title: IRF1 cooperates with ISGF3 or GAF to form de novo enhancers in murine macrophages (RNA-Seq)

first: Carolina

last: Chavez

address: 10833 LeConte Ave

institute: UCLA

summary: Exposure of macrophages to cytokines and pathogen-associated molecular patterns (PAMPs) can alter their subsequent stimulus responses, in part by epigenetic reprogramming. Our previous studies identified dynamic control of NFκB as a specificity mechanism for inducing hundreds of de novo enhancers in murine macrophages. A second set of hundreds of de novo enhancers are associated with the ISRE DNA binding element of the family of interferon regulatory factors (IRFs). In this project, we have dissected the roles of three endotoxin-responsive IRFs in macrophage de novo enhancer formation. While IRF3 was previously hypothesized to be a chromatin remodeling transcription factor, we found that its genetic requirement for enhancer formation (H3K4me1) is indirect, mediated by its role in type I IFN expression which activates the IRF9-containing ISGF3 transcription factor. However, our analysis shows that ISGF3 is unable to trigger enhancer formation on its own – it must cooperate with IRF1. Timecourse analysis of chromatin accessibility by ATAC-seq reveals that IRF1 plays a major role in the early steps of nucleosome eviction, while its partner ISGF3 then reinforces eviction and H3K4me1 deposition on neighboring nucleosomes. Further studies revealed that IRF1 can also cooperate with the type II IFN-induced GAF transcription factor, generating an additional set of IRF1-GAF-specific enhancers. Finally, global gene expression analysis by RNA-seq reveals that these IRF1-dependent enhancers are associated with potentiated expression of nearby genes in response to secondary immune threat exposure. Together our results reveal unexpected combinatorial coordination of IRF transcription factors in epigenomic reprograming to provide innate immune memory in a manner that is restricted to direct pathogen exposure or type II IFN-associated T-cell immunity, but not secondary innate immune stimulation via type I IFN.

overall_design: RNA-seq of bone marrow derived macrophages (BMDMs). Cells were stimulated with either LPS or IFNγ for 8 hours  and re-stimulated with LPS

first: Kelly

last: Lin

first: Alexis

last: Malveaux

first: Quen

last: Cheng

first: Alexander

last: Hoffmann


title: IRF1 cooperates with ISGF3 or GAF to form de novo enhancers in murine macrophages (ChIP-Seq)

status: Public on Feb 14 2024

city: Los Angeles

state: CA

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq for H3K4me1 in bone marrow derived macrophages (BMDMs) stimulated with LPS, IFNβ, or IFNγ.


title: Targeting Stem Cells and Dysplastic Features with Dual MEK/ERK and STAT3 Suppression in Gastric Carcinogenesis

city: Jejusi

first: Hyesung

last: Kim

address: Aran 13 gil, 15

department: Convergence Biomedical Science

country: South Korea

institute: Jeju National University College of medicine

type: Expression profiling by high throughput sequencing

summary: Pre-cancerous metaplasia progression to dysplasiasignificantlyincreases the risk of gastriccancer, and effective targeting strategies forpre-cancerouslesions are currently lacking.Weaimed to identify key signaling pathways critical for stem cell survival and function in dysplasia.Usingmouse and humanmetaplastic and dysplastic organoids, we evaluated responsestoPyrvinium, a putative anti-cancer drug.WhilePyrvinium induced growth arrest in metaplasticorganoids, itinducedcell death in dysplastic organoidsthrough a dual blockade of MEK/ERKand STAT3 signaling pathways. Pyrvinium specifically targeted stem cells andproliferating cellsin dysplastic organoids.Pyrviniumarrestedmetaplasia progression andpromoted repopulationof themousestomach mucosawith normal lineages.Furthermore, Pyrvinium exhibitedsuppressive effects on the growth and survival of human organoids with dysplastic features, through simultaneous blockingthe MEK/ERK and STAT3 signaling pathways.Therefore, ourfindings suggest that Pyrvinium is a promising therapeutic agent for reprogramming the pre-cancerous milieu to prevent of gastric cancer development.

overall_design: To evaluate transcriptomic alterations and identify subpopulations of dysplastic organoids affected by Pyrvinium treatment, we performed single-cell RNA-sequencing using cells from Meta4 organoids treated with either DMSO or Pyrvinium for 1 day before organoids exhibited morphological disruption.

first: Eunyoung

last: Choi


title: Laser Capture Microdissection Provides a Novel Molecular Profile of Human Primary Cutaneous Melanoma

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: Melanoma accounts for the majority of skin cancer related mortality. In-depth molecular analysis of neoplastic melanocytes in whole tissue biopsies is diluted by the inflammatory infiltration, which may obscure gene signatures specific to neoplastic cells. Thus, a method is needed to precisely uncover molecular changes specific to tumor cells from a limited sample of primary melanomas.

overall_design: We performed laser capture microdissection (LCM) and gene expression profiling of patient-derived frozen sections of pigmented lesions and primary cutaneous melanoma.

first: Kristina

last: Navrazhina

first: Samuel

last: Williams

first: Sandra

last: Garcet


title: Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease

city: Bandung

first: Popi

last: Septiani

state: West Java

address: Jl. Ganesha no. 10

department: School of Life Sciences and Technology

country: Indonesia

institute: Institut Teknologi Bandung

type: Non-coding RNA profiling by high throughput sequencing

summary: Cacao (Theobroma cacao) is a highly valuable crop with growing demands in the global market. However, cacao farmers often face challenges posed by black pod disease caused by Phytophthora spp. with P. palmivora as the most dominant. Regulations of various gene expression influence plant resistance to pathogens. One mechanism involves targeting mRNA of virulence genes in the invading pathogens, suppressing their infection. However, resistance also could be suppressed by plant-derived miRNAs that target their own defense genes. The objective of this study is to identify differentially expressed miRNAs in black pod resistant and susceptible Cacao varieties and to predict their targets in T. cacao and P. palmivora transcripts. In our research, 54 known miRNAs from 40 miRNA families and 67 Novel miRNAs were identified. As much as 17 miRNAs were differentially expressed in susceptible variety compared to resistant one, with 9 miRNAs were upregulated and 8 miRNAs downregulated. In T. cacao transcripts, the upregulated miRNAs were predicted to target several genes, including defense genes. The suppression of these defense genes can lead to a reduction in plant resistance against pathogen infection. While in P. palmivora transcripts, the upregulated miRNAs were predicted to target several genes, including P. palmivora effector genes and other important metabolism activities genes. In the future, limiting expression of miRNAs that target T. cacao's defense genes and applying miRNAs that target P. palmivora effector genes hold promise for enhancing cacao plant resistance against P. palmivora infection.

overall_design:
Identifying cacao pod miRNAs in resistant (TS858) and susceptible (Sulawesi 1) varieties with 2 replicates respectively.
Performed miRNA quantification using Rsubread and differentially expressed miRNA analysis using DeSeq2.

first: Karlia

last: Meitha

first: Yonadita

last: Pramesti

first: Devi

middle: U

last: Ningsih

first: Sulistyani

last: Pancaningtyas


title: IRF1 cooperates with ISGF3 or GAF to form de novo enhancers in murine macrophages (ATAC-Seq)

overall_design: ATAC-seq data from murine bone marrow-derived macrophages stimulated with 100ng/mL LPS (12 samples)


title: Nanostring gene expression profiling for markers of Alzheimer's disease in MAPT P301S;cTFEB;HSACre and MAPT P301S male and female mice

first: Constanza

middle: J

last: Cortes

state: California

address: 3715 McClintock Ave

institute: University of Southern California

summary: To assess the potential neuroprotective effects of overexpressing skeletal muscle Transcription Factor EB (TFEB) signaling in the context of age-associated neurodegenerative disease pathologies, we derived cTFEB;HSACre transgenic mice in the MAPT P301S tau hyperphosphorylated background and used the Nanostring nCounter® Alzheimer’s Disease panel to gain more precise insights into disease-relevant transcriptional changes in the hippocampus in both male and female mice with both Tau hyperphosphorylation and skeletal muscle TFEB overexpression. We confirmed significantly reduced transcriptional activation of the nCounter AD microglial activation module through signature scoring.

overall_design: In this study, we utilized 6-month-old male and female MAPT301s;cTFEB;HSACre transgenic and MAPT P301S mouse hippocampi and the Nanostring nCounter® Alzheimer’s Disease panel which directly assesses the expression of 770 genes curated from human and pre-clinical models of AD and robustly captures disease-relevant signatures to examine the effects of overexpressing skeletal muscle TFEB signaling on a target brain region in a mouse model of tau pathology.

first: Allison

last: Birnbaum

first: Kailin

last: Liu

first: Amber

middle: C

last: Nobles


title: scRNAseq of Hematopoietic stem cell populations from human cord blood

city: Barcelona

first: Alfonso

last: Saera-Vila

address: Dr. Trueta 179

country: Spain

institute: Sequientia Biotech

summary:
Single cell transcriptomic profiling (sc RNA-seq) of the two Human Hematopoietic Stem Cell Populations from cord blood:  18LinnegCD34posCD133pos (hereafter CBC1:CD34pos ) and 18LinnegCD34negCD133pos HSCs  (hereafter CBC3:CD34neg).
Purpose: to compare the single cells transcriptomic profiles of the two Human Hematopoietic Stem Cell Populations: CD34pos HSCs and CD34neg   HSCs in order to find unique homing molecules profile.
Results provide insight of highly expressed adhesion molecules in CD34neg   HSCs and their crucial role in interacting with the bone marrow microenvironment.

overall_design: FACS sorted cord blood cells were subjected to scRNAseq analyses

first: Asma

last: Al-Amoodi

first: Jing

last: Kai

first: Yanyan

last: Li

first: Jana

middle: S

last: Malki

first: Abdullah

last: Alghamdi

first: Satoshi

last: Habuchi

first: Jasmeen

last: Merzaban


title: Distinct transcriptomic signatures define febrile malaria depending on initial infective states, asymptomatic or uninfected

city: Nairobi

first: Kelvin

middle: Muteru

last: Kimenyi

department: Biochemistry

country: Kenya

institute: University of Nairobi

summary: Cumulative malaria parasite exposure in endemic regions often results in the acquisition of partial immunity and asymptomatic infections. However, there is limited information on how host-parasite interactions mediate maintenance of chronic symptomless infections that sustain malaria transmission. In this study, we identified uninfected and asymptomatic individuals and followed them until they manifested with symptoms of fever in the presence of malaria parasites and compared the gene expression profiles of peripheral blood mononuclear cells (PBMCs). The host response of asymptomatic children was characterized by downregulation of genes associated with inflammatory responses, compared to uninfected children and children with febrile malaria. They did show greater expression of some genes associated with the humoral response compared to uninfected children. Interestingly, the host responses during febrile infections that followed an asymptomatic infection featured stronger inflammatory responses, whereas the febrile host responses from previously uninfected children featured increased humoral immune responses.

overall_design: Peripheral blood monocytes were taken from a longitudinal cohort of individuals in a malaria endemic region to examine the immune response to infection. In the earliest sample, individuals were classed as either asymptomatically infected with malaria or uninfected. Individuals then received monitoring until they developed a febrile infection, whereupon a second sample was taken. Both paired samples (before and during febrile infection) and single samples from individuals seen in just one of the three states (asymptomatic, uninfected, febrile) are included here.

