title: Next Generation Sequencing Analysis of colon transcriptomes in BF638R bsh- and bF638R bsh+ colonized Cdx2Apcf/w mice.

city: Bethesda

first: Lulu

last: Sun

state: Maryland

address: 37 Convent Drive

institute: National Cancer Institute

summary: Bacteroides, that expresses bile salt hydrolase (BSH), is considered as a potential drug target for metabolic diseases. In the present study, BSH-expressing Bacteroides was found to be enriched in two different CRC mouse models and colonization of nonenterotoxigenic Bacteroides species, such as B. fragilis 9343 or B. vulgatus , enhanced CRC growth. Expression of the 9343 bsh gene in B. fragilis 638R, a bsh - lacking strain, enabled more bile acids to escape into the colon and accelerated CRC progression . The presence of BSH activated WNT signaling and  upregulated CCL28 expression dependent on b-catenin in colon tumors. The activated b-catenin/CCL28 axis elevated intra-tumororal immunosuppressive CD25+ FOXP3+ T reg cells. Anti-CCL28 antibody reversed microbial BSH amplificationinduced immunosuppression. Inhibition of BSH reduced CRC progression, coincident with suppression of WNT signaling and CCL28 expression. These findings provide a novel insight into the pro-carcinogenetic role of NTBF in CRC and characterize BSH as a potential target for CRC treatment.

overall_design: Bulk RNA-seq of RNA isolated from the colon of HFD-fed Cdx2Apcf/w mice that were colonized with  BF638R bsh- (WT B. fragilis 638R) and BF638R bsh+ (BSH-overexpressed B. fragilis 638R) .

first: Frank

middle: J

last: Gonzalez


title: Fatty acid binding proteins contribute to multiple myeloma cell maintenance through regulation of Myc, the unfolded protein response, and metabolism

status: Public on Dec 11 2022

city: Burlington

first: Julie

last: Dragon

state: VT

address: 95 Carrigan Dr

department: MMG

country: USA

institute: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE

type: Expression profiling by high throughput sequencing

summary: Multiple myeloma (MM) is an incurable plasma cell malignancy that causes anemia, osteolysis, hypercalcemia, and organ failure, with only a 53% 5-years survival rate. Herein, we present data demonstrating a novel target in MM: the fatty acid binding protein (FABP) family. In clinical data, FABP5 represented a novel biomarker for more aggressive cancer. FABP inhibitors decreased tumor burden in vitro and in vivo and increased survival in immunocompetent and immunocompromised mouse models. FABP5 was the most highly expressed FABP member in myeloma cells, and the most essential for their survival. CRISPR-Cas9 generated FABP5-KO MM.1S cells showed inhibited growth potential. RNA-sequencing and metabolic analysis identified new pathways of action for the FABPs, including MYC, the unfolded protein response (UPR), and metabolic changes. Collectively, our results demonstrate that FABPs comprise a novel, targetable, and safe, therapeutic avenue for MM and other cancers, and suggest inhibiting FABPs may be worthy of further study.

overall_design: MM.1S cells were cultured for 24 hours with 50 μM BMS309403, 50 μM SBFI-26 or the combination in a T25 at a density of 2.5x10^6 cells. mRNA was isolated with Qiazol and miRNeasy Mini Kit with on-column DNAse digestion  according to the manufacturer’s protocol.


title: Single cell analysis of senescent cells of old p16-FDR mice  (lung)

status: Public on Dec 10 2022

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: We report the analysis of single cell based sequencing to understand the cellular and molecular heterogeneity of senescent cell populations in vivo in multiple organ types. The findings will help characterise the roles different cell types play during the aging process.

overall_design: Examination of FACS sorted p16-FDR mCherry+ lung cells collected from aged mice (20-22 months) (n = 2)

first: Virinder

last: Reen

first: Husayn

middle: A

last: Pallikonda

first: Jodie

last: Birch

first: Scott

last: Haston

first: Jesus

last: Gil

first: Juan Pedro

last: Martinez-Barbera


title: Tead1 regulation of β-cells II

status: Public on Dec 14 2022

city: Pittsburgh

first: Vijay

middle: K.

last: Yechoor

state: PA

address: 200 Lothrop Street, BST 1058W

institute: University of Pittsburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Purpose: The goal of this study is to determine the regulatory role of Tead1 in β-cells by analyzing the Tead1 cistrome and open chromatin in β-cells
Methods: Isolated islets from WT C57bl6 mice of 12 weeks of age were flash frozen. For Chip-seq they were fixed with formaldehyde and then after sonication, IP was performed with Anti-Tead1 antibody or the IgG isotype control. For ATAC-seq 100,000 of the frozen nuclei were tagmented. After DNA extraction, library construction, sequencing was performed using Illumina Hi seq2500.
Conclusions: Our study represents the first detailed analysis of the Tead1 cistrome in beta cells.

overall_design: islated islets from 20 mice were pooled  into two separate pools of 10 each and processed for ChIP-seq and concurrent ATAC-seq

first: JeongKyung

last: Lee


title: Extracellular-acidosis restricts one-carbon metabolism and preserves T cell stemness (RNA-seq of sodium lactate samples)

status: Public on Dec 05 2022

city: Chengdu

first: chen

last: li

address: Renmin South Road

country: China

institute: Sichuan Univercity

summary: The accumulation of acidic metabolic waste products within the tumor microenvironment profoundly inhibits effector functions of tumor-infiltrating lymphocytes (TILs). However, it is unclear whether extracellular-acidosis impacts T cell metabolic fitness and differentiation status. Here, we surprisingly found that prolonged acid exposure reprogrammed T cell intracellular metabolism and mitochondrial fitness, and preserved T cell stemness. Elevated extracellular-acidosis impaired methionine uptake and metabolism via downregulating SLC7A5, therefore altering H3K27me3 deposition at the promoters of crucial T cell stemness genes. These changes promoted the maintenance of a “stem-like memory” state and improved long-term in vivo persistence and anti-tumor efficacy. Our findings not only reveal the unexpected roles of extracellular-acidosis in the maintenance of stem-like properties of T cells, but also advance our understanding of the direct involvement of methionine metabolism in T cell stemness.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cultured in control or 10mM lactic acid  conditions for 24 hours, and cultured in control or sodium lactate (10mM or 40mM) conditions for 12 days.

first: Guideng

last: Li

first: Lianjun

last: Zhang

first: Lu

last: Chen

first: Hongcheng

last: Cheng


title: Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution

status: Public on Dec 06 2022

city: Houston

first: Hongjie

state: TX

address: One Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

summary: Aging is accompanied by the functional decline of all tissues, but it is still largely unknown how aging impacts different tissues in a cell type-specific manner. Here, we present the Aging Fly Cell Atlas (AFCA) that includes single-nucleus transcriptomes of the entire Drosophila head and body from both males and females at four different ages. We characterize 162 distinct cell types and present an in-depth analysis of cell type-specific aging features, including changes of cell composition, gene expression, number of expressed genes, transcriptome noise, and cell identity. By combining all aging features, including aging clock models predicting a cell’s age, we find cell-type specific aging patterns. Adipose tissues showed the highest aging score, followed by two cell types from the reproductive system. This transcriptomic atlas provides a valuable resource for the community to study fundamental principles of aging in complex organisms.

overall_design: single nuclear RNA sequencing (snRNA-seq) of 30-, 50-, and 70-day-old Drosophila melanogaster

first: Tzu-Chiao

last: Lu


title: Tead1 regulation of β-cells

summary:
Purpose: The goal of this study is to determine the regulatory role of tead1 in β-cells by analyzing the transcriptomal changes with Tead1 deletion in β-cells

Methods: Isolated islet mRNA profiles of β-cell Tead1 KO mice compared to control floxed mice at 1 year of age were assessed by RNA-seq using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level using the CLC genomic workbench. qRT-PCR validation was performed using SYBR Green assays

Conclusions: Our study represents the first detailed analysis of beta cell transcriptomes following Tead1 deletion in beta cells.

overall_design: islated islet total RNA was used for libraby prep from 3 pooled samples for each of 2 samples for each genotype.


title: Complement lysis affects engraftment and efficacy of human mesenchymal stromal cell-based therapy

status: Public on Dec 07 2022

city: Hong Kong

first: Chun Ming

middle: Stanley

last: Wu

address: 21 Sassoon Road, Pokfulam, Hong Kong SAR, China

country: Hong Kong

institute: University of Hong Kong

summary: Acute Graft-versus-Host-Disease (aGVHD) is a life-threatening complication of allogeneic hematopoietic stem cell transplantation (HSCT). Transplantation of immunosuppressive human mesenchymal stromal cells (hMSCs) can protect against aGVHD post HSCT; however, their efficacy is limited by poor engraftment and survival. Moreover, infused MSCs can be damaged by activated complement, yet strategies to minimise complement injury of hMSCs and improve their survival are limited. Here, we report that hMSCs derived from three tissues divergently protected against aGVHD in a mouse model of this disease. Adipose tissue (AT)-hMSCs preferentially suppressed complement in vitro and in vivo, resisted complement lysis and survived better after transplantation when compared to bone marrow (BM)- and umbilical cord (UC)-hMSCs. AT-hMSCs also prolonged survival and improved the symptoms and pathological features of aGVHD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for different sources of Mesenchymal stem cells (MSCs) cells.

first: Stanley

middle: C

first: Ellen

middle: N

last: Poon

first: Godfrey

last: Chan


title: Extracellular-acidosis restricts one-carbon metabolism and preserves T cell stemness: RNA-seq

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control versus 10mM lactic acid or pH6.6 conditioned human T cells.


title: Single-cell transcriptional atlas revealed that the resident progenitor cell niche functions in TMJ disc development and injury

status: Public on Dec 01 2022

first: Xianni

last: Yang

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

summary: The biological characteristics of the temporomandibular joint (TMJ) disc involve complex changes in cell identity and extracellular matrix (ECM) composition to modulate jaw function during postnatal growth and aging. To better understand this process, we profiled and analyzed 39111 single-cell transcriptomes of TMJ disc cells from mice at different postnatal stages. Our data showed that TMJ disc cells are composed of 9 distinct clusters that can be divided into 4 principal cell types: fibroblasts (FBs), which were the most abundant, endothelial cells (ECs), macrophages (MPhs) and mural cells (MCs). FBs were found to exhibit heterogeneity in terms of biological processes related to ECM secretion and metabolic functions. The ECs and MPhs mainly clustered together in the junction of the anterior disc band and anterior attachment, indicating the potential importance of the inflammatory response in this region in the pathological process of disc diseases. Notably, we found for the first time that resident MCs are the source of the progenitor niche in TMJ discs. The pseudotime trajectory showed that MCs have 2 lineage fates: self-renewal or multidirectional differentiation toward functional cells. In MCs, the NOTCH3 and THY1 signaling pathways were ubiquitously active at all stages, coupled with specific gene expression of Notch3 and Thy1 in MCs, indicating the critical role of these molecules in MC characteristics. As an example, THY1+ cells in TMJ discs showed markedly stronger stem cell characteristics than THY1- disc cells in vitro and ex vivo. In addition, lineage tracing in vivo showed that the Myh11-CreER+ MC lineage proliferated and migrated to coordinate angiogenesis during disc injury but gradually lost its progenitor characteristics and ultimately became a functional cell for disc repair. Overall, we reveal multiple insights into the coordinated and temporal development of TMJ disc cells at different postnatal stages and are the first to describe the resident MC progenitor cell niche during TMJ disc growth and injury.

