title: A humanized mouse model for in vivo evaluation of iNKT cell responses

status: Public on Sep 25 2022

city: Bronx

first: XUSHENG

last: ZHANG

state: NY

address: 1300 Morris Park Ave

department: GENETICS

institute: ALBERT EINSTEIN COLLEGE OF MEDICINE

summary: Invariant natural killer T (iNKT) cells mediate immune responses when stimulated by glycolipid agonists presented by CD1d. In extensive studies of synthetic analogues of α-galactosyl ceramides, we identified numerous examples of significant differences in the recognition of specific glycolipids in wild type mice versus human iNKT cell clones or PBMC samples.  To predict human iNKT cell responses more accurately in a mouse model, we derived a mouse line in which compound genetic modifications were used to express a human-like iNKT cell TCR along with human CD1d in place of the endogenous mouse proteins.  Detailed transcriptional and phenotypic profiling demonstrated that these partially humanized mice developed an expanded population of T cells recognizing CD1d-presented glycolipid antigens, among which a subset characterized by expression of chemokine receptor CXCR6 had features characteristic of authentic iNKT cells.  Responses to iNKT cell activating glycolipids in these mice generated cytokine production in vitro and in vivo that showed a pattern of fine specificity that closely resembled that of cultured human iNKT cell clones.  Anti-tumor responses to variants of α‑galactosyl ceramide in VαKI mice also correlated with their potency for stimulating human iNKT cells.  This genetically modified mouse line provides a practical model for human presentation and recognition of iNKT cell activators in the context of a normally functioning immune system, and may furnish valuable opportunities for preclinical evaluation of iNKT cell-based therapies.

overall_design: iNKT and T cells were isolated to see if there are genetical differences or different sequences on their TCR among C57BL/6 and VαKI

first: Noemi

last: Saavedra Avila

first: David

last: Reynolds

first: Xusheng

last: Zhang

first: Robert

last: Dubin

first: Steven

last: Porcelli


title: Modeling pleomorphic rhabdomyosarcoma in mice

status: Public on Sep 26 2022

city: Memphis

first: Alessandra

last: d'Azzo

state: TN

address: 262 Danny Thomas Place

department: Genetics

country: USA

institute: St Jude Children's Research Hospital

summary: Here we used Ptch1+/-/ETV7TG/+/- mice with enhanced incidence of RMS to generate a model of pleomorphic RMS driven by haploinsufficiency of the lysosomal sialidase Neu1. These tumors share features and location with human RMS.

overall_design: We compared fourteen tumor samples taken from Neu1+/−/Ptch1+/−/ETV7 TG+/− (NPE) mice with seven tumor samples from Ptch1+/−/ETV7 TG+/− (PE) mice using the Mouse ClariomS array.

first: Eda

middle: R

last: Machado

first: Susanna

middle: M

last: Downing

middle: B

last: Finkelstein

first: Geoffrey

middle: A

last: Neale


title: Gene expression profile at single cell level of nervous system in sea cucumber.

status: Public on Sep 28 2022

city: Qingdao

first: Yingqiu

last: Zheng

address: Yushan Road 5

country: China

institute: Ocean university of China

type: Expression profiling by high throughput sequencing

summary: nervous system plays key roles in sea cucumber. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of diverse cells in the nervous system.

overall_design: The cell suspension was prepared from the fresh circumoral nerve ring tissue and was analysed under 10X Genomics sequencing platform.

first: Muyan

last: Chen


title: A comprehensive transcriptomic comparison of hepatocyte model systems

city: Utrecht

first: Arif Ibrahim

last: Ardisasmita

address: Heidelberglaan 100

department: Pediatrics

country: Netherlands

institute: University Medical Center Utrecht

summary: We generated intrahepatic cholangiocyte organoids and fetal hepatocyte organoids to compare their transcriptomic profile with liver tissue, primary human hepatocytes, and other hepatocyte model systems.

overall_design:
Comparative gene expression analysis of RNA-seq data for intrahepatic cholangiocyte organoids (expansion, 4d and 8d differentiation), fetal hepatocyte organoids and liver tissue. Each sample type has two biological replicates.

>>>Submitter states: due to GDPR, we were only allowed to upload de-identified  transcriptomic data (raw counts).<<<

first: Arif

middle: I

first: Imre

middle: F

last: Schene

first: Delilah

last: Hendriks

first: Benedetta

last: Artegiani

first: Sabine

last: Fuchs


title: Effect of Atm Inhibitor on Galactose-Induced Cataract in Rat Lens

status: Public on Sep 24 2022

city: Fukui

first: Masaya

last: Nagaya

address: 3-9-1 Bunkyo

country: Japan

institute: University of Fukui

summary:
Analysis of gene expression changes in galactose-induced cataracts when an Atm inhibitors is added.
A total of six samples were analyzed: a sample without induced turbidity (control), three samples in which turbidity was induced by galactose (galactose), and a sample with ATM inhibitor added (KU55933 or AZD0156).

overall_design: Genes that increased in galactose-treated lenses and reverted to their original state with ATM inhibitors were extracted.

