Pcgf6, RNF2, and the H2AK119ub in the control and Rif1-depleted mESCs.

overall_design: The overall genomic distribution of Rif1 manifested modest correlations with that of Pcgf6, RNF2, and the H2AK119ub.


title: NuRD complex recruitment to Thpok mediates CD4+ T cell lineage differentiation

city: Bethesda

first: Remy

last: Bosselut

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

summary: Although BTB-zinc finger (BTB-ZF) transcription factors control the differentiation of multiple hematopoietic and immune lineages, how they function is poorly understood. The BTB-ZF factor Thpok controls intrathymic CD4+ T cell development and expression of most CD4+- and CD8+-lineage genes. Here, we identify the nucleosome remodeling and deacetylase (NuRD) complex as a novel Thpok cofactor. We locate three amino-acid residues within the Thpok BTB domain that are required for both NuRD binding and Thpok functions, and show that NuRD recruitment recapitulates the functions of the Thpok BTB domain. NuRD mediates Thpok repression of CD8+-lineage genes, including the transcription factor Runx3, but is dispensable for Cd4 expression. We show that these functions cannot be performed by the BTB domain of the Thpok-related factor Bcl6, which fails to bind NuRD. Thus, cofactor binding critically contributes to the functional specificity of BTB-zinc finger factors, which control the differentiation of most hematopoietic subsets.

overall_design: Nuclei were isolated following the recommended protocol from 10X Genomics. Transposition and scATACseq capture was performed with the 10X Chromium Single Cell ATAC Solution (v1.0) , following the manufacturer's recommended protocol

first: L

middle: B

last: Chopp

first: Y

last: Gao

first: R


title: Higher susceptibility of males to bleomycin-induced pulmonary inflammation is associated with sex-specific transcriptomic differences in myeloid cells

city: Baton Rouge

first: Sonika

last: Patial

address: Baton Rouge, LA 70803

institute: Louisiana State University

summary: In this study, we subjected male and female mice to bleomycin-induced lung injury for 14-days. Bronchoalveolar lavage cells were isolated and subjected to RNA-sequencing. Four groups were compared. Saline-Males and females and bleomycin-males and females.

overall_design: Male and female C57BL/6 mice  were oropharyngeally given either saline or bleomycin (4U/Kg body weight) for 14-days. Bronchoalveolar cells were isolated and subjected to RNA-sequencing.

first: Richa

last: Lamichhane

first: Yogesh

last: Saini


title: Gene expression in MHCII restricted mature thymocytes from Thpok-RKF- or Thpok-RKF+ Thpokfl/flRunx3fl/dYFPCd4-Cre+ mixed Bone marrow chimera.

first: Yayi

address: 3016 Convert Drive

institute: National Cancer Institute

summary: Thpok-RKF which harbors a mutation in the BTB domain and disrupts the interaction between NuRD complex could not repress CD8 and CD8 lineage genes expression in Thpokfl/flRunx3fl/dYFPCd4-Cre+ from B2m-/- host. However, Thpok-RKF upregulates CD4 expression in these mice.

overall_design: Bone marrows from Thpokfl/flRunx3fl/dYFPCd4-Cre+ Thpok-RKF- or Thpok-RKF+ were mixed with CD45.1+CD45.2+ wild type bone marrow and transplanted into irradiated CD45.1+B2m-/- host mice. CD4+ SP, CD8+ SP, CD4+CD8+ cells from indicated mice were sorted. Gene expression was determined by RNA-seq.


title: Enhanced self-renewal of human pluripotent stem cells by simulated microgravity

city: Rochester

first: Tianle

last: Ma

state: MI

address: 115 Library Dr

institute: Oakland University

summary: We developed a fast-rotating clinostat to simulate micrigravity (µg) and investigated various effects (including proliferation, self-renewal, and cell cycle regulation) of simulated microgravity (sµg) on human pluripotent stem cells (hPSC). Cells were cultured in sµg and control condition in normal gravity (1g). We observed significant upregulation of protein translation of human pluripotency transcription factors in hPSC cultured in sµg condition compared to 1g. We also noted a significant increase in the expression levels of genes involved in telomere elongation. Our induced differentiation experiments showed that hPSC cultured in sµg condition were less susceptible towards differentiation compared to cells cultured in 1g condition as indicated by the significant delayed in the process of differentiation of the cell in sµg condition. These results suggest that sµg conditions enhance the self-renewal of hPSC. Our study further revealed that sµg enhanced the cell proliferation of hPSC by regulating the expression of cell cycle associated kinases. Moreover, RNAseq analysis indicated that in sµg condition the expression of pathways related to differentiation and development and down-regulated, while multiple components of the ubiquitin proteasome system are up-regulated, thus further contributing to an enhanced self-renewal of hPSC. These effects of sµg were not replicated in human fibroblasts. Taken together, these results highlight pathways and mechanisms in hPSC vulnerable to µg that impose significant impacts on human health and performance, physiology, and cellular and molecular processes.

overall_design: We performed a comparative gene expression profiling analysis of RNA-seq data for H1 and H9 human pluripotent stem cells after culturing them under normal gravity (1g) and simulated microgravity (near zero gravity).

first: Thea

last: Kirsch-Mangu

first: Schyler

last: Werth

first: Brooke

last: Shepard


title: Gene expression profiling by CRISPR/Cas13d-mediated CTSL knockdown in 293FT cells

status: Public on Jun 09 2022

city: Durham

first: Qianben

last: Wang

address: 905 S. Lasalle Street

institute: Duke University

summary: To examine the potential off-target effects by CRISPR/Cas13d-mediated CTSL knockdown in 293FT cells

overall_design: 293FT cells were transfected with non-targeting pre-gRNA control(gCtrl) or pre-gRNA targeting CTSL(gCTSL) expression plasmid in combination with Cas13d expression plasmid for 24h. RNA-seq was performed to characterize the differential expressed genes between gCtrl and gCTSL groups.

first: Zhifen

last: Cui

first: Furong

last: Huang

first: Yufan

last: Zhou


title: Gene expression in mature CD4 and CD8 from WT mice and mature CD4 from DBTBLZ or Mta2-DBTBLZ retrogenic mice

summary: T cell precursors develop into cytotoxic CD8 and helper CD4+ T cells in thymus. Thpok, a BTB/POZ family transcription factor, enforces commitment to the CD4 lineage and suppresses cytotoxic gene expression. However, it is still not fully understood how Thpok directs CD4 T cell development. Here, using mass-spectrometry, we identify nucleosome remodeling and deacetylase (NuRD) complex as a novel Thpok cofactor. We demonstrate that the Thpok BTB domain is essential for NuRD recruitment. Reconstituting NuRD binding to a BTB-less version of Thpok (which cannot bind NuRD) restored CD4 T cell in vivo. RNA sequencing showed that CD4 T cells expressing the reconstituted protein express a transcriptome similar to that of CD4 T cells expressing Thpok. Thus, our results demonstrate that NuRD recruitment is both necessary and sufficient for the function of the Thpok BTB domain in CD4 T cell development.

overall_design: Bone marrows from Cd4-Cre+Thpokfl/fl mice transduced with retrovirus expressing DBTBLZ or Mta2-DBTBLZ were transplanted into irradiated recipient mice. Mature CD4 cells from host expressing DBTBLZ or Mta2-DBTBLZ were sorted. Mature CD4 cells and mature CD8 cells from C57BL/6 mice were also sorted as control. Gene expression was determined by RNA-seq.


title: A truncated reverse transcriptase enhances prime editing by split AAV vectors

city: Aarhus

first: Zongliang

address: Høegh-Guldbergs Gade 10, C. F. Møllers Allé 6

country: Denmark

institute: Aarhus University

summary: To investigate if the truncated PE can be dilivered by dual AAV8 vectors for in vivo prime editing. We injected the dual AAV8 into 10-week-old C57BL/6J mice . Livers were isolated 4 weeks after injection and next generation sequencing showed an average of 1.4% and 5.4% precise prime editing with the low and high AAV doses, respectively (Figure 4D ). This demonstrates that PECO-Mini can be efficiently delivered by dual AAVs for in vivo prime editing.

overall_design: Dual AAV8 were injected into 10-week-old C57BL/6J mice intravenously at an equal vector amount of either 1x1011 or 1x1012 vg per vector. The mice without any treatment was used as control. We injected 3 mice for each type with a total of 9 mice.

first: Rasmus

last: Bak


title: tRNA-derived fragments regulate the functional maturation of neonatal β-cells

city: Lausanne

first: Mustafa

middle: Bilal

last: Bayazit

address: Rue du Bugnon 9

country: Switzerland

institute: University of Lausanne

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: CMN and CDT SADBE

city: Charlestown

first: David

last: Fisher

address: 149 13th Street

institute: Massachusetts General Hospital


title: The miR-15a/16-1 and miR-15b/16-2 clusters regulate early B cell development by limiting IL-7 receptor expression