overall_design: 5 samples from mouse TMJ disc tissues

first: Ruiye

last: Bi

first: Qing

last: Yin

first: Haohan

first: Yiru

last: Wang

first: Qianli

first: Han

last: Fang

first: Peiran

first: Ping

last: Lyu

first: Yi

last: Fan

first: Binbin

last: Ying

first: Songsong

last: Zhu


title: Physiological hypoxia improves growth and functional differentiation of human intestinal epithelial organoids.

status: Public on Dec 02 2022

city: Trondheim

first: Gunnar

middle: Andreas

last: Walaas

address: Prinsesse Kristinas gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

summary: The intestinal epithelium is an immunologically active barrier adapted for a low oxygen environment. Its role is implicated in the pathophysiology of various diseases, including inflammatory bowel disease (IBD) and colorectal cancer. Patient-derived intestinal epithelial organoids (IEOs) mimic the architecture and cell type composition of the intestine and can be used for disease modeling and personalized drug screening. IEOs are usually cultured in atmospheric oxygen concentrations (20% oxygen) without accounting for the physiological hypoxia in the colonic epithelium, where the oxygen concentration range from 3% to <1%.  Previously, we showed that human colon derived IEOs (colonoids) are viable and respond to the pro-inflammatory cytokines TNF and IL17 after short-term (40 hours) cultivation in low (2%) oxygen. We suggested that recapitulating the in vivo physiological oxygen environment (i.e., physioxia) will enhance the translational value of intestinal organoids as pre-clinical models. Here we evaluate whether human colonoids can be established and cultured in physioxia for the entire in vitro culture period and compare growth, differentiation, and immunological responses in colonoids at 2% and 20% oxygen.  Growth from single cells to differentiated organoids was monitored by brightfield images captured throughout cultivation and evaluated with a linear mixed model. Cell composition in undifferentiated vs. differentiated colonoids was identified by immunofluorescence staining of cell markers and single-cell RNA-sequencing. Enrichment analysis was used to identify transcriptomic differences within cell populations. Pro-inflammatory stimuli induced chemokines and Neutrophil gelatinase-associated lipocalin (NGAL) release were analyzed by Multiplex profiling and ELISA. Direct response to a lower oxygen level was analyzed by enrichment analysis of bulk RNA sequencing data.  Colonoids established in a 2% oxygen environment acquired a significantly larger cell mass compared to a 20% oxygen environment. There were significantly more cells with proliferation potential (KI67 positive) in undifferentiated than in differentiated colonoids; and significantly higher expression of cell markers for goblet cells (MUC2) and absorptive cells (MUC2 negative, CK20 positive) in differentiated colonoids. Enteroendocrine cells (CGA positive) were only present in differentiated colonoids. No differences in expression of any of the cell marker proteins were found between colonoids cultured in 2% and 20% oxygen, but the single-cell RNA-sequencing analysis identified differences in the transcriptome within stem-, progenitor- and differentiated cell clusters. Both colonoids grown at 2% and 20% oxygen secreted CX3CL1, CXCL2, CXCL5, CXCL6, CXCL10, CXCL12, CCL20, CCL25, and NGAL upon TNF + poly(I:C) treatment. However, there appeared to be a lower pro-inflammatory response in 2% oxygen.  Reducing the oxygen environment from 20% to 2% in differentiated colonoids altered the expression of genes related to differentiation, metabolism, mucus lining, and immune networks.  Our results suggest that colonoids studies can and should be performed in physioxia when the resemblance to in vivo conditions is important.

overall_design:
Gene expresion data of, untreated, undifferentiated and differentiated intestinal epithelial organoids  from 3 donors (3 undifferentiated biological replicates and 3 differentiated biological replicates).
***Please note that raw data is not provided as Norwegian law does not allow public access to human sequences raw data***

first: Shreya

last: Gopalakrishnan

first: Ingunn

last: Bakke

first: Helene

middle: K

last: Skovdahl

first: Arnar

last: Flatberg

first: Ann

middle: E

last: Østvik

first: Arne

last: Sandvik

first: Torunn

last: Bruland


title: Endothelial-to-osteoblast transition in normal mouse bone development and postnatal growth

first: Guocan

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

summary: To investigate the transcriptome of EC-OSB using Col1a1-GFP/Tie2-cre/Rosa-tdTomatodouble reporter mice, we sorted RFP+/GFP+ cells (EC-OSB) and RFP+ (non-EC-OSB cells) for RNA-seq analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EC-OSB (RFP+/GFP+ cells) and non-EC-OSB (RFP+ cells).

first: Song-Chang

last: Lin

first: Sue-Hwa


title: Extracellular-acidosis restricts one-carbon metabolism and preserves T cell stemness: CUT&Tag

first: chen

last: li

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) for the histone modifications H3K27me3and H3K4me3 in human T cells under control, lactic acid and lactic acid with 800μM methionine conditions.

first: Guideng

last: Li

first: Lianjun

last: Zhang

first: Lu

last: Chen

first: Hongcheng

last: Cheng


title: Extracellular-acidosis restricts one-carbon metabolism and preserves T cell stemness

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

overall_design: Refer to individual Series


title: H3K9me3 Impedes Cell Fate Transition between 2C-Like and Pluripotent States [ChIP-seq]

city: Shanghai

first: Yanping

last: zhang

address: Siping Road 1239

institute: Tongji University

summary: A small subgroup of embryonic stem cells (ESCs) exhibit molecular features similar to those of two-cell embryos (2C).  Multiple chromatin modifiers associated with H3K9 trimethylation (H3K9me3) have been implicated in the mediation of the 2C-like transition. However, it remains elusive how H3K9me3 is remodeled and its association with totipotent cells. Here, we analyze the genome-wide change in H3K9me3 in 2C-like transitions. We revealed that a large fraction of trophoblast-stem-cell specific enhancers undergoes loss of H3K9me3 exclusively in MERVL+/Zscan4+ cells during 2C-like transitions.

overall_design: Embryo stem cells histone profiles and 2 cell like ESCs were generated by deep sequencing, using Illumina GAIIx.

first: Rongrong

last: Le


title: H3K9me3 Impedes Cell Fate Transition between 2C-Like and Pluripotent States


title: Analysis of Polycomb Repressive Complex 1 subunits across cell cycle in pluripotent cells

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

summary: We report ChIP-seq of PRC1 proteins and 4sU-seq, mRNA-seq, Capture-C and 4C-seq data using mouse embryonic stem cells sorted in different phases of the cell cycle.

overall_design: ChIP-seq samples for Ring1b, Rybp, H2AK119ub1 and Cbx7 obtained from cell-cycle sorted FUCCI-mESCs (G1, S, G2 fractions). 4sU-seq data in cell cycle-sorted FUCCI-Ring1bfl/fl and FUCCI-Ring1b-/- mESCs. mRNA-seq data from cell cycle-sorted AID::Ring1b;FUCCI mESCs plated in differentiation media with IAA or without IAA during 6h. Capture-C data from G1 and G2 cell cycle-sorted FUCCI-Ring1bfl/fl and FUCCI-Ring1b-/- mESCs.  4C-seq data from G1 and G2 cell cycle-sorted FUCCI-Ring1bfl/fl and FUCCI-Ring1b-/- mESCs.

first: Helena

middle: G

last: Asenjo

first: Mencía

last: Espinosa

first: Lourdes

last: López-Onieva

first: María

last: Alcazar-Fabra

first: Amador

last: Gallardo

first: Emilia

last: Dimitrova

first: Angelika

last: Feldmann

first: Tomas

last: Pachano

first: Pedro

last: Carmona-Saez

first: Antonio

last: Sanchez-Pozo

first: Álvaro

last: Rada-Iglesias

first: Robert

last: Klose

first: David

last: Landeira


title: H3K9me3 Impedes Cell Fate Transition between 2C-Like and Pluripotent States [RNA-seq]

overall_design: Embryo stem cells transcriptome profiles and 2 cell like ESCs were generated by deep sequencing, using Illumina GAIIx.

last: Zhang


title: Human iPS cell-derived cartilage spatially and functionally replaces nucleus pulposus

status: Public on Nov 28 2022

city: Suita

first: Noriyuki

last: Tsumaki

state: Select One

address: 2-2 Yamadaoka

department: Department of Biochemistry and Molecular Biology

country: Japan

institute: Osaka University, Graduate School of Medicine

summary: Single cell RNA sequencing (scRNA-seq) analysis identified notochordal nucleus pulposus (NP) cells and chondrocyte-like NP cells in NP. Cells in human induced pluripotent stem cell-derived cartilage (hiPS-Cart) corresponded to chondrocyte-like NP cells but not to notochordal NP cells. hiPS-Cart cells changed their profile after implantation into intervertebral disks of nude rats, differentiating into two lineages that are metabolically distinct from each other. However, post-implanted hiPS-Cart cells corresponded to chondrocyte-like NP cells only and did not develop into notochordal NP cells.

