title: Single cell microarray analysis of mouse primordial germ cells with Prdm14 mutation.

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

country: Japan

institute: Nara Medical University

summary: Prdm14 is a critical gene for specifying mouse primordial germ cells (PGCs). The changes in expression in mouse PGCs caused by mutations of the Prdm14 gene were investigated at the single-cell level using microarray analysis.

overall_design: C57BL/6 mice with the Prdm14 (+/-) genotype (Yamaji et al., Nature Genetics, 2008) were crossed. Pregnant mice were sacrificed at embryonic day (E) 7.25 - 7.5 and embryos at the early-to-mid allantois bud stage were isolated. The base of the allantois bud, where primordial germ cells (PGCs) were clustered, was dissected using a glass knife and cells were dissociated with trypsin as described (Kurimoto et al., Genes and Development, 2008). Single cells were randomly isolated manually using a glass capillary as described (Kurimoto et al., Nature Protocols, 2007) and directly subjected to cDNA amplification (Kurimoto et al., Nucleic Acids Research, 2006). cDNAs of PGCs were identified based on Prdm1 expression using targeted PCR as described (Kurimoto et al., Genes and Development, 2008). Genotypes of Prdm14 were identified by PCR as described (Yamaji et al., Nature Genetics, 2008). cDNAs of PGCs with Prdm14 (+/+), (+/-), and (-/-) genotypes were then subjected to microarray analysis using the Affymetrix GeneChip Mouse Genome 430 2.0 Array. Microarray data was processed using dChip (Ver.1.3) with the PM/MM difference model.  Expression level of Dppa3 (1424295_at) were investigated.

first: Yukihiro

last: Yabuta

first: Mitinori

last: Saitou


title: Expression Signature of Human Endogenous Retroviruses in Chronic Lymphocytic Leukemia

status: Public on Apr 17 2024

city: Columbus

first: Alessandro

last: La Ferlita

state: OH

department: The James Comprehensive Cancer Center

country: USA

institute: The Ohio State University

type: Expression profiling by high throughput sequencing

summary: Chronic lymphocytic leukemia (CLL) is one of the most diagnosed forms of leukemia worldwide and it is usually classified into two forms: indolent and aggressive. These two forms are characterized by distinct molecular features that drive different responses to treatment and clinical outcomes. In this context, a better understanding of the molecular landscape of the CLL forms may potentially lead to the development of new drugs or the identification of novel biomarkers. Human Endogenous Retroviruses (HERVs) are a class of transposable elements that have been associated with the development of different human cancers, including different forms of leukemias. However, no studies about HERVs in CLL have ever been reported so far. Here, we present the first locus-specific profiling of HERV expression in both the aggressive and indolent forms of CLL. Our analyses revealed several dysregulations in HERV expression occurring in CLL and some of them were specific for either the aggressive or indolent form of CLL. Such results were also validated by analyzing an external cohort of CLL patients and by RT-qPCR. Moreover, in-silico analyses have shown relevant signaling pathways associated with them suggesting a potential involvement of the dysregulated HERVs in these pathways and consequently in CLL development.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of ten patients with the aggressive form of CLL carrying unmutated IGHV, ten patients with the indolent form of CLL carrying mutated IGHV, and four healthy donors.

first: Giovanni

last: Nigita

first: Liudmyla

last: Tsyba

first: Alexey

last: Palamarchuk

first: Salvatore

last: Alaimo

first: Alfredo

last: Pulvirenti

first: Veronica

last: Balatti

first: Laura

last: Rassenti

first: Philip

middle: N

last: Tsichlis

first: Thomas

last: Kipps

first: Yuri

last: Pekarsky

first: Carlo

middle: M

last: Croce


title: SARS-COV-2 putative mi-RNAs may target host immune system and cellular mechanisms to mediate pathogenesis-an in silico and in vivo study II

city: Lucknow

first: Vikas

last: Agarwal

state: Uttar Pradesh

address: SGPGIMS, Raebareli road

department: Clinical Immunology

country: India

institute: Sanjay Gandhi Postgraduate Institute of Medical Sciences

summary:
The exact role of epigenetics in the pathogenesis of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is unclear. Herein we have hypothesized that viral micro RNAs (miRNAs) may modulate host cellular and immune responses which may lead to varied clinical presentations. Using bioinformatics tools, we have first predicted putative miRNAs in the genotype of the SARS-CoV-2 and their potential gene targets. Thereafter, quantification of mRNA of key genes regulating inflammation, coagulation, neuropsychiatric functions, fibrosis and glucose metabolism was evaluated in the peripheral blood mononuclear cells and bone marrow of patients suffering from different severities of SARS-CoV-2 infection. Key genes regulating innate immunity, lymphopoiesis, T-cell and B-cell development, cytokine storm, coagulation pathways, fibrosis, neuropsychiatric manifestations, glucose metabolism, and olfaction were significantly downregulated in severe infection when compared with mild infection. Downregulated genes mRNA recovered to normal/near normal levels on recovery from infection. SARS-CoV-2 miRNAs appear promising players in the pathogenesis of COVID-19. Strategies silencing these miRNAs may be explored further as potential therapeutic targets.
Patients with severe illness were defined as: respiratory rate ≥30 per min or SpO2 <90% in ambient air, or acute respiratory distress syndrome or septic shock and those with mild illness as: patients with any of the symptoms like fever, cough, sore throat, malaise, headache, muscle pain, nausea, vomiting, diarrhea, loss of taste and smell, but no dyspnea, or abnormal chest imaging.  There were 4 severe SARS CoV-2 patients, Median age 57.5 years (Range 50-72 years), all males, median disease duration 7.5 days, duration of hospital stay 38 days with outcome as 3 deaths and one Post covid lung fibrosis. All 4 mild cases had median age 55.5 years (range 42-0 years), 3 males and one female, mean disease duration 2.8 days, mean duration of hospitalization 14.5 days and all recovered. Median age of all 4 recovered cases was 59 years (range 43-77 years), 3 males and one female, mean disease duration of 6 days, mean disease duration of 22 days and all recovered. There were 4 healthy subjects with median age 50 years (range 42-54 years) and there were 3 males and one female. All 3 patients who underwent bone marrow examination had severe Covid-19 and were different then the ones whose peripheral blood was analyed by qRT-PCR. Amongst Disease control subjects (n=3) who underwent  bone marrow examination, two had adult onset immune thrombocytopenia and one had a suspicion of myelodysplastic syndrome which was reported to be normal.

overall_design: Bone marrow samples of two each patients of severe SARS-CoV2 and disease controls were analyzed (in triplicate)

first: Mohit

middle: K

last: Rai

first: Sukanya

last: Tripathy

first: Anamika

last: Anuja

first: Durga

middle: P

last: Misra

first: Rupali

last: Awale

first: Latika

last: Gupta

first: Pankti

last: Mehta

first: Gaurav

last: Pande

first: Supriya

last: Sharma

first: Zia

last: Hashim

first: Alok

last: Nath

first: Mohan

last: Gurjar

first: Afzal

last: Azeem

first: Naveen

first: Sundaram

last: Gopalakrishnan

last: Koshy

first: Neha

last: Singh

first: Vishwesh

first: Ajmal

last: Khan


title: SARS-COV-2 putative mi-RNAs may target host immune system and cellular mechanisms to mediate pathogenesis-an in silico and in vivo study I

first: Vikas

last: Agarwal

summary:
The exact role of epigenetics in the pathogenesis of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is unclear. Herein we have hypothesized that viral micro RNAs (miRNAs) may modulate host cellular and immune responses which may lead to varied clinical presentations. Using bioinformatics tools, we have first predicted putative miRNAs in the genotype of the SARS-CoV-2 and their potential gene targets. Thereafter, quantification of mRNA of key genes regulating inflammation, coagulation, neuropsychiatric functions, fibrosis and glucose metabolism was evaluated in the peripheral blood mononuclear cells and bone marrow of patients suffering from different severities of SARS-CoV-2 infection. Key genes regulating innate immunity, lymphopoiesis, T-cell and B-cell development, cytokine storm, coagulation pathways, fibrosis, neuropsychiatric manifestations, glucose metabolism, and olfaction were significantly downregulated in severe infection when compared with mild infection. Downregulated genes mRNA recovered to normal/near normal levels on recovery from infection. SARS-CoV-2 miRNAs appear promising players in the pathogenesis of COVID-19. Strategies silencing these miRNAs may be explored further as potential therapeutic targets.
Patients with severe illness were defined as: respiratory rate ≥30 per min or SpO2 <90% in ambient air, or acute respiratory distress syndrome or septic shock and those with mild illness as: patients with any of the symptoms like fever, cough, sore throat, malaise, headache, muscle pain, nausea, vomiting, diarrhea, loss of taste and smell, but no dyspnea, or abnormal chest imaging.  There were 4 severe SARS CoV-2 patients, Median age 57.5 years (Range 50-72 years), all males, median disease duration 7.5 days, duration of hospital stay 38 days with outcome as 3 deaths and one Post covid lung fibrosis. All 4 mild cases had median age 55.5 years (range 42-0 years), 3 males and one female, mean disease duration 2.8 days, mean duration of hospitalization 14.5 days and all recovered. Median age of all 4 recovered cases was 59 years (range 43-77 years), 3 males and one female, mean disease duration of 6 days, mean disease duration of 22 days and all recovered. There were 4 healthy subjects with median age 50 years (range 42-54 years) and there were 3 males and one female.

overall_design: A total of 12 patients suffereing with SARS-CoV2 infection during first wave (May 2020 - January 2021), 3 during second wave April 2021-Septemer 2021 and 4 healthy controls samples of whole blood in triplicates were analyzed.

first: Mohit

last: Rai

first: Sukanya

first: Thomas


title: Meyoid-specific deficiency of Glutamine Synthetase Aggravates LPS/D-GalN-induced liver injury via the activation of monocyte-derived macrophages

city: Shanghai

first: Menglin

last: Shi

address: Dongan Road 130

country: China

institute: Fudan university

summary: Glutamine synthase (Glul) is a key enzyme to synthesize glutamine, but its function in acute liver injury (ALI) remains unclear. Here, we investigated the regulatory role of Glul on immnuity in LPS/D-GalN-induced ALI. The study firstly found that the expression of Glul in myeloid cells was inhibited following LPS/D-GalN challenge. Then myeloid-specific knockout Glul mice were generated, which showed more severe ALI and higher mortality due to the activation of monocyte-derived macrophages (MoMFs) and the secretion of CCL2, as well as the recruitment of CCR2+ monocytes. Notably, liver injury can be relieved with adeno-associated virus (AAV)-mediated hepatic delivery of Glul via tail vein injection in mice. In conclusion, this research validates the protective effect of Glul against ALI.