first: Fumito

last: Kanada

first: Yoshihiro

last: Takamura

first: Masaru

last: Inatani

last: Oki


title: System-wide identification of myeloid markers of TB disease and HIV-induced reactivation in the macaque model of Mtb infection and Mtb/SIV co-infection

status: Public on Sep 23 2022

city: San Antonio

first: Dhiraj

middle: Kumar

last: Singh

state: Texas

address: 8715 West Military Drive

department: Southwest National Primate Research Center

institute: Texas Biomedical Research Institute

summary: Mycobacterium tuberculosis (Mtb) has developed specialized mechanisms to parasitize its host cell, the macrophage. These mechanisms allow it to overcome killing by oxidative burst and persist in the wake of an inflammatory response. Mtb infection in the majority of those exposed is controlled in an asymptomatic form referred to as latent tuberculosis infection (LTBI). HIV is a well-known catalyst of reactivation of LTBI to active TB infection (ATB).  Through the use of nonhuman primates (NHPs) co-infected with Mtb and Simian Immunodeficiency Virus (Mtb/SIV), we are able to simulate human progression of TB/AIDS comorbidity. The advantage of NHP models is that they recapitulate the breadth of human TB outcomes, including immune control of infection, and loss of this control due to SIV co-infection. Using macaques infected with Mtb or Mtb/SIV and with different clinical outcomes we attempted to identify signatures between those that progress to active infection after SIV challenge (reactivators) and those that control the infection (non-reactivators).

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Two color M. mulatta 4x44k Agilent array

first: Deepak

last: Kaushal

first: Smriti

last: Mehra


title: Global early replication disrupts gene expression and chromatin conformation in a single cell cycle: subnucleosomal MNAse-Seq mapping

city: Cambridge

first: Philip

last: Zegerman

address: 80, Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The early embryonic divisions of many organisms, including fish, flies and frogs are characterised by a very rapid S-phase caused by high rates of replication initiation. In somatic cells, S-phase is much longer due to both a reduction in the total number of initiation events and the imposition of a temporal order of origin activation. The physiological importance of changes in the rate and timing of replication initiation in S-phase remains unclear. Here we assess the importance of the temporal control of replication initiation using a conditional system in budding yeast to drive the early replication of all origins in a single cell cycle. We show that global early replication disrupts the expression of over a quarter of all genes. By deleting individual origins we show that delaying replication is sufficient to restore normal gene expression, directly establishing replication timing control in this regulation. Global early replication disrupts nucleosome positioning and transcription factor binding during S-phase, suggesting that the rate of S-phase is important to regulate the chromatin landscape. Together these data provide new insight into the role of a temporal order of origin firing for coordinating replication, gene expression and chromatin establishment as occurs in the early embryo.

overall_design: Analysis of transcription-factor binding landscape using MNase-Seq upon a global advance in replication timing caused by overexpression of six limiting initiation factors (SSDDCS)

first: Miguel

last: Monteiro Santos

first: Mark

middle: C

last: Johnson

first: Lukáš

last: Fiedler


title: Global early replication disrupts gene expression and chromatin conformation in a single cell cycle: targeted origin deletion

overall_design: Examination of replication progression by high-throughput sequencing of DNA in four strains (sml1Δ SSDDCS ARS1008∆ ARS1009∆, sml1Δ ARS1008∆ ARS1009∆, sml1Δ ARS816∆ ARS818∆, sml1Δ SSDDCS ARS816∆ ARS818∆) which had two origins deleted at discrete locations.


title: Global early replication disrupts gene expression and chromatin conformation in a single cell cycle: transcription

overall_design: Analysis of transcription using RNA-Seq upon a global advance in replication timing caused by overexpression of six limiting initiation factors (SSDDCS)


title: Global early replication disrupts gene expression and chromatin conformation in a single cell cycle: replication timing

overall_design: Examination of replication progression by high-throughput sequencing of DNA in two strains (sml1_delta SSDDCS, sml1_delta) upon a genome-wide perturbation in the timing of replication initiation.


title: SARS-CoV-2 disrupt respiratory vascular barrier by suppressing Claudin-5 expression (additional RNA-seq data)

status: Public on Sep 22 2022

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: In the initial process of COVID-19, SARS-CoV-2 infects respiratory epithelial cells and then transfers to other organs via the blood vessels. It is believed that SARS-CoV-2 can pass the vascular wall by altering the endothelial barrier using an unknown mechanism. In this study, we investigated the effect of SARS-CoV-2 on the endothelial barrier using an airway-on-a-chip that mimics respiratory organs and found that SARS-CoV-2 produced from infected epithelial cells disrupts the barrier by decreasing Claudin-5 (CLDN5), a tight junction protein, and disrupting vascular endothelial cadherin (VE-cadherin)-mediated adherens junctions. Consistently, the gene and protein expression levels of CLDN5 in a COVID-19 patient’s lungs were decreased. CLDN5 overexpression or Fluvastatin treatment could rescue the SARS-CoV-2-induced respiratory endothelial barrier disruption. We therefore concluded that the downregulation of CLDN5 expression is a pivotal mechanism for SARS-CoV-2-induced endothelial barrier disruption in respiratory organs and that inducing CLDN5 expression is a novel therapeutic strategy against COVID-19.

overall_design: RNA-seq in the human lungs: Total RNA was collected from the lungs of healthy donors and COVID-19 patients, and then RNA-seq was performed.