middle: M

first: Mercy

middle: Y

last: Akinyi

first: Kioko

last: Mwikali

first: Tegan

last: Gilmore

first: Shaban

last: Mwangi

first: Elisha

last: Omer

first: Bonface

last: Gichuki

first: Juliana

last: Wambua

first: James

last: Njunge

first: George

last: Obiero

first: Philip

last: Bejon

first: Jean

last: Langhorne

first: Abdirahman

last: Abdi

first: Lynette

middle: I

last: Ochola-Oyier


summary: Cumulative malaria parasite exposure in endemic regions often results in the acquisition of partial immunity and asymptomatic infections. There is limited information on how host-parasite interactions mediate maintenance of chronic symptomless infections that sustain malaria transmission. Here, we have determined the gene expression profiles of the parasite population and the corresponding host peripheral blood mononuclear cells (PBMCs) from 21 children (<15 years). We compared children who were defined as uninfected, asymptomatic and those with febrile malaria. Children with asymptomatic infections had a parasite transcriptional profile characterized by a bias toward trophozoite stage (~12 hours-post invasion) parasites and low parasite levels, while earlier ring stage parasites were characteristic of febrile malaria. The host response of asymptomatic children was characterized by downregulated transcription of genes associated with inflammatory responses, compared with children with febrile malaria, which may lead to less cytoadherence of more mature parasite stages. Interestingly, the host responses during febrile infections that followed an asymptomatic infection featured stronger inflammatory responses, whereas the febrile host responses from previously uninfected children featured increased humoral immune responses. The priming effect of prior asymptomatic infection may explain the blunted acquisition of antibody responses seen to malaria antigens following natural exposure or vaccination in malaria endemic areas.

overall_design: To investigate the gene expression profiles of Plasmodium falciparum parasite isolates collected from paired asymptomatic [A] and subsequent febrile [F] malaria infections


title: Molecular Atlas of HER2+ Breast Cancer Cells Stimulated with EGF and HRG: Temporal Insights into Mechanisms in Trastuzumab Resistance [ATAC-Seq]

city: La Jolla

first: Shankar

last: Subramaniam

address: 3223 Voigt Dr

department: Bioengineering

institute: University of California San Diego

summary: Trastuzumab therapy in HER2+ breast cancer patients have mixed success owing to acquired resistance to therapy. In this study, we investigate the cellular mechanisms underlying acquired resistance using -sensitive and -resistant cancer cells (BT474 and BT474R) treated with endogenous ligands EGF and HRG, across time. Our measurements probe early receptor organization through microscopy, signaling events through multi-omic measurements and assess the cellular energetic state through mitochondrial measurements. Our integrative analyses of these multimodal measurements highlight differential mechanisms in both cell lines in response to ligands. In BT474, an active PI3K-AKT-mTORC1 signaling contributes to an active mitochondrial bioenergetic state (glycolysis and lipid metabolism) for both ligands EGF and HRG. A HIF1A mediated increase in cellular bioenergetics is also seen. In BT474R, there is a ligand-dependent activation of signaling cascades. In EGF treated BT474R, an EGFR driven IRF1/STAT1/STAT2 activation with likely impact on cellular bioenergetics is seen, whilst an AR mediated alteration of lipid metabolism is pronounced after HRG treatment.

overall_design: We performed qSMLM, RPPA, RNA and ATAC sequencing to dynamically interrogate the cell state as defined by HER2 receptor localization, downstream protein signaling, its transcriptomic landscape and the accessibility of chromatin in response to ligands in BT474 and BT474R cultured cell lines. To capture the temporal dynamics of ligand treatments, samples were sequenced at four timepoints, T0 (baseline, pretreatment only), at 1, 12 and 24hours.  Vehicle/water treated cells at each of the same timepoints were used as their respective controls (Figure 1a). Protein lysates were additionally collected at 30 minutes for RPPA measurements, to capture the phosphorylated protein dynamics All samples for the above measurements were obtained in duplicates (n=2) and differential analyses performed with respect to controls at a given timepoint.  Given the time complexity of qSMLM experiments, T0 was used as baseline control (n=2-3). Sample preparation, extraction, and imaging/sequencing protocols for each of the aforementioned are presented in detail within the Methods sections. Ligand concentrations were based on published studies7–11 and by titration experiments (data not shown).

first: Kavitha

last: Mukund

first: Jackelyn

last: Alva-Ornelas

first: Adam

last: Maddox

first: Divya

last: Murali

first: Darya

last: Veraksa

first: Andras

last: Saftics

first: Jerneja

last: Tomsic

first: David

last: Frankhouser

first: Megan

last: Razo

first: Tijana

last: Jovanovic-Talisman

first: Victoria

middle: L

last: Seewaldt


title: Molecular Atlas of HER2+ Breast Cancer Cells Stimulated with EGF and HRG: Temporal Insights into Mechanisms in Trastuzumab Resistance [RNA-Seq]


title: Molecular Atlas of HER2+ Breast Cancer Cells Stimulated with EGF and HRG: Temporal Insights into Mechanisms in Trastuzumab Resistance

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

overall_design: Refer to individual Series


title: PABPC1L promotes tryptophan metabolism and immune suppression by stabilizing IDO1 in renal cell carcinoma

city: Guangzhou

first: Jiaxing

last: Zhang

state: China

address: 58 Zhongshan 2nd Road

country: China

institute: First Affiliated Hospital of Sun Yat-sen University

summary: The tumor microenvironment (TME) in renal cell carcinomas (RCC) is marked by substantial immunosuppression and immune resistance though highly infiltrated by T cells. There is an urgent need to elucidate tumor immune evasion and to develop novel therapeutic target to boost the efficacy of immune checkpoint blockade (ICB) in RCC. Our study uncovers a mechanism wherein the polyadenylate-binding protein PABPC1L modulates indoleamine2, 3dioxygenase1 (IDO1), a prospective candidate for immunotherapy. PABPC1L, markedly upregulated in RCC, correlates with unfavorable prognosis and resistance to ICB. Overexpressed PABPC1L bolsters tryptophan metabolism and induces T-cell dysfunction by stabilizing IDO1. Conversely, silencing PABPC1L diminishes IDO1 expression, mitigates cytotoxic T-cell suppression, and enhances responsiveness to anti-PD-1 therapy. Our findings underscore PABPC1L's crucial role in facilitating immune evasion in RCC, making it a potential addition to ICB therapy.

overall_design: RNA-sequencing (RNA-seq) of 769-P cells revealed substantial transcriptional alterations upon PABPC1L knockdown

first: Junhang

last: Luo

first: Jiefeng

last: Yang


title: A retroviral link to vertebrate myelination

city: Cambridge

first: Tanay

last: Ghosh

address: Granta Park

department: Cambridge Institute of Science

country: United Kingdom

institute: AltosLabs

summary: Myelin, the insulating sheath that surrounds neuronal axons, is produced by oligodendrocytes in the central nervous system (CNS). This evolutionary innovation, which first appears in jawed vertebrates, enabled rapid transmission of nerve impulses, more complex brains and greater morphological diversity. Here we report that RNA level expression of RNLTR12-int, a retrotransposon of retroviral origin, is essential for myelination. We show RNLTR12-int-encoded non-coding RNA binds to the transcription factor SOX10 to regulate transcription of myelin basic protein (Mbp, the major constituent of myelin) in rodents. RNLTR12-int like sequences (which we nameRetroMyelin) are found in all jawed-vertebrates and we further demonstrate their function in regulating myelination in two different vertebrate phyla (zebrafish and frogs). Our study therefore suggests that retroviral endogenization was a key step in the emergence of vertebrate myelin.

overall_design: Differentiating oligodendrocyte progenitor cells (OPC) were transfected with siRNA against RNLTR12-int/control siRNA (siGENOME, Dharmacon). Transfected cells were kept at differentiating media for 4-5 days. 4 (control) to 3 (siRNLTR12-int)

first: Robin

last: Franklin


title: HO-1 attenuates testicular ischemia/reperfusion injury through activating the phosphorylated c-Jun-miR-221/222-TOX pathway [lncRNA+circRNA]

city: Hangzhou

first: Ning

last: He

state: Zhejiang

address: No. 79 Qingchun Road

department: Department of Urology

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

summary: Heme oxygenase(HO-1) has been shown to protect against I/R injury, but its effects on testicular I/R is very limited. Therefore, this study aims to investigate the effects of HO-1 on testicular I/R and the underlying mechanism.Knockout of HO-1 rats by TALEN technique.Immunofluorescence and immunohistochemistry was used to detect HO-1 nuclear translocation. Flow cytometry was used to detect cell apoptosis and cell cycle.High-resolution miRNA,mRNA sequencing, real-time PCR and western blot were performed to select testicular I/R injury related genes with strong conservation in HO-1 knockout rats.Double luciferase reporter assay was used to verify the relationship between c-Jun and miR-221/222.We found that HO-1 improved the pathological damage caused by testicular I/R in vivo. We verified the nuclear translocation of HO-1 and its protective effect on hypoxia/reoxygenation(H/R) damage in GC-1 cells.And our results indicated that HO-1 protein itself rather than heme breakdown metabolites might play a key role in testicular I/R.Gene sequencing was performed to screen out MiR221/222 and its downstream gene-thymocyte selection associated high mobility group box(TOX). In addition, we found that HO-1 increased phosphorylation of c-Jun in H/R group.We knocked down c-Jun in GC-1 cells and observed a decrease in the expression of miR-221/222.And we found by inhibiting HO-1,we observed a decrease in the expression of c-jun and miR-221/222,which could be rescued by adding c-jun. The dual luciferase reporter assay confirmed the interaction between c-Jun and miR-221/222. Collectively, HO-1 possesses a protective effect on testicular I/R via phosphorylated c-Jun-miR-221/222-TOX pathway.

overall_design: After anesthetizing the HO-1 wild-type(WT) rats or HO-1 knockout(HO-1-/-) rats, the left testicle was twisted clockwise 720°and fixed to the scrotal skin with silk thread. After 2 h of torsion, the testes were allowed to return to their natural position for 3 days,then the animals were sacrificed and testicular tissue was harvested.

first: Bo

last: Xie

first: Bing

last: Cheng

first: Lugeng

first: Yunfu

last: Liu


title: HO-1 attenuates testicular ischemia/reperfusion injury through activating the phosphorylated c-Jun-miR-221/222-TOX pathway [miRNA]

overall_design: After anesthetizing the HO-1 wild-type (WT) rats or HO-1 knockout (HO-1-/-) rats, the left testicle was twisted clockwise 720°and fixed to the scrotal skin with silk thread. After 2 h of torsion, the testes were allowed to return to their natural position for 3 days,then the animals were sacrificed and testicular tissue was harvested.


title: Transcription factor ATMIN facilitates chemoresistance in nasopharyngeal carcinoma

first: Linglong

last: Tang

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center


title: Transcription factor ATMIN facilitates chemoresistance in nasopharyngeal carcinoma [RNA-seq]

summary: Despite the docectaxel-cisplatin-5-fluorouracil (TPF) induction chemotherapy has greatly improved the patients' survival and became the standard of care for advanced nasopharyngeal carcinoma (NPC), some patients could not benefit from this therapy. The mechanism underlying the TPF chemoresistance remains unclear. Here, we identified ATMIN as a chemoresistance gene in response to TPF therapy in NPC patients. We found that USP10 deubiquitinates and stabilizes ATMIN protein. Knockdown of ATMIN inhibits the cell proliferation and facilitates the docetaxel-sensitivity of NPC cells in vitro and in vivo. Mechanistically, RNA-seq combined with ChIP-seq analysis suggests that ATMIN is associated with the cell death signaling. ATMIN transcriptionally activates LCK to facilitate cell proliferation and docetaxel-resistance. Our findings broaden the insight  into the mechanism of chemoresistance in NPC and the USP10-ATMIN-LCK axis provides potential therapeutic targets for the management of NPC.