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

country: Austria

institute: Medical University of Innsbruck, Biocenter

summary: Pleiotropic functions of miRNAs as transcriptional repressors have been reported for multiple biological processes. One prominent miRNA family is the miR-15 family, which is a well-established tumor-suppressor in B-cell chronic lymphocytic leukemia (CLL). The miR-15 family consists of three bicistronic clusters, miR-15a/16-1, miR-15b/16-2 and miR-497/195, all sharing the same seed sequence suggesting that loss one cluster can be functionally compensated by the remaining miR-15 family members. Thus, a combined deletion may be necessary to reveal its physiological function in vivo. A combined knockout of the most prominent miR-15 clusters, miR-15a/16-1 and miR-15b/16-2 in the hematopoietic system reveals a novel role of the miR-15 family in early B cell development highlighted by an increase of the pro-B cell compartment. Mechanistically, this effect is mediated by enhanced IL-7 receptor expression, which we identified as direct miR-15 target gene. Notably, elevated IL-7 receptor levels were sufficient to trigger increased activation of the STAT5 and PI3K/AKT pathways. Moreover, derepression of directly targeted cell cycle regulators such as Ccne1, Chek1 and Wee1 further facilitates G-to-S transition. Thus, by deregulating a target gene network of cell cycle and signaling mediators, loss of the miR-15 family establishes a pro-proliferative milieu manifesting in an enlarged pro-B cell pool.

overall_design: RNA sequencing data of FACS-sorted pro-B cells of 4 miR-15a/b+/+ Vav-Cre mice (controls) and 4 miR-15a/bfl/fl Vav-Cre mice.

first: Katharina

last: Hutter

first: Thomas

last: Rülicke

first: Lill

last: Andersen

first: Tamas

last: Szabo

first: Andreas

last: Villunger


title: Synergy of chemotherapy and macrophage depletion leads to T cell memory activation and durable triple negative breast cancer regression

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Chemotherapy and macrophage depletion leads to T cell memory activation and durable triple negative breast cancer regression in p53 null mouse models.

overall_design: RNA-seq was performed on 15 'p53 null' BalbC mouse samples, belonging to one of four different mouse models: 215R, T11, 225L, or 2208L.

first: Dan

last: Hollern


title: Deletion of the Lmna Gene in Fibroblasts Causes Senescence-Associated Dilated Cardiomyopathy

city: Houston

first: Priyatansh

last: Gurha

state: Texas

address: 6770 Bertner Ave

department: School of Medicine

institute: UTHealth

summary: Deletion of Lmna in PDGFRA+ cells cause dilated cardiomyoapthy.

overall_design: Total RNA obtained from PDGFRA+ cells  isolated from LV of  WT and Pdgfra-Cre: LmnaF/Fmice were  used for total RNA -seq.

first: Leila

last: Rouhi

first: Ali

middle: J

last: Marian


title: DCT SADBE RNA-Seq

summary: In this study we compared the RNA levels before and after treatment with SADBE

overall_design: Treatment on back skin of Dct-Cre NrasQ61R compared to acetone control

middle: E

first: Tal

last: Erlich

first: Max

last: von Franque

first: Yi

last: Zhang


title: tRNA-derived fragments regulate the functional maturation of neonatal β-cells [RNA-Seq]

summary: In neonatal islets from P10 rats, 3 sets of tRNA-derived fragments (tiRNA-5HisGTG/GluCTC/GluTTC) were inhibited with LNA inhibitiors ex vivo and mRNA-seq was performed to potentially identify the gene expression changes upon the inhibition

overall_design: mRNA-seq of neonatal (p10) rat islet cells transfected with control and tiRNA-5 inhibitors (n = 4 samples per condition)

first: Cecile

last: Jacovetti

first: Claudiane

last: Guay

first: Jonathan

last: Sobel

first: Flora

last: Brozzi

first: Cristina

last: Cosentino

first: Kejing

last: Wu

first: Adriana

last: Rodriguez-Trejo

first: Lisa

last: Stoll

first: Romano

last: Regazzi


title: tRNA-derived fragments regulate the functional maturation of neonatal β-cells [ncRNA-Seq]

first: Mustafa

last: Bayazit

summary: Annotation of tRNA fragments relies on the alignment of signals obtained from small RNA-seq on mature tRNA positions and requires the pretreatment of the RNA to remove tRNA modifications that may interfere with sequencing.

overall_design: Small RNA-seq of adult (p90) and neonatal (p10) rat islet cells and annotation of tRNA fragments (n = 3 samples per timepoint).


title: Gene expression profile of astrocytes derived from the cortex, hippocampus and hypothalamus of mice fed with standard chow (SC) or high-fat high-sugar (HFHS) diet

status: Public on Jun 08 2022

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

summary: Astrocytes exhibit a high molecular diversity within the same, as well as across different brain regions. Moreover, astrocytes are characterized by a region-specific role in the regulation of neuronal circuitries, which might be affected by specific diseases. Regarding metabolic control, selective perturbations in astrocytes trigger multiple alterations in energy balance and glucose homeostasis. Using RNA sequencing, we showed that astrocytes have a distinct transcriptomic profile dependent on their anatomical location in the brain, which is affected by hypercaloric diet.

overall_design: C57BL/6JRj mice were exposed to a SC or a HFHS (58%) diet at 8-9 weeks of age for 4 months. Afterwards, hypothalami, hippocampi, and half cortices derived from 2 animals were isolated and pooled together in distinct tubes. A number of 5-7 replicates per each group was used. ACSA2+ astrocytes were isolated from each sample by magnetic-activated cell sorting (MACS), and further processed for RNA-Sequencing analysis.

first: Luiza

last: Lutomska

first: Viktorian

last: Miok

first: Natalie

last: Krahmer

first: Ismael

last: González García

first: Tim

last: Gruber

first: Ophélia

last: Le Thuc

first: Cahuê

last: De Bernardis Murat

first: Beata

last: Legutko

first: Michael

last: Sterr

first: Gesine

last: Saher

first: Heiko

last: Lickert

first: Timo

last: Müller

first: Siegfried

last: Ussar

first: Matthias

last: Tschöp

last: García-Cáceres


title: IL-17A increases doxorubicin efficacy in triple negative breast cancer [bulk RNA-seq]

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

summary: Due to lack of targetable receptors and intertumoral heterogeneity, triple negative breast cancer (TNBC) remains particularly difficult to treat. Doxorubicin (DOX) is typically used as nonselective neoadjuvant chemotherapy, but the diversity of treatment efficacy remains unclear. Comparable to variability in clinical response, an experimental model of TNBC using a 4T1 syngeneic mouse model was found to elicit a differential response to a seven-day treatment regimen of DOX. Single-cell RNA sequencing identified an increase in T cells in tumors that responded to DOX treatment compared to tumors that continued to grow uninhibited. Additionally, compared to resistant tumors, DOX sensitive tumors contained significantly more CD4 T helper cells (339%), γδ T cells (727%), Naïve T cells (278%), and activated CD8 T cells (130%). Furthermore, transcriptional profiles of tumor infiltrated T cells in DOX responsive tumors revealed decreased exhaustion, increased chemokine/cytokine expression, and increased activation and cytotoxic activity. γδ T cell derived IL-17A was identified to be highly abundant in the sensitive tumor microenvironment. IL-17A was also found to directly increase sensitivity of TNBC cells in combination with DOX treatment. In TNBC tumors sensitive to DOX, increased IL-17A levels lead to a direct effect on cancer cell responsiveness and chronic stimulation of tumor infiltrated T cells leading to improved chemotherapeutic efficacy. IL-17A's role as a chemosensitive cytokine in TNBC may offer new opportunities for treating chemoresistant breast tumors and other cancer types.

overall_design: Cultured 4T1-Thy1.1 cells were exposed to combinations of doxorubicin and/or recombinant IL17A for 48 hours prior to RNA isolation to examine the effects of IL17A on doxorubicin response

first: Nicholas

last: Hum

first: Gabriela

last: Loots


title: FBXW7

city: Madrid

first: Orlando

last: Domínguez

address: Melchor F. Almagro 3

country: Spain

institute: CNIO

summary:
Purpose: FBXW7 is one of the most frequently mutated tumor suppressors, the deficiency of which has been associated with resistance to some anticancer therapies. Through bioinformatic analyses and genome-wide CRISPR screens, we here reveal that FBXW7 deficiency leads to multi-drug resistance (MDR), to a bigger extent than well-established MDR-drivers such as ABCB1. Proteomic data from FBXW7-deficient cells and human cancer samples identify the upregulation of mitochondrial function as a hallmark of FBXW7 deficiency, which has been previously linked to an increased resistance to chemotherapy. Accordingly, genetic or chemical targeting of mitochondria is preferentially toxic for FBXW7-deficient cells. For instance, targeting mitochondrial translation with the antibiotic Tigecycline efficiently kills FBXW7-deficient cells in vitro and in vivo, by a mechanism that involves activation of the Integrated Stress Response (ISR). Searching for additional drugs that overcome MDR in FBXW7-deficient cells, we found several targeted therapies such as Erlotinib, Dasatinib or Vemurafenib which unexpectedly also activate the ISR. Together, our study reveals that one of the most frequent mutations in cancer reduces the sensitivity to the vast majority of available therapies, and identifies a general principle to overcome such resistance.
Methods: This study was performed in 2 groups of DLD1 cells with duplicate samples per group. Both control (Wild Type, WT) and experimental (FBXW7 -/-, KO) were exposed to Tigecycline (10µM). DMSO was used as a control for the treatment. After 24h, the RNA was extracted and the transcriptome was profiled with RNA-Sequencing (RNA-seq) analysis.
Results: our study reveals that one of the most frequent mutations in cancer reduces the sensitivity to the vast majority of available therapies, and identifies a general principle to overcome such resistance.