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens

overall_design: We performed a single cell (sc)RNA-seq transcriptome analysis of nucleus pulposus (NP) and articular cartilage (AC) of cynomolgus monkey and compared the results with a scRNA-seq analysis of human induced pluripotent stem cell-derived cartilage (hiPS-Cart). Then hiPS-Cart was implanted into nuclectomized spaces of intervertebral disks of coccygeal vertebra in nude rats. Six weeks later, the implants were harvested and subjected to scRNA-seq analysis.

first: Hiroki

last: Hagizawa

first: Saeko

last: Koyamatsu

first: Shigeyuki

last: Shichino

first: Jyunko

last: Yamane

first: Wataru

last: Fujibuchi


title: Transcriptional Profiling of Dorsal Root Ganglion Neurons Following Sciatic Nerve Injury

status: Public on Nov 30 2022

city: Los Angeles

first: Yuyan

last: Cheng

state: CA

address: 695 Charles E Young Dr S Rm 2305

department: Neurology

institute: UCLA

summary: To elucidate transcriptional responses in peripherally injured neurons, we performed RNA-seq of dorsal root gangliona (DRG) sensory neurons at 1 and 5 days following sciatic nerve injury.

overall_design: Sciatic nerve crush was performed by exposing the left sciatic nerve at the level of sciatic notch and crushing with smooth forceps for 30s. L3-6 DRGs from naïve or crushed mice were dissected and vGLUT2-tdTomato labeled neurons were dissociated and selected by fluorescence-activated cell sorting (FACS), then mRNA purified and profiled by sequencing.

first: Vivek

last: Swarup

first: Daniel

last: Geschwind


title: Transcriptional Analysis of the Effects of Integrin-driven Axon Regeneration in the Spinal Cord

summary: To elucidate the mechanisms and down-stream pathways affected by activated integrin expression, we performed transcriptomic analyses of dorsal root gangliona (DRG) sensory neurons transduced with α9 integrin and its activator kindlin-1(α9k1), which enable axons to interact with tenascin-C, or controls, with and without dorsal root/central axotomy.

overall_design: Four experimental groups were created through injection of either AAV5-fGFP or AAV5-α9-V5 + AAV5-kindlin1-GFP into four cervical (left C5-C8) dorsal root ganglia (DRGs) with and without dorsal root crush. The groups were: i) α9-kindlin-1-GFP with dorsal root crush to enable axon regeneration in the spinal cord (α9k1-crush), ii) α9-kindlin-1-GFP with no axotomy in order to examine the effects of activated integrin expression without regeneration (α9k1-naïve), iii) GFP with axotomy to control for the effects of AAV injection and axotomy (GFP-crush), and iv) GFP with no axotomy to control for the effects of AAV injection (GFP-naïve). The DRGs were removed after 8 weeks, at which time many axons are actively regenerating in the spinal cord, and GFP-expressing neurons were dissociated and selected by fluorescence-activated cell sorting (FACS), then mRNA purified and profiled by sequencing.


title: Effects of interleukin-4 receptor blockade in experimental conjunctivitis evoked by skin inflammation

status: Public on Nov 16 2022

city: Cambridge

first: Franck

last: Rapaport

state: MA

address: 350 Water Street

department: PMCB

institute: Sanofi

summary: To characterize conjunctivitis and the effects of IL-4Ra signaling at the transcriptomic level, we performed RNA sequencing (RNA-Seq) on conjunctival tissues in OVA-challenged mice that received isotype or anti-IL-4Ra treatment, as well as control mice that were ocularly challenged with PBS (MC903+OVA/PBS)

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of conjunctiva tissues from three groups (n=5/group)

first: Hongwei

last: Han

first: Joseph

last: Gans

first: Javier

last: Escobedo

first: Srinivas

last: Shankara


title: Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development

status: Public on Nov 17 2022

city: La Jolla

first: Changuk

last: Chung

address: 9500 Gilman Dr

institute: UCSD

summary: Malformations of cortical development (MCD) are neurological conditions displaying focal disruption of cortical architecture and cellular organization arising during embryogenesis, largely from somatic mosaic mutations. Identifying the genetic causes of MCD has been a challenge, as mutations remain at low allelic fraction in brain tissue resected to treat epilepsy. Here, we report genetic atlas from 283 brain resections, identifying 69 mutated genes through intensive profiling of somatic mutations, combining whole-exome and targeted-amplicon sequencing with functional validation and single-cell sequencing. Genotype-phenotype correlation analysis elucidated specific MCD gene sets associating distinct pathophysiological and clinical phenotypes. Moreover, the unique spatiotemporal expression patterns deconvolved from single-nuclear transcriptional sequences of mutated genes in control and patient brains suggest critical roles driving excitatory neurogenic pools during brain development, and in establishing neuronal excitation after birth.

overall_design: A fresh-frozen brain tissue (~50 mg) was placed into a glass dounce homogenizer containing 1 ml cold lysis buffer (0.05% (v/v) NP-40, 10 mM Tris (pH 7.4), 3 mM MgCl2, 10 mM NaCl) and dounce 10 times with a loose pestle and following 10 times with a tight pestle. The homogenate was incubated for 10 min in RT. 9 ml of wash buffer (1% BSA in 1X PBS) was added to the homogenate and filtered by a 30 um cell strainer. The strained homogenate was spun down in 500 g to remove the supernatant. The pellet was resuspended with 5 ml of wash buffer. Straining and spinning down steps were performed once more, and the pellet was resuspended into 500 ul of wash buffer. 10 ul of nuclei resuspension was mixed with counting solution (0.02% Tween 20, 0.1ug/ml DAPI, 1% BSA in 1X PBS) and nuclei density was measured by manual nuclei counting using DAPI signal. The resuspension was diluted by wash buffer to make the desired concentration (800~1000 nuclei/ul). Maximum 2 samples were pooled together targeting 10000 nuclei per reaction. Gel beads emulsion (GEM) generation, cDNA, and sequencing library constructions were performed in accordance with instructions in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1). A library pool was sequenced with 800 million read pairs using NovaSeq 6000.

first: Xiaoxu

last: Yang

last: Gleeson


title: Repurposing Tamoxifen as Potential Host-Directed Therapeutic For Tuberculosis

status: Public on Nov 29 2022

city: Leiden

first: Ralf

last: Boland

address: Einsteinweg 55

department: IBL-ASH-CO

country: Netherlands

institute: Leiden University

summary: The global burden of tuberculosis (TB) is aggravated by the continuously increasing emergence of drug resistance, highlighting the need for innovative therapeutic options. The concept of host-directed therapy (HDT) as adjunctive to classical antibacterial therapy with antibiotics represents a novel and promising approach for treating TB. Here, we have focused on repurposing the clinically used anticancer drug tamoxifen, which was identified as a molecule with strong host-directed activity against intracellular Mycobacterium tuberculosis (Mtb). Using a primary human macrophage Mtb infection model, we demonstrate the potential of tamoxifen against drug-sensitive as well as drug-resistant Mtb bacteria. The therapeutic effect of tamoxifen was confirmed in an in vivo TB model based on Mycobacterium marinum infection of zebrafish larvae. Tamoxifen had no direct antimicrobial effects at the concentrations used, confirming that tamoxifen acted as an HDT drug. Furthermore, we demonstrate that the antimycobacterial effect of tamoxifen is independent of its well-known target the estrogen receptor (ER) pathway, but instead acts by modulating autophagy, in particular the lysosomal pathway. Through RNA sequencing and microscopic colocalization studies, we show that tamoxifen stimulates lysosomal activation and increases the localization of mycobacteria in lysosomes both in vitro and in vivo, while inhibition of lysosomal activity during tamoxifen treatment partly restores mycobacterial survival. Thus, our work highlights the HDT potential of tamoxifen and proposes it as a repurposed molecule for the treatment of TB.

overall_design: Zebrafish embryos and their were manually dechorionated at 24 hours post fertilisation (hpf) and at 30 hpf they were infected by injecting 200 colony forming units of M. marinum strain M into the blood island. After injections embryos were transferred into fresh egg water containing Tamoxifen (10uM), Amiodarone (10uM), or DMSO (equal v/v as treatments) incubated for 2 days at 28,5°C. After the incubation period, infected and uninfected embryos and their controls (10 per sample) were snap-frozen in liquid nitrogen and RNA was isolated for Illumina RNAseq analysis.

first: Matthias

middle: T

last: Heemskerk

first: Gabriel

last: Forn-Cuní

first: Cornelis

last: Korbee

first: Kimberley

middle: V

last: Walburg

first: Jeroen

last: Esselink

first: Carina

last: Carvalho dos Santos

first: Amy

middle: M

last: de Waal

last: van der Hoeven

first: Elisa

last: van der Sar

first: Herman

middle: P

last: Spaink

first: Michiel

last: van der Vaart

first: Mariëlle

last: Haks

first: Annemarie

middle: H

last: Meijer

first: Tom

last: Ottenhoff

first: Alex

middle: S

last: de Ries

first: Jiajun

last: Xie


title: A TLR7-nanoparticle adjuvant promotes broad immune  responses against heterologous strains of Influenza and SARS-CoV-2

status: Public on Nov 14 2022

city: Palo Alto

first: Meng

last: Sun

address: Biomedical Innovations Building 1300, 240 Pasteur Drive

institute: Stanford University

summary: Effective vaccines against viruses such as Influenza and SARS-CoV-2 must elicit a diverse repertoire of antibodies against multiple variant virus strains. However, antibody responses to current vaccines often lack cross-reactivity due to immunodominance. Here, we describe the synthesis of a toll-like receptor 7 agonist (TLR7)-nanoparticle adjuvant, TLR7-NP, constructed from TLR7 agonist-initiated ring-opening polymerization of lactide and self-assembly with poly(ethylene glycol)-b-poly(lactic-co-glycolic acid). TLR7-NP can enhance lymph node targeting, leading to persistent activation of immune cells. When mixed with Alum-adsorbed antigens, this TLR7-NP adjuvant elicited cross-reactive antibodies for both dominant and subdominant epitopes, as well as antigen-specific CD8+ T cell responses, in mice. TLR7-NP adjuvanted influenza subunit vaccine successfully protected mice from heterologous viral challenge. TLR7-NP also enhanced the antibody response to a SARS-CoV-2 subunit vaccine against multiple variants and revealed the mobilization of an antiviral response. We further demonstrate enhanced antigen-specific responses in human tonsil organoids with this novel adjuvant.

overall_design: The human tonsil cells were cultured to form organoids to test the vaccine and the adjuvants. We added a SARS-CoV-2 spike protein RBD nanoparticle (RBD-NP) with or without TLR7-NPs directly to the cultures. We harvested cells on day04 and day09. These cells were barcoded and FACS-sorted the live B cells for single-cell targeted RNA-seq with antibody-seq (CITE-seq). The library was prepared using the BD Rhapsody Targeted mRNA and AbSeq Reagent Kit (Cat. # 633774)and sequenced in one batch. Briefly, cells were captured with beads in microwell plates, followed by cell lysis, bead retrieval, cDNA synthesis, template switching and Klenow extension, and library preparation following the BD Rhapsody protocol. Libraries were prepared for sample tags, targeted mRNA using the customized Immune Response panel, and AbSeq. NovaSeq (Illumina, San Diego, CA) at Novogene USA Inc. (US Davis, CA) completed the sequencing.

first: Qian

last: Yin


title: Next Generation Sequencing Analysis of mouse tumors treated with rMVA

status: Public on Nov 10 2022

city: New York

first: Ning

last: Yang

state: NY

institute: MSKCC

summary: Based on RNA-seq technology, we studies gene expression profiles in tumor lysis isolated from mouse tumors before and after rMVA treatment. We identified differential gene expressions comparing treated tumors with non-treated tumors. The difference of tumor gene expression between WT and STING KO mice were also identified.

overall_design: WT C57B/6J or Sting1gt/gt mice were intradermally implanted with B16 cells at 5x10^5 cells at the left and right sides. After 7-10 days, tumors were injected with rMVA at 4x10^7 pfu. After 1 days, tumors were dissected and digested into single cells. The RNA was extracted and processed into RNA-seq.