overall_design: ATMIN is a transcription factor belonging to the zinc finger family. To explore the mechanisms underlying the oncogenic role of ATMIN in NPC, we performed RNA-seq after knocking down of ATMIN with siRNA.

first: Xue-Liang

last: Fang

first: Qing-Jie

last: Li

first: Jia-Yi

last: Lin

first: Cheng-Long

last: Huang

first: Sheng-Yan

first: Xi-Rong

last: Tan

first: Shi-Wei

first: Xun-Hua

last: Zhu

first: Jun-Yan

first: Sha

last: Gong

first: Han

last: Qiao

first: Ying-Qin

first: Jun

last: Ma

first: Yin

last: Zhao

first: Ling-Long


title: Transcription factor ATMIN facilitates chemoresistance in nasopharyngeal carcinoma [ChIP-seq]

overall_design: ATMIN is a transcription factor of the zinc finger family. To explore the mechanism underlying the oncogenic role and potential regulation targets of ATMIN in nasopharyngeal carcinoma, we performed ChIP-seq after over-expressing ATMIN.


title: Probe level meta analysis of microarray data to understand the role of retrotransposable elements in myelination.

first: Tanay

last: Ghosh

type:
Expression profiling by array
Third-party reanalysis

summary:
This study aim to understand the role of retrotransposable elements in myelination
Raw data with accession number GSE11218 and GSE5940 (using Affymetrix expresion GeneChIP Rat Genome 230 2.0 and 230A, respectively) were extracted fromm GEO. Probe level information was extracted using R library rat2302probe (for Rat genome 230 2.0) and rae230aprobe (for rat genome 230A). Unique probe sequence in 230 2.0 and 230A platform were retained and the intersect probes (90507 in number) between two platforms were used for analysis.  Background subtracted raw data were quantile normalized. Probes for which intensity were greater than. sample median level in at least half the arrays for one experimental condition in. a dataset were considered present; absent probes were removed. Further differentially expressed probbes between OL and OPC were identified by using R Bioconductor package 'limma'. P-values were adjusted to correct for multiple testing using FDR (Benjamini-Hochberg). Probes for which the difference between groups were > or = 2 fold and the adjusted P-value<0.05 were considered differentially expressed.

relation:
Reanalysis of: GSM282712
Reanalysis of: GSM282713
Reanalysis of: GSM282714
Reanalysis of: GSM282715
Reanalysis of: GSM282716
Reanalysis of: GSM282717
Reanalysis of: GSM282718
Reanalysis of: GSM282719
Reanalysis of: GSM138218
Reanalysis of: GSM138219
Reanalysis of: GSM138220
Reanalysis of: GSM138221
Reanalysis of: GSM138222
Reanalysis of: GSM138223
Reanalysis of: GSM138224
Reanalysis of: GSM138225
Reanalysis of: GSM138229

first: Robin


title: HO-1 attenuates testicular ischemia/reperfusion injury through activating the phosphorylated c-Jun-miR-221/222-TOX pathway

first: Ning


title: Itaconate suppresses atherosclerosis by impeding inflammation through Nrf2 signaling

city: Ann Arbor

first: Daniel

middle: R

last: Goldstein

state: MI

address: 2800 Plymouth Road

department: Department of Internal Medicine

institute: University of Michigan

summary: Itaconate has emerged as a critical immunoregulatory metabolite. Here, we examined the therapeutic potential of itaconate in atherosclerosis. We found that both itaconate and the enzyme that synthesizes it, aconitate decarboxylase 1 (Acod1, also known as “immune-responsive gene 1”/IRG1) are upregulated during atherogenesis in mice. Here we analzyed the anatomy of atherosclerotic plaques from wildtype and Acod1-/- mice through single cell RNA-seq.

overall_design: Wildtype and and Acod1-/- mice were injected with recombinant PCSK9-AAV intraperitoneally. 1 week after the injection, mice were given western diet for 10 weeks to increase cholesterol level and promote atherosclerosis. Aorta samples with atherosclerotic plaques from WT and Acod1-/- mice were analyzed by single cell RNA sequencing using the droplet based 10X Genomics pipeline.

first: Jianrui

last: Song

first: Yanling

last: Zhang

first: Ryan

last: Frieler

first: Anthony

last: Andren

first: Sherri

last: Wood

last: Tyrrell

first: Jane

last: Deng

first: Costas

last: Lyssiotis

first: Richard

last: Mortensen

first: Morgan

last: Salmon


title: ZFP36 disruption is insufficient to enhance the function of mesothelin-targeting human CAR-T cells

city: Philadelphia

first: David

last: Mai

state: PA

address: 8-189 Smilow Center for Translational Research

institute: University of Pennsylvania

summary: Loss of inflammatory effector function, such as cytokine production and proliferation, is a fundamental driver of failure in T cell therapies against solid tumors. Here, we used CRISPR/Cas9 to genetically disrupt ZFP36, an RNA binding protein that regulates the stability of mRNAs involved in T cell inflammatory function, such as the cytokines IL2 and IFNγ, in human T cells engineered with a clinical-stage mesothelin-targeting CAR to determine whether its disruption could enhance antitumor responses. ZFP36 disruption slightly increased antigen-independent activation and cytokine responses but did not enhance overall performance in vitro or in vivo in a xenograft tumor model with NSG mice. While ZFP36 disruption does not reduce the function of CAR-T cells, these results suggest that singular disruption of ZFP36 is not sufficient to improve their function and may benefit from a multiplexed approach.

overall_design: Differential gene expression analysis of bulk RNA-seq data for primary human T cells transduced with a mesothelin-targeting CAR with genetic disruption of ZFP36 or mock control.

first: Tifara

last: Boyce

first: Aakash

last: Mehta

first: Jordan

last: Reff

first: John

last: Scholler

first: Neil

last: Sheppard

first: Carl

middle: H

last: June


title: Single-cell analysis of uterosacral ligament revealed cellular heterogeneity  in women with pelvic organ prolapse

city: Taiyuan

first: Minna

last: Su

state: Shanxi

address: No.99 Longcheng Street, Xiaodian district

department: department of gynecology and obstetrics

institute: Shanxi Bethune Hospital

summary: Pelvic organ prolapse (POP) markedly affects the quality of life of women, including significant financial burden. Using single-cell RNA sequencing, we constructed a transcriptional profile of 30,452 single cells of the uterosacral ligament in POP and control samples for the first time, and identified 10 major cell types, including smooth muscle cells, endothelial cells, fibroblasts, neutrophils, macrophages, monocytes, mast cells, T cells, B cells, and dendritic cells. We performed subpopulation analysis and pseudo-time analysis of POP primary cells, and explored differentially expressed genes. We verified previous cell clusters of human neutrophils of uterosacral ligaments. We found a significant reduction in receptor-ligand pairs related to ECM and cell adhesion between fibroblasts and endothelial cells in POP. The transcription factors related to the extracellular matrix, development, and immunity were identified in USL. Here we provide insight into the molecular mechanisms of POP and valuable information for future research directions.

overall_design: We performed scRNA-seq of the USL in three patients with POP and one control patient who had undergone hysterectomy for hysteromyoma

first: Xiaochun

last: Liu


title: Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals [RNA-seq]

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

summary: Lactate is present at a high level in the microenvironment of mammalian preimplantation embryos in vivo and in vitro. However, its role in preimplantation development is unclear. Here, we report that lactate is highly enriched in the nuclei of early embryos when major zygotic genome activation (ZGA) occurs in humans and mice. The inhibition of its production and uptake results in developmental arrest at the 2-cell stage, major ZGA failure, and loss of lactate-derived H3K18lac, and the abnormal phenotypes could be recapitulated by overexpression of H3K18R mutation and rescued by addition of Lac-CoA. By profiling the landscape of H3K18lac in human and mouse preimplantation embryos, we show that H3K18lac is enriched on the promoter regions of most major ZGA genes and corelates with their expressions. Taken together, we demonstrate the important role for lactate in major ZGA via H3K18lac, showing a conserved metabolic mechanism underlies preimplantation development of mammalian embryos.

overall_design: RNA-seq libraries were prepared as described previously. Briefly, 5 embryos were used per group, and three replicates were performed for each group. Embryos were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the Phusion Hot Start II High-Fidelity PCR Master Mix (Thermo Fisher). Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Libraries were sequenced using the NovaSeq 6000 (Illumina, San Diego, CA) according to the manufacturer’s instructions.

first: Jingyu

last: Li

first: Weibo

last: Hou

first: Qi

last: Zhao

first: Wei

last: Han

first: Jianzhong

first: Shaorong

last: Gao

first: Guoning

last: Huang

first: Qingran

last: Kong


title: Global transcriptomic analysis of placenta from women with gestational SARS-CoV-2 infection during the 3rd trimester of pregnancy

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

summary: Transcriptomic analysis of the placenta in both maternal and fetal compartments was performed  to investigate the impact of maternal SARS-CoV-2 infection.

overall_design: 16 placental samples from women immediately after term delivery were collected, of which seven had confirmed SARS-CoV-2 infection by PCR before parturition. Extracted total RNA from placental tissues, separately from maternal and fetal compartments, constructed cDNA libraries, and sequenced them to assess mRNA and small RNA expression.

first: Nageswara

last: Rao Boggavarapu


title: Transcriptomics of Chronic Active Antibody-Mediated Rejection of Human Kidney Allografts and Identification of Intragraft Overexpression of Natural Kill Cell Cytotoxicity Gene Set

first: Yajas

last: Shah

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: The enigmatic natural killer (NK) cells mediate spontaneous cell-mediated cytotoxicity and antibody-dependent cell-mediated cytotoxicity via cell surface Fc receptors. The dual functionality of NK cells may enable their participation in chronic active antibody-mediated rejection (CA-ABMR), wherein evidence for complement activation is inconsistent. We RNA sequenced 57 human kidney allograft biopsies to determine whether NK cell cytotoxicity pathway gene set enrichment is an attribute of CA-ABMR. Among the 15,910 intragraft-expressed genes, 60 were uniquely overexpressed in CA-ABMR compared to active antibody-mediated rejection (active-ABMR) or acute T cell-mediated rejection (TCMR), versus no rejection (NR) biopsies. Cell type annotation showed enrichment for T cells and NK cells, and molecular pathways related to T cells and NK cells in CA-ABMR versus active-ABMR biopsies. NK cell cytotoxicity gene set enrichment in CA-ABMR than in ABMR biopsies, but not in TCMR, was confirmed by gene set variation analysis. Cellular deconvolution analysis divulged a higher proportion of NK cells in CA-ABMR compared to active-ABMR, but not in TCMR; immunohistochemistry of 138 consecutive clinically indicated allograft biopsies validated a higher proportion of CD56+ NK cells in CA-ABMR.  Principal component analysis of deconvolved immune cell transcriptomes separated CA-ABMR and TCMR from active-ABMR and NR biopsies. NK cell cytotoxicity pathway gene set was found to be enriched in rejection compared to no rejection biopsies in two publicly available kidney allograft microarray datasets. Altogether, CA-ABMR is exemplified by the overexpression of the NK cell pathway, and, surprisingly, compared to active-ABMR, is exemplified by key gene sets that are similar to TCMR.