title: A novel medication decision gene signature predicts response to individualized therapy and prognosis outcomes in hepatocellular carcinoma patients

city: Chengdu

first: Jiayin

last: Yang

state: Sichuan

address: 37 Guoxue Alley, Wuhou District

department: Department of Liver Surgery and Liver Transplantation Center

institute: West China Hospital of Sichuan University

summary:
Molecular targeted therapy has shown potential in hepatocellular carcinoma (HCC) patients, and immunotherapy applications are developing rapidly. However, clinical guidance for making individualized therapy decisions for HCC patients remains lacking.
To facilitate individualized and reasonable clinical guidance for each HCC patient, we constructed the MDH score.

overall_design: Sorafenib-resistant HCC cell lines generated from Huh7 and HepG2 parental cells were cultured

first: Yujun

last: Shi


title: LncRNA TP53TG1 plays an anti-oncogenic role in cervical cancer by synthetically regulating transcriptome profile in HeLa cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Long non-coding RNAs (lncRNAs) have been extensively studied as key regulators of cancer development in various cancers. TP53TG1 is a newly identified lncRNA in recent years, and several studies have shown that TP53TG1 may play oncogenic or anti-oncogenic roles in different cancers. Pan-cancer analysis showed that high TP53TG1 expression was significantly associated with better prognosis. Nevertheless, the role of TP53TG1 in the development of cervical cancer is unclear. In our study, we constructed a TP53TG1 overexpression model in HeLa cell line. We found that TP53TG1 overexpression significantly inhibited cell proliferation and induced apoptosis, and TP53TG1 may be a novel anti-oncogenic factor in cervical cancer. Mechanistically, overexpression of TP53TG1 could activate type I interferon signaling pathways and inhibits the expression of genes involved in DNA damage responses. Meanwhile, TP53TG1 could regulate the expression of a large number of RNA binding protein genes thereby potentially affecting the alternative splicing of genes involved in cell proliferation or apoptosis regulation. We also established a ceRNA network to predict the regulatory effect of TP53TG1 on gene expression through miRNA. Our study highlights the essential role of lncRNA TP53TG1 in the development of cervical cancer and suggests the potential regulatory mechanisms.

overall_design: We constructed a TP53TG1 overexpression model in HeLa cell line, coupled with RNA-seq sequences, to comprehensively reveal the biological function of TP53TG1 in HeLa cell and analyze the alterations of transcriptional profiles upon TP53TG1 overexpression.

first: YI

last: Cheng

last: Huang

first: Qingqing

last: Yin

first: Chao


title: Adaptive and innate immune responses in MAC lung disease

city: La Jolla

first: Cecilia

middle: Sofie

last: Lindestam

state: CA

address: 9420 Athena Circle

department: Sette

institute: La Jolla Institute for Immunology

summary: Immunological mechanisms of susceptibility to NTM disease are poorly understood. We evaluated innate and antigen-specific adaptive immune responses to Mycobacterium avium complex in individuals with MAC lung disease. We investigated the gene expression changes induced in PBMCs by polyclonal stimulation (anti-CD3, anti-CD28), Mav and Mtb lysates and a peptide pool (MTB300) in individuals with MAC lung disease (MACDZ), and healthy controls (IGRA+ and IGRA-).

overall_design:
RNAseq of sorted PBMC from cryopreserved PBMC of IGRA+ Healthy controls, IGRA- Healthy controls and individuals with MAC infection (MACDZ).

Mtb300 has been published in this paper:
https://pubmed.ncbi.nlm.nih.gov/27409590/

last: Lindestam Arlehamn

first: Rebecca

last: Kuan


title: Generation of a TPH2-EGFP reporter cell line for Purification and Monitoring of Human Serotonin neurons in vitro and in vivo

city: Shanghai

first: Ting

last: Xu

address: 1239 Siping Road

institute: Tongji University

summary: Generation of serotonin neurons (SNs) from human pluripotent stem cells (hPSCs) provides a promising platform to explore the mechanisms of serotonin-associated neuropsychiatric disorders. However, neural differentiation always yields heterogeneous cell populations, making it difficult to identify and purify SNs in vitro or track them in vivo following transplantation. Herein, we generated a TPH2-EGFP reporter hPSC line with insertion of EGFP into the endogenous tryptophan hydroxylase 2 (TPH2) locus using CRISPR-Cas9-mediated gene editing technology. This TPH2-reporter, which faithfully indicated TPH2 expression during differentiation, enabled us to obtain purified SNs for subsequent transcriptional analysis and study of pharmacological responses to antidepressants. In addition, the reporter system showed strong EGFP expression to indicate SNs, which enabled us to explore in vitro and ex vivo electrophysiological properties of SNs. In conclusion, this TPH2-EGFP reporter cell line might be of great significance for studies on human SN-related development and differentiation, drug screening, disease modeling, and cell replacement therapies.

overall_design: Comparative gene expression profiling of RNA-seq data from cells differentiated from hESCs to human serotonin neurons at three time points (Day0 (hESCs), Day21, Day42)

first: Jianfeng

last: Lu


title: RNA-Sequencing analysis of control and KDSR KO cancer cell lines

status: Public on Sep 27 2022

city: Worcester

first: Meghan

middle: E

last: Spears

state: MA

address: 364 Plantation St, LRB

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: The mRNA profiles of 3 cell lines (HUH7, DLD1, NCIH838) were analyzed by RNA-sequencing under control and KDSR KO conditions to identify gene expression changes induced by disruption of KDSR in cancer cells that are sensitive to its loss.