first: Adrian

middle: Y

last: Tan

first: Liang

last: Deng


title: Altered microRNA transcriptome in cultured human airway cells upon infection with SARS-CoV-2

status: Public on Nov 13 2022

city: Quebec

first: Patrick

last: PROVOST

state: QUEBEC

address: 2705 , Boulevard Laurier, Bloc T

department: Centre Hospitalier de l'Université Laval (CHUL) - Microbiology, Infectious diseases, Immunology

country: Canada

institute: CRCHU of Québec City - Université LAVAL

type: Non-coding RNA profiling by high throughput sequencing

summary: Numerous proteomic and transcriptomic studies have been carried out to better understand the current multi-variant SARS-CoV-2 virus mechanisms of action and effects. However, they are mostly centered on mRNAs and proteins. The effect of the virus on human post-transcriptional regulatory agents such as microRNAs (miRNAs) involved in the regulation of 60% of human gene activity remains poorly explored. Similar to what we have previously done with other viruses such as Ebola and HIV, in this study we investigated the miRNA profile of lung epithelial cells following infection with SARS-CoV-2. At the 24 and 72 hours post-infection, SARS-CoV-2 did not drastically alter the miRNome. About 90% of the miRNAs remained non-differentially expressed. The results revealed that miR-1246, miR-1290 and miR-4728-5p were the most upregulated over time. miR-196b-5p and miR-196a-5p were the most downregulated at 24 h while at 72 h, miR-3924, miR-30e-5p and miR-145-3p showed the highest level of downregulation. In the top significantly enriched KEGG pathways of genes targeted by differentially expressed miRNAs we found, among others, MAPK, RAS, P13K-Akt and renin secretion signaling pathways. By RT-qPCR, we also showed that SARS-CoV-2 may regulate several predicted host mRNA targets involved in the entry of the virus into host cells (ACE2, TMPRSS2, ADAM17 and FURIN), in renin–angiotensin system (RAS) (Renin, Angiotensinogen, ACE), innate immune response (IL-6, IFN1β, CXCL10, SOCS4) and fundamental cellular processes (AKT, NOTCH, WNT). Finally, we demonstrated by dual luciferase assay a direct interaction between miR-1246 and ACE-2 mRNA. This study highlights the modulatory role of miRNAs in the pathogenesis of SARS-CoV-2.

overall_design: We profiled the miRNome at two time points (24 h and 72 h) following SARS-CoV-2 infection of lung epithelial cells (Calu-3) by RNA-Sequencing (RNA-Seq)

first: Idrissa

last: Diallo

first: Rajesh

last: Jacob

first: Elodie

last: Vion

first: Robert

last: Kozak

first: Karen

last: Mossman

last: Provost


title: Regulation of antigen-specific CD4+ T cells by miR150

status: Public on Nov 08 2022

city: Farmington

first: Antoine

last: Menoret

state: CT

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

summary: Here were provide RNA-seq from C57BL6/J mouse antigen-specific CD4+ T cells (naïve and activated) that have or lack expression of miR150

overall_design: 4 groups - Naïve CD4+ T cells with and without miR150 expression; Activated CD4+ T cells with and without miR150 expression

first: Timofey

last: Karginov

first: Anthony

last: Vella


title: NR2F2 is a key downstream effector of NF1 loss in estorgen receptor positive breast cancer

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven


title: Genome-wide investigation of transcriptional regulation in malaria sporozoite

status: Public on Nov 05 2022

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university


title: Changes in microRNAs during storage and processing of breast milk of Korean mothers

status: Public on Nov 03 2022

city: Seoul

first: Dae Yong

last: Yi

address: Heukseok-ro 102

country: South Korea

institute: Chung-Ang University

summary: Human breast milk (HBM) is the ideal source of nutrients for infants and is rich in microRNA (miRNA). In recent years, expressed breast milk feeding rather than direct breastfeeding is becoming increasingly prevalent for various reasons. HBM requires storage and processing, which can cause various changes in the ingredients. We investigated how the miRNAs in HBM change due to processes often used in real life. HBM samples collected from 10 participants were each divided into 7 groups according to the storage temperature, thawing method, and storage period. And we analyzed the miRNA changes in each group. Significant changes in expression of several miRNAs were confirmed when HBM were heated by microwave immediately after collection, stored at room temperature for 1 week, or frozen for 1 week. Changes in expression were also dependent on the frozen period or thawing method. However, there was no change in the miRNA expression in all samples refrigerated for 1 week. The expression of miRNA can change depending on the diverse processing, storage, and thawing methods of breast milk, and refrigerated storage may be an ideal method to maintain a state of miRNA.

first: Jun

last: Kim

first: Ki-Uk

first: Hyeyoung

last: Min

first: Eun

last: Lee

first: Ji

last: Park

first: Su

first: Sin

middle: W

last: Yun

first: Soo

last: Chae

first: In

last: Lim

first: Jeonglyn

last: Song

first: Insoo

last: Kang

first: Dae


title: Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution

status: Public on Oct 31 2022

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

summary: Human brain development is underpinned by cellular and molecular reconfigurations continuing into the third decade of life. To reveal cell dynamics orchestrating neural maturation we profiled human prefrontal cortex gene expression and chromatin accessibility at single-cell resolution, from gestation to adulthood. Integrative analyses define the dynamic trajectories of each cell type, revealing major gene expression reconfiguration at the prenatal-to-postnatal transition in all cell types followed by continuous reconfiguration into adulthood, and identifying regulatory networks guiding cellular developmental programs, states, and functions. We uncover links between expression dynamics and developmental milestones, characterize the diverse timing of when cells acquire adult-like states, and identify molecular convergence from distinct developmental origins. We further reveal cellular dynamics and their regulators implicated in neurological disorders. Finally, using this reference we benchmark cell identities and maturation states in organoid models. Together, this captures the dynamic regulatory landscape of human cortical development.

overall_design: Single cell transcriptome and chromatin accessibility analysis of normal human prefrontal cortex development from gestation to adulthood. Consists of 29 samples for single nucleus RNA-seq (snRNA-seq) and 17 samples for single nucleus Assay for Transposase-Accessible Chromatin using sequencing (snATAC-seq), including 16 paired samples from the same donors with broad temporal coverage from fetal to adulthood stages of the Brodmann area 8, 9, 10, and 46 prefrontal cortex regions. Also includes 3 cerebral organoid snRNA-seq datasets

first: Charles

middle: A

last: Herring

first: Rebecca

last: Simmons

first: Saskia

last: Freytag

first: Daniel

last: Poppe

first: Sam

last: Buckberry

first: Luciano

last: Martelotto


title: Genome-wide investigation of transcriptional regulation in malaria sporozoite [ChIP-Seq]

first: masao

last: yuda

summary: Sporozoite is the stage in which malaria parasites initially infect the vertebrate host. Elucidation of gene regulation in this stage will promote the investigation of mechanisms of liver infection by this parasite and contribute to development of strategies for preventing the malaria transmission. AP2-Sp is a transcription factor essential for formation of sporozoites or sporogony, which take place in oocysts on the midgut of infected mosquitoes. To understand the role of this transcription factor in the transcriptional regulatory system of this stage we performed ChIP-seq analysis using whole mosquito midguts containing late oocysts as start materials and explore its target genes genome-widely. Target genes were composed of 640 genes, which encompassed various functional categories and were contained genes involved in distinct processes parasites pass through in this stage, from sporogony to development into the liver stage. Furthermore, RNA-seq analysis showed that these genes constituted majority of the genes highly expressed in in this stage.  These results suggested that this TF determines basal pattern of gene expression of this stage by targeting a broad range of genes directly.

overall_design: Mosquito midgut was dissected and fixed immediately in 1% paraformaldehyde solution and kept in it until dissection of all mosquitoes were completed. ChIP-seq was performed in the same procedure as reported previously. Briefly, fixed midguts were sonicated with Bioruptor (Tosho Denki, Yokohama, Japan) in 0.25 ml of lysis buffer. After centrifugation at 4℃, supernatant was subjected to ChIP with anti-GFP antibodies, and harvested DNA fragments were subjected to sequencing. Input DNAs were obtained from the chromatin without IP by the same procedure. Sequencing was performed with SOLID 5500 system (Life Technologies) in experiment 1 and illumine NextSeq system in experiment 2.

first: Masao

last: Yuda

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Tsubasa

last: Nishi

first: Yuho

last: Murata


title: Transcriptome and metabolome analysis reveals anthocyanin biosynthesis pathway associated with poplar (Populus deltoids) leaf color formation

city: Guiyang

first: yunfeng

last: wei

address: Huaxi District, Guiyang City

institute: Guizhou University

summary: Colored-leaf plants are increasingly popular and have been attracting more and more attentions. However, studies about the anthocyanin components and molecular mechanisms of anthocyanin biosynthesis in QHP and ZSY was still unclear. In present study, an integrated metabolite and transcriptome profiling analysis was performed to explore the anthocyanin compositions and the specific regulatory network of  anthocyanin biosynthesis in purple leaves of QHP and ZSY. A total of 39 anthocyanin compounds were detected based on the LC-MS/MS analysis. Of these, 12 cyanidins, 7 pelargonidins, 5 delphindins, and 5 procyanidins are the major anthocyanin compounds, which were significantly differentially accumulated in purple leaves of QHP and ZSY. The major genes associated with anthocyanin biosynthesis, including structural genes and TFs, were differentially expressed in the purple leaves of QHP and ZSY through RNA-seq data analysis, some of which were further assessed by qRT-PCR. Correlation between RNA-seq analysis and metabolite profiling showed that the expression pattern of some differentially expressed genes in anthocyanin biosynthes pathway were closely correlated with the differential accumulation of anthocyanins. In addition, one member of SG5 subgroup of R2R3-MYB TFs, Podel.04G021100, shows a similar expression pattern to some structure genes and closely correlates with sixteen anthocyanin compounds, indicating that the MBY TF (Podel.04G021100) may be involved in the regulation of anthocyanin biosynthesis. The above results not only make us systematic and comprehensive understand the anthocyanin components and corresponding molecular mechanisms of anthocyanin biosynthesis in purple leaves of QHP and ZSY, but also contribute to the promotion and application of anthocyanins in colored-leaf poplars.

first: Xuqian

last: Peng

first: YuJie

last: Ai

first: XiaoJing

last: Wang

first: WeiBing

last: Zhuang


title: Deep RNA-seq of male and female murine sensory neuron subtypes after nerve injury

status: Public on Oct 29 2022

city: Oxford

first: Allison

last: Barry

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

summary: Primary afferent pathophysiology is thought to be a key driver in painful conditions, with dorsal root ganglia (DRG) neurons being well described for their role in driving both acute and chronic pain. These neurons encompass a diverse collection of subtypes that are grouped by various factors, each intrinsically related. These include size, myelination, conduction velocity, projection patterns, end organs, and general function. More recently, these subpopulations have been well documented through single cell and single nuclear RNA-seq in mice and human. This diversity is lost during bulk RNA-seq, due to the consolidation of all subtypes together. In single cell datasets, pseudo-bulk samples can be generated for each cluster, but this relies on a well-defined clustering that can be lost after nerve injury. As such, changes at a subtype level remain unclear in painful states. Here, we address this gap through the deep transcriptional profiles of multiple murine DRG populations in acute and chronic pain states while considering sex differences. We have studied the molecular changes in five populations: Scn10a-expressing DRG, peptidergic and non-peptidergic nociceptors, as well as C-LTMRs and Ntrk2-expressing A-LTMRs. In a naive state, we find subtype specific sexual dimorphism in a small number of genes. This does not translate to a strong interaction of sex and injury, as the injury response seems to be consistent across sexes at the neuronal transcript level.  We also see both stereotypes and unique subpopulation signatures in injured states after nerve injury at both an acute (3 day) and chronic (4 week) timepoint, with notable changes in C-LTMR and NP populations, as well as a distinct transcriptional program in AB-RA + Ad-LTMRs by 4 weeks compared to the other subtypes in the study. This data has been deposited in a searchable database to increase accessibility at https://livedataoxford.shinyapps.io/drg-directory/.