overall_design: This study was performed in 2 groups of DLD1 cells with duplicate samples per group. Both control (Wild Type, WT) and experimental (FBXW7 -/-, KO) were exposed to Tigecycline (10µM). Subsequent transcriptome differences were exposed by RNA-seq analysis.

first: Laura

last: Sanchez-Burgos

first: Belen

last: Navarro

first: Santiago

last: García

first: Hector

last: Tejero

first: Marta

last: Antón

first: Fátima

last: Al-Shahrour

first: O

last: Fernandez-Capetillo


title: IL-17A increases doxorubicin efficacy in triple negative breast cancer [single-cell RNA-seq]

overall_design: Single-cell RNA sequencing was performed on mammary fat pad 4T1-Th1.1 tumors in BALB/c mice that were administered doxorubicin


title: Transcriptional Reprogramming during Floral Fate Acquisition I

city: Lyon

first: Antoine

last: Larrieu

address: 46, allée d'Italie,

country: France

institute: ENS Lyon

summary: To gain insight into the auxin-dependent network during flower initiation, we used complementary RNAseq-based genomic analyses to obtain a global vision of the auxin-regulated gene network in the SAM before progressively converging on the identification of a high-confidence core network acting during the early phases of flower initiation.

overall_design: Transcriptome profiling of dissected wild-type meristems (Col-0) and pin-shaped meristems of mutants pin1-7, pid-9 and mpS319 (all loss-of-function alleles in Col-0 accession).

first: Teva

last: Vernoux


title: Genes regulated by WIPK and SIPK in wounded tobacco leaves

city: Minamiminowa

first: Shinpei

last: Katou

state: Kamiina, Nagano

department: Faculty of Agriculture

institute: Shinshu University

summary: WIPK and SIPK, two tobacco MAPKs, are rapidly activated by wounding. Goal is to identify the genes regulated by WIPK and SIPK. For this purpose, we produced transgenic tobacco plants in which expression of WIPK and SIPK is suppressed by RNAi (WIPK/SIPK-suppressed plants).

overall_design:
Search for genes regulated by WIPK and SIPK in wounded tobacco leaves
Single experiment


title: IL-17A increases doxorubicin efficacy in triple negative breast cancer


title: Transcriptional Reprogramming during Floral Fate Acquisition II

overall_design: We profiled the transcriptome of NPA pins treated with or without auxin for 30 or 120 minutes to analyze the dynamics of early auxin responses.


title: Transcriptome profile of livers from hepatocyte-specific Slc25a34 knockout mice on chow and fast-food diet

city: Pittsburgh

first: Andrew

middle: W.

last: Duncan

state: PA

address: 450 Technology Drive, Suite 300

department: Pathology

institute: University of Pittsburgh

summary: Identifcation of diferentially expressed genes in livers of mice maintained on chow diet or fast-food diet when Slc25a34 is deleted in hepatocytes.

overall_design: LoxP sites were inserted into the promoter and intron 1 of Slc25a34 genomic DNA to generate a floxed allele. To specifically delete Slc25a34 in hepatocytes from 2-month-old floxed mice, Cre recombinase was delivered by adeno-associated virus driven by the thyroxine binding globulin (TBG) promoter, AAV8-TBG-Cre, which targets >95% of hepatocytes, generating a hepatocyte-specific Slc25a34 knockout (Slc-HKO). As a control, Slc25a34 floxed mice were injected with AAV8-TBG-GFP, which does not affect Slc25a34 expression (WT control). Mice were maintained on chow diet for 1 month after AAV8 injection and then maintained on either chow diet for 2 additional months or FFD for 2 months. RNA was isolated from whole liver after fasting for 16 hours (Slc-HKO, n = 3 / diet; WT control, n = 3 / diet).

first: Nairita

last: Roy

first: Sierra

middle: R

first: Joseph

last: Locker

middle: W


title: Mouse models of CMN and comparison to human CMN

first: David

last: Fisher

summary: In this study we compared the RNA levels of two CMN mouse models.

overall_design: Normal skin, nevi skin and tumor from nevi was taken from both models (Dct-Cre NrasQ61R and Tyr-CreERT2 NrasQ61R)

first: Tal

last: Erlich

first: Max

last: Von Franque

first: Yi

last: Zhang


title: FoxA1 and FoxA2 regulate growth and cellular identity in NKX2-1-positive lung adenocarcinoma (scRNA-Seq)

city: Salt Lake City

first: Eric

last: Snyder

state: UT

address: 2000 Circle of Hope Drive

institute: University of Utah, Huntsman Cancer Institute

summary: Changes in cellular identity (also known as histologic transformation or lineage plasticity) can drive malignant progression and resistance to therapy in multiple types of cancer, including lung adenocarcinoma (LUAD). The lineage specifying transcription factors FoxA1 and FoxA2 (FoxA1/2) regulate identity in NKX2-1/TTF1-negative LUAD. However, their role in NKX2-1-positive LUAD has not been systematically investigated. We find that Foxa1/2 knockout severely impairs tumorigenesis in KRAS-driven genetically engineered mouse models and human cell lines. Foxa1/2 deletion leads to collapse of a dual-identity state, marked by co-expression of pulmonary and gastrointestinal transcriptional programs, that has been implicated in LUAD progression. Mechanistically, loss of FoxA1/2 leads to aberrant NKX2-1 activity and genomic localization, which inhibits tumorigenesis and drives alternative cellular identity programs associated with non-proliferative states. This work demonstrates that FoxA1/2 expression is a novel lineage-specific vulnerability in NKX2-1-positive LUAD and identifies mechanisms of response and resistance to targeting FoxA1/2 in this disease.

overall_design: scRNAseq of murine lung adenocarcinoma (WT and FoxA1/2-negative)

middle: L

first: Grace

last: Orstad

first: Gabriela

last: Fort

first: Brian

last: Lohman


title: Transcriptional Reprogramming during Floral Fate Acquisition III

overall_design: To further define a high-confidence auxin-dependent network acting during flower initiation, we consolidated our SAM auxin response transcriptome by also profiling the transcriptome of an inducible repressor of auxin signaling (pRPS5A-GR-bdl (Weijers et al., 2006), Figure 1B) using inflorescence tissues treated with or without 10µM dexamethasone (dex) for 2 hours.


title: Transcriptional Reprogramming during Floral Fate Acquisition

overall_design: Refer to individual Series


title: Klf5 promotes alveolar epithelial type 1 cell lineage commitment during lung development and regeneration

city: Philadelphia

first: Michael

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Alveolar epithelial cell fate decisions drive lung development and regeneration. Using transcriptomic and epigenetic profiling coupled with genetic mouse and organoid models, we identified Klf5 as a critical regulator of alveolar epithelial cell fate across the lifespan. During prenatal lung development and alveologenesis, Klf5 enforces alveolar epithelial type 1 (AT1) cell lineage fidelity. While it is dispensable for both adult AT1 and alveolar epithelial type 2 (AT2) cell homeostasis, Klf5 regulates AT2 cell plasticity after injury. Klf5 represses AT2 cell proliferation and enhances AT2-AT1 cell differentiation in a spatially restricted manner in both infectious and non-infectious models of acute respiratory distress syndrome. Moreover, ex vivo organoid assays reveal that Klf5 modulates AT2 cell fate decisions through reducing AT2 cell sensitivity to inflammatory signaling. These data highlight a major transcriptional regulator of AT1 cell lineage commitment and of the AT2 cell response to inflammatory crosstalk during lung regeneration.

overall_design: Adult control and Klf5-deficient mouse AT2 cells were isolated 3 days after hyperoxic lung injury.

first: Derek

middle: C

last: Liberti

first: Micheal

first: Edward

last: Morrisey


title: Regulatory programs of B-cell activation and germinal center reaction allow for B-ALL escape from CD19 CAR T-cell therapy

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

summary: CAR T-cell therapy has led to tremendous successes in the treatment of B-cell malignancies. However, 30%-50% of treated patients relapse – often with reduced target antigen expression. We report that anti-CD19 CAR T-cells cause a rapid reduction of CD19 expression within hours in CAR-T exposed CD19+ B-ALL cells. Initially, anti-CD19 CAR T-cells cause CD19 clusters at the T-cell – leukemia cell interface followed by CD19 internalization and decreased CD19 surface expression. Subsequently, CD19 expression is repressed by transcriptional rewiring. Using single-cell RNA-seq and single-cell ATAC-seq we demonstrate that a subset of CD19low cells that are refractory to CAR T-cell killing employ transcriptional programs of physiological B-cell activation and germinal center reaction in order to sustain decreased CD19 expression. Inhibiting B-cell activation programs with the BTK inhibitor ibrutinib increased the cytotoxic efficacy of anti-CD19 CAR T-cells without effecting CAR T-cell viability. These results demonstrate transcriptional plasticity as an underlying mechanism of CAR T-resistance and highlight the importance of combining CAR T-cell therapy with targeted therapies that aim to overcome this plasticity.

overall_design: Single cell expression and chromatin accessibility profiles of NALM-6 B-ALL cells exposed to CAR T-cells or uninfected T-cells.