overall_design: Compare the mRNA profiles of 3 cancer cell lines under CTRL (non-targeting guide) and KDSR KO mediated by CRISPR-cas9. Each condition was analyzed in biological triplicate for a total of 18 samples.

first: Dohoon

last: Kim

first: Rui

last: Li

first: Lihua

middle: J

last: Zhu

first: Eduardo

last: Torres


title: Global early replication disrupts gene expression and chromatin conformation in a single cell cycle

first: Philip

last: Zegerman

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

overall_design: Refer to individual Series


title: Global early replication disrupts gene expression and chromatin conformation in a single cell cycle: MNAse-Seq mapping

overall_design: Analysis of nucleosome landscape using MNase-Seq upon a global advance in replication timing caused by overexpression of six limiting initiation factors (SSDDCS)

first: Miguel

last: Monteiro Santos

first: Mark

last: Johnson

first: Lukáš

last: Fiedler


title: The SPARC complex defines RNAPII promoters in Trypanosoma brucei

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Crescent

institute: Wellcome Centre for Cell Biology


title: RNA-seq from ventricles of cardiomyocyte-specific PGC-1α4 overexpressing mice

city: Kuopio

first: Tomi

last: Tuomainen

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

summary: We investigated gene expression changes in the cardiac tissue of a transgenic mouse model overexpressing Peroxisome proliferator-activated receptor gamma coactivator 1-alpha isoform 4 (PGC-1α4) specifically in cardiomyocytes at the neonatal stage and at the age of four weeks.

overall_design: Mice carrying Myh6-cre transgene were crossed with mice carrying floxed Pgc-1α4 transgene in Rosa26 locus to produce animals with cardiomyocyte-specific Pgc-1α4 overexpression. Male mice positive for both transgenes were sacrificed at the age of 1-2 days (neonatal) and at the age of four weeks, and ventricular part of neonatal and left ventricle of 4-week-old animals were flash frozen in liquid nitrogen. Mice positive only for floxed Pgc-1α4 transgene were used as a control. Number of replicates for each experimental group is four.

first: Pasi

last: Tavi


title: An atlas of human dental pulp cells in multiple spatial and temporal levels based on single-cell sequencing analysis

city: Beijing

first: Huihui

last: Ren

address: No.22, Zhongguancun Nandajie, Haidian District

institute: Peking University School and Hospital of Stomatology

summary: The specific cellular heterogeneity of dental pulp cells, especially dental stem cells in different spatial and temporal level was proviede. So we used single cell RNA sequencing to analysis this question.

overall_design: We harvested one sample from human dental pulp of third molar less than 1/3 root completed from a 13-year old child

first: Quan

last: Wen

first: Qingxuan

last: Zhao

first: Yuming


title: PCSK9 deficiency results in a specific shedding of excess LDLR in female mice only: Role of hepatic cholesterol

city: Montreal

first: Annik

last: PRAT

state: QC

address: 110 Pine Avenue West, Biochemical Neuroendocrinology

country: Canada

institute: IRCM (Montreal)

summary:
PCSK9 promotes the lysosomal degradation of cell surface LDL receptor (LDLR). We analyzed how excess LDLR
generated by PCSK9 deficiency is differently handled in male and female mice to possibly unveil the mechanism
leading to the lower efficacy of PCSK9 mAb on LDL-cholesterol levels in women. Analysis of intact or ovariectomized
PCSK9 knockout (KO) mice supplemented with placebo or 17β-estradiol (E2) demonstrated that female,
but not male mice massively shed the soluble ectodomain of the LDLR in the plasma. Liver-specific PCSK9 KO or
alirocumab-treated WT mice exhibit the same pattern. This shedding is distinct from the basal one and is
inhibited by ZLDI-8, a metalloprotease inhibitor pointing at ADAM10/ADAM17. In PCSK9 KO female mice, ZLDI-
8 raises by 80 % the LDLR liver content in a few hours. This specific shedding is likely cholesterol-dependent: it is
prevented in PCSK9 KO male mice that exhibit low intra-hepatic cholesterol levels without activating SREBP-2,
and enhanced by mevalonate or high cholesterol feeding, or by E2 known to stimulate cholesterol synthesis via
the estrogen receptor-α. Liver transcriptomics demonstrates that critically low liver cholesterol in ovariectomized
female or knockout male mice also hampers the cholesterol-dependent G2/M transition of the cell cycle. Finally,
higher levels of shed LDLR were measured in the plasma of women treated with PCSK9 mAb. PCSK9 knockout
female mice hormonally sustain cholesterol synthesis and shed excess LDLR, seemingly like women. In contrast,
male mice rely on high surface LDLR to replenish their stocks, despite 80 % lower circulating LDL.