overall_design: To study the NK cell cytotoxicity pathway transcriptome in caABMR biopsies (N=15), we selected three comparator groups: active antibody-mediated rejection (aABMR, N=7), acute T cell-mediated rejection (TCMR, N=17), and normal/no rejection (N=18). We excluded mixed rejection, BK virus nephropathy, and other diagnoses. For the purpose of this study, prior to the processing of the samples for RNA isolation, each biopsy was read again by both the transplant pathologists independent of each other and reported based on the Banff 2017 update of the Banff ‘97 classification (2, 3). Subsequently, prior to data analysis, we reviewed the biopsies again; all 57 biopsies still met the criteria for their respective diagnostic categories when reclassified using the Banff 2019 update (4). The biopsies we selected were as pristine as possible in terms of their diagnostic phenotype.

first: Manikkam

last: Suthanthiran

first: Olivier

last: Elemento

first: Thangamani

last: Muthukumar


title: HSP90, a potential common therapeutic target for suppressing skin injury caused by exposure to chemically diverse classes of blistering agents

city: Vestavia Hills

first: Ritesh

last: Srivastava

state: Alabama

address: 1670 University Blvd.

department: Dermatology

institute: University of Alabama at Birmingham

summary: Vesicants such as arsenicals and mustards produce highly painful cutaneous inflammatory and blistering responses, hence, developed as chemical weapons during World War I/II. Here, using lewisite and sulfur mustard surrogates namely phenylarsine oxide (PAO) and 2-chloroethyl ethyl sulfide (CEES) respectively, we defined a common underlying mechanism of toxic action by these distinct classes of vesicants. Murine skin exposure to these chemicals causes skin inflammation and tissue destruction characterized by increase in skin bifold thickness, Draize score, infiltration of inflammatory cells and appearance of apoptotic epidermal and dermal cells. RNAseq analysis identified ~346 inflammatory genes that were commonly altered by both PAO and CEES along with identification of cytokine signaling activation as top canonical pathway. Activation of several of these inflammatory genes and pathways are associated with phosphorylation-dependent activation of heat shock protein 90 (pHSP90). Topical treatment with known HSP90 inhibitors, SNX-5422 and IPI-504 post PAO or CEES skin challenge significantly attenuates these chemical-induced skin damage (reduction in overall skin injury and clinical scores). In addition, highly upregulated inflammatory genes Saa3, Cxcl1, Ccl7, IL-6, Nlrp3, Csf3, Chil3 etc. by both PAO and CEES, significantly diminished by the treatment with these HSP90 inhibitors. These drugs not only reduced PAO or CEES-induced pHSP90 expression but also its client proteins NLRP3, pP38 and expression of their targeted inflammatory genes. These data confirm a critical role of HSP90 as a shared underlying molecular signaling of toxicity by these two distinct vesicants and provide effective and novel medical countermeasure to suppress vesicants pathogenesis.

overall_design: Analysis of RNAseq data for mouse skin exposed with either vehicle (control) or chemicals phenylarsine oxide (PAO) or 2-chloroethyl ethyl sulfide (CEES). We also tested effects of SNX-5422, a HSP90 inhibitor on PAO or CEES-altered genes.

middle: K

first: Suhail

last: Muzaffar

first: Jasim

last: Khan

first: David

last: Crossman

first: Mohammad

last: Athar


title: Ongoing Production of Tissue-Resident Macrophages from Hematopoietic Stem Cells in Healthy Adult Macaques [RNA-seq]

city: Bethesda

first: Jason

last: Brenchley

state: MD

address: 4 Center Drive

institute: NIAID

summary: To understand the ontogeny and longevity of tissue-resident macrophages in nonhuman primates (NHPs), we employ a model of autologous hematopoietic stem progenitor cell (HSPC) transplantation with HSPCs genetically modified to be marked with clonal barcodes, allowing for subsequent analysis of clonal ontogeny.

overall_design: Macrophages from animals that had been transplanted with barcode- and GFP-labeled stem cells were compared with non-GFP macrophages and macrophages from control, unmanipulated animals.

first: Andrew

last: Rahmberg

first: Chuanfeng

last: Wu

first: Taehoon

last: Shin

first: So

middle: G

last: Hong

first: Luxin

last: Pei

first: Tovah

middle: E

last: Markowitz

first: Heather

middle: D

last: Hickman

first: Cynthia

last: Dunbar


title: RNF185 control of COL3A1 expression impacts prostate cancer migration and metastatic potential

first: Ze'ev

middle: A.

last: Ronai

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: RNF185 is a RING finger domain-containing ubiquitin ligase implicated in ER associated degradation. Analysis of prostate tumor patient data revealed a negative correlation between RNF185 expression and prostate cancer progression and metastasis. Likewise, several prostate cancer cell lines exhibited greater migration and invasion capabilities in culture, upon RNF185 depletion. Subcutaneous inoculation of mouse prostate cancer MPC3 cells that stably express shRNA against RNF185 into B6 mice, resulted in larger tumors and more frequent lung metastases. RNA-sequencing and Ingenuity Pathway Analysis identified wound healing and cellular movement among the most significantly upregulated pathways in RNF185-depleted prostate cancer cells, compared with control. Gene Set Enrichment Analyses that were performed in both patients harboring low RNF185 expression, and in RNF185-depleted cell lines, confirmed deregulation of genes implicated in EMT. Among those, COL3A1 was identified as the primary mediator of RNF185 ability to impact the migration phenotype. Correspondingly, enhanced migration of RNF185 KD prostate cancer cells was abolished upon COL3A1 inhibition.  Taken together, our results identify RNF185 as gatekeeper of prostate cancer metastasis, in part by its control of COL3A1 transcription.

overall_design: Gene expression comparison of  RNF185 KD and control in MPC3 cell line using RNA-seq.

first: Benjamin

last: Van Espen

first: Ze’ev

middle: A


title: The effects of epicardial-specific deletion of Sox9 on parietal mitral valve leaflet development

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: The overall goal of this study is to determine the transcriptomic consequences of the absence of epicardial-derived cells in the parietal leaflets of the atrioventricular valves as a consequence of epicardial deletion of Sox9.

overall_design: Isolated parietal mitral valve leaflets from 5 biological replicates of control (Sox9 fl/fl) and 4 littermate epicardial-knockout (Wt1-cre; Sox9 fl/fl) mice at postnatal day 5 were compared by RNA-seq.

middle: B

last: Harvey

first: Andy

last: Wessels


title: RNA-seq of Yra1 associated mRNAs

city: Davis

first: Ben

last: Montpetit

address: One Shields Ave

department: Viticulture and Enology

institute: University of California, Davis

summary: Gene expression results from mRNA - RNA-binding protein (RBP) interactions within messenger ribonucleoprotein (mRNP) particles. We identified heterogeniety of nuclear mRNP composition involved in mRNA biogenesis and export with different occupancy and stoichiometry of RNA-binding proteins. Especially, mRNA export adopter protein Yra1 showed large variation of its stoichiometry on single mRNPs. We identified stoichiometry of Yra1 in the nuclear cap binding complex (Cbp80) bound mRNPs and it can be dissected into two categories (one and multiple Yra1 bound mRNPs). Multiple Yra1 containing mRNPs specifically co-occupied with THO complex (Hpr1). To investigate gene dependency to form different Yra1 stoichiometry mRNPs, we performed RNA-IP experiment for Yra1 with two step purification by Cbp80/Yra1 and Hpr1/Yra1.

overall_design: RNA-seq of Cbp80/Yra1 and Hpr1/Yra1 co-occupied mRNPs isolated by two-step pulldown of Cbp80/Yra1 and Hpr1/Yra1 as well as total RNA isolated from pre-pulldown cell lysate. For the first pulldown, mRNPs are isolated by protein A (PrA) tagged Cbp80 or Hpr1. No PrA tagged strain was used as negative control. The isolated mRNPs are further selected by Yra1 pulldown to analyze Yra1 bound mRNPs.

first: Ryuta

last: Asada

last: Dominguez


title: Protective Effects of Apigenin on the Brain Transcriptome with Aging in Mice

city: Fort Collins

first: Alyssa

middle: N

last: Cavalier

state: CO

address: 1582 Campus Delivery, Moby Reception

department: Health and Exercise Science

institute: Colorado State University

summary:
Age is the primary risk factor for many chronic diseases and cognitive decline during brain aging may increase dementia risk. Hallmarks of brain aging including neuronal dysfunction and glial contribute to reduced cognitive function, and there is a persistent lack of effective treatments. Bioactive plant compounds called “nutraceuticals” can target age-related cellular processes and may protect cognitive function. Apigenin is a flavone found in plants such as chamomile and can inhibit hallmarks of aging such as cellular senescence, mitochondrial dysfunction, and impaired proteostasis. However, the underlying mechanisms of apigenin in the brain are not fully understood.
Here, we characterized brain transcriptome changes in young and old mice given apigenin in drinking water and examined potential mechanisms in human astrocytes. Consistent with previous studies, we observed improved novel object recognition in old mice treated with apigenin versus old controls. Transcriptome analyses in old controls found differentially expressed genes related to immune responses, inflammation, and cytokine regulation versus young. Fewer differences were observed in old apigenin-treated versus old controls, but these changes were related to development, behavior, and antiviral responses. The majority of upregulated genes in old mice were downregulated with apigenin treatment and associated with immune responses. Similarly, the genes that were reduced with aging, but increased in old apigenin-treated mice were related to pathways important for neurological function/disease, cellular maintenance, and homeostatic signaling. We also found that glial cells drove the majority of the transcriptome differences with aging and apigenin-treatment. To explore the mechanism of action for apigenin in glial cells, we treated replicatively aged astrocytes with apigenin and observed reduced markers of inflammation and cellular senescence. Collectively, our data support the role of apigenin as a protector of cognitive and neuronal function protectant through the suppression of neuroinflammatory genes and proteins and may be especially important in non-neuronal cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of whole brain tissue from young and old C57BL/6N mice

first: Thomas

last: LaRocca


title: Epigenetic Regulation of Ameloblast Differentiation by HMGN Proteins

first: Bing

last: He

address: 30 Convent Dr MSC 4370

institute: NIDCR/NIH

summary:
To investigate the molecular mechanism of nucleosomal binding proteins HMGN regulating ameloblast differentiation
We performed RNA-seq analysis of dental epithelium cells that were dissected from WT and DKO (Hmgn1-/-; Hmgn2-/-) mouse molars at three developmental stages.

overall_design: Compare gene expression profile of WT and DKO dental epithelium cells.

first: Michael

last: Bustin


title: Gene expression analysis of yeast grown at 25, 30 and 37°C

summary: Differentially expression analysis to evaluate transcriptome comparing among 25, 30 and 37°C grown yeast cells.

overall_design: Tota RNA isolated from yeast cells grown in 25, 30 and 37°C.