first: Nam

last: Im

first: Amy

last: Guillaumet-Adkins

first: Megha

last: Wal

first: Anna

last: Rogers

first: Julia

last: Frede

first: Praveen

last: Anand

first: Sarah

last: Stegmann

first: Johannes

middle: M

last: Waldschmidt

first: Noori

last: Sotudeh

first: Leili

last: Niu

first: Jordan

last: Voisine

first: Michal

last: Schweiger

first: Clemens

last: Grassberger

first: Jens

last: Lohr


title: A target expression threshold dictates invader defense and autoimmunity by CRISPR-Cas13 [Genome wide screen]

city: Wuerzburg

first: Chase

last: Beisel

address: Josef Schneider Strasse , D15

institute: HIRI

summary: The study investigates how varying target expression levels influences self-targeting and defense using Cas13a. We see how immunity is activated only over a target transcription threshold, which is variable between targets. A gRNA library targeting transcripts from the whole coding genome of E. coli MG1655 confirms the importance of the transcription threshold in determining immunity and shows that most of the cellular transcripts do not induce cytotoxicity.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Comparison of enriched spacers between cells with and without Cas13a nuclease. Two biological replicates for each condition.

first: Elena

last: Vialetto

first: Yanying

last: Yu

first: Scott

middle: P

last: Collins

first: Katharina

last: Wandera

first: Lars

last: Barquist


title: TRAP-seq of samples isolated from  DHPG-stimulated WT and Fmr1-/y hippocampal slices

status: Public on Jun 07 2022

city: Edinburgh

first: Emily

last: Osterweil

state: Scotland

address: Hugh Robson Building, 15 George Square

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

summary: Sequencing files from TRAP-seq samples isolated from  DHPG-stimulated WT and Fmr1-/y hippocampal slices

overall_design: Hippocampal slices were prepared from 6 littermate pairs of WT and Fmr1-/y mice expressing EGFP-L10a in CA1 pyr neurons. Slices were stimulated with DHPG to induce LTD and TRAP performed to isolate ribosome-bound mRNAs. Both TRAP samples and samples of the total hippocampal lysate were processed for Illumina sequencing.

first: Sang

middle: S

last: Seo

first: Manuela

last: Rizzi


title: Genome-wide chromatin occupancy of MIR205HG/LEADR in prostate basal epithelial cells

city: Milan

first: Paolo

last: Gandellini

state: Milan

address: Via celoria 26

department: Bioscience

country: Italy

institute: University of Milan

summary: Aside serving as host gene for the microRNA miR-205, MIR205HG transcribes for a nuclear chromatin-associated long noncoding RNA (lncRNA) able to restrain the differentiation of prostate basal cells, a finding that led to its reannotation as LEADR (Long Epithelial Alu-interacting Differentiation-related RNA). In our previous work (PMID: 30659180), we showed that genes that are modulated upon manipulation of MIR205HG/LEADR are characterized by the presence of an Alu sequence in their promoters. Notably, an Alu element also spans the first and second exon of MIR205HG/LEADR, thus suggesting its possible involvement in target selection and binding. Here, we performed Chromatin Isolation by RNA precipitation followed by DNA-sequencing (ChIRP-seq) to map MIR205HG/LEADR chromatin occupancy at a genome-wide level in prostate basal cells.

overall_design: Chromatin Isolation by RNA precipitation followed by DNA-sequencing (ChIRP-seq) for MIR205HG/LEADR long noncoding RNA in RWPE-1 cells, performed in three replicates. LacZ probes used as control.

first: Eugenia

last: Bezzecchi

first: Giulia

last: Pagani


title: A target expression threshold dictates invader defense and autoimmunity by CRISPR-Cas13 [RNA-seq]

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA-seq of transcripts during early (OD 0.5) and late (OD 0.8) exponential growth phase from E. coli MG1655. Two biological replicates for each timepoint.

middle: G


title: A target expression threshold dictates invader defense and autoimmunity by CRISPR-Cas13

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


title: Influence of sire fertility status on conceptus-induced transcriptomic response of the bovine endometrium

city: columbia

first: Hongyu

last: Liu

state: mo

address: 920 east campus drive.

institute: university of missouri

summary: The aim of this study was to examine the effect of sire fertility status on conceptus-induced changes in the endometrial transcriptome. Holstein Friesian bulls (3 High fertility, HF, 3 Low fertility, LF) were selected from the Irish national population of AI bulls (minimum of 500 inseminations/bull) based on adjusted fertility scores (HF: +4.37% and LF: -12.7%; mean = 0%). To generate elongated conceptuses, Day 7 blastocysts produced in vitro using sperm from these six bulls were transferred in groups of 5-10 to synchronized heifers (n=7 heifers per bull; total 42 heifers). Conceptuses were recovered following slaughter on Day 15 (recovery rate: HF 59.4% vs. LF 45.0%; P<0.05). In parallel, Day 15 endometrial explants were recovered from synchronized cyclic heifers (n=4). Explants from each heifer were co-cultured for 6 h in RPMI medium with (i) nothing, control (ii) 100 ng/ml ovine recombinant interferon tau (IFNT) (iii) a single conceptus from each high fertility bull, or (iv) a single conceptus from each low fertility bull. To minimize variation, explants from the same uterus were used across all treatments, replicated across 4 heifers. After 6 h, explants were snap frozen and stored at -80°C. Extracted mRNA was subjected to RNA-seq (Illumina NextSeq 500) and the resulting data were analyzed through a bioinformatic pipeline with R software.

overall_design: Endometrial explants were co-cultured for 6 h in RPMI medium with (i) nothing, control (ii) 100 ng/ml ovine recombinant interferon tau (IFNT) (iii) a single conceptus from each high fertility bull, or (iv) a single conceptus from each low fertility bull.

last: O’Callaghan

first: Jose

last: Sánchez

first: Maria

last: Rabaglino

first: Michel

last: McDonald

first: Thomas

last: Spencer

first: Sean

last: Fair

first: David

middle: A

last: Kenny

first: Pat

last: Lonergan


title: TRAP-seq from hippocampus isolated from WT and Fmr1-/y mice bred to Snap25-EGFPL10a mice

summary: Ribosome-bound mRNAs isolated from neurons in the hippocampi of Fmr1-/y mice and littermate WT controls

overall_design: TRAP-seq was performed on hippocampi isolated from 4 littermate pairs of WT and Fmr1-/y mice expressing EGFP-L10a in a pan-neuronal Snap25-EGFPL10a line

middle: K


title: RNA-seq of liver of mice exposed to varying food availability

city: Münster

first: Marisol

last: Herrera-Rivero

state: NRW

address: Albert-Schweitzer-Campus 1

institute: University of Münster

overall_design: Match and mismatch conditions of high (ad libitum) and low (90% of ad libitum intake) food availability from adolescence to early adulthood in female C57BL/6J mice

first: Janina

last: Feige-Diller

first: Anika

last: Witten

first: Monika

last: Stoll

first: Sylvia

last: Kaiser

first: S

middle: H

last: Richter

first: Norbert

last: Sachser


title: ECM dimensionality tunes actin tension to regulate endoplasmic reticulum function and spheroid phenotype

city: San Francisco

first: Valerie

last: Weaver

address: 513 Parnassus Avenue, HSE 560

department: Surgery

institute: UCSF

summary: Patient-derived organoids and cellular spheroids recapitulate tissue physiology with remarkable fidelity. We investigated how engagement with a reconstituted basement membrane (rBM) in three dimensions (3D) supports the polarized, stress resilient tissue phenotype of mammary epithelial spheroids. Cells interacting with rBM in 3D had reduced levels of total and actin-associated filamin and decreased cortical actin tension that increased plasma membrane protrusions to promote negative plasma membrane curvature and plasma membrane protein associations linked to protein secretion. By contrast, cells engaging rBM in 2D had high cortical actin tension that forced filamin unfolding and endoplasmic reticulum (ER) associations. Enhanced filamin-ER interactions increased levels of PKR-like ER kinase effectors and ER-plasma membrane contact sites that compromised calcium homeostasis and diminished cell viability. Consequently, cells with low cortical actin tension had reduced ER stress and survived better. Consistently, cortical actin tension in cellular spheroids regulated polarized BM membrane deposition and sensitivity to exogenous stress. The findings implicate cortical actin tension-mediated filamin unfolding in ER function, and underscore the importance of tissue mechanics in organoid homeostasis.

overall_design: RNAseq data from MCF10A cultured in 2D or 3D at three timepoints

first: Connor

last: Stashko

first: Kai

last: Fuiboon

first: V


title: CX DHPG TRAP-seq

first: Emily

last: Osterweil

summary: Sequencing files from TRAP-seq samples isolated from  DHPG-stimulated WT and Fmr1-/y hippocampal slices incubated with vehicle or 200 nM CX-5461

overall_design: Hippocampal slices were prepared from 4 littermate pairs of WT and Fmr1-/y mice expressing EGFP-L10a in CA1 pyr neurons. Slices were pre-incubated with 200nM CX-5461 or vehicle then stimulated with DHPG to induce LTD. TRAP was performed to isolate ribosome-bound mRNAs.

first: Sang

last: Seo

first: Manuela

last: Rizzi


title: Transcription factor-driven coordination of cell cycle exit and lineage-specification in vivo during granulocytic differentiation [ChIP-Seq_2]