overall_design: we extracted RNA from liver tissues in Glullflox/flox and GlulΔlyz2 mice treated with LPS/D-GalN or H2O and then performed mRNA transcriptome analysis

first: Jianghong

last: Yu

first: Yumeng

last: Guo

first: Huilu

last: Zhang


title: Gene expression profile at single cell level of Peritoneal Cells in Patients with Gastric Cancer

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of Peritoneal Cells in Patients with Gastric Cancer.

overall_design: Gastric cancer patients  peritoneal Cells were collected from either malignant astices fluid or peritoneal washing  and analyzed using scRNAseq to identify the tumor microenviroment and different gene expression profile.

first: Yanghee

last: Woo


title: RECQL4 is not critical for firing of human DNA replication origins

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

summary: RECQL4, a member of the RecQ helicase family, plays a role in maintaining genomic stability, but its precise function remains unclear. The N-terminus of RECQL4 has similarity to Sld2, a protein required for the firing of DNA replication origins in budding yeast. Consistent with this sequence similarity, Xenopus RECQL4 has been implicated in initiating DNA replication in oocyte extracts. To determine whether human RECQL4 is required for firing of DNA replication origins, we generated cells in which both RECQL4 alleles were targeted, resulting in either lack of protein expression (Knock-Out) or expression of a full-length, mutant protein lacking helicase activity (Helicase Dead). Surprisingly, both the RECQL4 Knock-Out and Helicase Dead cells were viable and exhibited essentially identical origin firing profiles as the parental cells. Analysis of the rate of fork progression revealed normal rates in the RECQL4 Knock Out cells, but decreased rates in the RECQL4 inactive cells. Thus, while budding yeast Sld2 is required for DNA replication origin firing, our evidence suggest that human RECQL4 has assumed a role in the regulation of replication fork progression.

overall_design: EdUseq data of RECQL4  WT and mutant cells (CRISPR KOs bearing frameshifts to the N-terminal (fsN)or helicase (fsN) domain of the protein and helicase inactive mutants (KM)), under normal (NE) and overexpression (OE) conditions of ectopic CCNE, addressing the origin firing profile (EdUseq), fork progression (EdUseq_RXX) and Mitotic DNA synthesis profiles (MiDASseq)

first: Laura

last: Padayachy

first: Sotirios

middle: G

last: Ntallis

first: Thanos

middle: D

last: Halazonetis


title: Bulk and single cell RNA-seq of MCF7 and MCF7 TDP2-KO cells treated with/without estrogen

city: Los Angeles

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

summary: To investigate the function of tyrosyl-DNA phosphodiesterase 2 (TDP2) in estrogen receptor (ER) positive breast cancer, we perfomed bulk and single-cell RNA-seq on MCF7 and MCF7 TDP2-KO cells treated with/without estrogen .

overall_design: bulk and single cell RNA-seq of MCF7 and MCF7 TDP2-KO cells treated with or without estrogen (17beta-estradiol, E2).

first: Hisashi

last: Tanaka

first: Sungyong

last: You

first: Nicholas

last: Manguso


title: SARS-COV-2 putative mi-RNAs may target host immune system and cellular mechanisms to mediate pathogenesis-an in silico and in vivo study

first: Vikas

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

overall_design: Refer to individual Series


title: Transcriptome of human peripheral blood regulatory T cells with distinct ex vivo expansion profile

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: The UCSF Treg cell therapy program manufactured over 60 human regulatory T cell (Treg) products under the GMP condition in support of 9 clinical trials between 2011 and 2021. These products were manufactured using two alternative protocols of either two rounds of polyclonal stimulations (PolyTregs) or first allogeneic B cell stimulation followed by polyclonal stimulation (arTregs).  A high degree of individual variability in Treg expansion with both protocols was observed.  RNA-seq analysis was performed on freshly isolated peripheral blood Tregs to identify transcriptome profile associated with Treg expansions.

overall_design: A total of 19 individuals with sufficient archived pre-expansion PBMCs were selected for RNA-seq analysis.  Among these, 6 were classified as high expanders, 6 were mid expanders, and 7 were low expanders.  Tregs were purfied from cryopreserved PBMCs using FACS based on the phenotype of CD4+CD25+CD127lo/-.  Total RNA was extracted for RNAseq.

first: Qizhi

last: Tang

first: Yani

last: Peng

first: Alberto

last: Senchez-Fueyo

first: Sandy

last: Feng


title: Modeling clonal evolution in Fanconi anemia

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: Transcriptomic comparison of stages of clonal evolution of Fanconi anemia modeled using induced pluripotent stem cells.

overall_design:
iPSCs bearing defined mutations were differentiated to HSPCs, and RNA was isolated for RNA-seq.

**The submitter declares that the raw data will be submitted to dbGaP**

first: Grant

last: Rowe


title: Nucleosome reorganisation in breast cancer tissues

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Background
Nucleosome repositioning in cancer is believed to cause many changes in genome organisation and gene expression. Understanding these changes is important to elucidate fundamental aspects of cancer. It is also important for medical diagnostics based on cell-free DNA (cfDNA), which originates from genomic DNA regions protected from digestion by nucleosomes.

Results
We have generated high-resolution nucleosome maps in paired tumour and normal tissues from the same breast cancer patients using MNase-assisted histone H3 ChIP-seq and compared them with the corresponding cfDNA from blood plasma. This analysis has detected single-nucleosome repositioning at key regulatory regions in a patient-specific manner and common cancer-specific patterns across patients. The nucleosomes gained in tumour versus normal tissue were particularly informative of cancer pathways, with ~ 20-fold enrichment at CpG islands, a large fraction of which marked promoters of genes encoding DNA-binding proteins. The tumour tissues were characterised by a 5–10 bp decrease in the average distance between nucleosomes (nucleosome repeat length, NRL), which is qualitatively similar to the differences between pluripotent and differentiated cells. This effect was correlated with gene activity, differential DNA methylation and changes in local occupancy of linker histone variants H1.4 and H1X.

Conclusions
Our study offers a novel resource of high-resolution nucleosome maps in breast cancer patients and reports for the first time the effect of systematic decrease of NRL in paired tumour versus normal breast tissues from the same patient. Our findings provide a new mechanistic understanding of nucleosome repositioning in tumour tissues that can be valuable for patient diagnostics, stratification and monitoring.

overall_design:
MNase-assisted DNA-sequencing (MNase-seq) breast tissues from Breast Cancer patients paired with normal surrounding tissue. In addition, MNase- assisted Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3 as well as cell-free DNA sequencing obtained from the same patients' blood plasma.
**RAW data not available due to patient privacy concerns**

first: Divya

middle: R

last: Jacob

first: Wilfried

last: Guiblet

first: Hulkar

last: Mamayusupova

first: Mariya

last: Shtumpf

first: Luminita

last: Ruje

first: Svetlana

last: Gretton

first: Isabella

last: Ciuta

first: Milena

last: Bikova

first: Clark

last: Correa

first: Emily

last: Dellow

first: Shivam

last: Agrawal

first: Navid

last: Shafiei

first: Anastasija

last: Drobysevskaja

first: Chris

last: Armstrong

first: Jonathan D.

last: Lam

first: Yevhen

last: Vainshtein

first: Christopher

middle: T

last: Clarkson

first: Graeme

middle: J

last: Thorn

first: Kai

last: Sohn

first: Madapura

last: Pradeepa

first: Anuradha

last: Apte

first: Sankaran

last: Chandrasekharan

first: Greg

last: Brooke

first: Elena

last: Klenova

first: Victor

last: Zhurkin


title: Identification of different miRNAs in Alzheimer's disease and vascular cognitive impairment and dementia

city: changchun

first: weijie

last: zhai

address: jiefangdalu

department: neurology and nurosience center

institute: the first hospital of jilin university

type: Non-coding RNA profiling by high throughput sequencing

summary: There are many subtypes of dementia without any minimally invasive, low-cost and efficient diagnostic biomarkers. MicroRNA (miRNA) are easily gained and accessible from patients, which may be a promising biomarker for dementia diagnosis and differential diagnosis. We make a completely expression analysis of serum miRNA from 24 participants including post-stroke cognitive impairment (PSCI) group (n=6), post-stroke non-cognitive impairment (PSCI) group, Alzheimer's Disease (AD) group (n=6) and normal control group (NC) group (n=6). Different expression miRNA (DE -miRNA) were screened by LIMMA ebayes method, Benjamini-Hochberg check and fold change (P < 0.05, |log2FC|≥1), we construct a DE-miRNA-key gene-signaling pathway network, the roles of DE-miRNA and related genes and signaling pathways in AD and PSCI were deduced through comprehensive network construction and literature search.

overall_design: Totally, plasma of 24 patients who have been admitted to The Department of Neurology at the First Hospital of Jilin University between 2021 and 2022 were selected. We conduct a comprehensive miRNA expression analysis of plasma samples from group1:post-stroke cognitive impairment (PSCI) group (n=6), group 2: post-stroke non-cognitive impairment (PSCI) group, group 3: Alzheimer's Disease (AD) group (n=6) and group 4: normal control group (NC) group (n=6).

first: Li

last: Sun

first: Weijie

last: Zhai

first: Meng

last: Zhao


title: The lower the better? Impact of radiation dose reduction on radiation-induced lung fibrosis molecular signature: approach towards preclinical model perfection

city: Seodaemun-gu

first: Jaeho

last: Cho

state: Seoul

address: Yonsei-ro

department: Department of Radiation Therapy

country: South Korea

institute: Yonsei University

summary: Radiation-induced pulmonary fibrosis (RIPF) is the most common bottleneck of radiation therapy (RT) that limits its tumor-killing effect. Up to date, there is no effective therapeutic agent for RIPF treatment due to absence of realistic preclinical models. Lungs of mice exposed to focal, highly localized dose of 75Gy-100Gy represents short time-taking (up to 6 weeks) modality for mimicking recent advanced RT, stereotactic body RT-associated lung fibrosis. However, extensive fibrosis and possibility of animal lethality resulted from exposure to high dose raises a question regarding the appropriate dose threshold for limiting unnecessary responses and obtain clinically relevant results. We observed in preliminary trials that lung tissues of 65Gy-exposed mice are still able to develop inflammation and fibrosis at the same time cap. But the molecular changes associated with dose reduction is still unknown. To examine this, bulk RNA from 65Gy and 75Gy irradiated as well as normal lung tissues of mice were obtained, and analysed using computational approach to uncover the transcriptomal similarities and differences between the differentially irradiated samples. Differentially expressed genes (DEGs) were analysed and 2-week and 6-week intersected DEGs as well as 65 and 75Gy exclusive DEGs at 2-week and 6-week time points were detected using venn diagramme. Expression direction of intersected DEGs between 65Gy and 75Gy was checked and found to be consistent at both inflammation and fibrosis stages proven visually by MDS and heatmap graphs. All-times intersected DEGs are 488 and involved in inflammation, cytokine production, and cell proliferation; 2-week intersected DEGs are 221 and involved in cell cycle and DNA damage; 6-week intersected DEGs are 403 and involved in immunoglobin production, extracellular matrix (ECM) deposition, and ECM-receptor interactions. Interestingly, only 75Gy exclusive DEGs of 2 and 6 weeks presented inflammation and fibrosis-related biological process, respectively. These include anti-inflammatory process, cytokine production, EMT, vasculogenesis, and angiogenesis. These results suggested that 65Gy maybe a better dose for delivering less exaggerated, clinically relevant inflammation and fibrotic events, and thus, it can be utilised in establishing appropriate preclinical models for studying RIPF pathology and therapy.