overall_design: Here, we perform comparative gene expression profiling analysis of bulk RNA-seq of murine sensory neuron subtypes at two timepoints after nerve injury (SNI), with sex differences. Sensory neurons were labelled through previously available transgenic lines crossed to fluorescent reporters for FACS, allowing for bulk purified (via FACS) subtype-specific samples.     Once all samples were collected, samples were thawed on ice, vortexed, and randomized into a 384-well plate. Non-directional libraries were prepared together using NEB Ultra low/Smarter library prep, as per manufacture instructions by the Oxford Genomics Centre at the Wellcome Trust Centre for Human Genetics.  Libraries were amplified (21 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers (based on Lamble et al. 2013). Individual libraries were normalized using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation before pooling together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer. Sequencing was performed over three independent runs, and merged after quality control. Paired end sequencing was performed using a NovaSeq6000 platform using the S2/S4 reagent kit v1.5. Samples were sequenced with a 150~bp read length, at a depth of 30 million reads per sample.

first: Georgios

last: Baskozos

first: David

middle: L

last: Bennett


title: Effect of neuron-specific spliced XBP1 (XBP1s) overexpression on gene expression in the mouse brain

status: Public on Oct 22 2022

city: Durham

first: Wei

last: Yang

state: NC

address: 303 Research Drive

department: Anesthesiology

institute: Duke University Medical Center

summary: One major component of cellular proteome resides in the endoplasmic reticulum (ER), the key organelle for protein biogenesis in the secretory pathway. Disruption of ER proteostasis leads to ER stress, which subsequently activates multiple adaptive stress response pathways, collectedly termed as the unfolded protein response (UPR). One UPR branch is mediated by IRE1(inositol-requiring enzyme 1). Activation of the IRE1 UPR branch generates a potent transcriptional factor: spliced X-box–binding protein-1 (XBP1s). Since activation of this UPR branch has been shown to be neuroprotective in brain ischemia/stroke, it is critical to identify the XBP1s-regulated genes in neurons in vivo and thus help determine the molecular mechanisms underlying the beneficial effects exerted by this UPR branch. In this study, we performed RNA-Seq analysis on the hippocampus from XBP1s conditional transgenic mice.

overall_design: Compare gene expression between control mice and XBP1s conditional transgenic (TRE-XBP1s;Camk2a-tTA ) mice (n = 4).


title: Gene expression and VDJ TCR profile of follicular T cells  from  immunized with nuclear proteins and control mice

status: Public on Oct 25 2022

city: Ann Arbor

first: Irina

last: Grigorova

address: 1150 W MEDICAL CENTER DR

department: Microbiology and Immunology

institute: University of Michigan

summary: Analysis of follicular helper and follicular regulatory T cell subsets suggests that acquasition of nuclear proteins by antigen-specififc B cells promotes an increase in follicular regulatory T cells with immunosupressive gene expression profile

overall_design: Four C57BL/6J mice were subcutaneously immunized with SA-DEL (streptavidin linked to biotinylated Duck Egg Lysozyme) in Ribi adjuvant. At 8 d.p.i. two mice were boosted with SA-NucPrs (streptavidin linked to biotinylated nuclear proteins, including bovine nucleosomes, Jo-1, Scl-70, Ro, SmRNP)  in Ribi  and two mice boosted with SA in Ribi for control. Follicular T cells (CD4+PD1hiCXCR5hi) were sorted from draining lymph nodes of mice at day 11 after immunization into PBS + 2% FBS.  Single cell suspensions were subjected to counting and viability checks on the LUNA Fx7 Automated Cell Counter (Logos Biosystems) and diluted to a concentration of 700 -1000 cells/ul. Single cell libraries were generated using the 10x Genomics Chromium Controller with Immune Profiling reagents following the manufacturer’s protocol (10x Genomics). Final library quality was assessed using the LabChip GX (PerkinElmer). Libraries were subjected to paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10x Genomics) was used to align reads and generate count matrices. Barcodes with mitochondrial reads > 5% were removed. Preprocessing, clustering, and dimensionality reduction were performed using Loupe Browser and Loupe V(D)J browser (10x genomics, Cell Ranger). Graph-based clustering of Tfrs were visualized in 2D using UMAP algorithm.

first: Fang

last: Ke


title: APOE4 drives transcriptional heterogeneity and maladaptive immunometabolic responses of astrocytes (Spatial)

status: Public on Oct 20 2022

city: Lexington

first: Joshua

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

institute: University of Kentucky

summary: Apolipoprotein 4 (APOE4), is the strongest genetic risk allele associated with the development of late onset Alzheimer’s disease (AD). Across the CNS, astrocytes are the predominant expressor of Apoe while also being critical mediators of neuroinflammation and cerebral metabolism. APOE4 has been consistently linked with dysfunctional neuro-immunometabolism, however insights into the molecular constituents driving these responses remain unclear. Utilizing complimentary approaches across humanized ApoE expressing mice and isogenic IPS astrocytes, we demonstrate that harboring ApoE4 alters astrocyte immunometabolic response to pro-inflammatory stimuli. Our findings demonstrate that ApoE4-expressing astrocytes acquire distinct transcriptional repertoires at the single-cell and spatially-resolved domains, which driven, in-part, by preferential utilization of the cRel transcription factor. Further, inhibiting cRel translocation abrogated inflammatory-induced glycolytic shift and ultimately resulted in significantly dampened glycolysis-associated metabolites in tandem with mitigating production of multiple pro-inflammatory cytokines. Altogether, our findings elucidate novel cellular underpinnings by which ApoE4 drives maladaptive immunometabolic responses of astrocytes.

overall_design: Male, targeted replacement humanized APOE33 and APOE44 mice were used for these studies. 5mg/kg LPS was administered systemically via IP injection and mice were euthanized 24hrs later.


title: APOE4 drives transcriptional heterogeneity and maladaptive immunometabolic responses of astrocytes (bulk RNA-Seq)

overall_design: Isogenic APOE33 and APOE44 astrocytes (see 10.1016/j.cell.2022.05.017) were seeded in 24 well plate at a density of ~109k cells/well. Cells were treated with vehicle or 3ng/mL IL-1a, 30ng/mL TNF, and 400ng/mL C1q for 4 hours. Following treatment, media was apirated, cells washed with sterile DPBS. Following wash, cells were lysed with RLTplus buffer and RNA harvested per manufacturer's suggested protocol (Qiagen # 74034).


title: APOE4 drives transcriptional heterogeneity and maladaptive immunometabolic responses of astrocytes

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

overall_design: Refer to individual Series


title: Wireless, closed-loop, smart bandage with integrated sensors and stimulators for advanced wound care and accelerated healing

status: Public on Oct 14 2022

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

summary: We quantify the effects of electrical stimulation on murine cells at the cellular and transcriptomic level using single cell RNA-sequencing. We characterize circulating cells and compare them to unstimulated circulating cells.

overall_design: scRNA-seq was performed on murine cells collected from parabiome excisional wounds. Cells labeled as GFP+ were isolated and sequenced to analyze cells in the circulation that hone to the wound upon treatment.

first: Artem

last: Trotsyuk

first: Yuanwen

last: Jiang

first: Zhenan

last: Bao

first: Geoffrey

last: Gurtner


title: MUC1-C IS A MASTER REGULATOR OF MICA/B NKG2D LIGAND AND EXOSOME SECRETION IN HUMAN CANCER CELLS

status: Public on Oct 17 2022

city: Boston

first: Yoshihiro

last: Morimoto

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: MUC1-C regulates expression of  MICA/B NKG2D LIGAND AND enhance EXOSOME SECRETION IN HUMAN CANCER CELLS

overall_design: RNA-seq in colorectal cancer and lung cancer cell lines


title: APOE4 drives transcriptional heterogeneity and maladaptive immunometabolic responses of astrocytes (scRNA-Seq)


title: Obp56h RNA seq

status: Public on Oct 13 2022

city: Greenwood

first: Heather

last: Flanagan-Steet

state: SC

address: 101 Gregor Mendel circle

institute: Greenwood Genetic Center

summary: Insect odorant-binding proteins (OBPs) are members of a rapidly evolving multigene family traditionally thought to facilitate chemosensation. However, studies on Drosophila have shown that members of this family have evolved functions beyond chemosensation, as evident from their expression in reproductive tissues and the brain.  Previous studies implicated diverse functions of Obp56h, a member of the largest gene cluster of the D. melanogaster Obp repertoire. Here, we examined the effect of CRISPR/Cas9-mediated deletion of Obp56h on two fitness phenotypes, resistance to starvation stress and heat stress, and on locomotion and sleep phenotypes. Obp56h-/- mutants show a strong sexually dimorphic effect on starvation stress survival, with females being more resistant to starvation stress than the control. In contrast, Obp56h-/- females, but not males, are highly sensitive to heat stress. Both sexes show changes in locomotion and sleep patterns.  Transcriptional profiling of RNA from heads of Obp56h-/- flies and the wildtype control reveal differentially expressed genes, including gene products associated with antimicrobial immune responses and members of the Turandot family of stress-induced secreted peptides. In addition, differentially expressed genes of unknown function were identified in both sexes.  Genes encoding components of the mitochondrial electron transport chain, cuticular proteins, gene products associated with regulation of feeding behavior (Lst and CCHa2), ribosomal proteins, lncRNAs, snoRNAs, tRNAs, and snRNAs show changes in transcript abundances in Obp56h-/- females. These differentially expressed genes are likely to contribute to Obp56h-mediated effects on the diverse phenotypes that arise upon deletion of this odorant binding protein.

overall_design: 2 genotypes- control and Obp56h null adult fly heads; 2 replicates per sex per genotype

first: Sneha

last: Mokashi

first: Robert

last: Anholt


title: Next Generation Sequencing Analysis of Wild Type and cGAS-/- BMDC infected with MVA or MVAΔE5R

status: Public on Oct 06 2022

first: Ning

summary: Based on RNA-seq technology, we studies gene expression profiles in BMDC before and after MVA or MVAΔE5R infection. We identified genes which expression dependent on cGAS comparing WT and cGAS-/- cells after MVA infection. The difference genes bewteen MVA and MVAΔ5R were also identified.