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

institute: University of Copenhagen

summary: Differentiation of multipotent stem cells into mature cells is fundamental for development and homeostasis of mammalian tissues, and requires the coordinated induction of lineage-specific transcriptional programs and cell cycle withdrawal. To understand the underlying regulatory mechanisms of this fundamental process, we investigated how the tissue-specific transcription factors, CEBPA and CEBPE, coordinate cell cycle exit and lineage-specification in vivo during granulocytic differentiation. We demonstrate that CEBPA promotes lineage-specification by launching an enhancer-primed differentiation program and direct activation of CEBPE expression. Subsequently, CEBPE confers promoter-driven cell cycle exit by sequential repression of MYC target gene expression at the G1/S transition and E2F-meditated G2/M gene expression, as well as by the up-regulation of Cdk1/2/4 inhibitors. Following cell cycle exit, CEBPE unleashes the CEBPA-primed differentiation program to generate mature granulocytes. These findings highlight how tissue-specific transcription factors coordinate cell cycle exit with differentiation through the use of distinct gene regulatory elements.

overall_design: ChIP-seq of CEBPA and H3K27ac in WT and Cebpe KO MY1+2, MM populations of granulocytic differentiation. ChIP-seqs were performed in biological duplicates.

first: Kim

last: Theilgaard-Mönch

first: Sachin

last: Pundhir

first: Kristian

last: Reckzeh

first: Jinyu

last: Su

first: Marta

last: Tapia

first: Benjamin

last: Furtwängler

first: Johan

last: Jendholm

first: Janus

last: Jacobsen

first: Marie

last: Haseman

first: Kasper

last: Knudsen

first: Jack

last: Cowland

first: Anna

last: Fossum

first: Erwin

last: Schoof

first: Mikkel

middle: B

last: Schuster

middle: T


title: Ornithine Decarboxylase Activity in Gastric Epithelial Cells Contributes to the Pathogenesis of Helicobacter pylori

city: Nashville

first: Keith

last: Wilson

state: TN

address: 2215 Garland Ave

department: Medicine

institute: Vanderbilt University Medical Center

summary: RNA sequencing by Illumina NovaSeq6000 was performed on  gastric tissues of Odc fl/fl and Odc_Delta_Epi mice infected or not with H. pylori PSS1 for 4 weeks to determine the role of epithelial ODC in H. pylori pathogenesis

overall_design: RNA was extracted from 4 mice per genotype either uninfected or infected

first: Johanna

last: Sierra

first: Yvonne

last: Latour

first: Alain

last: Gobert


title: AMPK is involved in regulating the utilization of carbon sources, conidiation, pathogenicity, and stress response of the nematode-trapping fungus Arthrobotrys oligospora

city: Kunming

first: wenjie

last: wang

address: Kunming

institute: Yunnan University

summary: Transcriptomic profile between the wild-type strain and ΔAosnf1 showed that differentially expressed genes were enriched on peroxisome,endocytosis, fatty acid degradation, and multi-lipid metabolism (sphingolipid, ether lipid, glycerolipid, and glycerophospholipid).

overall_design: RNA-seq analysis between six wild-type samples and six ΔAosnf1 mutant samples, with three biological replicates per sample, and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Wenjie

last: Wang

first: Yining

last: Zhao

last: Bai


title: Combinatorial genetics reveals the DOCK1-RAC2 axis as a specific target for the treatment of NPM1;Cohesin mutated AML

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: Acute myeloid leukemia (AML) is driven by mutations that occur in numerous combinations. A better understanding of how mutations interact with one another to cause disease is critical to developing targeted therapies. Approximately 50% of patients that harbor a common mutation in NPM1 (NPM1cA) also harbor a mutation in the cohesin complex. As cohesin and Npm1 are known to regulate gene expression, we sought to determine how cohesin mutation alters the transcriptome in the context of NPM1cA. We utilized inducible Npm1cAflox/+ and Smc3flox/+ mouse models to examine this genetic interaction. While Npm1cA/+;Smc3 /+ mice developed AML with similar latency as Npm1cA/+ mice, RNA sequencing suggests that the Npm1cA; Smc3 /+ mutational combination uniquely alters the transcriptome. We found that the Rac1/2 nucleotide exchange factor Dock1 was uniquely upregulated in Npm1cA/+;Smc3 /+ HSPCs. Knockdown of Dock1 resulted in decreased growth and adhesion and increased apoptosis specifically in Npm1cA/+;Smc3 /+ AML. Higher Rac activity was also observed in Npm1cA/+;Smc3 /+ vs. Npm1cA/+ AMLs. Importantly, the Dock1/Rac pathway is targetable in Npm1cA/+;Smc3 /+ AMLs. Our results suggest that Dock1/Rac represent unique targets for the treatment of patients harboring both the NPM1cA and cohesin mutations and support the use of combinatorial genetics to identify novel precision oncology targets.

overall_design: RNA-seq of 4 conditions, 3 replicates each

first: Alison

last: Meyer

first: Kirthi

last: Pulakanti


title: The Integrated "Multiomics" Landscape at Peak Injury and Resolution From Alcohol-Associated Liver Disease

status: Public on Jun 06 2022

city: Chicago

first: Natalia

last: Nieto

state: IL

address: 909 S. Wolcott Ave

institute: University of Illinois at Chicago

summary: To investigate the the liver transcriptome at peak injury and during early and late resolution from alcohol-induced liver injury in mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data during progression and resolution of alcoholic liver disease in mice.

first: Sukanta

last: Das


title: Global enrichment of FoxM1 bound chromatin in Huh7 cell line

first: Vaibhav

last: Chand

address: 900S Ashland Ave

department: Biochemistry and Molecular Genetics

summary: FoxM1 is an oncogenic transcription factor that has been linked to the genesis and progression of cancer. FoxM1 not only upregulates cell proliferation and survival genes, but also represses tumor suppressor genes according to our prior study. This ChIP-Seq is a part of our endeveavor to creat a map of the FoxM1 occupied chromatin area in order to better understand the FoxM1 role in tumorigenesis. We present the results of a high-throughput profile of Chromatine alteration in mammalian cells using ChIP-Seq. We developed genome-wide chromatin-state maps of the human HCC cell line Huh7 by extracting approximately 3 billion bases of sequence from chromatin immunoprecipitated DNA in approxiamtoly 33 million reads. We discovered that FoxM1 successfully distinguishes between expressed, stably repressed and poised genes  and therefore reflect cell state and lineage potential. This research lays the groundwork for using extensive chromatin profiling to characterize the genes controlled by the oncogeneic transcription factor FoxM1 and their role in the development of FoxM1-induced cancers.

overall_design: Chromatin occupancy of oncogenic transcription factor FoxM1 in Huh7-HCC line is genererated in this study

first: Pradip

last: Raychaudhuri


title: Transcription factor-driven coordination of cell cycle exit and specification of cell identify during granulocytic differentiation [ChIP-Seq]

first: Bo

last: Porse

summary: Differentiation of multipotent stem cells into mature cells is fundamental for development and homeostasis of mammalian tissues. However, how this temporal process of cell cycle exit and induction of lineage-specific transcription programs is coordinated remains largely unknown. To understand the underlying mechanisms, we investigated how the tissue-specific transcription factors CEBPA and CEBPE coordinate cell cycle exit and lineage-specification during granulocytic differentiation. We demonstrate that CEBPA promotes lineage-commitment by launching an enhancer-primed differentiation program and direct activation of CEBPE expression. Subsequently, CEBPE confers promoter-driven cell cycle exit by sequential repression of MYC target gene expression at the G1/S transition and E2F-meditated G2/M gene expression, as well as by the up-regulation of Cdk1/2/4 inhibitors. Following cell cycle exit, CEBPE unleashes the CEBPA-primed differentiation program to generate mature granulocytes.  These findings highlight how tissue-specific transcription factors coordinate cell cycle exit with terminal differentiation through the use of distinct gene regulatory elements.

overall_design: ChIP-seq of CEBPE in WT and CEBPA KO MY1+2, MM, BC and PMN populations of granulocytic differentiation. ChIP-seqs were performed in biological duplicates.

first: Kim

last: Theilgaard-Mönch

first: Sachin

last: Pundhir

first: Kristian

last: Reckzeh

first: Johan

last: Jendholm

first: Janus

last: Jacobsen

first: Marie

last: Haseman

first: Kasper

middle: J

last: Knudsen

first: Jack

last: Cowland

first: Anna

last: Fossum


title: Metabolic lactate production coordinates vasculature development and progenitor behavior in the developing mouse neocortex

city: Beijing

first: Xiaoxiang

last: Dong

address: Shuangqing Road, Haidian District, Beijing

institute: TSINGHUA UNIVERSITY

summary: Proper neural progenitor behavior in conjunction with orderly vasculature formation is fundamental to the development of the neocortex. However, the mechanisms coordinating neural progenitor behavior and vessel growth remain largely elusive. Here we show that robust metabolic production of lactate by radial glial progenitors (RGPs) co-regulates vascular development and RGP division behavior in the developing mouse neocortex. RGPs undergo a highly organized lineage progression program to produce diverse neural progeny. Systematic single cell metabolic state analysis revealed that RGPs and their progeny exhibit distinct metabolic features associated with specific cell types and lineage progression statuses. Symmetrically dividing, proliferative RGPs preferentially express a cohort of genes that support glucose uptake and anaerobic glycolysis. Consequently, they consume glucose in anaerobic metabolism and produce a high level of lactate, which promotes vessel growth. Moreover, lactate production enhances RGP proliferation by maintaining mitochondrial length. Together, these results suggest that specific metabolic states and metabolites coordinately regulate vasculature formation and progenitor behavior in neocortical development.