first: Andrew


title: Distinct transcriptomic responses to Ab plaques, neurofibrillary tangles, and APOE in Alzheimer’s disease

city: Ludwigshafen

first: Astrid

last: Wachter

address: Knollstrasse

country: Germany

institute: AbbVie Deutschland GmbH & Co. KG

summary:
INTRODUCTION: Omics studies have revealed that various brain cell types undergo profound molecular changes in Alzheimer’s disease (AD) but the spatial relationships with plaques and tangles and APOE-linked differences remain unclear.
METHODS: We performed laser capture microdissection of Ab plaques, the 50mm halo around them, tangles with the 50mm halo around them, and areas distant (>50mm) from plaques and tangles in the temporal cortex of AD and control donors, followed by RNA-sequencing.
RESULTS: Ab plaques exhibited upregulated microglial (neuroinflammation) and downregulated neuronal (neurotransmission/energy metabolism) genes, whereas tangles had mostly downregulated neuronal genes. Ab plaques had more differentially expressed genes than tangles. We identified a gradient Ab plaque>peri-plaque>tangle>distant for these changes. AD APOEe4 homozygotes had greater changes than APOEe3 across locations, especially within Ab plaques.
DISCUSSION: Transcriptomic changes in AD consist primarily of neuroinflammation and neuronal dysfunction, are spatially associated mainly with Ab plaques, and are exacerbated by the APOEe4 allele.

overall_design: Abeta plaques, the 50um halo around them, tangles with a 50um halo around them, and areas distant (>50um) from plaques and tangles in the temporal cortex of 10 Alzheimer's disease cases (n=5 APOEe4/e4, n=4 APOEe3/e3, and n=1 APOEe3/e4) were profiled, along with 8 age- and sex-matched control donors

first: Sudeshna

last: Das

first: Zhaozhi

last: Li

first: Srinija

last: Alla

first: Ayush

last: Noori

first: Aicha

last: Abdourahman

first: Joseph

last: Tamm

first: Maya

last: Woodbury

first: Robert

middle: V

last: Talanian

first: Knut

last: Biber

first: Eric

last: Karran

first: Bradley

middle: T

last: Hyman

first: Alberto

last: Serrano-Pozo


title: Activation of Hydroxy-carboxylic Acid Receptor 1 effect on cardiomyocytes

city: Nantong

first: Mengkang

last: Fan

state: Jiangsu

address: Xisi Road No.20

institute: Affiliated Hospital of Nantong University

summary:
Our aim is to explore the effect of Hydroxy-carboxylic Acid Receptor 1 on cardiomyocytes.  Neonatal rat cardiomyocytes (NRCMs) were isolated and cultured. Subsequently, NRCMs were treated with the agonist of Hydroxy-carboxylic Acid Receptor 1 (HCAR1), 3Cl-HBA at 40 μM for 48 h(HBA1,HBA2 and HBA3)  or DMSO as control(C1,C3 and C3). RNA was extracted using the KAPA RiboErase RNA-Seq kit (Roche, Basel, Switzerland), and was analysed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) for quality control. The libraries were sequenced on an Illumina HiSeq X Ten platform.  DESeq2 was used to analyse RNA-seq data.
Neonatal rat cardiomyocytes (NRCMs) were isolated and cultured. Subsequently, NRCMs were treated with the agonist of Hydroxy-carboxylic Acid Receptor 1 (HCAR1), 3Cl-HBA (40 μM for 48 h) or DMSO as control. RNA was extracted using the KAPA RiboErase RNA-Seq kit (Roche, Basel, Switzerland), and was analysed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) for quality control. The libraries were sequenced on an Illumina HiSeq X Ten platform.

overall_design: Lihong, Yao

first: Hongzhuan

last: Sheng


title: Transcriptomics of Marburg virus-infected proximal tubular cells

city: Frankfurt am Main

first: Benjamin

middle: Florian

last: Koch

address: Theodor-Stern-Kai 7

department: Nephrology

institute: Goethe University Hospital

summary: Marburg virus, a member of the Filoviridae, is the causative agent of Marburg virus disease (MVD), a hemorrhagic fever with a case fatality rate of up to 90%. Acute kidney injury is common in MVD and is associated with increased mortality, but its pathogenesis in MVD remains poorly understood. Interestingly, autopsies show the presence of viral proteins in different parts of the nephron, particularly in proximal tubular cells (PTC). These findings suggest a potential role for the virus in the development of MVD-related kidney injury. To shed light on this effect, we infected primary human PTC with Lake Victoria Marburg virus and conducted transcriptomic analysis at multiple time points. Unexpectedly, infection did not induce marked cytopathic effects in primary tubular cells at 20 and 40 hours post infection. However, gene expression analysis revealed robust renal viral replication and dysregulation of genes essential for different cellular functions. The gene sets mainly downregulated in PTC were associated with the targets of the transcription factors MYC and E2F, DNA repair, the G2M checkpoint, as well as oxidative phosphorylation. Importantly, the downregulated factors comprise PGC-1α, a well-known factor in acute and chronic kidney injury. By contrast, the most highly upregulated gene sets were those related to the inflammatory response and cholesterol homeostasis. In conclusion, Marburg virus infects and replicates in human primary PTC and induces downregulation of processes known to be relevant for acute kidney injury as well as a strong inflammatory response.

overall_design: Analysis of MARV (strain musoke-80)-infected primary human proximal tubular cells

middle: F

first: Olga

last: Dolnik


title: Regionally defined stem cell growth directs cell fate during intestinal nutrient adaptation

city: Canterbury

first: Jerome

last: Korzelius

state: Kent

address: Ingram Building, University of Kent

institute: University of Kent

summary: The adult intestine is a regionalized organ, whose size and cellular composition is adjusted in response to nutrient status. This involves dynamic regulation of intestinal stem cell (ISC) proliferation and differentiation. How nutrient signaling integrates with mechanisms controlling cell fate to achieve regional changes in intestinal cell composition remains unclear. Here we show that nutrient adaptation involves highly region-specific control of intestinal cell size, number and differentiation. Our data uncovered a mechanism by which mTOR complex 1 activation increases ISC size in a region-specific manner. This promotes Delta expression to direct cell fate towards the absorptive enteroblast lineage, while inhibiting secretory enteroendocrine cell differentiation. Thus, ISC size acts as an early fate determinant allowing regional control of intestinal cell differentiation in response to nutrition.

overall_design: We compared RNA-Seq profiles of G1 and G2  ISCs expressing CFP/YFP-Fucci using FACS sorting and RNA isolation from sorted G1 (CFP) and G2 (CFP+YFP) cells

first: Jaakko

last: Mattilla

first: Arto

last: Viitanen

first: Gaia

last: Fabris

first: Ville

last: Hietakangas


title: Gene expression profile at single cell level of Min6 cells (GCs) from CRISPR-Cas9 edited cells

city: Beijing

first: Gongxin

last: Peng

address: NO.5 Dongdan Santiao

institute: Peking Union Medical College

summary: Single cell RNA sequencing (scRNA-seq) was used to find the key potassium channels in insulin secretion.

overall_design: We used a system involving CRISPR–Cas9-mediated knockout of all 83 K+ channels and scRNA-seq in Min6 β cell line to identify genes associated with insulin secretion.

first: Ru-Xuan

last: Zhao

first: Jing

last: Lu

first: Juan-Juan

last: Zhu

first: Ting-Ting

last: Shi

first: Feng-Ran

last: Xiong

first: Ying-Chao

last: Zhang

first: Gong-Xin

first: Jin-Kui

last: Yang


title: Combined inhibition of TOP1 and PARP: a synergistic therapeutic strategy for PTEN-deficient glioblastoma

city: BETHESDA

first: Zachary

last: Sergi

address: 37 CONVENT DR

department: Neuro-Oncology Branch

institute: National Cancer Institute

summary: Deletions or loss-of-function mutations in phosphatase and tensin homolog (PTEN) are common in glioblastoma (GBM) and have been associated with defective DNA damage repair. Here we investigated whether PTEN deficiency presents a vulnerability to a simultaneous induction of DNA damage and suppression of repair mechanisms by combining topoisomerase I (TOP1) and PARP inhibitors. Patient-derived GBM cells and isogenic PTEN-null and PTEN-WT glioma cells were treated with LMP400 (Indotecan), a novel non-camptothecin TOP1 inhibitor alone and in combination with a PARP inhibitor, Olaparib or Niraparib. RNAseq analysis was performed to identify treatment-induced dysregulated pathways. We found that GBM cells lacking PTEN expression are highly sensitive to LMP400, while rescue of the PTEN expression reduces sensitivity to the treatment. Combining LMP400 with Niraparib leads to synergistic cytotoxicity by inducing G2/M arrest, DNA damage, suppression of homologous recombination (HR)-related proteins and activation of caspase 3/7 activity significantly more in PTEN-null cells compared to PTEN-WT cells. LMP400 and Niraparib are not affected by ABCB1 and ABCG2, the major ABC drug efflux transporters expressed at the blood-brain barrier (BBB), thus suggesting that these drugs should penetrate the BBB. Animal studies confirmed both an anti-glioma effect and sufficient BBB penetration to prolong survival of mice treated with the drug combination. In conclusion, our findings provide proof of concept for the combined treatment with LMP400 and Niraparib in a subset of GBM patients with PTEN deficiency.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GSC827 cells treated with LMP400, Olaporib, combination treatment, or untreated. Each group was comprised of 2 biological replicates.

first: Zach

first: Madison

last: Butler

first: Parthav

last: Jailwala

first: Vishal

last: Koparde

first: Yin

last: Da


title: Gene expression profiling of white bass when fed fish meal or fish meal replacement diets

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: White bass (Morone chrysops) are a popular sportfish throughout the southern United States, and one parent of the commercially successful hybrid striped bass (M. chrysops x M. saxatilis).  Currently, white bass are cultured using diets formulated for other carnivorous fish, such as largemouth bass (Micropterus salmoides) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-Cision). Significant differential expressed genes and gene ontology of pairwise comparisons between control diet and each test diet are presented and discussed.

overall_design: A total of 54 liver tissue samples from white bass were used in this study. Juvenile fish (approximately 40 g each) were placed in replicate tanks (n=3) and fed either a control or test diet over a 60-day period. Then, three fish from each tank (n=9 total per control or test diet) were collected and liver extracted for RNA-seq.

middle: W

first: Anna

last: Rawles

first: Carl

last: Webster


title: Integrative Transcriptomic and Metabolomic Profiling Unravels Anti-Apoptotic and Anti-Inflammatory Properties of Qing-Jin-Hua-Tan Decoction in Chronic Obstructive Pulmonary Disease

city: Chengdu

state: Sichuan

address: No.33, Mashi Street, Wenjiang District

institute: Chengdu Fifth People's Hospital

summary:
Qing-Jin-Hua-Tan decoction (QJHTD) is a classic traditional Chinese medicine (TCM) prescription that has proven appropriate for the treatment of inflammatory lung diseases including chronic obstructive pulmonary disease (COPD), but its mechanism of action on COPD is still perplexing. We aim to explore the molecular machinery underpinning the curative effects of QJHTD on COPD.
We confirmed in vitro anti-apoptotic and anti-inflammatory activities of QJHTD using the BEAS-2B and RAW264.7 cells challenged by cigarette smoke (CS) extract (CSE) and lipopolysaccharide (LPS) after chemical analysis of QJHTD. In vivo therapeutic activities of QJHTD were evaluated in the CS-LPS-exposed BALB/c mice. The phenotype data showed that anti-apoptotic and anti-inflammatory properties featured prominently in COPD treatment with QJHTD. Network pharmacology-based prediction followed by transcriptomic analysis of mouse lung tissue revealed that inhibiting such signaling pathways as IL-1β, IL-6, TNF, IκB-NF-κB, TLR, MAPK, and apoptosis contributed to the anti-COPD mechanism of QJHTD. Metabolome profiling unveiled the dominant role of dampening apoptosis and sphingolipid (SL) metabolism with choline (Ch) metabolism boosted in QJHTD modality for COPD. Integrative transcriptome-metabolome analysis unraveled the bridge between SL metabolism and apoptosis. In silico molecular docking revealed that acacetin as an active compound in QJHTD could bind with high affinities to the target proteins including MEK1, MEK2, ERK1, ERK2, Bcl2, NF-κB, and alCDase. These findings provide comprehensive insights into the molecular profile of QJHTD action against COPD and justify theoretical promise in a novel pharmacotherapy for the multifactorial disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lung tissue in the BALB/c mice with COPD (Model group), the COPD mice treated with the agent QJHTD (QJHTD group), and the normal mice (Control group).