overall_design: 65Gy and 75Gy irradiated and non-irradiated lung tissue taken from left lung of mice strain C57BL/6 after 2 weeks and 6 weeks of exposure time had been RNA extracted and RNA was sequenced for RNA-seq analysis.

first: Mohamed

middle: E

last: Farh

first: Hyun

last: Kim

first: Sang

middle: Y

first: Jae

middle: H

last: Lee

first: Sun

first: Ha

first: Yu

last: Choi

first: Insuk


title: p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response

city: Badalona

first: Biola

last: Javierre

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles , s/n

institute: Josep Carreras Leukaemia Research Institute


title: Sequencing of AsPC-1 cells with CYP3A5 expression modulation

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Purpose: To understand the transcriptome-wide effect of CYP3A5 knockdown or over-expression in AsPC-1 cells

overall_design:
Methods: We obtained expression profiles of cancer cell line AsPC-1 by RNA-sequencing in various conditions.
mRNA profiles of each cell line were obtaiend in triplicate using Illumina-based RNA-Sequencing. Sequencing was conducted as paired-end 100bp reads. The respective controls groups are labeled with "NC" which are samples without Doxycycline, and siNC which are treated with siNon-targeting

first: Ming

last: Shao

middle: C

first: Taosheng

last: Chen


title: p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response [PCHiC]

summary: Activation of the p53 tumor suppressor triggers a transcriptional program to control cellular response to stress. However, the molecular mechanisms by which p53 controls gene transcription are not completely understood. Here, using a multi-omics integration framework, we uncover the critical role of spatio-temporal genome architecture in this process. We demonstrate that p53 drives direct and indirect changes in genome compartments, topologically associating domains and DNA loops within minutes of its activation, which escort the p53 transcriptional program along time. Focused on p53-bound enhancers, we report a core transcriptional program of 340 genes directly regulated by p53 over distance, most of these not previously identified. Finally, we showcase that p53 controls transcription of distal genes through newly formed and pre-existing enhancer-promoter loops in a cohesin dependent manner. Taken together, our findings demonstrate a previously unappreciated architectural role of p53 as regulator at distinct topological layers and provide a reliable set of new p53 direct target genes that may help future designs of p53-based cancer therapies.

overall_design: PCHiC, a version of the Hi-C tecnique that is enriched to capture a list of baits (promoters).

first: François

last: Serra

first: Andrea

last: Nieto-Aliseda

first: Llorenç

last: Rovirosa

first: Mónica

last: Cabrera-Pasadas

first: Lucía

last: Fanlo

first: Aleksey

last: Lazarenkov

first: Blanca

last: Urmeneta

first: Andrei

middle: L

last: Okorokov

first: Peter

last: Fraser

first: Jose

last: Sardina

first: Alfonso

last: Valencia


title: Condensin I folds the C. elegans genome

city: Bern

last: Meister

state: Schweiz

address: Baltzerstrasse 4

department: Institute of Cell Biology

institute: University of Bern


title: Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish

status: Public on Apr 16 2024

city: Research Triangle Park

first: Ciro

middle: Maurizio

last: Amato

state: NC

address: 111 Tw Alexander Dr

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

summary: Previous studies have suggested that adamts9 (a disintegrin and metalloprotease with thrombospondin type-1 motifs, member 9), an extracellular matrix (ECM) metalloprotease, participates in primordial germ cell (PGC) migration and necessary for female fertility. In this study, we found that adamts9 knockout (KO) led to reduced body size, and female to male sex conversion in adult mature zebrafish prior to or after 90 days post fertilization (dpf); however, primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation, significantly reduced number and size of Stage IB follicles (equivalent to primary follicle) in early juveniles of adamts9 KO, and arrested development at Stage IB follicles in mid- or late-juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq, we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together, our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish, and loss of adamts9 in zebrafish leads to ovarian follicle arrest, female infertility, and sex conversion in late juveniles and mature adults.

overall_design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence, we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.

first: Jonathan

last: Carver

first: Humphrey

last: Yao

first: Zhu

last: Yong


title: Blocking CD226 regulates ILC2 effector function and alleviates airway hyperreactivity

first: Yoshihiro

last: Sakano

address: 1450 Biggy street

department: Molecular Microbiology & Immunology

institute: Unversity of Southern California

summary: Type 2 innate lymphoid cells (ILC2s) play a pivotal role in type 2 asthma. CD226 is a costimulatory molecule involved in various inflammatory diseases. Here, we aimed to investigate CD226 expression and function within human and mouse ILC2s, and to assess the impact of targeting CD226 on ILC2-mediated airway hyperreactivity (AHR). Our findings demonstrated an inducible expression of CD226 in activated ILC2s, enhancing their cytokine secretion and effector functions. Blocking CD226 ameliorates ILC2-dependent AHR in IL-33 and Alternaria Alternata-induced models. Interestingly, CD226 is expressed and inducible in human ILC2s, and its blocking reduces cytokine production. Finally, we showed that peripheral ILC2s in asthmatic patients exhibited elevated CD226 expression compared to healthy controls.Our findings underscore the potential of CD226 as a novel therapeutic target in ILC2s, presenting a promising avenue for ameliorating AHR and allergic asthma.

overall_design: mRNA profiles of mouse lung ILC2s from WT mice that were treated  with isotype control or anti-CD226 antibody were generated by deep sequencing, in duplicates, using a NextSeq 500.


title: A germline PAF1 paralog complex ensures cell type-specific gene expression

city: Aarhus

last: Andersen

state: Denmark

address: Universitetsbyen 83

department: MBG

country: Denmark

institute: Aarhus University

summary: Animal germline development and fertility rely on paralogs of general transcription factors that recruit RNA polymerase II to ensure cell type-specific gene expression. It remains unclear whether gene expression processes downstream of such paralog-based transcription is distinct from that of canonical RNA polymerase II genes. In Drosophila, the testis-specific TBP-associated factors (tTAFs) activate over a thousand spermatocyte-specific gene promoters to enable meiosis and germ cell differentiation. Here we show that efficient termination of tTAF-activated transcription requires a testis-specific Polymerase Associated Factor 1 Complex (tPAF) composed of paralogs of canonical Polymerase Associated Factor 1 Complex (PAF1C) proteins. Defective transcription termination in tPAF mutants causes aberrant expression of hundreds of downstream genes due to read-in transcription, compromising cell type-specific gene expression in spermatocytes. Consistently, tPAF is required for the segregation of meiotic chromosomes, sperm individualisation, and male fertility. Comparative in vivo proximity labeling assays of tPAF and PAF1C showed tPAF-specific association with tTAF as well as connections to central RNA polymerase II termination factors. Our study uncovers transcription termination as a developmentally regulated process required for cell type-specific gene expression.

overall_design:
To investigate the impact of the tPAF complex on testis gene expression two RNA-seq experiments were conducted: bulk RNA-seq and RNA-seq using sorted spermatocytes.
For bulk testis RNA-seq, samples were prepared from dissected testis of control and  flies mutant for each of the four tPAF genes For sorted spermatocyte RNA-seq, control genotype was compared to mutants of the Paf1L and Leo1L tPAF genes.

first: Astrid

last: Pold Vilstrup


title: Pronounced early differentiation underlies zebra finch gonadal germ cell development.

city: New York

first: Wei

last: Wang

state: New York

address: 1230 York Ave.

department: Bioinformatics Resource Center

institute: The Rockefeller University

summary: We applied single-cell RNA sequencing to investigate inter-species differences in germ cell development between chicken and zebra finch (Taeniopygia castanotis, formerly Taeniopygia guttata castanotis), a Neoaves songbird species and a common model of vocal learning.

sample_organism:
Gallus gallus
Taeniopygia guttata

platform_organism:
Gallus gallus
Taeniopygia guttata

overall_design: Early embryonic male and female gonads (HH28; n=2 per sex and species) were dissected and dissociated into a single-cell suspension using a 0.05% Trypsin solution. Library preparation was done using 10X Genomics 3' v3.1 kit. Sequencing was done using Illumina NovaSeq S2 flowcell.

first: Matthew

last: Biegler

first: Erich

last: Jarvis

first: Anna

last: Keyte

first: Paul

last: Collier


title: PEX5 integrates p38 MAPK signaling pathway and taurine metabolism to regulate cellular senescence in lung fibroblasts

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

summary: Chronic lung diseases significantly impact the aging population globally, but their etiology is largely unknown, and the therapeutic options are minimal. Cellular senescence has been increasingly recognized as an essential driving mechanism for chronic lung diseases. Remodeling in subcellular compartments is commonly observed in senescent cells, which reciprocally regulates the senescent progression. Roles of peroxisomes in cellular senescence have been documented, but the molecular mechanisms for this regulation remain poorly understood. Here, we showed that the peroxisome pathway and the shuttling receptor PEX5 are downregulated during replicative and oxidative senescence in human fetal lung fibroblast 1 (HFL-1) cells. PEX5 knockdown can induce senescence via transcriptional suppression of LAMP1 and autophagic flux. Further study revealed that activation of the p38 MAPK signaling pathway and subsequent nuclear localization of transcription factor EB (TFEB) are the significant retrograde signals contributing to the PEX5 regulation of cellular senescence. Metabolomics analysis identified a substantial increase in taurine levels in cells with PEX5 overexpression. Reciprocally, treatment of cells with taurine enhanced PEX5 levels in the senescent HFL-1 cells and the lungs of aged mice and alleviated senescence, suggesting the presence of a taurine-dependent response in PEX5 regulation of cellular senescence. Collectively, our findings provided new insights into the peroxisomal regulation of cellular senescence by integrating the p38 MAPK retrograde signaling pathway and taurine metabolism, which may help develop anti-aging strategies to treat chronic lung diseases.

overall_design: To investigate the impact of the shuttling receptor PEX5 for peroxisomes on gene expression in lung fibroblasts, cells were transduced with lentivirus supernatants of Flag, PEX5, shNC, shPEX5-1 or shPEX5-2 for 24 hours. 3 days post-infection, gene expression profiling was conducted using RNA-seq data obtained from three independent replicates.