overall_design: Comparative gene expression profiling analysis of E10.5 RGP treated with LDH inhibitor (GSK) by Bulk RNA-seq, and treated with DMSO as a control, each group contains three replicates.

first: Qiangqiang

last: Zhang

first: Xiangyu

last: Yu

first: Ding

last: Wang

first: Jiaming

last: Ma

first: Jian

first: Song-Hai

last: Shi


title: Transcription factor-driven coordination of cell cycle exit and specification of cell identify during granulocytic differentiation [RNA-Seq]

first: Bo

overall_design: Examined transcriptome of different populations along granulocytic and monocytic lineage, along with four populations (GP, PM, MY1+2 and MM) for which transcriptiome upon CEBPE KO was also examined.

first: Mikkel

last: Schuster


title: Rapid, scalable assessment of SARS-CoV-2 cellular immunity by whole-blood PCR

city: New York

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Fast, high-throughput methods for measuring the level and duration of protective immune responses to SARS-CoV-2 are needed to anticipate the risk of breakthrough infections. Here we report the development of two quantitative PCR assays for SARS-CoV-2- specific T cell activation. The assays are rapid, internally normalized and probe-based: qTACT requires RNA extraction and dqTACT avoids sample preparation steps. Both assays rely on the quantification of CXCL10 messenger RNA, a chemokine whose expression is strongly correlated with activation of antigen-specific T cells. On restimulation of whole-blood cells with SARS-CoV-2 viral antigens, viral-specific T cells secrete IFN-γ, which stimulate monocytes to produce CXCL10. CXCL10 mRNA can thus serve as a proxy to quantify cellular immunity. Our assays may allow large-scale monitoring of the magnitude and duration of functional T cell immunity to SARS-CoV-2, thus helping to prioritize revaccination strategies in vulnerable populations.

overall_design: Total RNA was extracted from whole blood after overnight stimulation with a SARS-CoV-2 spike peptide pool (SpG) or DMSO control. The cohort consists of 11 naïve donors, 8 COVID-19 convalescent donors, and 16 vaccinated donors.

first: M

last: Schwarz

first: D

last: Torre

first: E

last: Guccione


title: NFKB2 Knockdown Reduces Expression of HR-Related Genes

first: Brian

last: Budke

address: 920 E 58th St

department: Radiation and Cellular Oncology

institute: University of Chicago

summary: Homologous recombination (HR) serves multiple roles in DNA repair that are essential for maintaining genomic stability. The central HR protein, RAD51, is frequently overexpressed in human malignancies, thereby elevating HR proficiency and promoting resistance to DNA-damaging therapies. Here we find that non-canonical NF-κB factors control the expression of RAD51 andother HR-promoting proteins.  Transcriptional silencing of p100/p52 reduces RAD51 protein levels in multiple human cancer subtypes.  RNA-seq after p100/p52 silencing identifies RAD51 as the most differentially expressed gene among 40 genes with known relevance to HR.  While p100/p52 depletion inhibits HR function in human tumor cells, it does not influence the function of other double-strand DNA repair pathways including single-strand annealing, microhomology mediated annealing, or non-homologous end joining.

overall_design: U2OS cells were transfected with siRNA at 75 nM total using Lipofectamine RNAiMAX. Total RNA was collected 48 hours later and submitted to the Functional Genomics Facility core at the University of Chicago for QC, library preparation, and sequecing using an Illumina HiSeq 4000 instrument.

first: Budke

last: Brian

first: Zhong

last: Alison

first: Sullivan

last: Katherine

first: Park

last: Chanyoung

first: Gittin

last: David

first: Kountz

last: Tim

first: Connell

last: Philip


first: NORC

last: Boston

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

summary: We systematically determined the extent to which APPBP2 loss stimulate beige adipocyte biogenesis in a PRDM16-dependent fashion. To this end, we ran RNA-seq analysis in adipocytes that lack APPBP2 and/or PRDM16. By overlapping the transcriptome data with published dataset of brown/beige fat (Chondronikola et al., 2016; Perdikari et al., 2018; Shinoda et al., 2015a), we found that APPBP2 loss significantly increased 72 genes whose expression was enriched in brown adipocytes relative to white fat.  Among 72 brown/beige fat-enriched genes, we found that 90.28% (65/72 genes) of them were regulated in a PRDM16-dependent manner.  The data suggest that PRDM16 is required for the majority, if not all, of APPBP2’s action on brown fat genes

overall_design: mRNA profiles of vehicle or cAMP treated inguinal adipocytes that lack APPBP2 and/or PRDM16

first: Shingo

last: Kajimura

first: Qiang


title: Epigenome analysis of CD4+ T cells from non-pregnant, 1st and 2nd trimester pregnant women

city: Linköping

first: Sandra

last: Hellberg

address: Universitetssjukhuset

country: Sweden

institute: Linköping University

type: Methylation profiling by genome tiling array

summary:
Epigenetics may play a central, but yet unexplored, role in the profound changes that the maternal immune system undergoes during pregnancy. We investigated changes in the methylome in isolated circulating CD4+ T cells in non-pregnant and pregnant women, during the 1st and 2nd trimester, using the Illumina Infinium Human Methylation 450K array, and explored how these changes were related to autoimmune diseases that are known to be affected during pregnancy. Pregnancy was associated with thousands of methylation differences, particularly during the 2nd trimester, where the majority of sites were hypermethylated, indicating transcriptional repression. Using a network-based modular approach disclosed several genes and pathways related to T cell signalling and activation. The pregnancy module was significantly enriched for disease-associated methylation changes related to multiple sclerosis, rheumatoid arthritis and systemic lupus erythematosus. The directionality of the changes was also in line with the previously observed effect of pregnancy on the disease activity, with a negative correlation for multiple sclerosis and rheumatoid arthritis that improves during pregnancy, and a positive correlation for systemic lupus erythematosus, a disease that instead worsens. In summary, this systems medicine approach supports the importance of the methylome in immune regulation of CD4+ T cells during pregnancy.
Samples included twelve (n=12) non-pregnant women, elven (n=11) 1st trimester pregnant women and twelve (n=12)

overall_design: Methylation changes during pregnancy was analyzed in CD4+ T cells were isolated from peripheral blood using positive selection from pregnant and non-pregnant women. Genomic DNA was extracted from all samples and bisulphite converted. The converted DNA was hybridized to the Ilumina Infinium 45K Human Methylation BeadChip v1.2

first: Mika

last: Gustafsson


title: Self-amplifying Loop of NF-κB and Periostin Initiated by PIEZO1 Accelerates Mechano-induced Senescence of Nucleus Pulposus Cells and Intervertebral Disc Degeneration

city: Guangzhou,

first: Jinna

last: Wu

state: Guangdong,

address: 58 Zhongshan Road 2

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: Abnormal mechanical load is a main risk factor of intervertebral disc degeneration (IDD), and cellular senescence is a pathological change in IDD. Additionally, extracellular matrix (ECM) stiffness promotes human nucleus pulposus cells (hNPCs) senescence. However, the molecular mechanism underlying mechano-induced cellular senescence and IDD progression is not yet fully elucidated. First, we demonstrated that mechano-stress promoted hNPCs senescence via NF-κB signaling. Subsequently, we identified periostin as the main mechano-responsive molecule in hNPCs through unbiased sequencing, which was transcriptionally upregulated by NF-κB p65; moreover, secreted periostin by senescent hNPCs further promoted senescence and upregulated the catabolic process in hNPCs through activating NF-κB, forming a positive loop. Both Postn (encoding periostin) knockdown via siRNA and periostin inactivation via neutralizing antibodies alleviated IDD and NPCs senescence. Furthermore, we found that mechano-stress initiated the positive feedback of NF-κB and periostin via PIEZO1. PIEZO1 activation by Yoda1 induced severe IDD in rat tails without compression, and Postn knockdown alleviated the Yoda1-induced IDD in vivo. Here, we reported for the first time that self-amplifying loop of NF-κB and periostin initiated via PIEZO1 under mechano-stress accelerated NPCs senescence, leading to IDD. Furthermore, periostin neutralizing antibodies, which may serve as potential therapeutic agents for IDD, interrupted this loop.

overall_design: mRNA profiles and ATAC-seq of human nucleus pulposus cells cultured on 1kPa and 40kPa hydrogel

first: Yuyu

last: Chen

first: Zhiheng

last: Liao

first: Taifeng

last: Zhou


title: Single cell transcriptome analysis of endocrine pancreas development in mice

city: Stanford

first: Seung

last: Kim

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

summary: In this study, we used SMART-Seq2 single cell analysis to delineate the molecular mechanisms underlying gene expression changes during endocrine pancreas differentiation

overall_design: 495 cells were sequenced isolated from mouse embryonic pancreas on embryonic day (E) E15 and E17. Two different strains were used, Neurog3-eGFP knock in line and Neurog3-Cre; Rosa-mTmG

first: Eliza

last: Duvall

first: H. Efsun

last: Arda


title: Cellular RNA Targets of Cold Shock Proteins CspC and CspE and Their Importance for Serum Resistance in Septicemic Escherichia coli

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: We performed a global analysis to identify transcripts that interact with CspC and CspE (CLIP-seq), focusing on virulence-related genes.