overall_design: Effect of placebo or 17b-estradiol supplementation in WT or PCSK9 KO ovariectomized mice

first: Anna

last: Roubtsova

last: Prat


title: ER stress transforms stochastic olfactory receptor gene choice into stereotypic axon guidance programs

city: New York

first: Hani

last: Shayya

state: New York

address: 3227 Broadway

department: Biochemistry and Mol Biophysics

institute: Columbia University

summary: Olfactory sensory neurons (OSNs) transform the stochastic choice of one out of >1000 olfactory receptor (OR) genes into precise and stereotyped axon targeting of OR-specific glomeruli in the olfactory bulb. Here, we show that the PERK arm of the unfolded protein response (UPR) regulates both the glomerular coalescence of like axons, and the specificity of their projections. Subtle differences in OR protein sequences lead to distinct patterns of endoplasmic reticulum (ER) stress during OSN development, converting OR identity into distinct gene expression signatures. We identify the transcription factor Ddit3 as a key effector of PERK signaling that maps OR-dependent ER signaling patterns to the transcriptional regulation of axon guidance and cell adhesion genes, instructing targeting precision. Our results extend the known functions of the UPR from a quality control pathway that protects cells from misfolded proteins, to a sensor of cellular identity that interprets physiological states to direct axon wiring.

overall_design: 80 bulk RNA-seq libraries prepared using the Takara SMARTER Stranded Total RNA-seq Kit v2 - Pico Input Mammalian. Five experiments are included. (1) FAC-sorted developmental OSN populations (INP, iOSN, mOSN). (2) FAC-sorted high and low stress iOSNs (iRFP) and mOSNs (iRFPGFP) from Atf5(rep/+); Omp(iresGFP/+) mice (Ctrl1-6). (3) FAC-sorted high and low stress iOSNs (iRFP) and mOSNs (iRFPGFP) from Atf5(rep/+); Omp(iresGFP/+); P2(M71iresLacZ/+) mice (Swap1-3). (4) FAC-sorted GFP and tdtomato-positive OSNs from 4-week-old Mor28 Ddit3 WT, Het and cKO mice. (5) FAC-sorted tdtomato+ OSNs from p9 Omp-iresCre; Ddit3 WT, Het and cKO mice.

first: Stavros

last: Lomvardas


title: Ovarian cancer cell fate regulation by the dynamics between saturated and unsaturated fatty acids

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: The goal of this study was to determine how the balance between SFAs and UFAs tightly controlled by SCD, regulates OC cell survival and tumorigenicity.

overall_design: 1) SCD was stably knocked down by shRNA in OVCAR-5 cells and cultured in low serum condition for 48 hours. Global effects on the transcriptome were examined by RNA-sequencing between shSCD vs shCtrl (in biological triplicates).

first: Guangyuan

first: Horacio

last: Cardenas

first: Hao

last: Huang


title: SARS-CoV-2 disrupts respiratory vascular barriers by suppressing Claudin-5 expression

first: Kazuo

last: Takayama

overall_design: The PET membrane to which HMVEC-L was adhered was mechanically recovered from the airway-on-a-chip, and then total RNA was collected and RNA-seq was performed.


title: Single-cell RNA Sequencing Demonstrates Inter-Patient Heterogeneity and Altered Tumor Microenvironment in Invasive and Intraductal Cribriform Prostate Cancer

city: Nashville

first: Hong Yuen

last: Wong

state: Tennessee

address: 2220 Pierce Ave # PRB648, Preston Research Building

department: Medicine

institute: VUMC

summary: ICC and IDC are aggressive histological subtypes of prostate cancer that are associated with progression to lethal disease. To delineate cancer cell intrinsic as well as tumor microenvironmental factors that contribute to ICC/IDC aggressiveness, this study examined paired ICC/IDC-enriched and benign-enriched prostate samples obtained from radical prostatectomy (RP) by scRNAseq, TCR sequencing and histology. ICC/IDC cancer cells had robust inter-patient heterogeneity but upregulated similar pathways (MYC and TNF via NFĸB) and targets with potential for therapeutic intervention (PSMA and B7-H3). ICC/IDC was associated with increased neovasculature, and cancer foci were densely circumscribed by immunosuppressive CAF likely derived from APOD+ peri-epithelial fibroblast progenitors. The ICC/IDC TME had fewer and more dysfunctional T cells and increased M2 polarization of two macrophage subtypes compared to benign prostate. These findings support that ICC/IDC are hallmarked by several aggressive features that likely contribute to their association with lethal prostate cancer.

overall_design: scRNA-seq (whole transcriptome and TCR) performed on paired ICC/IDC-enriched and benign-enriched prostate samples obtained from radical prostatectomy.

first: Paula

last: Hurley

first: Quanhu

last: Sheng


title: Transcriptome-wide m6A methylome analysis uncovered the changes of m6A   modification in oral pre-malignant cells compared with normal oral epithelial cells