first: Lingjun

last: Zheng

first: Xiong

last: Su


title: Apobec-Mediated Retroviral Hypermutation In Vivo is Dependent on Mouse Strain

city: Austin

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

summary: Retroviruses cause lifelong infections resulting from their ability to thwart innate immunity. The Apobec family of cytidine deaminases are part of the innate immune response that recognizes and mutates foreign nucleic acids, including those from multiple viruses. Multiple retroviral antagonists of Apobecs have been identified, including mouse mammary tumor virus (MMTV)-encoded Rem protein. Previous experiments have shown that Rem-null MMTV or closely related TBLV proviruses from BALB/c tumors accumulate G-to-A and C-to-T mutations typical of Apobecs compared to wild-type proviruses expressing Rem. The difference in mutations between Rem-expressing and non-expressing MMTV strains largely disappeared in mice lacking the Apobec family member, activation-induced cytidine deaminase (AID). These results suggested that Rem is an AID antagonist. In this study, we attempted to study AID-mediated mutations of TBLV proviruses lacking Rem expression obtained from tumors in C57BL/6 (B6) wild-type and AID-knockout backgrounds. Surprisingly, no differences in G-to-A mutations were observed in TBLV proviruses regardless of Rem expression, yet such mutations were significantly reduced in proviruses obtained from mA3/AID-double knockout mice relative to those from wild-type B6 or AID-knockout mice. Many cellular mRNAs involving the innate immune response, but not Apobecs, were elevated in the absence relative to the presence of Rem expression on the B6 AID-knockout background. These results revealed that Apobec-mediated mutagenesis is dependent on mouse strain and suggested a second means of Rem-dependent immune evasion.

overall_design: Each of two mouse mammary tumor virus (MMTV) strains (TBLV-WT = Rem-expressing or TBLV-SD = lacks Rem expression) was used to generate tumors in C57BL/6 (B6) mice or AID-knockout B6 mice. Three tumors from each mouse strain and virus were extracted for total DNA, and used for PCR to amplify the envelope-LTR region of the TBLV genome. Libraries of viral PCR fragments were prepared prior to MiSeq sequencing and comparison to the cloned TBLV-WT sequence (total of 12 samples). Nanopore sequencing was employed for high-throughput sequence analysis of TBLV proviruses from tumors induced by low-dose TBLV infection. For Nanopore sequencing, we used DNA extracted separately from three tumors for each mouse strain/virus strain combination. Mouse strains used for virus infection were wild-type B6, AID-knockout, and mA3-AID double knockout (6 tumors/strain X 3 strains = 18 tumors for Nanopore sequencing). DNA samples from each of the 18 samples was used for PCR to amplify the envelope-LTR region of the TBLV genome. Libraries of viral PCR fragment were prepared prior to Nanopore sequencing and comparison to the cloned TBLV wild-type (Rem+) sequence.

first: Hyewon

last: Byun

first: Gurvani

last: Singh

first: Wendy

last: Xu

first: Poulami

last: Das

first: Alejandro

last: Reyes

first: Dennis

last: Wylie

first: Mario

last: Santiago

first: Mary

last: Lozano

first: Jaquelin

last: Dudley


title: Single cell RNA-seq of aortas from Tet2flox/flox and Tet2SMC-KO mice receiving high-dosed cholecalciferol

city: Guangzhou

first: Xuejiao

last: Fan

state: Guangdong

address: Tianhe District, Jinsui Road

department: Institute of Pediatrics

institute: Guangzhou Women and Children’s Medical Centre

summary: To investigate the role of TET2 in osteogenic differentiation of smooth muscle cells (SMCs) in vivo, we performed single cell RNA-seq in cholecalciferol overload-induced calcified aortas of Tet2flox/flox and SMC specific Tet2 knock-out mice (Tet2SMC-KO).

overall_design: We performed single cell RNA sequencing (scRNAseq) of aorta tissues from the Tet2flox/flox mice receiving vehicle (WT) or high-dosed cholecalciferol (WT_VD) and Tet2SMC-KO mice receiving high-dosed cholecalciferol (KO_VD) , 3 replicates of each group.

first: Zhi

last: Zeng

first: Wai Ho

last: Tang


title: Integrated transcriptome and Ribosome Profiling analyses elucidate the liver response of rainbow trout (Oncorhynchus mykiss) to heat stress [Ribo-seq]

city: Lanzhou

first: guiyan

last: zhao

address: Yingmen Village 1

institute: Gansu Agricultural University

summary: Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. Through comprehensive multi-omics analysis, we revealed the dynamic translational pattern of rainbow trout liver under heat stress for the first time. Comparative analysis of ribosome analysis data with RNA-seq data showed that the fold changes of gene expression at the transcriptional level were highly correlated (R2 = 0.83) with those at the translational level globally. In total, 2,203 genes exhibited significant alterations exclusively within the translational level. However, the limited overlap in response genes between transcription and translation under heat stress suggests that these two processes may independently modulate the cellular response to thermal challenges. Significant changes in the translation efficiency of 809 genes were observed under heat stress. Further analysis indicated that the translation efficiency of genes were strongly influenced by sequence characteristics such as GC content, coding sequence length and NMFE. Moreover, 3,468 putative uORFs were identified in 2,676 genes, which potentially modulating translation efficiency of mORFs. These findings provide a novel perspective for understanding the physiological adaptations of rainbow trout in response to changes in ambient temperature.

overall_design: Ribosome profiling expression  in the liver of rainbow trout (Oncorhynchus mykiss) at 18C and heat stress (24C)  for 8 h

first: Zhe

last: Liu

first: Gui-yan

last: Zhao


title: Transcriptomic analysis of C. elegans mutants which do not respond to oomycete exposure

city: London

first: Michalis

last: Barkoulas

address: SAF Building, South Kensington

institute: Imperial College London

summary: We have established epidermal expression of chil-27p::GFP as the marker for activation of oomycete recognition response (ORR) in C. elegans. Through a forward genetic screen, we identified clec-27, clec-35, and ceh-37 to be the key players required for activating chil-27p::GFP upon exposure to the oomycete Myzocytiopsis humicola extract. To determine if activation of entire ORR is affected in these mutants, we analyzed their transcriptome in the presence and absence of extract and compared with that of wildtype C. elegans.

overall_design: Comparative gene expression of M. humicola extract treated N2, ceh-37(ok642), clec-27(icb104), and clec-35(icb105) animals at L4 stage with untreated controls.

first: Kenneth

first: Manish

last: Grover


title: Role of CASZ1 in keratinocyte differentiation [RNA-seq]

city: Beer Sheva

first: Idan

last: Cohen

address: David Ben Gurion Blvd 1

department: Microbiology, Immunology and Genetics

country: Israel

institute: Ben-Gurion University

summary: Here we indentified CASZ1 as an essential regulator of the epidermal differentiation program.

overall_design: Differentiated human epidermal keratinocytes  were treated with CASZ1 shRNA or control shRNA, cells were isolated and RNA was apurified and analyzed by RNA-seq.

first: Liat

last: Oss-Ronen


title: ACCELERATED CD8+ T CELL MATURATION IN INFANTS WITH PERINATAL HIV INFECTION

city: Miami

first: Akshay

last: Iyer

state: FL

institute: University of Miami

summary: In perinatal HIV infection, early ART initiation is recommended but questions remain regarding infant immune responses to HIV and impact of HIV on immune development. Using single cell transcriptional and phenotypic analysis we evaluated the T cell compartment at pre-ART initiation of infants with perinatally acquired HIV from Maputo, Mozambique (TARA cohort). CD8+ T cell maturation subsets exhibited altered distribution in HIV exposed infected (HEI) infants relative to control infants (HIV exposed uninfected) with reduced naïve, increased effectors, higher frequencies of activated T cells, and lower frequencies of cells with markers of self-renewal. Additionally, a cluster of CD8+ T cells identified in HEI displayed gene profiles consistent with cytotoxic T lymphocytes (CTL) and showed evidence for hyper expansion. Longitudinal phenotypic analysis revealed accelerated maturation of CD8+ T cells was maintained in HEI despite viral control. The results point to a HIV directed immune response that is likely to influence reservoir establishment.

overall_design: Investigate gene expression profiles and T cell and B cell clonality in PBMC from 1 month old infants that aquired HIV perinatally.

first: Lesley

last: De Armas

first: Savita

last: Pahwa


title: Fibrin promotes oxidative stress and neuronal loss in traumatic brain injury via innate immune activation

city: San Francisco, CA

first: Katerina

last: akassoglou

address: 1650 Owens st

institute: Gladstone Institutes

summary: Traumatic brain injury (TBI) causes significant blood-brain barrier (BBB) breakdown, resulting in the extravasation of blood proteins into the brain. The impact of blood proteins, especially fibrinogen, on inflammation and neurodegeneration post-TBI is not fully understood, highlighting a critical gap in our comprehension of TBI pathology and its connection to innate immune activation. We combined vascular casting with 3D imaging of solvent-cleared organs (uDISCO) to study the spatial distribution of the blood coagulation protein fibrinogen in large, intact brain volumes and assessed the temporal regulation of the fibrin(ogen) deposition by immunohistochemistry in a murine model of TBI. Fibrin(ogen) deposition and innate immune cell markers were co-localized by immunohistochemistry in mouse and human brains after TBI. We assessed the role of fibrinogen in TBI using unbiased transcriptomics, flow cytometry and immunohistochemistry for innate immune and neuronal markers in Fggγ390–396A knock-in mice, which express a mutant fibrinogen that retains normal clotting function, but lacks the γ390–396 binding motif to CD11b/CD18 integrin receptor. We show that cerebral fibrinogen deposits were associated with activated innate immune cells in both human and murine TBI. Genetic elimination of fibrin-CD11b interaction reduced peripheral monocyte recruitment and the activation of inflammatory and reactive oxygen species (ROS) gene pathways in microglia and macrophages after TBI. Blockade of the fibrin-CD11b interaction was also protective from oxidative stress damage and cortical loss after TBI. These data suggest that fibrinogen is a regulator of innate immune activation and neurodegeneration in TBI. Abrogating post-injury neuroinflammation by selective blockade of fibrin’s inflammatory functions may have implications for long-term neurologic recovery following brain trauma.

overall_design: C57BL/6 and Fggg390-396A mice underwent controlled cortical impact (CCI), a model of TBI. 24h post CCI, CD45lowCD11b+ and CD45hiCD11b+ immune cells were sorted from ipsilaterial brain regions and profiled via bulk RNA-seq. See Methods of publication for detailed experimental details.

first: Andrew

middle: S

last: Mendiola

last: Akassoglou

first: Jae

last: Ryu


title: Role of CASZ1 in keratinocyte differentiation [CUT&RUN]

overall_design: Differentiated human epidermal keratinocytes  were  isolated and analyzeb by CUT&RUN.