overall_design: We used CLIP-seq, which combines UV cross-linking, immuno-precipitation and RNA sequencing and compared samples of three biological cross-linked conditions with three biological non cross-linked conditions for both CspC and CspE

first: Yael

last: Yair

first: Charlotte

last: Michaux


title: Transcriptome analysis of Arabidopsis dry seeds

city: Valencia

first: Javier

last: Forment

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (UPV-CSIC)

summary: We report the dry seed transcriptome of 13 wild type accessions of Arabidopsis thaliana

overall_design: Total RNA of dry seed were extracted and sequenced

first: Jose

last: Gadea


title: Lung in C57BL mice: Control vs cigarette smoke exposure

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

institute: Osaka Metropolitan University Graduate School of Medicine

summary: The gene expression profling between Control and  cigarette smoke exposure for 2 or 4 weeks in lung of C57BL male mice.

overall_design: Male 10-week-old C57BL mice were exposed to clean air (control) or mainstream cigarette smoke for 1 h/day (10 to 11 AM), 5 days/ week, for 2 or 4 weeks. After treatment, mice were sacrificed, and removed lungs. Control and cigarette smoke exposure. 5 and 5 control male mice, 5 and 4 cigarette smoke exposure male mice for 2 and 4 weeks, respectively. Mixed 4 or 5 samples from each group for each array.


title: Gruffi removes stressed cells from brain organoid datasets

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

institute: IMP/IMBA

summary: Organoids enable disease modeling in complex and structured human tissue, in vitro. Like most 3D cultures, they lack sufficient oxygen supply, leading to cellular stress. These negative effects are particularly prominent in complex models, like brain organoids, where they can prevent proper lineage commitment. Here, we analyze brain organoid and fetal single cell RNA sequencing (scRNAseq) data from published and new datasets totaling about 190,000 cells. We describe a unique stress signature found in all organoid samples, but not in fetal samples. We demonstrate that cell stress is limited to a defined organoid cell population, and present Gruffi, an algorithm that uses granular functional filtering to identify and remove stressed cells from any organoid scRNAseq dataset in an unbiased manner and validate our findings on six further datasets from different organoid protocols and early brains. Our data show that adverse effects of cell stress can be corrected by bioinformatic analysis, improving developmental trajectories and resemblance to fetal data.

overall_design: Generation of new and re-analysis of published organoid scRNA seq datasets

first: Ábel

last: Vértesy

first: Oliver

last: Eichmüller

first: Julia

last: Naas

first: Christopher

last: Esk

first: Sabrina

last: Ladstaetter

first: Christoph

last: Bock

first: Arndt

last: von Haeseler

first: Juergen

last: Knoblich


title: Mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance: Minigene library DNA-seq

status: Public on Jun 05 2022

city: Mainz

first: Julian

last: König

address: Ackermannweg 4

department: Biology

institute: Institute of Molecular Biology, Mainz

summary: We developed a massively parallel reporter assay to determine the splicing effects of all mutations in the region comprising CD19 exons 1-3. Despite the great success of CART-19 (chimeric antigen receptor-armed autologous T-cells) immunotherapy to treat B-cell acute lymphoblastic leukaemia (B-ALL), many patients relapse due to loss of the targeted CD19 epitope. Since epitope loss can be caused by CD19 exon 2 mis-splicing, we set out to learn the regulatory code that controls CD19 alternative splicing.

overall_design: DNA-seq from the CD19 minigene variants transfected into NALM-6 cells

first: Mariela

last: Cortés-López

first: Laura

last: Schulz

first: Mihaela

last: Enculescu

first: Claudia

last: Paret

first: Bea

last: Spiekermann

first: Anke

last: Busch

first: Anna

last: Orekhova

first: Fridolin

last: Kielisch

first: Mathieu

last: Quesnel-Vallières

first: Manuel

last: Torres-Diz

first: Jörg

last: Faber

first: Yoseph

last: Barash

first: Andrei

last: Thomas-Tikhonenko

first: Kathi

last: Zarnack

first: Stefan

last: Legewie


title: Melanoma GEMM Tumors, untreated or vemurafenib treated [bulk RNA-seq]

status: Public on Jun 03 2022

city: South San Francisco

first: Dorothee

last: Nickles

state: CA

address: 1 DNA Way

institute: Genentech

summary: Emerging research suggests that multiple tumor compartments can influence treatment responsiveness and relapse, yet the search for therapeutic resistance mechanisms remains largely focused on acquired genomic alterations in cancer cells. Here, we show how treatment-induced changes occur in multiple tumor compartments during tumor relapse and can reduce benefit of follow-on therapies. By utilizing serial biopsies, next generation sequencing and single cell transcriptomics, we tracked the evolution of multiple cellular compartments within individual lesions during first-line treatment response, relapse and second-line therapeutic interventions in an autochthonous model of melanoma. We discovered that while treatment-relapsed tumors remained genetically stable, they converged on a shared resistance phenotype characterized by dramatic changes in tumor cell differentiation state, immune infiltration and extracellular matrix (ECM) composition. Similar alterations in tumor cell differentiation were also observed in more than half of our treatment-relapsed patient tumors. Tumor cell state changes were coincident with ECM remodeling and increased tumor stiffness, which alone was sufficient to alter tumor cell fate and reduce treatment responses in melanoma cell lines in vitro. Despite the absence of acquired mutations in the targeted pathway, resistant tumors showed significantly decreased responsiveness to second-line therapy intervention within the same pathway. The ability to preclinically model relapse and refractory settings - while capturing dynamics within and crosstalk between all relevant tumor compartments - provides a unique opportunity to better design and sequence appropriate clinical interventions.

overall_design:
bulk RNA-seq
This study is related to GSE126714.

first: Melissa

last: Juntilla


title: Neuropilin-2 regulates androgen-receptor transcriptional activity in advanced prostate cancer

city: Omaha

first: Samikshan

last: Dutta

state: NE

address: 42 and Emile

department: BMB

institute: univ of nebraska medical center

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

overall_design: Refer to individual Series


title: Extracellular Vesicles Carry Distinct Proteo-Transcriptomic Signatures That are Different from Their Cancer Cell of Origin (22RV1 cell line only)

first: Navneet

last: Dogra

address: 1 Gustave L. Levy Pl

summary: Circulating extracellular vesicles (EVs) contain molecular footprints - lipids, proteins, metabolites, RNA, and DNA - from their cell of origin and may provide non-invasive access for detection, characterization, and monitoring of diseases. Consequently, EV-associated RNA and proteins have gained widespread interest in developing liquid-biopsy assays for cancer. Yet, an integrative proteo-transcriptomic landscape of EVs and a direct comparison with their cell of origin remains relatively unexplored. Here, we report that EVs enrich for distinct molecular cargo and their proteo-transcriptome does not linearly correlate with their cell of origin. Our sub-cellular compartment analyses revealed that EV enrich 2-6 times more cytoskeletal and extracellular proteins, while their donor cells cargo 3-10 times more nuclear and mitochondrial proteins. EVs predominantly enrich (40-60%) for small RNA between ~15-200 nucleotides, which include miRNAs, siRNAs, tRNA, 5S rRNAs, and snRNAs, associated with cell differentiation, development, and Wnt signaling signatures. Finally, our integrated proteo-transcriptomic analyses reveal that EVs are enriched with specific small RNAs (RNY3, vtRNA, and MIRLET-7) and their complementary proteins (YBX1, IGF2BP2, SRSF1/2). These analyses suggest that RNA-protein complexes may constitute a functional interaction network inside EVs to protect and regulate access to EV-RNA. To ensure that our analyses are unbiased and independent of the cell of origin, EV isolation methods, site of experimentation, site of data generation, and methodologies applied for RNAseq and mass spectrometry, we have generated and curated comprehensive datasets of proteomics and transcriptomics from a total of 12 cancer cell lines, their EVs, and prostate cancer patientsÕ serum EVs (A detailed description is provided in Fig. 1). These combined analyses demonstrated that irrespective of the cell of origin and other aforementioned conditions, EVs enrich for distinct RNA and protein signatures that do not linearly correlate with their cell of origin.

overall_design: In this study, we have generated and curated comprehensive datasets of proteomics and transcriptomics from a total of 12 cancer cell lines, their EVs, and prostate cancer patientsÕ serum EVs

first: Tzu-Yi

last: Chen

first: Edgar

last: Gonzalez-Kozlova

first: Gustavo

last: Stolovitzky


title: Neuropilin-2 regulates androgen-receptor transcriptional activity in advanced prostate cancer [ChIP-seq]

summary:
Our study using prostate cancer tissues and cell lines observed that neuropilin-2 (NRP2) can translocate to the nucleus of advanced prostate cancer cells. NRP2 is present in the nuclear membrane and near to the nuclear pore. To understand the functions of nuclear NRP2 in prostate cancer, we have performed NRP2-specific chromatin immunoprecipitation DNA-sequencing (ChIP-seq) in prostate cancer cell. Our results showed NRP2 forms a complex with transcription factors and pore proteins, which helps the transcription factors to be recruited at the promoter regions of genes.  The nature of the interaction between NRP2-transcription factors is dynamic and depends on various physiological and pathological conditions.
The ChIP-seq was carried in duplicate using adenocarcinoma cell lines.

overall_design: D,Klinkebiel

first: S

first: K

last: Datta


title: Neuropilin-2 regulates androgen-receptor transcriptional activity in advanced prostate cancer [RNA-seq]

summary: Gene expression was first compared between control and NRP2 depletd condition in prostate adenocarcinoma cell line LNCaP C4-2B . In the next set, we compared the gene  expression between control and AR deplted state in LNCaP C4-2B cells.