overall_design: BMDC cells siolated from WT or cGAS-/- mice were infected with MVA or MVAΔE5R at MOI 10 for 6 h.

first: Adrian

last: Tan

first: Liang

last: Deng


title: RNAseq after cortical spreading depolarization (SD)

status: Public on Oct 05 2022

city: Albuquerque

first: Michela

last: Dell'Orco

state: NM

address: 1 University of New Mexico, MSC08 4740

institute: University of New Mexico

summary: The present study aimed to perform an extensive, unbiased RNA sequencing (RNA-seq) analysis to identify biological pathways, as well as related diseases and functions, modified by SD in healthy brains. SDs were induced repetitively (2 hours, 30 min intervals) in healthy, female mice and monitored with intrinsic optical signal (IOS) imaging. SD induction was with either focal application of KCl in C57Bl/6 mice or with optogenetic stimulation in Thy1-ChR2-YFP mice. Two hours after onset of SD, total cortical RNA was extracted and subjected to Illumina paired-end RNA sequencing to identify differentially expressed genes (DEGs; fold change >1.25, p-value <0.05). We identified 101 significantly upregulated genes after KCl-induced SDs and 136 after optogenetic induction; of these 57 (31.7%) genes were in common.

overall_design: SDs were induced repetitively (4 SDs in 2 hours at 30 min intervals) in healthy, 7- to 8-week-old female mice and SDs were confirmed with intrinsic optical signal imaging. SD induction was with either focal application of KCl (NaCl for sham controls, n=6) in C57Bl/6 mice or with optogenetic stimulation (2 mW for 20 seconds) in Thy1-ChR2-YFP heterozygous mice (n=6).

first: William

last: Shuttleworth


title: Transmicron: Accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens

status: Public on Oct 01 2022

city: München

first: Roland

last: Rad

address: Ismaninger Strasse 22

department: Institute of Molecular Oncology and Functional Genomics

country: Germany

institute: Technical University of Munich

summary: Transposon screens are powerful in vivo assays used to identify loci driving carcinogenesis. These loci are identified as Common Insertion Sites (CIS), i.e. regions with more transposon insertions than expected by chance. However, the identification of CIS is strongly affected by biases in the insertion behaviour of transposon systems. Here, we introduce Transmicron, a novel method that differs from previous methods by i) modelling neutral insertion rates based on chromatin accessibility, transcriptional activity, and sequence context, and ii) estimating oncogenic selection for each genomic region using Poisson regression to model insertion counts while controlling for neutral insertion rates. To assess the benefits of our approach, we generated a dataset applying two different transposon systems under comparable conditions. Benchmarking for enrichment of known cancer genes showed improved performance of Transmicron against state-of-the-art methods. Modelling neutral insertion rates allowed for better control of false positives and stronger agreement of the results between transposon systems. Moreover, using Poisson regression to consider intra-sample and inter-sample information proved beneficial in small and moderately-sized datasets. Transmicron is open-source and freely available. Overall, this study contributes to the understanding of transposon biology and introduces a novel approach to use this knowledge for discovering cancer driver genes.

overall_design: A cohort of diffuse large B cell lymphomas (DLBCLs) developed in PB ITP mice (n=30) and SB ITP mice (n = 11) as well as tail tissue as a control tissue (n = 12 for PB and n = 11 for SB).

first: Julia

last: Weber

first: Anja

last: Pfaus

first: Lena

first: Mathias

last: Friedrich


title: How thermal challenges change gene regulation in the songbird brain and gonad: implications for sexual selection in our changing world

city: Bloomington

first: Kimberly

last: Rosvall

state: IN

address: Dept of Biology, Indiana Univ., 1001 E. 3rd St, Jordan Hall

institute: Indiana University

summary: In a rapidly warming world, exposure to high temperatures may impact fitness, but the gene regulatory mechanisms that link sublethal heat to sexually selected traits are not well understood, particularly in endothermic animals. Our experiment used zebra finches (Taeniopygia guttata), songbirds that experience extreme temperature fluctuations in their native Australia. We exposed captive males to an acute thermal challenge (43°C) compared with thermoneutral (35°C) and lower (27°C) temperatures. We found significantly more heat dissipation behaviors at 43°C and heat retention behaviors at 27°C, temperatures previously shown to reduce song production and fertility. Next, we characterized gene expression in tissues important for mating effort – the posterior telencephalon, for its role in song production, and the testis, for its role in fertility and hormone production. Differential expression of hundreds of genes in the testes, but few in the brain, suggest the brain is more buffered from extreme temperatures. Nevertheless, dopaminergic signaling in the brain co-varied with heat dissipation behaviors, providing a mechanism by which temporary thermal challenges may alter motivational circuits for song production. In both brain and testis, we also observed quantitative continuous variation between thermally sensitive gene networks and individual differences in thermoregulatory behavior, indicating that mechanisms of thermal-behavioral tolerance have microevolutionary potential. Taken together, these results suggest that selection for thermal tolerance could impact performance of sexually selected traits, and in turn, sexual selection in a warming world could influence how thermal tolerance evolves.

overall_design: 2 tissues (posterior telencephalon and testis) were collected from 24 male zebra finches exposed to temperatures above (Ta = 43°C), within  (Ta = 35°C), or below their thermoneutral zone (Ta = 27°C);  total RNA was extracted and run on a Nextseq platform.

first: Sara

last: Lipshutz

first: Clara

middle: R

last: Howell

first: Aaron

last: Buechlein

first: Doug

middle: B

last: Rusch

first: Elizabeth

last: Derryberry


title: Gene expression changes in mouse neuroepithelial organoids in response to all-trans retinoic acid.

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

summary: We describe the transcriptomic changes in neuroepithelial organoids in response to all-trans retinoic acid.

overall_design: Organoids were grown via clonal growth from R1 mouse ES cells seeded in Matrigel and cultured in N2B27 medium at 37C, 5% CO2 as described (Meinhardt et al. Stem Cell Reports 2014, Ishihara et al. Methods in Mol. Bio. 2017). At Day 2 (=48 hrs post seeding), organoids were treated with or without 250 nM all trans retinoic acid. Organoids were extracted from the Matrigel at Day 2 or at 8, 18, 30, 42, 54, 66, and 78 hrs post Day 2. Three biological replicates were prepared for each cell population, yielding 45 independent samples for RNA extraction.

first: Elena

last: Gromberg

first: Keisuke

last: Ishihara

first: Elly

last: Tanaka


title: Morphine PVT TRAPSeq

status: Public on Oct 04 2022

city: Philadelphia

first: Julie

last: Blendy

state: PA

address: 125 S 31st St Room 2109A

department: Pharmacology

institute: University of Pennsylvania

summary: Using an oral self-administration paradigm, we have seen morphine  increase neural activity in the Paraventricular Nucleus of the Thalamus (PVT). Morphine binds primarily to Mu Opioid Receptors (MORs), which are highly expressed in the PVT. Translating Ribosome Affinity Purification (TRAP)-Sequencing was conducted on PVT neurons that express MORs

overall_design: 11 days of 0.5mg/ml morphine dissolved in 0.2% saccharin in the drinking water. Just 0.2% saccharin in the drinking water was used as controls

first: Darrell

last: Eacret

first: Elisabetta

last: Manduchi

first: Jonathan

last: Schug


title: DNA methylation entropy as a measure of stem cell replication and aging [RNA-seq]

status: Public on Sep 30 2022

city: Camden

first: Jean-Pierre

last: Issa

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

summary: We report age related gene expression changes in mice in Small intestine, Colon, 3  different aging timepoints (4 month, 12 month, 24 month)

overall_design: RNA was isolated from each section of the intestine at different time point and rRNA-seq was performed.

first: Himani

last: Vaidya

first: Hyeseon

last: Jeong

first: Kelsey

last: Keith

first: Gennaro

last: Calendo

first: Shinji

last: Maegawa

first: Jozef

last: Madzo

first: Jarosalv

last: Jelinek


title: T cell transcriptome after immunofilament or dendritic cell stimulation

city: Nijmegen

first: Lea

last: Weiss

address: Geert Grooteplein Zuid 28, Dept Tumor Immunology, Route 278

institute: Radboud Institute for Molecular Life Sciences, Radboudumc

summary: In this study we developed immunofilaments - nanosized synthetic polymers - for the antigen-specific activation of T cells. Immunofilaments effectively stimulate CD8+ T cells, but it is unclear how well this stimulation compares to natural dendritic cell activation. In this study, we want to investigate the pathways triggered by the immunofilament and the dendritic cell.

overall_design: RNA-seq profiling of sorted viable CD8+ OT-I T cells after different timepoints (0 hrs (only unstimulated), 8 hrs and 22 hrs) of stimulation. Cells were stimulated with either dendritic cells pulsed with the SIITFEKL-antigen or immunofilaments decorated with SIITFEKL loaded major histocompatibility complex (MHC) and Interleukin-2 (IL-2). Similarities and differences after the stimulation with either immunofilaments or dendritic cells were obtained by comparing to the 0 hr unstimulated timepoint.

first: Guido

last: van Mierlo

first: Marjolein

last: Schluck

first: Carl

last: Figdor


title: DNA methylation entropy as a measure of stem cell replication and aging

type: Methylation profiling by high throughput sequencing


title: CXCR1 and Its Downstream NF-κB Inflammation Signaling Pathway as a Key Target of Guanxinning Injection for Myocardial Ischemia/reperfusion Injury

status: Public on Sep 27 2022

city: Tianjin

first: Guangxu

last: Xiao

address: Beihua South Road, JingHai District

institute: Tianjin University of Traditional Chinese Medicine

summary: To investigate the therapeutic effect of Guanxinning injection (GXNI) on myocardial ischemia/reperfusion injury (MIRI) mice, we established MIRI model by ligating the left anterior descending (LAD) coronary artery of mice for 30 minutes and then reperfusion for 24 hours. We then performed RNA-seq on myocardial tissue of mice in the sham group, MIRI group and GXNI treatment group.

overall_design: The significant differential expressed genes were analyzed in myocardial tissue of mice in the sham group, MIRI group and GXNI treatment group.

first: Ming

last: Lyu

first: Yan

last: Zhu


title: Novel insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis.

status: Public on Sep 26 2022

city: Cincinnati

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Pulmonary alveolar microlithiasis (PAM) is an autosomal recessive lung disease caused by a deficiency in the pulmonary epithelial Npt2b sodium-phosphate co-transporter that results in accumulation of phosphate and formation of hydroxyapatite microliths in the alveolar space. The single cell transcriptomic analysis of a PAM lung explant showing a robust osteoclast gene signature in alveolar monocytes and the finding that calcium phosphate microliths contain a rich protein and lipid matrix that includes bone resorbing osteoclast enzymes suggested a role for osteoclast-like cells in the defense against microliths.

overall_design:
Using the 10x Chromium platform sequencing, transcriptomes of single cells from human lung explant of PAM patient and normal human donor lung were analyzed.
Submitter states that raw data will be submitted to dbGap.