first: Xin

last: Shen

first: Long

last: Wang


title: Impact of heavy metals on cold acclimation of Salix viminalis roots

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

summary: Frost is a major abiotic stress limiting plant growth and development. Climate change models predict an increase in the magnitude and frequency of late-frost events, which, together with an observed loss of soil insulation, will significantly damage roots. To withstand freezing stress, plants have evolved an adaptative process known as cold acclimation. While this process is well documented, it is known that the plant response to multiple stresses is unique and cannot be deduced from the response to each stress taken separately. Here, we investigate the impact of long-term metal exposure on the cold acclimation of Salix viminalis roots. To do so, we used physiological, transcriptomic and proteomic approaches. We found that while metal exposure significantly affected plants morphology and physiology, it did not impede cold acclimation. The impact of the simultaneous exposure to metals and cold acclimation on the transcriptome was unique, while at the proteomic level, the cold acclimation component seemed to be dominant. Further analysis revealed that metals strongly and negatively impacted the cellular antioxidant system. While this should have led to a loss of frost tolerance, it was not observed. A group of proteins was identified that could have played a role in compensating the impediment of the antioxidative system in metal-exposed roots.

overall_design: Cuttings of 10 cm of one individual S. viminalis were rooted in containers filled with a mix of 25 kg of potting soil and 17.5 kg sand under a controlled environment (23/20°C, 60% relative humidity, 16/8h photoperiod). After three weeks, plantlets were transferred to individual pots and half of them were exposed to a mixture of heavy metals (1.5 ppm Cd, 175 ppm Cu, 30 ppm Ni, 500 ppm Zn). After 40 days, half of the plants were randomly chosen and cold-acclimated (7/5°C, 60% relative humidity, 16/8h photoperiod) while the remaining was kept under control conditions. A total of four temperature-polymetallic contamination combinations were obtained, namely Control soil Temperate (CT), Control soil Cold acclimated (CC), Metals-polluted soil Temperate (MT) and Metals-polluted soil Cold acclimated (MC). Three biological replicates per conditions were analysed using RNA-Seq approach

first: Valentin

last: Ambroise

first: Jean-Francois

last: Hausman

first: Ann

last: Cuypers

first: Céline

middle: C

last: Leclerc

first: Marijke

last: Jozefczak

first: Jenny

last: Renaut

first: Sébastien

last: Planchon

first: Kjell

last: Sergeant


title: Smurf1 modulates Smad signaling pathway in fibrotic cataract formation

city: Guangzhou

first: Fanying

last: Jiang

address: No. 7, Jinsui Road

institute: Zhongshan Ophthalmic Center, Sun Yat-Sen University

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Tracking the role of Aire in immune tolerance to the eye with a TCR transgenic mouse model

city: SAN FRANCISCO

first: Mianmian

last: Yin

state: CA

address: 513 Parnassus Avenue

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

summary: Roughly one-half of mice with partial defects in two immune tolerance pathways (AireGW/+Lyn-/- mice) spontaneously develop severe damage to their retinas due to T cell reactivity to Aire-regulated interphotoreceptor retinoid-binding protein (IRBP). Single cell T cell receptor (TCR) sequencing of CD4+ T cells specific for a predominate epitope of IRBP showed a remarkable diversity of autoantigen-specific TCRs with greater clonal expansions in mice with disease. TCR transgenic mice made with an expanded IRBP-specific TCR (P2.U2) of intermediate affinity exhibited strong but incomplete negative selection of thymocytes. This negative selection was absent in IRBP-/- mice and greatly defective in AireGW/+ mice. Most P2.U2+/- mice and all P2.U.2+/-AireGW/+ mice rapidly developed inflammation of the retina and adjacent uvea (uveitis). Aire-dependent IRBP expression in the thymus also promoted Treg differentiation, but the niche for this fate determination was small, suggesting differences in antigen presentation leading to negative selection vs. thymic Treg differentiation and a stronger role for negative selection in preventing autoimmune disease in the retina.

overall_design: To characterize the diversity of the spontaneous autoimmune P2 response, the single cell TCR sequencing and mRNA sequencing were performed for the P2+ cells from LN of AireGW/+ Lyn-/- mice with (two dataset) and without uveitis

first: Jennifer

last: Smith

first: Marissa

last: Chou

first: Jackie

last: Chan

first: Rachel

middle: R

last: Caspi

first: Douglas

last: Gould

first: Mark

middle: S

last: Anderson

first: Anthony

middle: L

last: DeFranco

first: Yingyos

last: Jittayasothorn


title: Pinpointing the tumor-specific T-cells via TCR clusters

city: Moscow

first: Ekaterina

last: Serebrovskaya

address: Ostrovityanova st., 1

country: Russia

institute: Russian National Research Medical University

summary: Adoptive T cell transfer (ACT) is a promising approach to cancer immunotherapy, but its efficiency fundamentally depends on the extent of tumor-specific T-cell enrichment within the graft. This can be estimated via activation with identifiable neoantigens, tumor-associated antigens (TAAs), or living or lyzed tumor cells, but these approaches remain laborious, time-consuming, and functionally limited, hampering clinical development of ACT. Here, we demonstrate that homology cluster analysis of T cell receptor (TCR) repertoires efficiently identifies tumor-reactive TCRs allowing to: 1) detect their presence within the pool of tumor-infiltrating lymphocytes (TILs); 2) optimize TIL culturing conditions, with IL-2low/IL-21/anti-PD-1 combination showing increased efficiency; 3) investigate surface marker-based enrichment for tumor-targeting T cells in freshlyisolated TILs (enrichment confirmed for CD4+ and CD8+ PD-1+/CD39+ subsets), or re-stimulated TILs (informs on enrichment in 4-1BB-sorted cells). We believe that our approach to the rapid assessment of tumor-specific TCR enrichment should accelerate T cell therapy development.

overall_design: Dataset consists of 336 files. CD39+PD-1+ (double-positive or DP) and not-DP CD4+ and CD8+ TILs were freshly isolated and sorted from metastasized lymph nodes of 8 melanoma patients (2 biological replicas per sample). For one patient, CD8+ DP and not-DP TILs were expanded ex vivo and stimulated with tumor-associated antigens mix. CD137-high cells were sorted for NGS (1 biological replica per sample).  Additionally, bulk TILs TCR repertoires were obtained from uncultured TILs of one melanoma patient (8 biological replicas), and TILs of 3 melanoma patients cultured in different expansion conditions (4,6, and 12 biological replicas per condition respectively).

first: Mikhail

last: Goncharov

first: Dmitry

last: Chudakov


title: Diet-induced plasticity of life-history traits and gene expression in outbred Drosophila melanogaster population

city: Cambridge

first: Soumen

last: Khan

address: Babraham Hall

department: Epigenetics

institute: Babraham Institute

summary: Food is a fundamental requirement for organisms to develop, survive and reproduce. However, access to an optimum diet is not always guaranteed, resulting in a mismatch between the diet and the organism's needs. To comprehend the consequences of this mismatch, it becomes crucial to explore how different compositions of an organism's diet impact its overall performance. In this context, we tested the effect of isocaloric diets with different protein to carbohydrate ratios on eight key life history traits in a large (n = ~2,100) outbred Drosophila melanogaster population. We report accelerated pre-adult development and increased reproductive output, without affecting pre-adult viability and body size, in flies fed on low carbohydrate diet. We also observe that high carbohydrate content in diet shortens fly lifespan. In support, we found that increasing carbohydrate content in food led to faster aging by impairing locomotor activity and gut integrity. Additionally, we noted that the composition of the diet had an impact on gene expression patterns with high carbohydrate diets upregulating genes and high protein diets downregulating them. These results collectively provide a comprehensive understanding of how the balance of macronutrients in an organism's diet intricately shapes its traits.

overall_design: Whole RNA was isolated from female flies subject to different dietary conditions (P:C 0.25, P:C 0.40, P:C 0.55, P:C 0.70), on the 13th day post egg collection. RNA libraries prepared using  NEBNext Ultra II RNA Library Prep Kit for Illumina, using standard protocol. Sequencing was carried out on Novaseq6000 platform using 150*2 paired end chemistry. All experiments were carried out on three independnt biological replicates. Raw reads were trimmed and aligned to the BDGP6 genome using Hisat2. DeSeq2 was used to identify differentially expressed genes between different groups

first: Sudipta

last: Tung


title: Transcriptional modifications between Treg from healthy donors (HD) and Treg from patients suffering from warm autoimmune hemolytic anemia (wAIHA)

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

summary: We assessed Next Generation RNA Sequencing of circulating Treg from PBMC of HD or wAIHA patients and our results showed that Treg have an activated profile with sustained transcriptional and translational activity, as well as strong engagement of the TCR and TNF-a signaling pathway during wAIHA.

overall_design: Circulating regulatory T cells were sorted by Fluorescent Activated Cell sorting (FACS) from thawed PBMCs, according to their phenotype: FVS780- CD3+ CD4+ CD25hi CD127-. Four samples were obtained from HD and 5 from wAIHA patients.

first: Marion

last: Ciudad

first: Sylvain

last: Audia

first: Corentin

last: Richard


title: Single-cell transcriptomic analysis of tumor-infiltrated immune cells from myeloid-specific Usp18 knockout mice

city: La Jolla

first: Sayuri

last: Miyauchi

address: 3855 Health Sciences Drive

institute: University of California, San Diego

summary: Ubiquitin specific peptidase 18 (USP18) inhibits type I interferon response and mediates ISG15-deconjugation. Here, we examined the role of USP18 in myeloid-linage cells in tumor development. B16F10 melanoma grown in control or myeloid-specific Usp18 knockout mice were analyzed. Single-cell transcriptomic analysis revealed that the profile of tumor-infiltrated immune cells were altered with Usp18 deletion. We observed that increase in M1-polarized macrophages and decrease in myeloid-derived suppressor cells, resulting enhanced anti-tumor microenvironment in Usp18 conditional knockout mice.

overall_design: B16F10 melanoma was subcutaneously injected into control (Usp18f/f)  or myeloid-specific Usp18 knockout (Usp18f/f LysM-Cre) mice. Tumors were harvested 14 days after tumor injection. Single cell suspension was prepared from harvested tumors. 4 tumors per group were pooled. Live CD45+ cells were sorted on BD FACSAria. Libraries of aproximately 8,000 cells were constructed with 10x Genomics Chromium Single Cell 3' Reagent Kits v3 and sequenced on Illumina HiSeq 4000. Reads were aligned using CellRanger (v3.0.1).