title: New perspective on the origin of adaptive evolution: a study on cytidine deaminase in lampreys

city: Dalian

first: Zihao

last: Yan

state: Liaoning

address: Ganjingzi District

department: School of Life Science

institute: Liaoning Normal University

summary: This study evaluates the similarity of adaptive immune mechanisms between jawless and jawed vertebrates using lamprey cytidine deaminase (CDA). We identified the ancestral gene Lr-CDAs of the AID/APOBEC deaminase family and evaluated its biological function in vivo. Lr-CDA1 deletion affected the assembly of three types of variable lymphocyte receptors (VLRs). We identified a switch-like region in lamprey gVLRs bound to Lr-CDAs, which upon repression, downregulated VLRB expression. Overall, we propose that lampreys have an early form of class switch recombination (CSR) that is mediated by Lr-CDAs and acts on gVLRs, affecting the assembly, maturation, and diversity regulation of VLR genes in Lethenteron reissneri. This CSR process in lampreys is linked to tumorigenesis and chromosomal translocation markers via Lr-CDAs.

overall_design:
We conducted a gene knockout experiment on Lr-CDA1 and collected embryos identified as successful CDA1 knockouts.
Then, we conducted gene expression profiling analysis using the RNA-seq data obtained from the CDA1 knockout experimental group and the control group.
By comparing the gene expression profiles between experimental and control groups using RNA-seq data analysis, we aim to identify genes that interact with or are regulated by CDA1.

first: Yinglun

last: Han


title: Gene expression profile at single cell level of Gli1+ progenitors from the metaphysis of distal femur and proximal tibia in response to MPS.

city: Chendu

first: Fangyuan

last: Shen

state: --- Select a state ---

address: No.29 Jiuyanqiao Wangjiang Road, Chengdu, 610064

institute: Sichuan University

summary: Gli1+ progenitors are considered as metaphyseal mesenchymal progenitors in the distal femur and proximal tibia under the growth plate. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of Gli1+ progenitors in response to methylprednisolone.

overall_design: Gli1+ progenitors of the Gli1-CreERT2; tdTomato mice were isolated by Flourescence-activated cell sorting (FACS) according to the presence or absence of PE signal and analyzed using scRNAseq.

first: Puying

last: Yang

first: Yu

last: Shi


title: Transcriptomic alterations in cortical astrocytes following the development of post-traumatic epilepsy

city: Blacksburg

first: Michelle

middle: Lynne

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Tech

summary: We aimed to identify molecular signatures of astrocytes isolated from the cortex in sham or CCI injured mice with or without spontaneous recurrent seizures

overall_design: Utilizing the murine unilateral focal control cortical impact (CCI) injury, we evaluated seizure onset using 24/7 EEG video analysis at 2-4 months post-injury. Isolation of region-specific astrocytes and RNA-seq was performed to determine differential gene expression in PTE+ vs. PTE- that may comport with the epileptogenic process

last: Theus


title: Transcriptomics changes upon WNK1 knockdown in JJN3 cells

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

summary: We performed RNA-seq in JJN3 human multiple myeloma cells with or without WNK1 knockdown to profile global transcriptomic changes

overall_design: RNA-seq in JJN3 cells tranduced with NS or WNK1 shRNA

first: Tianyi

last: Ye


title: Transcriptomics changes upon WNK463 treatment in JJN3 cells

summary: We performed RNA-seq in JJN3 human multiple myeloma cells treated with WNK463 to profile global transcriptomic changes

overall_design: RNA-seq in JJN3 cells treated with WNK463 (1μΜ) for 0/2/6 hours


title: Exosomal miRNA profile of BNCT treated glioblastoma cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: An increase in 380 miRNAs (ratio>2) and a decrease in 145 miRNAs (ratio<0.5) were detected in BNCT cells compared with non-irradiated cells.

overall_design: miRNA in exosomes from BNCT-treated glioblastoma cells and non-treated cells were investigated with microarray

first: Natsuko

first: Tadatoshi

last: Kinouchi


title: Global mapping of H3K27ac and RPB1 occupancy upon WNK463 treatment

summary: ChIP-seq for H3K27ac and RPB1 in JJN3 cells treated with DMSO or WNK463


title: WNK463 effect on JJN3 cells

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

overall_design: Refer to individual Series


title: Cancer-associated Fibroblast Spatial Heterogeneity and EMILIN1 Expression in Cancer Stroma Modulate TGF-b Activity and CD8+ T-Cell Infiltration in Breast Cancer

city: Montpellier

first: Andrei

last: Turtoi

address: 208 Avenue des Apothicaires

country: France

institute: Institut de Recherche en Cancérologie de Montpellier

summary: The tumor microenvironment (TME) and its multifaceted interactions with cancer cells are major targets for cancer treatment. Single-cell technologies have brought major insights into the TME, but the resulting complexity frequently precludes conclusions on function. Therefore, we combined single-cell RNA sequencing and spatial transcriptomic data to explore the relationship between different cancer-associated fibroblast (CAF) populations and immune cell exclusion in breast tumors. Our data show for the first time the degree of spatial organization of different CAF populations in breast cancer. We found that IL-iCAFs, Detox-iCAFs, and IFNγ-iCAFs tended to cluster together, while Wound-myCAFs, TGFb-myCAFs, and ECM-myCAFs formed another group that overlapped with elevated TGF-b signaling. Differential gene expression analysis of areas with CD8+ T-cell infiltration/exclusion within the TGF-b signaling-rich zones identified elastin microfibrillar interface protein 1 (EMILIN1) as a top modulated gene. EMILIN1, a TGF-b inhibitor, was upregulated in IFNγ-iCAFs directly modulating TGFb immunosuppressive function. Histological analysis of 74 breast cancer samples confirmed that high EMILIN-1 expression in the tumor margins was related to high CD8+ T-cell infiltration, consistent with our spatial gene expression analysis. High EMILIN-1 expression was also associated with better prognosis of patients with breast cancer, underscoring its functional significance for the recruitment of cytotoxic T cells into the tumor area. In conclusion, our data show that correlating TGF-b signaling to a CAF subpopulation is not enough because proteins with TGF-b-modulating activity originating from other CAF subpopulations can alter its activity. Therefore, therapeutic targeting should remain focused on biological processes rather than on specific CAF subtypes.

overall_design: Spatial gene expression analysis of 4 breast cancer samples of different HER2 and HR status was done with the Visium Spatial Gene Expression Reagent Kit (10x Genomics) following the manufacturer’s user guide.

first: Takehiko

last: Yokobori


title: Truncated protein isoforms generate diversity of protein localization and function in yeast

city: Berkeley

first: Gloria

last: Brar

state: CA

address: 616 Barker Hall

department: Molecular and Cell Biology

institute: UC Berkeley

summary: Genome-wide measurements of ribosome occupancy on mRNA transcripts have enabled global empirical identification of translated regions. These approaches have revealed an unexpected diversity of protein products, but high-confidence identification of new coding regions that entirely overlap annotated coding regions – including those that encode truncated protein isoforms – has remained challenging. Here, we develop a sensitive and robust algorithm focused on identifying N-terminally truncated proteins genome-wide, identifying 388 truncated protein isoforms, a more than 30-fold increase in the number known in budding yeast. We perform extensive experimental validation of these truncated proteins and define two general classes. The first set lack large portions of the annotated protein sequence and tend to be produced from a truncated transcript. We show two such cases, Yap5truncation and Pus1truncation, to have condition-specific regulation and functions that appear distinct from their respective annotated isoforms. The second set of N-terminally truncated proteins lack only a small region of the annotated protein and are less likely to be regulated by an alternative transcript isoform. Many localize to different subcellular compartments than their annotated counterpart, representing a common strategy for achieving dual localization of otherwise functionally identical proteins.

overall_design: To investigate the function of a truncated isoform of Pus1 in S. cerevisiae, we generated strains capable of expressing truncated Pus1 under control of an anhydrotetracyclin (aTC)-inducible promoter, in either a WT or PUS1 delete background. aTC-treated and vehicle (DMS0)-treated control samples were included. Samples were collected during vegetative exponential growth, at 3h post-dilution in YEPD. 2 replicates for each condition are included.

first: Andrea

last: Higdon

first: Nathan

last: Won

middle: A


title: Precise immuno-fluorescence canceling enables highly multiplexed imaging

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation


title: Long-term multi-modal recording reveals unpredictable nongenetic adaptation routes in dormant breast cancer cells. [gBarcodes]

first: Heena

last: Dhiman

address: 72 Du Cane Road

summary: Patients diagnosed with hormone dependent breast cancer (HDBC) receive five or more years of adjuvant endocrine therapies (ET). Adjuvant treatment delays relapse by targeting hidden micro-metastatic deposits, yet up to 50% of treated patients experience recurrent disease, often many years after surgery. The mechanisms driving these subtype-specific clinical dynamics are largely unknown but likely involve dormancy2. We developed two approaches to study the long-term fate of dormant cells in unprecedented details. Firstly, we took advantage of a rare cohort of patients treated upfront with first line ETs until progression to dissect the contribution of genomic events to tumour awakening. Next, we developed a first of its kind in vitro evolutionary study to systematically record adaptive strategies of individual clonal lineages in parallel unperturbed systems during a period of several months. Collectively our data suggest that ETs induce an inherently unstable persister dormant state in a stochastically selected fraction of lineages. Over time, single cells spontaneously escape dormancy and divergently adapt via heritable transcriptional reprogramming, often developing distinct collateral resistance. Overall, this study uncovers previously unsuspected roles for non-genetic plasticity during dormancy with profound clinical implications for breast cancer.

overall_design: RNAseq data for TRADITIOM High

first: Dalia

last: Rosano

first: Emre

last: Sofyali

first: Diana

last: Ivanoiu


title: Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells

type: Genome variation profiling by high throughput sequencing


title: Long-term multi-modal recording reveals unpredictable nongenetic adaptation routes in dormant breast cancer cells. [WGS]

summary: Patients diagnosed with hormone dependent breast cancer (HDBC) receive five or more years of adjuvant endocrine therapies (ET). Adjuvant treatment delays relapse1,2 by targeting hidden micro-metastatic deposits, yet up to 50% of treated patients experience recurrent disease, often many years after surgery1. The mechanisms driving these subtype-specific clinical dynamics are largely unknown but likely involve dormancy2. We developed two approaches to study the long-term fate of dormant cells in unprecedented details. Firstly, we took advantage of a rare cohort of patients treated upfront with first line ETs until progression to dissect the contribution of genomic events to tumour awakening. Next, we developed a first of its kind in vitro evolutionary study to systematically record adaptive strategies of individual clonal lineages in parallel unperturbed systems during a period of several months. Collectively our data suggest that ETs induce an inherently unstable persister dormant state in a stochastically selected fraction of lineages. Over time, single cells spontaneously escape dormancy, often without developing resistance. Ultimately, single lineages and divergently divergently adapt via heritable transcriptional reprogramming, often developing distinct collateral resistance. Overall, this study uncovers previously unsuspected roles for non-genetic plasticity during dormancy with profound clinical implications for breast cancer.