first: Yasuaki

last: Uehara

first: Yusuke

last: Tanaka

first: Shuyang

last: Zhao

first: Nikolaos

last: Nikolaidis

first: Lori

last: Pitstick

first: Huixing

last: Wu

first: Jane

middle: J

last: Yu

first: Erik

last: Zhang

first: Yoshihiro

last: Hasegawa

first: John

last: Noel

first: Jason

middle: C

last: Gardner

first: Elizabeth

last: Kopras

first: Wendy

middle: D

last: Haffey

first: Kenneth

last: Greis

first: Jinbang

last: Guo

last: Woods

first: Kathryn

last: Wikenheiser-Brokamp

first: Jennifer

last: Kyle

first: Charles

last: Ansong

first: Steven

last: Teitelbaum

first: Yoshikazu

last: Inoue

first: Göksel

last: Altinişik

first: Francis

middle: X

last: McCormack


title: Dual Chemical Labeling Enables Nucleotide-Resolution Mapping of DNA Abasic Sites and Common Alkylation Damage in Human Mitochondrial DNA

status: Public on Sep 24 2022

city: Riverside

first: Chaoxing

last: Liu

address: 900 University Ave

institute: University of California, Riverside

summary: Understanding the genomic locations of DNA modifications is pivotal for deciphering their roles in gene regulation, mutagenesis, and pathology. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the specificity of labeling and enrichment of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mitochondrial DNA (mtDNA) from cultured human cells under different biological conditions. Also, we demonstrated the broader applicability of the method in sequencing additional DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.

overall_design: We created a dual chemical labeling-assisted sequencing which is a sensitive and specific approach for sequencing AP sites and other DNA modifications. When coupled with parallel sample processing and lesion-specific repair enzymes, DCL-seq is promised to be a powerful approach for sequencing multiple DNA modifications in a biological sample.

first: Wenyan

last: Xu

first: Ching-Hsin

last: Yang

first: Brandon

last: Le

first: Yu

last: Chen

first: Linlin

last: Zhao


title: DNA methylation entropy as a measure of stem cell replication and aging [BiSulfite-seq]

first: Jean-Pierre

last: Issa

summary: We report age related DNA methylation changes in mice in Small intestine, Colon, Heart, Lungs, Liver, Spleen, Kidney and Whole hlood  across 3  different aging timepoints (4 month, 12 month, 24 month). For small intestine and colon there are 4 aging time points ( 4 month, 12 month, 18 month and 24 month)

overall_design: DNA was isolated from each tissue and time point and reduced representation bisulfite sequencing (RRBS) was performed.

first: Himani

last: Vaidya

first: Hyeseon

last: Jeong

first: Kelsey

last: Keith

first: Gennaro

last: Calendo

first: Shinji

last: Maegawa

first: Jozef

last: Madzo

first: Jarosalv

last: Jelinek


title: Epigenetic priming improves salvage chemotherapy in diffuse large B-cell lymphoma via endogenous retrovirus-induced cGAS-STING activation

city: Seoul

first: Junshik

last: Hong

state: Seoul

address: 101 Daehak-ro, Jongno-gu

department: Department of Internal Medicine

institute: Seoul National University

summary: RNA sequencing of low-dose 5-azacytidine treated and PBS treated DLBCL cell lines to measure transcriptional changes in gene and endogenous retrovirus expression

overall_design: RNA sequencing using RNA obtained from low-dose 5-azacytidine treated DLBCL cell lines and PBS treated controls

first: Jun


title: Loss of tight junctions disrupts gastrulation patterning and increases differentiation towards the germ cell lineage in human pluripotent stem cells

status: Public on Sep 23 2022

city: San Francisco

first: Ivana

last: Vasic

state: CALIFORNIA

address: 1650 Owens St

institute: Gladstone Institute

summary: To investigate the role of tight junctions in BMP4 signaling and differentiation, we knocked down TJP1 in human pluripotent stem cells using CRISPRi, and examined gene expression via RNA sequencing of TWT (no KD) and TKD (TJP1 KD) cells in the untreated pluripotent (P) state and after BMP4 differentiation (B).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TWT and TKD cells cultured on standard plates (S) and transwells (T), in the pluripotent (P) and BMP4 differentiated (B) conditions.


title: Gene expression analysis of phage Alderaan infected mycelium from S. venezuelae

status: Public on Sep 22 2022

city: Jülich

first: Tom

last: Luthe

address: Wilhelm-Johnen-Strasse

institute: Forschungszentrum Jülich

summary: To gain insights into the processes underlying adaptation to phage infection, we performed RNA-seq analysis of infected mycelium from the plaque interface of S. venezuelae wild type harvested 24 h and 72 h after infection with Alderaan.

overall_design: Sampling for the gene expression analysis was done with infected and uninfected control samples in duplicates for the two time points 24 h and 72 h on agar plates.

first: Julia

last: Frunzke


title: CCL17 promotes colitis-associated tumorigenesis dependent on the microbiota

city: Planegg

first: Rebecca

last: Metzger

address: Großhaderner Strasse 9

institute: LMU

summary:
• CCL17 expression is increased in colitis-associated colon tumors
• Single-housed CCL17-deficient mice develop fewer tumors dependent on the microbiota
• Reduced tumor numbers coincide with increased apoptosis during tumor initiation

overall_design: Sorted cells from tumors from CCL17 ko mice cohoused with control mice or CCL17 ko mice separately housed after AOM DSS treatment

first: Rupert

last: Öllinger


title: Single Cell Transcriptional and Chromatin Accessibility Profiling on the human adult kidneys with autosomal dominant polycystic kidney disease

status: Public on Sep 18 2022

city: St. Louis

first: Yoshiharu

last: Muto

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

summary: We performed single nucleus ATAC (snATAC-seq) and RNA (snRNA-seq) sequencing to generate paired, cell-type-specific chromatin accessibility and transcriptional profiles of the adult human kidney with autosomal dominant polycystic kidney disease.  snATAC-seq on 5 samples (control1/2/3/4/5) were already done and deposited on GSE151302 as Healthy1-5 (GSM4572187-4572191, respectively)

overall_design: n=8 ADPKD and n=5 control human adult kidney cortex samples were analyzed with snRNA-seq and snATAC-seq (10xGenomics platform). snATAC-seq sequencing of 5 samples (control1/2/3/4/5).

first: Y

first: B

last: Humphreys


title: Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition

status: Public on Sep 12 2022

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary: To understand the effect of SET protein accumulation on genomic function we used different accumulating models, cells and in vivo, that we analyzed with different techinques up to the single level. SET accumulation is known to be caused by the accumulation of its direct interactor SETBP1, when mutated, the causative gene of Schinzel Giedion syndrome. SET has been shown to be able to interfere with histones acetylation, thus we wanted to investigated the functional effect on the genome function and cell fate commitment.

sample_organism:
Danio rerio
Homo sapiens
Mus musculus

platform_organism:
Danio rerio
Homo sapiens
Mus musculus

overall_design: Genomic analysis of human cells (IPSCs, NPCs, Neurons), Zebrafish brain embryo, mouse embryonic and post natal cortex, to understand the effect of SET accumulation on genome function

first: Mattia

last: Zaghi

first: Edoardo

last: Bellini

first: Alessandro

last: Sessa

first: Vania

last: Broccoli


title: Transcriptional responses of CDCA treated Staphylococcus aureus cells

status: Public on Oct 15 2022

city: Beijing

first: Qing

last: Wei

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Analysis of Staphylococcus aureus  treated by CDCA. Staphylococcus aureus cells are evaluated with RNA-seq to understand the genes affected by this antibacterial agent. Our results provide new vision on the mode of action by CDCA.

overall_design: We used three Staphylococcus aureus replicates and three CDCA-treated Staphylococcus aureus replicates to compare the differential gene expression.

first: Yi

last: Wang


title: miR-210 expression is strongly hypoxia-induced in anaplastic thyroid cancer cell SW1736

status: Public on Sep 08 2022

city: Baltimore

first: Bonita

last: Powell

state: MD

address: 733 N Broadway, MRB 8 829

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: Anaplastic thyroid carcinoma (ATC) is a rare but deadly form of thyroid cancer. Hypoxia is frequent in aggressive solid tumors like ATC and can promote resistance to therapy via the hypoxia-inducible factor (HIF) pathway. miR-210 has been previously identified as a direct target of hypoxia-inducible factor 1 (HIF-1) and is upregulated in many solid tumors. Here we show that miR-210 expression is upregulated in ATC cell line SW136 in hypoxia relative to normoxia. Identifying and targeting hypoxic cells is an attractive approach to detecting and treating ATC.

overall_design: ATC cell line SW1736 was cultured in hypoxia (2%O2) or Normoxia (21% O2) for 72hrs.Total RNA was extracted from Hypoxic and Normoxic SW1736 cells for small RNA sequencing.

first: Andrey

last: Turchinovich

first: Kenneth

last: Witwer


title: Differential gene expression between DLD-1 cells lines with moderately and significantly upregulated levels of Snail

status: Public on Sep 03 2022

city: Cambridge

first: Fatima

last: Junaid

address: Puddicombe Way

institute: Cancer Research UK - CI

summary: Using human colon cancer DLD-1 cells, we engineered a cell line with a doxycycline-inducible single-copy of Snail and compared it to an existing EMT models in DLD-1 where Snail was introduced by episome transfection. Induction of the single-copy line (Snail-lo) with doxycycline increased Snail expression to a level similar to that observed in cancer cell lines spontaneously expressing Snail and results in partial EMT.  In comparison, higher levels of overexpression arising from introduction of episomal-Snail (Snail-hi), results in complete EMT.

overall_design: The changes in expression of 84 epithelial-mesenchymal transition (EMT)-associated genes in were measured in Snail-lo and Snail-hi cells using a QIAGEN RT2 Profiler PCR Array Human Epithelial to Mesenchymal Transition and its accompanying data analysis package (QIAGEN PCR Array Data Analysis Software). There were three biological repeats per line.


title: Analysis of red blood cells from rainbow trout Oncorhynchus mykiss infected by Tetracapsuloides bryosalmonae

status: Public on Aug 31 2022

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

summary: The myxozoan Tetracapsuloides bryosalmonae is the causative agent of proliferative kidney disease (PKD) – a disease of salmonid fishes, notably of the commercially farmed rainbow trout Oncorhynchus mykiss. Both wild and farmed salmonids are threatened by this virulent/deadly disease, which is often expressed by swollen kidneys. In order to understand the causes and consequences of the disease, we studied the immune response towards the parasite. To profile the influence of the disease on these cells, we produced a transcriptome of teleost RBCs in health and disease. Compared to erythrocytes originating from healthy fish, PKD fundamentally altered RBCs in their metabolism, adhesion, and response to inflammation.