first: Dong-Er

last: Zhang


title: Transcriptome analysis of Mapt-EGFP+ and Mapt-EGFP- myenteric cells

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary:
Mapttm1(EGFP)Klt/J mice (Mapt-EGFP; The Jackson Laboratory, Bar Harbor, ME, USA; stock 004779) carry a knock-in of the EGFP coding sequence in the first exon of the microtubule-associated protein tau (Mapt) gene producing a cytoplasmic EGFP fused to the first 31 amino acids of MAPT. EGFP expression marks neurons including enteric neurons regardless of their lineage, closely patterning the expression of neuron-specific beta-tubulin III (TUBB3). Mapt-EGFP ice were backcrossed to C57BL/6J (Jackson Laboratory strain #:000664) for three to five generations at Mayo Clinic. Six male and six female Mapt-EGFP mice (54-98 days of age) underwent surgical laparotomy in 3 groups (surgery #1: 1 male and 1 female, surgery #2: 3 males and 1 female, surgery #3: 2 males and 4 females) under pentobarbital (50mg/kg) anesthesia. The celiac ganglion of each mouse was injected with 3-5 μL of 25 mg/mL Alexa Fluor 647-labeled cholera toxin subunit B (CTB-AF647; Thermo Fisher Scientific, Waltham, MA, USA) with the intention of labeling the cell soma of intestinofugal neurons in the myenteric plexus of the colon. The animals were killed 3-4 days after surgery. The muscularis externa of the colon from each Mapt-EGFP mouse was pooled together between all mice of the same surgery date (2, 4, and 6 mice) and mechanically and enzymatically dissociated into single cells with a two-step process that first enriches for cells within myenteric ganglia (PMCID: PMC8114175). The pooled cells from each group of mice formed one biological replicate and subjected to FACS immediately after dissociation to generate populations of Mapt-EGFP+ neurons with or without the CTB-AF647 tracer and Mapt-EGFP− non-neuronal cells. The frequency of Mapt-EGFP+CTB-AF647+ neurons was approximately 125-fold lower than that of Mapt-EGFP+CTB-AF647− neurons and RNA from these preparations did not pass quality control. Therefore, only data from Mapt-EGFP+CTB-AF647− neurons were analyzed and referred to as Mapt-EGFP+ cells. Total RNA was isolated from Mapt-EGFP+ colonic neurons and Mapt-EGFP− myenteric cells using RNA-Bee (AMSBIO, Cambridge, MA, USA) and purified with RNeasy Mini Kit (Qiagen, Germantown, MD, USA). RNA quality was tested using Agilent Electropherogram (Agilent Technologies, Santa Clara, CA, USA) and hybridized to Affymetrix Mouse Genome 430.2 gene expression microarrays (Thermo Fisher Scientific, Waltham, MA, USA).
This study utilized Affymetrix Mouse Genome 430.2 oligonucleotide microarray analysis to charaterize the transcriptome of Mapt-EGFP+ neurons and Mapt-EGFP- non-neuronal myenteric cells isolated from the colon of Mapttm1(EGFP)Klt/J mice.

overall_design: Total RNA from GFP+ myenteric cells (neurons) and GFP- myenteric cells sorted from Mapttm1(EGFP)Klt/J mice was isolated. Oligonucleotide micorarray studies using Affymetrix Mouse Genome 430.2 GeneChips were performed in 3 biological replicate samples of each sorted cell type with each replicate representing cells isolated from 2, 4  or 6 mice.

first: Fei

last: Gao

first: David

last: Linden


title: A six-gene prediction model for tumor response to induction chemotherapy in locoregionally advanced laryngo-hypopharyngeal carcinoma

city: beijing

first: Chen

last: Tan

state: BEIJING

address: BEIJING DONGJIAOMIN NO 1

institute: Capital Medical University

summary: This study aimed to develop a novel gene expression signature that can predict tumor response to induction chemotherapy (IC) before treatment. RNA sequencing (RNA-seq) was used to screen the differentially expressed genes (DEGs) between response and non-response in 54 samples (discovery cohort). Random forest (RF) and receiver operating characteristic (ROC) analyses were performed to further screen principal genes using the RNA-seq data of 27 cases (training cohort). qRT-PCR was used to confirm the relative expression of the selected genes between 57 non-response tissues and 55 response tissues (validation cohort). K-means was used to stratify all patients into two clusters according to the 6-gene signature. Kaplan-Meier analysis was used to estimate overall survival in the two clusters. The log-rank survival test was performed to compare the differences between the two clusters. In the discovery phase, 107 DEGs were obtained. It effectively distinguished tumors from normal tissues and distinguished response tumors from non-response tumors by RNA sequencing. In the training phase, the top 50 genes were selected by RF, which showed distinct transcriptome segregation between response and non-response tumors. Then, the performance of the 50 genes was evaluated to predict the tumor response of IC using ROC analysis. Among them, 10 genes were chosen for which the area under the curve was more than 80%. In the validation phase, six genes (CD72, NRIP1, THBS4, ABCA9, SNED1, and GIMAP7) were significantly overexpressed in non-response tissues compared to response tissues (p < 0.05). Finally, the 6-gene signature was developed, which was highly accurate in predicting the short-term tumor response to IC (AUC= 0.949) and was also an independent prognostic factor for predicting the overall survival of locoregionally advanced laryngeal and hypopharyngeal carcinoma (LA-LHC) patients. The 6-gene signature can effectively predict tumor response to IC and overall survival, which lays the foundation for a more individualized therapeutic strategy for LA-LHC patients.

overall_design: mRNA profiles from human laryngo-hypopharyngeal carcinoma were generted by deep sequencing.

first: Ru

last: Wang

first: Lingwa

first: Yifan

last: Yang

first: Shizhi

last: He

first: Meng

last: Lian

first: Wenbin

last: Xu

first: Ling

last: Feng

first: Jugao

last: Fang


title: An ESR1 neoepitope vaccine targeting resistance mutations induces cross-protective anti-tumor immune responses against ER+ Breast Cancer

city: Durham

first: Erika

last: Crosby

state: NC

address: 203 Research Dr. MSRBI Room 407

institute: DUKE UNIVERSITY MEDICAL CENTER

summary: Estrogen receptor α (ER) positivity defines ~75% of breast cancers (BCs), treated with a variety of estrogen-targeting therapies. However, ~25% of patients with localized disease and nearly all metastatic disease patients develop resistance to such therapies. One major mechanism of resistance occurs through gain-of-function mutations in the gene encoding ER (ESR1), which occurs after prolonged endocrine therapy. These gain-of-function mutations render ESR1 constitutively active and represent critical neoepitopes of ER+ BC.  We here confirm that these mutations permit ligand-independent estrogen signaling, as well as stimulate alternate pathways to enhance BC oncogenicity in vivo. As these oncogenic ESR1-mutated genes (ESR1mut) may be a significant, predictable contributor to the development of acquired resistance to endocrine therapy, we explored the potential of vaccination targeting these neoepitopes. In our study, we confirmed that these peptides are presented by MHC complexes and capable of stimulating CD8+ T-cell responses. Using recombinant adenoviral vectors encoding ESR1mut, we also demonstrate the induction of ESR1-specific immunity to generate anti-tumor responses against ESR1mut-expressing BC. Finally, we improved the safety profile, ESR1-specific immunity and anti-tumor efficacy of our vaccines using c-terminal subunit ESR1mut targeting, which has the potential to prevent the outgrowth of resistant ER+ BCs and improve patient outcomes.

overall_design: MCF7 cells were transfected with WT or mutant ESR1 and cultured with or without estrogen. Cells were harvested and replicates sequenced for gene expression changes.

first: Zachary

last: Hartman


title: Genome-wide analysis of POLR2, CTCF, RAD21, and H3K9ac binding in N1E115 cells

summary: Neuronal nitric oxide synthase 1 (NOS1) produces the gaseous signaling molecule nitric oxide (NO), which plays important roles in the development and function of the nervous system. The regulation of Nos1 gene expression is incompletely understood. Here, we explored the role of physiological hypoxia in the control of Nos1 transcription and the underlying mechanisms using N1E115 mouse neuroblastoma cells as a model. N1E115 cells were cultured for 3 days at high (20%) and low (4%) oxygen levels. Following the verification of upregulation of Nos1 mRNA and protein levels in response to 4% oxygen, we analyzed the genome-wide distribution of CTCF, RAD21, total and S2- or S5-phosphorylated RNA polymerase II, and the histone mark H3K9ac by chromatin immunoprecipitation-sequencing.

overall_design: Libraries were made from chromatin-immunoprecipitated DNA isolated from N1E115 cells cultured in the presence of 20% or 4% oxygen (at ambient barometric pressure) using antibodies against CTCF, RAD21, H3K9ac, POLR2, POLR2S2p, and POLR2S5p and sequenced on Illumina HiSeq 4000 platform.


title: Genome-wide analysis of H3K4me3 in NOS1+ mouse enteric neurons

summary: Neuronal nitric oxide synthase 1 (NOS1) produces the gaseous signaling molecule nitric oxide (NO), which plays important roles in the development and function of the nervous system. The regulation of Nos1 gene expression is incompletely understood. Here, we analyzed the genome-wide distribution of the histone mark H3K4me3 in FACS-purified nitrergic enteric neurons by chromatin immunoprecipitation-sequencing.

overall_design: Libraries were made from chromatin-immunoprecipitated DNA isolated from sorted NOS1+ mouse enteric neurons using anti-H3K4me3 antibodies and sequenced on Illumina HiSeq 4000 platform.


title: Genome-wide analysis of histone marks in N1E115 cells

summary: Neuronal nitric oxide synthase 1 (NOS1) produces the gaseous signaling molecule nitric oxide (NO), which plays important roles in the development and function of the nervous system. The regulation of Nos1 gene expression is incompletely understood. Here, we explored the role of physiological hypoxia in the control of Nos1 transcription and the underlying mechanisms using N1E115 mouse neuroblastoma cells as a model. N1E115 cells were cultured for 3 days at high (20%) and low (4%) oxygen levels. Following the verification of upregulation of Nos1 mRNA and protein levels in response to 4% oxygen, we analyzed the genome-wide distribution of the histone marks H3K27ac, H3K27me3, H3K36me3, H3K4me1, and H3K4me3 by chromatin immunoprecipitation-sequencing.

overall_design: Libraries were made from chromatin-immunoprecipitated DNA isolated from N1E115 cells cultured in the presence of 20% or 4% oxygen (at ambient barometric pressure) using antibodies against H3K27ac, H3K27me3, H3K36me3, H3K4me1, and H3K4me3 and sequenced on Illumina HiSeq 2500 or 4000 platform.


title: Transcriptome analysis of N1E115 cells cultured in the presence of 20% or 4% O2

summary: Neuronal nitric oxide synthase 1 (NOS1) produces the gaseous signaling molecule nitric oxide (NO), which plays important roles in the development and function of the nervous system. The regulation of Nos1 gene expression is incompletely understood. Here, we explored the role of physiological hypoxia in the control of Nos1 transcription and the underlying mechanisms using N1E115 mouse neuroblastoma cells as a model. N1E115 cells were cultured for 3 days at high (20%) and low (4%) oxygen levels. Following the verification of upregulation of Nos1 mRNA and protein levels in response to 4% oxygen, we performed transcriptome analysis using stranded total RNA-sequencing.