overall_design: WGS data for TRADITIOM High


title: Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [RNA-Seq]

summary: Patients diagnosed with hormone dependent breast cancer (HDBC) receive five or more years of adjuvant endocrine therapies (ETs). Adjuvant ETs delay relapse by targeting clinically undetectable micro-metastatic deposits, yet up to 50% of patients receiving ET relapse at a constant rate over the course of decades after surgery. The mechanisms driving these clinical dynamics are largely unknown but likely involve dormancy. We developed two approaches to study the fate of dormant cells in long-term experiments. Firstly, we profiled samples from late relapse (10-35 yrs.) and patients treated with 16-44 months of neoadjuvant ETs until progression to dissect the contribution of genetic and transcriptional changes to tumour awakening. Next, we developed a first of its kind in vitro evolutionary study to systematically record adaptive strategies of individual lineages in unperturbed parallel experiments through several months. Collectively our data demonstrate that ETs induce a heritable cell state transition into dormancy via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably via epigenetic erosion. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs with profound implications for breast cancer.


title: Reliance of neuronal gene expression on cohesin scales with chromatin loop length (5C)

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: 5C-seq from Rad21lox/lox;NexCre/+ and Rad21+/+;NexCre/+ dissociated cortical neurons at Day In Vitro (DIV10) without stimulation or after treatment with TTX/D-AP5 and 1h of KCl depolarization.  And, 5C of and doxycycline treated Rad21-TEV primary neurons transduced with NLS-TEV

overall_design: 5C-seq from Rad21lox/lox;NexCre/+ and Rad21+/+;NexCre/+ dissociated cortical neurons at Day In Vitro (DIV10) without stimulation or after treatment with TTX/D-AP5 and 1h of KCl depolarization.  And, Total of 8 samples analysed; 2 replicates of Rad21-tev primary neurons 24h following doxycyline treatment (6 hours, 100ng/ml), 2 replicates of Rad21-tev primary neurons 24h following vehicle treatment. 2 replicates of Rad21-tev primary neurons 7 days following doxycycline treatment (6 hours, 100ng/ml), 2 replicates of Rad21-tev primary neurons 7 days following vehicle treatment.

first: Matthias

last: Merkenschlager

first: Jonathan

last: Beagan

first: Felix

last: Weiss

first: Yi-Fang

last: Wang


title: RNA sequencing in iAM-1 differentiated cells and RnSbk2 knockdown

city: Leiden

first: Pim

last: van Gorp

state: Zuid-Holland

address: Albinusdreef 2

department: Experimental Cardiology

country: Netherlands

institute: Leiden University Medical Center

overall_design: Examination of transcriptome of conditionally immortalized neonatal rat atrial myocytes treated with lentiviral shRNA RnSbk2 knockdown constructs

first: P

first: A

last: de Vries


title: RHAMMB promotes metastasis of pancreatic neuroendocrine tumor

city: New York

first: Nancy

last: Du

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Analysis of molecular mechanisms by which RHAMMB promote metastasis of pancreatic neuroendocrine tumor.

overall_design: The transcriptomes of N134 subcutaneous tumors (N134_SC), N134-RHAMMB subcutaneous tumors (N134_RHB_SC), and N134-RHAMMB liver mets (N134_RHB_met) were profiled and the differential expressed genes were identified.

first: Yi-Chieh

middle: N

first: Xiang

last: Chen


title: Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq]


title: Exercise intervention during pregnancy induces promoter methylation alterations in maternal blood and cord blood

city: Beijing

first: Jie

last: Yan

address: Xi'anmen Street

institute: Peking University First Hospital

summary:
Maternal blood, as well as umbilical cord blood samples, were collected and DNA methylation levels were determined by Illumina MethylationEPIC microarray.
Methods: Twenty-four subjects were chosen from a previous clinical study. Overweight/obese pregnant women (body mass index ≥24kg/m2) who had an uncomplicated pregnancy at <12+6 weeks of gestation were randomly allocated to either an exercise or a control group. Patients allocated to the exercise group performed 3 exercise bouts per week (at least 30 min/session with a rating of perceived exertion between 12-14) via a cycling program that was initiated within 3 days of randomization until 37 weeks of gestation. Patients allocated to the control group continued their usual daily activities. Maternal blood, as well as umbilical cord blood samples, were collected and DNA methylation levels were determined by Illumina MethylationEPIC microarray.

overall_design: Bisulphite converted DNA from the 96 samples were hybridised to the Illumina MethylationEPIC microarray.

first: Huixia

last: Yang


title: Effect of shear stress on Chromatin structure

city: Riverside

first: Brendan

last: Gongol

address: 900 University Ave

institute: University of California, Riverside

summary: This study aimed to investigate chromatin accessibility in endothelial cells under pulsatile shear stress (PS) and Oscillatory shear stress (OS). The ATACseq signals were measured at four-time points (0, 2, 8, and 16 hr) under PS or OS. Three replicates were used for each condition and time point.

overall_design: HUVECS were cultured in M199 medium (Gibco) supplemented with 15% fetal bovine serum (FBS) , 1 ng/ml recombinant human fibroblast growth factor, 90 μg/ml heparin, 20 mM HEPES (pH 7.4), and 100 U/ml penicillin-streptomycin. Samples for ATAC sequencing were collected at 0, 2, 8, 16hr following exposure to shear stress.  Three biological replicates were collected for each treatment and each at each time point. Following treatment, nuclei were isolated from ECs lysed in lysis buffer containing 10 mmol/L Tris-HCl, 10 mmol/L NaCl, 3 mmol/L MgCl2, and 0.1% NP-40. Resulting nuclei were incubated in 50 transposition buffer (Nextera DNA Library Preparation Kit; Illumina) and DNA samples were purified with Qiagen MinElute PCR purification kit followed by library preparation and  paired-end sequencing on an Illumina NextSeq 500 sequencing platform.

first: John

last: Shyy

first: Ming

last: He


title: Gene expression of rat BMSCs stimulated with or without dexamethasone

status: Public on Apr 15 2024

city: Wuhan, Hubei, China

first: yongle

last: yu

state: 湖北

address: Wuhan, Hubei, China

institute: 武汉大学第二临床学院

summary: Steroid-induced avascular necrosis of the femoral head (SANFH) is closely associated with the imbalance between adipogenic and osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). Additionally, epigenetic regulation plays a critical role in this process. Our previous research found that during BMSC adipogenic differentiation, C/EBPα enhances the histone H3K27 acetylation modification at the PPARγ promoter, promoting sustained adipogenic differentiation of BMSCs, suggesting that Histone deacetylases (HDACs) may play an important role in BMSC adipogenic differentiation. However, identifying specific HDAC target genes requires further investigation. This study combines cell experiments with clinical specimen experiments to screen specific HDAC genes involved in BMSC adipogenic differentiation and explore their preliminary functions. Our findings indicate that HDAC10 influences the progression of steroid-induced avascular necrosis of the femoral head by regulating BMSC adipogenic differentiation, possibly through its association with PPARγ histone acetylation. These discoveries provide promising directions for the treatment of steroid-induced avascular necrosis of the femoral head.

overall_design: The BMSC of rats was cultured to 80%, and the samples were collected after 4 days of culture with or without 100uM dexamethasone

first: Yong-Le

last: Yu

first: Ping

last: Duan

first: Lin

last: Zheng

first: Jun-Miao

last: Xu

first: Hui

first: Jia-Dong

first: Xing

last: Ye

first: Zhong-Xuan

last: Zhu

first: Zhen-Yu

last: Pan


title: Apobec-Mediated Retroviral Hypermutation In Vivo is Dependent on Mouse Strain [RNA-seq]

city: Austin

first: Anna

last: Battenhouse

address: 100 East 24th St., Stop A5000

institute: The University of Texas at Austin

summary: Retroviruses cause lifelong infections resulting from their ability to thwart innate immunity. The Apobec family of cytidine deaminases are part of the innate immune response that recognizes and mutates foreign nucleic acids, including those from multiple viruses. Multiple retroviral antagonists of Apobecs have been identified, including mouse mammary tumor virus (MMTV)-encoded Rem protein. Previous experiments have shown that Rem-null MMTV or closely related TBLV proviruses from BALB/c tumors accumulate G-to-A and C-to-T mutations typical of Apobecs compared to wild-type proviruses expressing Rem. The difference in mutations between Rem-expressing and non-expressing MMTV strains largely disappeared in mice lacking the Apobec family member, activation-induced cytidine deaminase (AID). These results suggested that Rem is an AID antagonist. In this study, we attempted to study AID-mediated mutations of TBLV proviruses lacking Rem expression obtained from tumors in C57BL/6 (B6) wild-type and AID-knockout backgrounds. Surprisingly, no differences in G-to-A mutations were observed in TBLV proviruses regardless of Rem expression, yet such mutations were significantly reduced in proviruses obtained from mA3/AID-double knockout mice relative to those from wild-type B6 or AID-knockout mice. Many cellular mRNAs involving the innate immune response, but not Apobecs, were elevated in the absence relative to the presence of Rem expression on the B6 AID-knockout background. These results revealed that Apobec-mediated mutagenesis is dependent on mouse strain and suggested a second means of Rem-dependent immune evasion.

overall_design: Each of two mouse mammary tumor virus (MMTV) strains (TBLV-WT = Rem-expressing or TBLV-SD = lacks Rem expression) was used to generate tumors in C57BL/6 (B6) mice or AID-knockout B6 mice. For RNAseq, we extracted four or five tumors induced by infection with TBLV-WT (Rem+) or TBLV-SD (Rem-) either in wild-type B6 mice or AID-knockout mice. Total RNA was extracted separately from each tumor for analysis and used for library preparation prior to sequencing.

first: Hyewon

last: Byun

first: Gurvani

last: Singh

first: Wendy

middle: K

first: Poulami

last: Das

first: Alejandro

last: Reyes

first: Dennis

last: Wylie

first: Mario

last: Santiago

first: Mary

middle: M

last: Lozano

first: Jaquelin

middle: P

last: Dudley


title: Direct and indirect effetcs of CYTOR lncRNA regulate HIV gene expression

city: Beer Sheva

first: Ran

middle: Taube Pathology Rm

last: Taube

state: ISRAEL

address: Biotechnology Building 3, room 324

department: Microbiology

institute: Ben Gurion University

summary:
The implementation of antiretroviral therapy (ART) has effectively restricted the transmission of Human Immunodeficiency Virus (HIV) and improved overall clinical outcomes. However, a complete cure for HIV remains out of reach, as the virus persists in a stable pool of infected cell reservoir that is resistant to therapy and thus a main barrier towards complete elimination of viral infection. While the mechanisms by which host proteins govern viral gene expression and latency are well-studied, the emerging regulatory functions of non-coding RNAs (ncRNA) in the context of T cell activation, HIV gene expression and viral latency have not yet been thoroughly explored.
Here, we report the identification of the Cytoskeleton Regulator (CYTOR) long non-coding RNA (lncRNA) as an activator of HIV gene expression that is upregulated following T cell stimulation. Functional studies show that CYTOR suppresses viral latency by directly binding to the HIV promoter and associating with the cellular positive transcription elongation factor (P-TEFb) to activate viral gene expression. CYTOR also plays a global role in regulating cellular gene expression, including those involved in controlling actin dynamics. Depletion of CYTOR expression reduces cytoplasmic actin polymerization in response to T cell activation. In addition, treating HIV-infected cells with pharmacological inhibitors of actin polymerization reduces HIV gene expression. We conclude that both direct and indirect effects of CYTOR regulate HIV gene expression.