overall_design: The aim of this work was to characterize the population of RBCs in PKD-diseased trout. We investigated the RBC-specific phenotype that may be a cause or a consequence of the anemia or hypergammaglobulinemia associated with PKD. To this end, we compared the RBC transcriptome of four healthy SPF versus four PKD-diseased rainbow trout using a salmonid-specific microarray.

first: Tomáš

last: Korytář

first: Justin

last: Chan

first: Dirk

last: Koczan

first: Filip

last: Dyčka

first: Amparo

last: Sánchez


title: FOXA1 Shapes the Chromatin State of ILC and Drives Differential Response to Aromatase Inhibitors and Tamoxifen [WGS]

city: Boston

first: Rinath

last: Jeselsohn

address: 450 Brookline Ave, D728

institute: DFCI

summary: Invasive lobular breast cancer (ILC) is the second most common histological sub-type of breast cancer. Although the majority of ILC are strongly hormone receptor positive and are of low-intermediate grade, they present a number of clinical challenges. These challenges include limitations in physical exam and breast imaging for early detection, decreased response to chemotherapy and prospective evidence for differences in the benefit from specific adjuvant endocrine treatment regimens when compared to invasive ductal cancer (IDC). In addition to loss of e-cadherin, ILCs possess genetic alterations that are suggestive of a unique estrogen receptor(ER) axis, including an increase in the frequency of FOXA1 mutations and decrease in GATA3 truncating mutations. We performed a randomized Phase II clinical trial, Palbociclib and Endocrine therapy for Lobular breast cancer Preoperative Study (PELOP), in which patients were stratified by histological subtype and found that the magnitude of the difference between the benefit from letrozole compared tamoxifen is significantly higher in ILC versus IDC. To elucidate the mechanism underlying this divergent response we comprehensively studied the ER axis in experimental models of ILC and IDC and clinical samples and show that ILC harbors a unique ER transcriptional axis that stems from increased FOXA1 chromatin binding and an altered chromatin state. These findings provide insights to the unique pattern of response to endocrine treatment in ILC and mechanisms of resistance to endocrine treatment, and offer new treatment strategies to improve outcomes for patients with this breast cancer subtype."

overall_design: Whole Genome Sequencing of ductal (MCF7 and T47D) and lobular (MDA134 and SUM44) cells using Illumina HiSeq X.


title: FOXA1 Shapes the Chromatin State of ILC and Drives Differential Response to Aromatase Inhibitors and Tamoxifen [GATA3 ChIP-seq]

summary: Invasive lobular breast cancer (ILC) is the second most common histological sub-type of breast cancer. Although the majority of ILC are strongly hormone receptor positive and are of low-intermediate grade, they present a number of clinical challenges. These challenges include limitations in physical exam and breast imaging for early detection, decreased response to chemotherapy and prospective evidence for differences in the benefit from specific adjuvant endocrine treatment regimens when compared to invasive ductal cancer (IDC). In addition to loss of e-cadherin, ILCs possess genetic alterations that are suggestive of a unique estrogen receptor(ER) axis, including an increase in the frequency of FOXA1 mutations and decrease in GATA3 truncating mutations. We performed a randomized Phase II clinical trial, Palbociclib and Endocrine therapy for LObular breast cancer Preoperative Study (PELOP), in which patients were stratified by histological subtype and found that the magnitude of the difference between the benefit from letrozole compared tamoxifen is significantly higher in ILC versus IDC. To elucidate the mechanism underlying this divergent response we comprehensively studied the ER axis in experimental models of ILC and IDC and clinical samples and show that ILC harbors a unique ER transcriptional axis that stems from increased FOXA1 chromatin binding and an altered chromatin state. These findings provide insights to the unique pattern of response to endocrine treatment in ILC and mechanisms of resistance to endocrine treatment, and offer new treatment strategies to improve outcomes for patients with this breast cancer subtype."

overall_design: GATA3 ChIP-seq of ductal (MCF7 and T47D) and lobular (MDA134 and SUM44) cells in hormone deprivided condition (WM) plus estrogen; in duplicates, using Illumina NextSeq500.


title: FOXA1 Shapes the Chromatin State of ILC and Drives Differential Response to Aromatase Inhibitors and Tamoxifen [H3K27ac ChIP-seq]

overall_design: H3K27ac ChIP-seq of ductal (MCF7 and T47D) and lobular (MDA134 and SUM44) cells in hormone deprivided condition (WM) plus estrogen; in duplicates, using Illumina NextSeq500.


title: FOXA1 Shapes the Chromatin State of ILC and Drives Differential Response to Aromatase Inhibitors and Tamoxifen [HiChIP-seq]

overall_design: HiChIP-seq of ductal (MCF7 and T47D) and lobular (MDA134 and SUM44) cells in hormone deprivided condition (WM) plus estrogen using Illumina NovaSeq6000.


title: Analysis of histone antibody specificity directly in sequencing data using siQ-ChIP

city: Grand Rapids

first: Ariana

last: Kupai

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: We previously developed sans spike-in quantitative chromatin immunoprecipitation sequencing (siQ-ChIP), a technique that introduces an absolute quantitative scale to ChIP-seq data. The absolute scale is possible because the IP step of ChIP is a competitive binding reaction and produces a classical binding isotherm when antibody or epitope is titrated. The mathematical model that led to siQ-ChIP also predicts that sequencing samples from along an isotherm can reveal differential preferences of the antibody for specific chromatin regions, if the antibody binds with different strengths to different regions. In this paper, we directly test this prediction with several histone post-translational modification (PTM) antibodies. When titrating these antibodies, we identified on- and off-target interactions directly in ChIP-seq. Antibodies that displayed mostly on-target interactions had small, uniform responses for different regions of chromatin, while antibodies that contained off-target interactions had large, variable responses, indicating differences in binding affinity for different chromatin regions. The generation of an isotherm is essential to perform siQ-ChIP analysis. Therefore, we also present a detailed and simplified wet lab protocol, optimized to reproducibly achieve a binding isotherm. We highlight several benchmarks of success that can be used to gain confidence in ChIP experiments, serving as a guide for the practice of siQ-ChIP. Collectively, these studies demonstrate an optimized siQ-ChIP protocol that can be used to determine histone PTM antibody specificity directly in sample chromatin without any exogenous spike-in reagents and at minimal sequencing depth.

overall_design: HeLa ChIP-Seq

first: Robert

last: Vaughan

first: Scott

last: Rothbart

first: Bradley

last: Dickson


title: Chromatin Accessibility differentiates Invasive Lobular from Invasive Ductal Breast cancer and Dictates Response to Endocrine Treatment

overall_design: ATAC-seq of ductal (MCF7 and T47D) and lobular (MDA134 and SUM44) cells, as well as MDA134 witn and without an shRNA for FOXA1, in hormone deprivided condition (WM) plus estrogen; in duplicates, using Illumina NextSeq500.


title: FOXA1 Shapes the Chromatin State of ILC and Drives Differential Response to Aromatase Inhibitors and Tamoxifen [ER ChIP-seq]

overall_design:
ER ChIP-seq of ductal (MCF7 and T47D) and lobular (MDA134 and SUM44) cells, as well as cells from a pleural effusion of a ILC patient  in hormone deprivided condition (WM) plus estrogen or tamoxifen; in duplicates, using Illumina NextSeq500.

ER ChIP-seq of lobular (MDA134) cells, in hormone deprivided condition (WM) plus estrogen or tamoxifen; in duplicates, using Illumina NextSeq500.


title: FOXA1 Shapes the Chromatin State of ILC and Drives Differential Response to Aromatase Inhibitors and Tamoxifen [FOXA1 ChIP-seq]

summary: Invasive lobular breast cancer (ILC) is the second most common histological sub-type of breast cancer. Although the majority of ILC are strongly hormone receptor positive and are of low-intermediate grade, they present a number of clinical challenges. These challenges include limitations in physical exam and breast imaging for early detection, decreased response to chemotherapy and prospective evidence for differences in the benefit from specific adjuvant endocrine treatment regimens when compared to invasive ductal cancer (IDC). In addition to loss of e-cadherin, ILCs possess genetic alterations that are suggestive of a unique estrogen receptor(ER) axis, including an increase in the frequency of FOXA1 mutations and decrease in GATA3 truncating mutations. We performed a randomized Phase II clinical trial, Palbociclib and Endocrine therapy for LObular breast cancer Preoperative Study (PELOP), in which patients were stratified by histological subtype and found that the magnitude of the difference between the benefit from letrozole compared tamoxifen is significantly higher in ILC versus IDC. To elucidate the mechanism underlying this divergent response we comprehensively studied the ER axis in experimental models of ILC and IDC and clinical samples and show that ILC harbors a unique ER transcriptional axis that stems from increased FOXA1 chromatin binding and an altered chromatin state. These findings provide insights to the unique pattern of response to endocrine treatment in ILC and mechanisms of resistance to endocrine treatment, and offer new treatment strategies to improve outcomes for patients with this breast cancer subtype.

overall_design: FOXA1 ChIP-seq of ductal (MCF7 and T47D) and lobular (MDA134 and SUM44) cells, as well as cells from a pleural effusion of a ILC patient  in hormone deprivided condition (WM) plus estrogen; in duplicates, using Illumina NextSeq500.


title: Role of lamin A in regulation of DNA Damage Response pathways in ovarian cancer

status: Public on Aug 23 2022

city: Kolkata

first: Kaushik

last: Sengupta

state: West Bengal

address: 1/AF Bidhannagar

department: Biophysics and Structural Genomics

country: India

institute: Saha Institute of Nuclear Physics

summary: A-type lamins, the key structural components of the nucleus, are emerging as regulators in the maintenance of nuclear architecture and genome organization. Extensive research for the last two decades has enormously contributed in understanding the roles of lamins in various signaling mechanisms which frequently go awry in neoplasias. It is interesting to know that alteration in lamin A/C expression and distribution drives tumorigenesis thus modifying its expression can be a potent therapeutic approach. One of the important signatures of a cancer cell is its inability to repair DNA damage which befalls due to a number of genomic defects that transform the cells to be sensitive to chemotherapeutic agents. Also, the errors in DNA repair mechanism are accompanied by high replication rate. This genomic and chromosomal instability is the most conventional feature found in cases of high grade ovarian serous carcinoma. Here, we report elevated levels of lamins in OVCAR3 cells (High grade ovarian serous carcinoma cell line) with respect to IOSE (Immortalised ovarian surface epithelial cells) and the altered damage repair machineries in both the cell lines. We have analysed the changes in global gene expression in sequel to DNA damage induced by etoposide in lamin A upregulated ovarian carcinoma background and reported a number of differentially expressed genes associated with pathways conferring cellular proliferation and chemoresistance. We highlight new avenues unravelling the role of an upregulated lamin A in confronting chemically induced genomic instability in the context of ovarian cancer.

overall_design: Comparative gene expression profiling of RNA Sequencing data of DMSO(Vehicle/Mock) treated and Etoposide treated OVCAR3 (High grade ovarian serous carcinoma cell line) cells. All the samples were studied in duplicates.

first: Duhita