status: Public on Sep 21 2022

city: Guangzhou

first: LiuTao

last: Chen

address: Waihuan West Road 132, University TownHigher Education Mega Center

institute: The Sun YAT-SEN UNIVERSITY

summary: As the most common post-transcriptional RNA modification, m6A methylation extensively regulates the structure and function of RNA. The dynamic and reversible  modification of m6A is coordinated by m6A writers and erasers. m6A reader proteins  recognize m6A modification on RNA, mediating different downstream biological   functions. mRNA m6A modification and its corresponding regulators play an   important role in cancers, but its characteristics in the precancerous stage are still   unclear. In this study, we used oral precancerous DOK cells as a model to explore the   characteristics of transcriptome-wide m6A modification and major m6A regulator  expression in the precancerous stage compared with normal oral epithelial cell HOEC  and oral cancer cell SCC-9 through MeRIP-seq and RT-PCR. Compared with HOEC   cells, we found 1180 hyper-methylated and 1606 hypo-methylated m6A peaks and 354   differentially expressed mRNAs with differential m6A peaks in DOK cells. Although   the change of m6A modification in DOK cells was less than that in SCC-9 cells,   mRNAs with differential m6A in both cell lines were enriched into many identical GO   terms and KEGG pathways. Among the 20 known m6A regulatory genes, FTO,   ALKBH5, METTL3 and VIRMA were slightly upregulated or downregulated in   DOK cells, but the expression of 10 genes such as METTL14/16, FTO and   IGF2BP2/3 changed significantly in SCC-9 cells. Our data suggest that precancerous   cells showed, to some extent, changes of m6A modification. Identifying some key  m6A targets and corresponding regulators in precancerous stage may provide potential   intervention targets for the prevention of cancer development through epigenetic   modification in the future.

overall_design: Transcriptome-wide m6A sequencing was performed as described previously .  Briefly, total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA)   and quantified. RNA integrity was evaluated by Bioanalyzer 2100 (Agilent, CA,   USA). Poly (A) RNA was purified using Dynabeads Oligo (dT)25-61005 (Thermo   Fisher, CA, USA) and fragmented into about 100nt using Magnesium RNA   Fragmentation Module (NEB, USA). The RNA fragments were divided into two   portions, one was kept as input and the other was used to enrich m6A-methylated   RNA fragments by immunoprecipitation with m6A-specific antibody (Synaptic   Systems, Germany). RNA-seq library preparation included double stranded cDNA  synthesis, addition of A-tailing, adapter ligation, amplification of ligated products, and   library purification. The paired-end sequencing (PE150) of libraries was performed on   Illumina Novaseq™ 6000 platform (LC-Bio Technology CO., Ltd., Hangzhou, China),  following the manufacturer’s protocol.

first: Xun

first: Liutao

first: Yi

last: He


title: Alpha4 is Critical for Adipocyte Maintenance and Mitochondrial Homeostasis through Regulation of Insulin Signaling

city: Kumamoto

first: masaji

last: sakaguchi

address: 1-1-1 Honjo, Chuoku

department: Metabolic Medicine

institute: Kumamoto University

summary: Insulin signaling is mediated via a network of protein phosphorylation. Dysregulation of this network is central to obesity, type 2 diabetes and metabolic syndrome. Here we have investigated the role of phosphatase binding protein Alpha4 (α4) that is essential for the Ser/Thr protein phosphatase PP2A in insulin action/resistance in adipocytes. Unexpectedly, adipocyte-specific inactivation of α4 impairs insulin-induced Akt-mediated Ser/Thr phosphorylation despite a decrease in the PP2A levels. Interestingly, loss of α4 also reduces insulin-induced insulin receptor Tyr phosphorylation. This occurs through decreased association of α4 with Y-box protein 1 (YBX1), resulting in the enhancement of the Tyr phosphatase PTP1B expression. Moreover, adipocyte-specific knockout of α4 results in impaired adipogenesis and altered mitochondrial oxidation leading to increased inflammation, systemic insulin resistance, hepatosteatosis, islet hyperplasia, and impaired thermogenesis. Thus, the α4 /YBX1-mediated pathway of insulin receptor signaling is essential for maintaining insulin sensitivity, normal adipose tissue homeostasis and systemic metabolism.

overall_design: iWAT and BAT mRNA profiles of Control and Ai-α4KO mice.

first: Masaji

last: Sakaguchi


title: MtTRC-1, a Novel Transcription Factor, Regulates Cellulase Production via Directly Modulating the Genes Expression of the Mthac-1 and Mtcbh-1 in Myceliophthora Thermophila

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

institute: TIB CAS

summary: In thermophilic fungi, work on the ER stress and UPR signalling is largely unknown,we here identified a new Cys2His2 transcription factor and found its knockout strain with significantly decreased cellulases production on crystalline cellulose.Here, we show that loss-of-function mutations of this regulator resulted in the reduced expression of Mthac-1 via RNA-seq under Avicel and artificial ER-stress.

overall_design: mRNA profiles of Myceliophthora thermophila cells exposed to 4h Avicel,6h Avicel and 4h starch.

first: Qian

last: Liu

first: Defei

last: Li

first: Chaoguang

last: Tian


title: Study of microRNA associated with lenvatinib’s anti-tumor effect in hepatocellular carcinoma cell line

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Lenvatinib treatment markedly altered miRNA expression in vitro, and the various miRNAs induced by lenvatinib may also contribute to tumor growth inhibition in vitro.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 2555 human miRNA probes in the HuH-7 cell line in vitro that was treated with and without lenvatinib.