overall_design: HIV infected Jurkat T Jlat 6.3 cells were stimulated and cells that carry active or latent HIV were subjected to RNA-Seq

first: Kuzmina

last: Alona


title: Exploring the utility of circulating miRNAs as diagnostic biomarkers of fasciolosis

city: Ultimo

first: Dayna

last: Sais

state: New South Wales

address: 15 Broadway

country: Australia

institute: University of Technology Sydney

summary: Effective management and control of parasitic infections on farms depends on their early detection. Traditional serological diagnostic methods for Fasciola hepatica infection in livestock are specific and sensitive, but currently the earliest detection of the parasite only occurs at approximately three weeks post-infection. At this timepoint, parasites have already entered the liver and caused the tissue damage and immunopathology that results in reduced body weight and loss in productivity. Here, we investigated whether the differential abundance of micro(mi)miRNAs in sera of F. hepatica-infected sheep has potential as a tool for the early diagnosis of infection. Using miRNA sequencing analysis, we discovered specific profiles of sheep miRNAs at both the pre-hepatic and hepatic infection phases in comparison to non-infected sheep. In addition, six F. hepatica-derived miRNAs were specifically identified in sera from infected sheep. Thus, a panel of differentially expressed miRNAs comprising four sheep (miR-3231-3p; miR133-5p; 3957-5p; 1197-3p) and two parasite miRNAs (miR-124-3p; miR-Novel-11-5p) were selected as potential biomarkers. The expression of these candidates in sera samples from longitudinal sheep infection studies collected between 7 days and 23 weeks was quantified using RT-qPCR and compared to samples from age-matched non-infected sheep. We identified oar-miR-133-5p and oar-miR-3957-5p as promising biomarkers of fasciolosis, detecting infection as early as 7 days. The differential expression of the other selected miRNAs was not sufficient to diagnose infection; however, our analysis found that the most abundant forms of fhe-miR-124-3p in sera were sequence variants (IsomiRs) of the canonical miRNA, highlighting the critical importance of primer design for accurate diagnostic RT-qPCR. Accordingly, this investigative study suggests that certain miRNAs are biomarkers of F. hepatica infection and validates miRNA-based diagnostics for the detection of fasciolosis in sheep.

overall_design: Performed small-RNA sequencing on total RNA isolated from serum harvested from sheep infected with Fasciola hepatica at different timpoints including, 0, 2, 9, 14 and 18 days post infection and 3, 7, 10, 14 weeks post infection and 14 weeks uninfected. Sheep and Fasciola hepatica miRNAs were assessed.

first: Sumaiya

last: Chowdhury

first: Alison

last: Ricafrente

first: Sheila

last: Donnelley

first: Nham

last: Tran


title: RNA Seq of IAPP expressing SC-β cells

city: Cambridge

first: Jeffrey

last: Davis

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: Islet transplantation for treatment of diabetes is limited by availability of donor islets and requirements for immunosuppression. Stem cell-derived islets might circumvent these issues. SC-islets effectively control glucose metabolism post transplantation, but do not yet achieve full function in vitro with currently published differentiation protocols. We aimed to identify markers of mature subpopulations of SC-β cells by studying transcriptional changes associated with in vivo maturation of SC-β cells using RNA-seq and co-expression network analysis. The β cell-specific hormone islet amyloid polypeptide (IAPP) emerged as the top candidate to be such a marker. IAPP+ cells had more mature β cell gene expression and higher cellular insulin content than IAPP- cells in vitro. IAPP+ INS+ cells were more stable in long-term culture than IAPP- INS+ cells and retained insulin expression after transplantation into mice. Finally, we conducted a small molecule screen to identify compounds that enhance IAPP expression. Aconitine up-regulated IAPP and could help to optimize differentiation protocols.

overall_design:
ANGIs iPS cells were differentiated into stage 6 SC-β cells for two weeks and sorted into two populations of INS+ IAPP+ and INS+ IAPP- cells . After FACS isolation of these subpopulations RNA was collected and analyzed by RNA Seq

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no Raw data due to European GDPR law
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first: M

last: Ryaboshapkina


title: Spatiotemporal transcriptomic changes of human ovarian aging and the key regulatory role of FOXP1

city: Wuhan

first: Shixuan

last: Wang

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: The understanding of how aging affects the cellular and molecular components of the human ovary and contributes to age-related fertility decline is still limited. Here, we systematically characterize human ovarian aging by combining single-cell RNA sequencing and spatial transcriptomics. We provide a comprehensive understanding  of human ovarian aging and a resource for the development of new diagnostic biomarkers and therapeutic strategies.

overall_design: The ovarian tissues of the 15 cases were divided into 3 groups based on ovarian function: young group (Y, 18-28 y), middle-aged group (M, 36-39 y), and old group (O, 47-49 y). We generated scRNA-seq data for 9 ovarian tissues (from 9 women) and ST-seq data for 28 ovarian tissues (from 15 women).

first: Meng

last: Wu

first: Weicheng

last: Tang


title: Primordial germ cell DNA demethylation and development require DNA translesion synthesis

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

type: Methylation profiling by high throughput sequencing

summary: Mutations in DNA damage response (DDR) factors are associated with human infertility, which affects up to 15% of the population. It remains unclear if the role of DDR is solely in meiosis. One pathway implicated in human fertility is DNA translesion synthesis (TLS), which allows replication impediments to be bypassed. We find that TLS is essential for pre-meiotic germ cell development in the embryo. Loss of the central TLS component, REV1, significantly inhibits the induction of human PGC-like cells (hPGCLCs). This is recapitulated in mice, where deficiencies in TLS initiation (Rev1-/- or PcnaK164R/K164R) or extension (Rev7-/-) result in a >150-fold reduction in the number of primordial germ cells (PGCs) and complete sterility. In contrast, the absence of TLS does not impact the growth, function, or homeostasis of somatic tissues. Surprisingly, we find a complete failure in both DNA demethylation, a critical step in germline epigenetic reprogramming, and in activation of the germ cell transcriptional program. Our findings show that for normal fertility, DNA repair is required not only for meiotic recombination but for completion of DNA demethylation and the progression of PGC development.

overall_design: Bisulfite sequencing of Pcna knockout and wildtype mouse PGCs

first: Pranay

last: Shah

first: Ross

last: Hill

first: Stephen

last: Clark

first: Camille

last: Dion

first: Abdulkadir

last: Abakir

first: Mark

last: Arends

first: Harry

last: Leitch

first: Wolf

last: Reik

first: Gerry

last: Crossan


title: Single-cell RNA sequencing of circulating OR tumor infiltrating mock-electroporated and BTLA-knockout 41BBzeta CART19 cells

city: Philadelphia

first: Puneeth

last: Guruprasad

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Single-cell gene expression of 4-1BBzeta CART19 cells in both the peripheral blood (model 1) and tumor-infiltrating (model 2) of OCI-Ly18 DLBCL-bearing mice. Cells were captured and processed using 10X 5' v2 Chemistry GEX

overall_design: CART19, produced from a healthy human donor, were infused into OCI-Ly18 bearing mice. In model 1: on day -10, 5 × 1e6  luciferase+ OCILy18 cells were implanted subcutaneously into NSG mice. On day 0, 4 × 1e6 cells WT (n=8 mice) or BTLA KO (n=6 mice) CART19 cells were infused into tumor bearing mice. On day 16, mice were bled via retro-orbital sinus; human T cells from individual mice were barcoded, pooled based on condition (WT or BTLA KO) and sorted via FACS (CD3+CD2+CD5+). In model 2:  5 × 1e6 OCI-Ly18 were implanted into NSG mice on day -14. Then, on day 0, 4 × 1e6 WT (n=2 mice) or BTLA KO (n=2 mice) CART19 were infused via tail vein. On day 11 post-infusion, tumors were resected, minced, and filtered (70 µm & 40 µm). Mice tumor suspensions were pooled per condition (2 per arm); TILs were then sorted via FACS (CD2+CD5+).

first: Guruprasad

last: Puneeth

first: Chen

last: Linhui

first: Ruella

last: Marco


title: The difference between intraepithelial mast cells and lamina propria mast cells (ATAC-seq)

first: Liu

last: Yang

address: Qinghuayuan street

institute: Tsinghua University

summary: Type 2 immune responses are crucial for protection against helminth infections and for the maintenance of tissue homeostasis, yet the underlying mechanisms of immune activation remain incompletely understood. Here, we study the role of mast cells in type 2 immunity. While the number of lamina propria residing mast cells (termed LPMCs hereinafter) remained stable, intraepithelial mast cells (termed IEMCs hereinafter) markedly expanded during the course of type 2 responses. We uncovered a new type 2 response mechanism depending on the crosstalk between mast cells and epithelial cells, and defined the function of intraepithelial mast cells.

overall_design: H. polygyrus larvae were used to infect WT mice. After 14 days, IEMCs and LPMCs were sorted from infected intestinal epithelium and LP, respectively.

first: Xiaoyu

last: Hu


title: Differences in Nature Killer cell Response and Interference with Mitochondrial DNA induced Apoptosis in Moxifloxacin Environment

city: Shanghai

first: Mengqing

last: Wang

address: No. 415 Fengyang Road, Huangpu District, Shanghai, China

department: Department of Emergency and Critical Care

institute: Shanghai Changzheng Hospital of Naval Medical University

summary: In light of the widespread adoption of antibiotics, the imperative to promptly manage and regulate their use, ensuring accuracy and safety, is evident. Such misuse can lead to frequent adverse drug reactions, causing unnecessary harm, and prolonged erroneous use may culminate in irreversible injuries and fatalities. Of particular concern is the prevalent use of moxifloxacin (MXF), a fourth-generation fluoroquinolone antibiotic, across various infections and disease prevention scenarios. This have been reported to have immunomodulatory effects on a variety of immune cells and even anti-proliferative and pro-apoptotic effects, but the mechanism of action is not fully clear. There exists an urgent necessity to investigate the safety and mechanisms of action on immunomodulation of this drugs.