overall_design: Libraries were made from total RNA  isolated from N1E115 cells cultured in the presence of 20% or 4% oxygen (at ambient barometric pressure) using the Illumina TruSeq® Stranded Total RNA LT - (with Ribo-Zero™ Human/Mouse/Rat) - Set A kit and sequenced on the Illumina HiSeq 4000 platform.


title: Genome-wide analysis of HIF1A and ARNT binding in N1E115 cells

summary: Neuronal nitric oxide synthase 1 (NOS1) produces the gaseous signaling molecule nitric oxide (NO), which plays important roles in the development and function of the nervous system. The regulation of Nos1 gene expression is incompletely understood. Here, we explored the role of physiological hypoxia in the control of Nos1 transcription and the underlying mechanisms using N1E115 mouse neuroblastoma cells as a model. N1E115 cells were cultured for 3 days at high (20%) and low (4%) oxygen levels. Following the verification of upregulation of Nos1 mRNA and protein levels in response to 4% oxygen, we analyzed HIF1A and ARNT binding by chromatin immunoprecipitation-sequencing.

overall_design: Libraries were made from chromatin-immunoprecipitated DNA isolated from N1E115 cells cultured in the presence of 20% or 4% oxygen (at ambient barometric pressure) using HIF1A and ARNT antibodies and sequenced on Illumina HiSeq 2500 platform. 20%O2_HIF1A_replicate2 and 4%O2_HIF1A_replicate2 as well as their inputs, 20%O2_input5 and 4%O2_input5, were generated by combining reads from two sequencing runs.


title: LAG-3- and CXCR5-expressing CD4 T cells display progenitor-like properties during chronic visceral leishmaniasis

status: Public on Feb 13 2024

city: Laval

first: Simona

last: Stager

state: Quebec

address: 531 Boul. des Prairies

department: Centre Armand-Frappier

country: Canada

institute: INRS

summary: In chronic infections, sustaining the CD4 T cell responses is crucial for pathogen clearance.  The expression of inhibitory receptors such as LAG-3 or Lymphocyte activation gene 3 is usually associated with immune suppression and T cell exhaustion. However, LAG-3 also serves as an immune checkpoint molecule and is implicated in proliferation control and cell survival. In this study, we have utilized a mouse model of visceral leishmaniasis (VL), to characterize a subset of LAG-3- and CXCR5-expressing CD4 T cells. These LAG-3+CXCR5+PD-1lo/int CD4 T cells exist in naïve mice, they expand during VL, and are antigen specific. Importantly, the RNAseq analysis showed that these cells highly express gene signatures associated with self-renewal capacity, indicating that these cells might act as progenitors. Additionally, upon adoptive transfer into Rag1-/- mice followed by challenge with Leishmania donovani, these LAG-3+CXCR5+ PD-1lo/int CD4 T cells gave rise to different types of T effector and regulatory subsets, demonstrating their differentiation potential. These cells were also observed in mice infected with LCMV clone-13 and Heligmosomoides polygyrus bakeri. In summary, we propose that these LAG-3+CXCR5+ PD-1lo/int CD4 T cells that exhibit progenitor-like capacities could be implicated in maintaining CD4 T cell responses in chronic infections.

overall_design: LAG-3+ CXCR5+ PD-1lo/int CD4 T cells (referred to as TLCPlo/int cells in the associated article) and CXCR5+ PD-1hi Tfh cells (mostly germinal center Tfh cells) were purified by cell sorting from spleens of Leishmania donovani-infected mice (n = 6) at 21 days post infection. We performed bulk-RNA-seq to compare TLCPlo/int cells with GC-Tfh cells, as the initial flow cytometry analysis showed that these two populations shared similar markers such as CXCR5, PD-1, ICOS and TCF-1.

first: Sharada

last: Swaminathan

last: Stäger


title: The Hxk1 protein of Candida albicans influences gene expression of both metabolic and virulence related genes

city: Merced

first: Clarissa

last: Nobile

state: California

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

summary: The Hxk1 protein of Candida albicans is a moonlighting protein with a wide variety of functions. It phosphorylates N-acetylglucosamine (GlcNAc) which is necessary for different purposes in the cell including energy and chitin production. Further, this protein is a regulator for morphogenesis independent of its function during GlcNAc catabolism.To identify the regulatory role of Hxk1 and putative downstream regulator Hxk2, we performed CUT&RUN experiments for GFP-tagged Hxk1 strains and GFP-tagged Hxk2 strains.

overall_design: CUT&RUN for 3 biological replicates of GFP-tagged Hxk1, GFP-tagged Hxk2 and corresponding IgG negative controls.

first: Stefanie

last: Wijnants

first: Dimitrios

last: Sofras

first: Wouter

last: Van Genechten

first: Rudy

last: Vergauwen

first: Ashley

last: Valle Arevalo

first: Deepika

last: Gunasekaran

first: Craig

last: Ennis

first: Sabrina

last: Jenull

first: Karl

last: Kuchler

middle: J

first: Patrick

last: Van Dijck


title: PMI-controlled mannose metabolism and glycosylation determines tissue tolerance and virus fitness

city: Hong Kong

first: Peng

last: Luo

address: 21 Sassoon Rd

institute: The University of Hong Kong

summary: This study explored the regulatory effect of D-mannose on host immunometabolic responses after viral infection. The results showed that D-mannose can compete with glucose for transporters and hexokinase, inhibiting glycolysis, reducing mitochondrial reactive oxygen species and succinate-induced HIF-1α, thereby reducing virus-induced inflammatory cytokine production. Even with delayed combinatorial treatment of D-mannose and antiviral monotherapy after viral infection, a synergistic effect was still observed in mouse models. Phosphomannose isomerase (PMI) activity determines the benefits of D-mannose, as simultaneous PMI depletion and mannose supplementation impaired cell viability. PMI inhibition can suppress replication of various viruses by affecting host and viral surface protein glycosylation. However, D-mannose does not inhibit PMI activity or viral fitness. In summary, PMI-centered therapeutic strategies can eliminate viral infections, while D-mannose treatment reprograms glycolysis to control collateral damage.

overall_design: This study used a mouse model, divided into control group (Mock Infection), virus infection group (H1N1), and D-mannose treatment after viral infection group (H1N1-Mannose), with 3 mice per group. Metabolic changes, inflammatory factor expression, viral load and other indicators were measured at different time points after viral infection or treatment. By comparing the control group and the viral infection group, the impact of viral infection on mouse immune metabolism was evaluated. By comparing the viral infection group and the treatment group, the regulatory effect of D-mannose treatment on metabolism and inflammation was assessed.

first: Shuofeng

last: Yuan

first: Ronghui

last: Liang


title: Phenotypic Plasticity upon GSC Differentiation

city: Lille

first: Mohamed

last: Elati

address: Bd du Professeur Jules Leclercq

institute: University of Lille

summary:
At the cellular level, the malignant characteristics of GBM are largely attributed to GBM stem cells (GSCs). These cells, endowed with stem-like properties, can self-renew, generate diverse cancerous cell populations, and initiate tumors in vivo.
The GSC lines, NCH644 and NCH421k, when cultured as neurospheres (NS) — a condition that preserves their stem-like state, as evidenced by the expression of stem cell markers like SOX2, CD133, and Nestin — were found to align with the PN subclass and CL-B/C respectively.

overall_design: For the NCH644 and NCH421k lines in both stem-like and differentiated states, total RNA was isolated, and biotinylated single-strand cDNA targets were prepared using the Ambion WT Expression Kit (Cat #4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat #900671), following manufacturer guidelines. The cDNAs were hybridized onto GeneChip® Human Gene 2.0 ST arrays (Affymetrix), targeting over 40,000 RefSeq transcripts and approximately 11,000 LncRNAs. Chips were processed and scanned using Affymetrix equipment and software. Raw data was then analyzed and processed using Affymetrix Expression Console software version 1.4.1 with the default RMA settings.

first: Sophie

last: Foppolo

first: Christelle

last: Thibault

first: Monique

last: Dontenwill


title: Colony stimulating factor-1 receptor drives glomerular parietal epithelial cell activation in focal segmental glomerulosclerosis

city: Hospitalet de Llobregat

first: ANNA

last: SOLA

state: --- Select One ---

address: Pavelló de Govern, Avda Mare de Déu de Bellvitge, Lab 4120

institute: IDIBELL

summary: Parietal epithelial cells (PECs) are part of renal progenitor cells with similarities to bone marrow stem cell niche. In focal segmental glomerulosclerosis (FSGS) PECs become activated and contribute to extracellular matrix deposition. Colony stimulating factor-1 (CSF-1), a hematopoietic growth factor, acts via its specific receptor, CSF-1R, and has been implicated in several glomerular diseases, although its role on PEC activation is unknown. We found that CSF-1R was upregulated in PECs and podocytes from human biopsies with FSGS. Through in vitro studies, we demonstrated that PECs constitutively express CSF-1R. Incubation with CSF-1 induced CSF-1R upregulation and significant transcriptional regulation of genes involved in pathways associated with PEC activation. Specifically, CSF-1/CSF-1R activated the ERK1/2 pathway and upregulated CD44 in PECs, while both ERK and CSF-1R inhibitors reduced CD44 expression. Our functional studies showed that CSF-1 induced PEC proliferation and migration, while reducing the differentiation of PECs into podocytes. These results were validated in the Adriamycin-induced FSGS experimental model. Importantly, treatment with either the CSF-1R-specific inhibitor GW2580 or Ki20227 provided a robust therapeutic effect. In conclusion, we provide the first evidence of the role of the CSF-1/CSF-1R pathway in PEC activation in FSGS, paving the way for future clinical studies investigating the therapeutic effect of CSF-1R inhibitors on FSGS in humans.

overall_design: To investigate the functional changes induced by CSF-1 through its specific receptor in human PECs, we performed an RNA-seq experiment. Normalized gene expression profiles were compared between cells treated with CSF-1 for 24 hours (T24H sample) and untreated cells (CTL sample)

first: Anna

last: Sola

first: Josep

middle: M

last: Cruzado


title: Altered RNAs in patients of temporal lobe epilepsy

city: shanghai

first: che

last: che

state: - None -

address: ruijin second road, No 197, huangpu district，shanghai

institute: ruijin hospital

summary: Over the past decades, the immune responses have been suspected of participating in the mechanisms for epilepsy. To assess the immune related pathway in temporal lobe epilepsy (TLE), we explored the altered immune pathways in TLE patients with and without hippocampal sclerosis (HS).We analyzed RNA-seq data from 3 TLE-HS and 3 TLE-nonHS patients, including identification of differentially expressed RNA, function pathway enrichment, the protein-protein interaction network and construction of ceRNA regulatory. network. We illustrated the immune related landscape of molecules and pathways on human TLE-HS. Also, we identified several differential immune related genes like HSP90AA1 and SOD1 in TLE-HS patients. Further ceRNA regulatory network analysis found SOX2-OT connected to miR-671-5p and upregulated the target gene SPP1 in TLE-HS patients. Also, we identified both SOX2-OT and SPP1 were significantly upregulated in five different databases including TLE-HS patients and animal models