first: M

last: Nakahara

first: T

last: Masaki


title: Nanomolar inhibition of SARS-CoV-2 infection by N-terminally extended HR2 peptides

city: Berkeley

first: Timothy

last: Eisen

state: CALIFORNIA

address: Stanley Hall

institute: UC Berkeley

summary: Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies through changes of epitopes on the receptor binding domain of the viral spike glycoprotein (S). Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors which block formation of the HR1HR2 six-helix bundle of the SARS-CoV-2 spike protein and thus interfere with viral membrane fusion; HR2 derived peptides are validated inhibitors of this process. Here, we identify a short N-terminal region that, when appended to the helical region of an HR2 peptide from previous studies, leads to potent inhibition of fusion. The extended peptide shows an ~100-fold increase in efficacy compared with the previously used 36-amino-acid version of HR2, effectively achieving single-digit nanomolar inhibition of SARS-CoV-2 in cell-based fusion, VSV-SARS-CoV-2 chimera, and authentic SARS-CoV-2 infection assays. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. Structural studies of the HR1HR2 bundle reveal the formation of an extended, stabilized N-terminus that interacts with the HR2 triple helix, further stabilizing the HR1HR2 bundle. Together, these results suggest that regions outside the previously studied HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: High-throughput screening for peptide binders of the HR1-portion of the spike protein using mRNA display

first: Kailu

last: Yang

first: Chuchu

last: Wang

first: Alex

last: Kreutzberger

first: Ravi

last: Ojha

first: Suvi

last: Kuivanen

first: Sergio

last: Couoh

first: K

last: White

first: Richard

last: Held

last: Pfuetzner

first: Luis

last: Esquivies

first: Serena

last: Muratcioglu

first: Subu

last: Subramanian

first: Kendra

last: Marcus

first: John

last: Kuriyan

first: Olli

last: Vapalahti

first: Giuseppe

last: Balistreri

first: Tomas

last: Kirchhausen

first: Axel

middle: T

last: Brunger


title: mTOR- and LARP1-dependent regulation of TOP mRNA poly(A) tail and ribosome loading [polysome fractionation]

city: Nagoya

first: Koichi

last: Ogami

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

institute: Nagoya University

summary: Translation of TOP mRNAs encoding protein synthesis machinery is strictly regulated by an amino acid sensing mTOR pathway.  However, its regulatory mechanism remains elusive.  Here, we demonstrate that TOP mRNA translation positively correlates with its poly(A) tail length under mTOR active/amino acid-rich condition, suggesting that TOP mRNAs are post-transcriptionally controlled by poly(A) tail length regulation.  Consistent with this, tail length of TOP mRNAs dynamically fluctuates in response to amino acid availability.  Poly(A) tail shortens under mTOR active/ amino acid-rich condition, whereas the long-tailed TOP mRNAs accumulate under mTOR inactive/amino acid-starved (AAS) condition.  An RNA-binding protein LARP1 that specifically binds to TOP mRNAs is indispensable for the process.  We also show that LARP1 interacts with non-canonical poly(A) polymerases, PAPD4, PAPD5 and PAPD7 and induces post-transcriptional polyadenylation of the target when tethered to the mRNA.  Our findings illustrate that LARP1 contributes to the selective accumulation of TOP mRNAs with long poly(A) tail under AAS, resulting in accelerated ribosomal loading onto TOP mRNAs for the resumption of translation after AAS.

overall_design: 5’ capped polyA RNAs purified from free, monosomal, light-polysomal and heavy-polysomal fractions were analyzed by direct RNA-sequencing using the Oxford Nanopore’s MinION.


title: Single cell analysis of menstrual endometrial tissues defines phenotypes associated with endometriosis

city: Mahasset

first: Andrew

last: Shih

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

summary:
Background. Endometriosis is a common, complex disorder which is underrecognized and subject to prolonged delays in diagnosis. It is accompanied by significant changes in the eutopic endometrial lining.
Methods . We have undertaken the first single cell RNA-sequencing (scRNA-Seq) comparison of endometrial tissues in freshly collected menstrual effluent (ME) from 33 subjects, including confirmed endometriosis patients (cases) and controls as well as symptomatic subjects (who have chronic symptoms of endometriosis but have not been diagnosed).
Results . We identify a unique subcluster of proliferating uterine natural killer (uNK) cells in ME-tissues from controls that is almost absent from endometriosis cases, along with a striking reduction of total uNK cells in the ME of cases (p<10 -16 ). In addition, an IGFBP1+ decidualized subset of endometrial stromal cells are abundant in the shed endometrium of controls when compared to cases (p<10 -16 ) confirming findings of compromised decidualization of cultured stromal cells from cases. By contrast, endometrial stromal cells from cases are enriched in cells expressing pro-inflammatory and senescent phenotypes. An enrichment of B cells in the cases (p=5.8 x 10 -6 ) raises the possibility that some may have chronic endometritis, a disorder which predisposes to endometriosis.
Conclusions . We propose that characterization of endometrial tissues in ME will provide an effective screening tool for identifying endometriosis in patients with chronic symptoms suggestive of this disorder. This constitutes a major advance, since delayed diagnosis for many years is a major clinical problem in the evaluation of these patients. Comprehensive analysis of ME is expected to lead to new diagnostic and therapeutic approaches to endometriosis and other associated reproductive disorders such as female infertility.

overall_design: Single cell RNA-sequencing (scRNA-Seq) of endometrial tissues in freshly collected menstrual effluent (ME) from 33 subjects, including confirmed endometriosis patients (cases) and controls as well as symptomatic subjects (who have chronic symptoms of endometriosis but have not been diagnosed).