overall_design: The study involved the in vitro treatment of peripheral blood mononuclear cells (PBMC) from healthy adults (n=3) with MXF (10ug/ml) for 24 hours. Single-cell sequencing was employed to delineate the impacts of MXF on various immune cell taxa both before and after its administration. Subsequent to MXF exposure, the identification of subsets displaying the most significant damage in Natural Killer (NK) cells was accomplished, followed by the screening of pivotal differential genes. Phenotyping of the most affected NK cell subsets was executed using flow cytometry. The exploration of drivers influencing NK cell differentiation stimulated by MXF was achieved through mimetic time-series analysis. The differential genes extensively down-regulated in NK cells were localised within the mitochondrial respiratory chain complexes. The endpoints of MXF-induced stress damage in NK cells were identified through assays measuring mitochondrial respiratory chain complexes I, III, IV, and ATP synthase activity. Additionally, assessments included mitochondrial membrane potential, reactive oxygen species, and mitochondrial electron microscopy.

first: Wenfang

last: Li

first: Weiwei

last: Jiang

first: Hao

last: wu


title: scRNA-seq of mouse CD45+ aortic cells with CITE-seq and cell Hashing after continuous or alternate diet

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

overall_design: We performed single-cell RNA-seq analysis with CITE-seq and cell hashing of total viable aortic cells from Ldlr-/- mice fed a continuus or alternate high fat diet, as well as control C57BL6 aortas

first: Clement

last: Cochain

first: Antoine-Emmanuel

last: Saliba

first: Alma

last: Zernecke


title: The miR390/TAS3/ARF module governs the expression of an LBD transcription factor to regulate nodulation and root architecture in Medicago truncatula

city: Villa Elisa-La Plata

first: Maria

middle: Eugenia

last: Zanetti

state: BUENOS AIRES

department: Instituto de Biotecnología y Biología Molecular

country: Argentina

institute: Universidad Nacional de La Plata

summary: The microRNA390 targets the TAS3 transcript leading to the production of trans-acting small interference RNAs that subsequently post-transcriptionally repress the mRNAs encoding the Auxin Response Factors (ARF)2, ARF3, and ARF4. This module has been linked to the development of lateral organs in both aerial and underground tissues. Previously, we have shown that the miR390/TAS3/ARFs module mediates the control of lateral roots and symbiotic nodules in legumes. Here, we show that a member of the Lateral Organ Boundaries Domain (LBD) family of transcription factors, designated as MtLBD17/29a, is a target of the miR390/TAS3/ARFs module. Transcriptomic, RT-qPCR and promoter fusion analysis revealed that MtLBD17/29a is induced under symbiotic conditions, whereas no induction was observed in roots overexpressing miR390 or silenced in ARF2/3/4. ChIP-PCR experiments demonstrated that MtARF2 directly binds to an Auxin Response Element (ARE) present in the MtLBD17/29a promoter activating its expression. Knockdown of MtLBD17/29a reduced the length of primary and lateral roots and increasing the density of lateral roots, whereas overexpression of MtLBD17/29a produced the opposite phenotype. Interestingly, both knockdown and overexpression of MtLBD17/29a resulted in a significant reduction in the number of nodules and infection events, as well as impaired the induction of the symbiotic genes Nodulation Signaling Pathway (NSP) 1 and 2, reminiscent of the phenotype observed in ARF2/3/4 silenced roots. These results demonstrate that MtLBD17/29 is regulated by the miR390/TAS3/ARFs module and a direct target of ARF2, revealing a new lateral root regulatory hub recruited by legumes to act in the root nodule symbiotic program.

overall_design: RNA-seq libaries were genetated from Medicago truncatula roots overexpressiong the microRNA390 (OX390) and form roots transformed with the empty vector (EV) at 48 hours post-inoculation with water (mock) or with S. meliloti (Sm)

first: Cristina

last: Kirolinko

first: Karen

last: Hobecker

first: Marianela

last: Cueva

first: Florencia

last: Botto

first: Aurelie

last: Chris

first: Andreas

last: Niebel

first: Federico

last: Ariel

first: Flavio

last: Blanco

first: Martín

last: Crespi

first: María


title: The difference between intraepithelial mast cells and lamina propria mast cells

first: Liu

last: Yang

overall_design: H. polygyrus lavae were used to infect WT mice. After 14 days, IEMCs and LPMCs were sorted from infeceted intestinal epithelium and LP, respectively.

first: Xiaoyu

last: Hu


title: Impact of azide metabolic glycoengineering and bioorthogonal click chemistry cell-cell tethering in adipose tissue-derived mesenchymal stromal cells

city: Aveiro

first: Pedro

last: Lavrador

address: Campus Universitário de Santiago, Universidade de Aveiro

department: CICECO - Aveiro Institute of Materials

country: Portugal

institute: University of Aveiro

summary: We report RNA sequencing data from adipose tissue-derived mesenchymal stromal cells (hASCs) functionalized via metabolic glycoengineering with pendant azide sialosides. Beyond the impact of this cell surface engineering on transcriptome, we explore the expression profiles of azide-hASCs covalently tethered to an interfacial glycosaminoglycan via bioorthogonal click chemistry and yielding a 3D multicellular construct. We find global gene expression changes in response to metabolic glycoengineering in 2D cell culture conditions as well as those arising from cell-to-cell tethering into 3D environments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hASCs in three conditions (2D Native, 2D Glycoengineered and 3D Day 1 Cellgels)

first: Beatriz

last: Moura

first: José

last: Almeida-Pinto

first: Vítor

last: Gaspar

first: João

middle: F

last: Mano


title: Single-cell TCR profiling of CSF and blood cells of PWH reveals persistent and shared infected T cell clones across tissue compartments even after ART

city: New Haven

first: Meng

last: Wang

state: CT

address: 300 George St

institute: Yale University

summary: The brain is a site of persistent infected cells during HIV infection. However, the dynamics of central nervous system (CNS) infection and T cell trafficking in people living with HIV (PWH) are incompletely understood. We profiled the single cell T cell repertoire and host transcriptome from paired blood and cerebrospinal fluid (CSF) from PWH and uninfected controls. We detected HIV RNA-producing cells in 8/11 (72.7 %) CSF samples and 6/11 (54.5 %) blood samples, with a higher frequency of infected single CD4 T cells in CSF than in blood. Infected CSF T cells displayed a unique transcriptional profile compared to uninfected CSF T cells. Most infected T cell clones were not shared across tissue; however, in a subset of participants we detected identical T cell clones that were infected in both CSF and blood. Longitudinally following one PWH before and at three time points after initiating ART, we found infected T cell clones that persisted after ART initiation, in both CSF and blood, including a T cell clone that expanded in the CSF several months after ART initiation. Our findings suggest that infected T cells traffic to the CNS where they undergo clonal expansion despite ART, contributing to the CNS reservoir.

overall_design: Asymptomatic PWH P2 - P7 were enrolled (n = 7), and all were stable on ART (median 16 years) with suppressed plasma viral loads (< 50 copies/mL) and a median CD4 count of 503. One additional PWH was enrolled (P1) with newly diagnosed HIV and not yet on ART, and had a plasma viral load of 257,000 copies/mL. Control participants C1 - C6 were healthy volunteers recruited from the surrounding community for research sampling (n = 6) plus one hospitalized individual C1 undergoing a workup for gait instability. All control participants were confirmed HIV-negative by plasma enzyme immunoassay and screened for confounding neurological conditions. All participants consented to large-volume lumbar puncture (up to 30cc CSF removed) and blood draw for research purposes, or to donate additional CSF and blood samples collected during clinical standard-of-care procedures. Participant P1 underwent longitudinal study visits and consented to provide blood and CSF samples at HIV diagnosis/baseline and three, six, and nine months after initiating ART. The gene expression and T cell receptors of the peripheral blood and CSF samples were then measured using 5’ V(D)J 10x Genomics paired scRNA-seq and TCR-seq. Sequencing data for C1 - C3 was previously published on SRA (study accession: SRP312293, C1_BLD_RNA: SRR14076861, C1_BLD_TCR: SRR14076833, C1_CSF_RNA: SRR14076871, C1_CSF_TCR: SRR14076842, C2_BLD_RNA: SRR14076860, C2_BLD_TCR: SRR14076832, C2_CSF_RNA: SRR14076869, C2_CSF_TCR: SRR14076841, C3_BLD_RNA: SRR14076858, C3_BLD_TCR: SRR14076831, C3_CSF_RNA: SRR14076868, C3_CSF_TCR: SRR14076840).

first: Jennifer

last: Yoon

first: Hailey

last: Reisert

first: Bibhuprasad

last: Das

last: Chiarella

first: Elias

last: Halvas

first: Alina

last: Pang

first: Joshua

last: Cyktor

first: Serena

last: Spudich

first: Yuval

last: Kluger

first: Michael

middle: J

last: Corley

first: Shelli

last: Farhadian


title: 5' gene expression (GEX) single-cell RNA sequencing of four (4) Hodgkin Lymphoma patient tumor biopsies

first: Puneeth

last: Guruprasad

summary: Hodgkin lymphoma tumors are characterized by profound infiltration of immune cells. We used scRNA-seq to analyze the cellular composition of the tumor microenvironment in Hodgkin lymphoma.

overall_design: Fresh tumor tissue was obtained from four Hodgkin lymphoma patient biopsies (core-needle). Tumor cells were processed, resuspended in PBS + 0.04% BSA, and run on 10X Chromium Controller

first: Guruprasad

last: Puneeth


title: RNA sequencing of mouse myoblast cells C2C12 with and without lenvatinib treated after 4 days differentiated.

city: Chiba

first: Junjie

last: Ao

state: Chiba

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

department: Department of Gastroenterology

institute: Graduate School of Medicine, Chiba University

summary: Transcriptome were compared between lenvatinib-treated and untreated C2C12 cells. 145 up-regulated genes and 285 down-regulated genes were identified by setting a 2-fold change and p < 0.05 threshold.

overall_design: In this study, we used 3 control (lenvatinib untreated) and 3 lenvatinib-treated C2C12 cells' RNA to performe RNA sequencing, respectively.

last: Qiang

first: Masato

last: Nakamura


title: Comparative Transcriptome Analysis of Two Rice Genotypes with Varying Tolerance to Salt Stress

city: Islamabad

first: Muhammad Ramzan

last: Khan

address: Park Rd

department: National Institute Of Genomics And Advanced Bio-Technology (NIGAB)

country: Pakistan

institute: National Agricultural Research Centre

summary:
The goals of this study were to compare the transcriptome of two rice genotypes under salt stress by RNA-Seq.
We performed differential gene expression analysis by comparing samples of same genotypes in control and stress conditions and different genotypes in the same condition.

overall_design: Gene expression profiling by high throughput sequencing.

first: Muhammad

last: Ramzan

first: Nageen

last: Zahra

first: Imdadullah

last: Zaid