overall_design: The gene expression was analyzed in triplicate in each conditions. Following Neuropilin-2 or AR depletion by siRNA for 48hrs, gene expression was carried out


title: Impact of fetal exposure to mycotoxins on longissimus muscle fiber hypertrophy and miRNA transcriptome

city: Clemson

first: Susan

last: Duckett

state: SC

address: 112 Biosystems Research Complex

department: Animal and Veterinary Sciences

institute: Clemson University

summary: Longissimus muscle samples were collected from lambs exposed in utero to mycotoxins (E-, endophyte-free tall fescue seed without ergot alkaloids or E+, endophyte-infected tall fescue seed containing ergot alkaloids) during mid-gestation (MID; E+/E-; N) or late-gestation (LATE; E-/E+; T) harvested at two developmental stages (FETAL, gestational d133) or (MKT, near maturity, 250 d of age). Muscle samples were examined to determine the impact of in utero mycotoxin exposure on skeletal muscle fiber hypertrophy and the miRNA transcriptome at FETAL and MKT.

overall_design: This study is comprised of 12 samples. There are 4 groups with 3 replicates each. There are two stages of development: fetal and wether. For each life stage, there is a group exposed in utero to mycotoxins (endophyte-infected tall fescue seed containing ergot alkaloids) during mid-gestation (MID; N) or late-gestation (LATE; T).

first: Maslyn

last: Greene

first: Aliute

middle: N

last: Udoka

first: Rhonda

last: Powell

first: Rooksana

middle: E

last: Noorai

first: Terri

last: Bruce


title: CLIP-Seq of ZCCHC14 binding sites in HAV infected cells

city: CHAPEL HILL

first: Jason

last: Whitmire

state: NC

address: 5062 Genetic Medicine Bldg

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

summary: We analyzed RNAs bound to FLAG tagged ZCCHC14 protein in HAV infected 293T cells using enhanced crosslinking-immunoprecipitation (eCLIP) and next generation sequencing (NGS), in order to identify ZCCHC14 binding sites on cellular and HAV RNAs.

overall_design: Examination of RNA sequences bound to FLAG tagged ZCCHC14 protein in HAV infected 293T  cells.

first: Li

last: You

first: Lemon

last: Stanley


title: RNA-sequencing of undifferentiated and differentiated mouse skeletal muscle cells following the depletion of SETD2

city: Chapel Hill

first: Jimena

last: Giudice

address: 6340B MBRB, Campus Box 7545

department: Cell Biology and Physiology

institute: UNC - Chapel Hill

summary: undifferentiated mouse skeletal muscle cells (myoblasts) and differentiated mouse skeletal muscle cells (myotubes) were subjected to treatment with siRNAs targeting SETD2 or a non-targeting siRNA (si-Ctrl). Differential gene expression analysis and splicing analysis was performed on the resulting data.

overall_design: 18 samples total, 9 myoblast, 9 myotube each with three conditions (si-Ctrl, si-Setd2#1, and si-Setd2#2) and three biological replicates of each condition

first: Hannah

last: Wiedner


title: The function of Wtap in N6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells [YTHDF2-iCLIP]

city: Planegg-Martinsried

first: Taku

last: Kureha

address: Grosshaderner Str. 9

department: Institute for Immunology

institute: Ludwig-Maximilians-Universität

summary: T cell antigen receptor (TCR) signaling controls the development, activation and survival of T cells by involving several layers and numerous mechanisms of gene regulation. N6-methyladenosine (m6A) is the most prevalent mRNA modification affecting splicing, translation and stability of transcripts. Here, we describe the Wtap protein as essential for m6A methyltransferase complex function and reveal its crucial role in TCR signaling. Wtap and m6A methyltransferase functions were required for the differentiation of thymocytes, control of activation-induced death of peripheral T cells and prevention of colitis by enabling gut RORγt+ regulatory T cell function. Transcriptome and epitranscriptomic analyses reveal that m6A modification destabilizes Orai1 and Ripk1 mRNAs. Lack of post-transcriptional repression of the encoded proteins correlated with increased store-operated calcium entry (SOCE) activity and diminished survival of T cells. These findings uncover how m6A modification impacts on TCR signal transduction and determines activation and survival of T cells.

overall_design: Examination of transcriptome in WT or Wtap KO CD4+ T cells. m6A-CLIP or YTHDF2-iCLIP experiments were performed on polyA+ RNA from mouse CD4+ cells with 3 or 2 biological replicates, respectively.

last: Ito-Kureha

first: Vigo

last: Heissmeyer


title: The function of Wtap in N6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells [RNA-seq]


title: Mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance: Minigene library RNA-seq

first: Julian

last: König

overall_design: PolyA selected RNA from the expressed CD19 minigene variants introduced in NALM-6 cells

first: Mariela

last: Cortés-López

first: Laura

last: Schulz

first: Mihaela

last: Enculescu

first: Claudia

last: Paret

first: Bea

last: Spiekermann

first: Anke

last: Busch

first: Anna

last: Orekhova

first: Fridolin

last: Kielisch

first: Mathieu

last: Quesnel-Vallières

first: Manuel

last: Torres-Diz

first: Jörg

last: Faber

first: Yoseph

last: Barash

first: Andrei

last: Thomas-Tikhonenko

first: Kathi

last: Zarnack

first: Stefan

last: Legewie


title: Neurovascular dysfunction in GRN-associated frontotemporal dementia identified by single-nucleus RNA-sequencing of human cerebral cortex

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

institute: UMCG

summary: Frontotemporal dementia (FTD) is the second most prevalent form of early-onset dementia, affecting predominantly frontal and temporal cerebral lobes. Heterozygous mutations in the progranulin gene (GRN) cause autosomal-dominant FTD (FTD-GRN), associated with TDP-43 inclusions, neuronal loss, axonal degeneration and gliosis, but FTD-GRN pathogenesis is largely unresolved. Here we report single-nucleus RNA sequencing of microglia, astrocytes and the neurovasculature from frontal, temporal and occipital cortical tissue from control and FTD-GRN brains. We show that fibroblast and mesenchymal cell numbers were enriched in FTD-GRN, and we identified disease-associated subtypes of astrocytes and endothelial cells. Expression of gene modules associated with blood–brain barrier (BBB) dysfunction was significantly enriched in FTD-GRN endothelial cells. The vasculature supportive function and capillary coverage by pericytes was reduced in FTD-GRN tissue, with increased and hypertrophic vascularization and an enrichment of perivascular T cells. Our results indicate a perturbed BBB and suggest that the neurovascular unit is severely affected in FTD-GRN.

overall_design: Bulk RNAseq of NEUNpos and OLIG2pos nuclei from CTR and FTD-GRN brains. Single-nucleus RNAseq of NEUNnegOLIG2neg nuclei from the same samples.

first: Lucia

last: Giannini

first: Nieske

last: Brouwer

first: Shamiram

last: Melhem

first: Danielle

last: Seilhean

first: Isabelle

last: Le Ber

first: Alwin

last: Kamermans

first: Gijs

last: Kooij

first: Helga

last: de Vries

first: Erik

last: Boddeke

first: Harro

last: Seelaar

first: John

last: van Swieten

first: Bart

last: Eggen


title: Hematopoietic Loss of Y Chromosome Leads to Cardiac Fibrosis and Dysfunction and is Associated with Death due to Heart Failure [bulkRNAseq_HeartNeutrophils]

status: Public on Jun 02 2022

city: Nagoya

first: Hayato

last: Ogawa

state: Aichi

address: Tsurumai-cho 65

department: Department of Cardiology

institute: Nagoya University Graduate School of Medicine

summary: Hematopoietic mosaic loss of Y chromosome (mLOY) is associated with increased risk of mortality and a variety of age-related diseases in men, but causal and mechanistic relationships have yet to be established. Here it is shown that mice reconstituted with bone marrow cells lacking the Y chromosome display increased mortality and age-related profibrotic pathologies including a progressive decline in cardiac function. Accelerated cardiac dysfunction and fibrosis were also observed in younger mice subjected to a pressure-overload model of heart failure. Bone marrow-derived, cardiac macrophages lacking the Y chromosome exhibited polarization toward a more fibrotic and less inflammatory phenotype. Treatment with a TGFb1  neutralizing antibody led to greater amelioration of heart failure in mice reconstituted with mLOY compared to wild-type bone marrow. Consistent with these data, a prospective study in men revealed that mLOY in blood is associated with an increased risk for cardiovascular disease and heart failure-associated mortality. Together, these results indicate that hematopoietic mLOY contributes to heart failure in men.

overall_design: NOT PROVIDED; REQUESTED

first: Nicholas

last: Chavkin

first: Anupreet

last: Kour

first: Keita

last: Horitani

first: Soichi

last: Sano

first: Kenneth

last: Walsh


title: Hematopoietic Loss of Y Chromosome Leads to Cardiac Fibrosis and Dysfunction and is Associated with Death due to Heart Failure.


title: RIP-seq for Ddx3xb in zebrafish embryos

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.

overall_design: RIP-seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at 2 and 4 hpf including two biological replicates

first: B

last: Shi

first: J

last: Heng

last: Zhou

first: Y

last: Yang

first: F

last: Liu


title: Phase separation of Ddx3xb helicase regulates maternal-to-zygotic transition in zebrafish