first: Robert

middle: P

last: Adelson

first: Himanshu

last: Vashistha

first: Houman

last: Khalili

first: Ashima

last: Nayyar

first: Radha

last: Puran

first: Rixsi

last: Herrera

first: Prodyot

middle: K

last: Chatterjee

first: Annette

last: Lee

first: Alexander

last: Truskinovsky

first: Kristine

last: Elmaliki

first: Margaret

last: DeFranco

first: Christine

middle: N

last: Metz

first: Peter

last: Gregersen


title: Translational profiling of neuronal subtypes reveals early vulnerability of somatostatin-expressing neurons in pre-symptomatic fatal familial insomnia

city: Linköping

first: Susanne

last: Bauer

address: BKV, Cellbiologi Pl 10

department: BKV

country: Sweden

institute: Linköpings universitet

summary: Selective neuronal vulnerability is a common, yet poorly understood characteristic of neurodegenerative diseases and is particularly prominent in familial prion diseases, such as Creutzfeldt-Jakob disease (CJD) and fatal familial insomnia (FFI), where different mutations in the prion protein manifest as neuropathologically distinct diseases. To determine how presence of mutant prion protein influences gene expression at pre-symptomatic stages, we used RiboTag to isolate cell type-specific, translating RNA from GABAergic, glutamatergic, somatostatin- (SST) and parvalbumin-expressing neurons of 9-month-old knock-in mice of CJD and FFI.

overall_design: We analyzed four cell types (Gad2+, PV+, SST+, vGluT2+) in three genotypes (FFI, CJD and WT control). Cell type-specific RNA was obtained from in two brain regions (cerebrum sans olfactory bulb, and cerebellum). For cerebellum, only Gad2+ and vGluT2+ were analyzed. For each analyzed RiboTag sample set (genotype_celltype_region) 3-7 biological replicates were prepared and sequenced. Cell type-specific RNA was obtained using the RiboTag Immunoprecipitation method from brain tissue homogenates (details below). For a subset of samples, total RNA was isolated from brian homogenates as input control. Differential expression anaysis was performed for each sample set, comparing FFI vs. Control or CJD vs. Control.

first: Walker

middle: S

last: Jackson


title: Identification of genes differentially expressed in HAX1-deficient HL-60 cells

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: RNA sequencing was performed to compare levels of intracellular transcripts in HL-60 WT and HL-60 HAX1 KO cells. Experiment was performed to check influence of HAX1 protein on cellular transcriptome (in HL-60 cell line)

overall_design: 12 samples: 4 control samples obtained from HL-60 cells, 4 samples obtained from HL-60 HAX1 KO #1 cells, 4 samples obtained from HL-60 HAX1 KO #2 cells

first: Ewa

last: Grzybowska

first: Maciej

last: Wakuła

first: Małgorzata

last: Rydzanicz


title: Small-molecule Activators Specific to Adenine Base Editors through Blocking Canonical TGF-beta Pathway

status: Public on Sep 20 2022

city: Shanghai

first: Mingliang

last: zhang

address: No.280 Chongqing South Road

institute: Shanghai Jiao Tong University school of medicine

summary: ABEs were developed to catalyze an A-to-G conversion, thus holding therapeutic potentials for treating the major class of human pathogenic SNPs. However, robust and precise editing at diverse genome loci in a controllable manner remains challenging. Here, through a high-throughput chemical screen of ~ 8,000 small molecules, we identified and validated a spectrum of small molecules that target the canonical TGF-beta pathway as ABE activators. Among those, SB505124, a selective ALK5 inhibitor, promotes ABE editing most. Treating cells with SB505124 dramatically enhanced on-target editing at multiple genome loci, including the refractory regions, while exhibiting little effect on off-target conversion on the genome, eliminating the major concern for clinical applications. Furthermore, SB505124 facilitates the editing of disease-associated genes in vitro and in vivo. Intriguingly, SB505124 serves as a specific activator by selectively promoting the activity of ABEs, rather than CBEs or Cas9. Our finding equips the ABE with precise chemical control, and more importantly, reveals a so-far-unreported role of the canonical TGF-beta pathway on gene editing.

overall_design:
Cells were seeded on 24-well plates, transfected with a plasmid expressing ABE7.10 and gRNA targeting site 18. Twelve hours after transfection, cells were re-plated into 24-well plates as 1.4×10^5 cells per well. The chemicals were added individually. Seventy-two hours after treatment, the total RNA was isolated by TRNzol Universal reagent according to the standard protocol then used to construct high-throuput sequencing libraries for RNA-seq.
ITD 1 is a selective inhibitor of TGF-β signaling.  SB-505124 is a selective inhibitor of TGF-β Receptor type I receptors.

last: Zhang

first: Yudong

last: Yang


title: Dosage effect of TGF-beta on EMT induction of MCF10A cells (experiment1)

city: Yokohama

first: Kazuhide

last: Watanabe

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: Riken

summary: Epithelial-mesenchymal transition (EMT) is a key cellular process involved in development and disease progression. Single-cell transcriptomes can reveal intermediate EMT states observed in tumors, but previous studies focused on time-dependent responses in epithelial cells after stimulation with EMT signals as an in vitro model for understanding EMT progression, so it was unclear how transcriptomes can change in response to different levels of EMT inducer. Here, we performed single-cell RNA-sequencing with human mammary epithelial cells treated with various concentrations of TGF-β. We found that the dose-dependent EMT harbors multiple intermediate states at the single-cell level after two weeks of treatment, suggesting a stable EMT continuum. After correcting batch effects from experiments, we performed comparative analyses of the dose- and time-dependent EMT. We found that the dose-dependent EMT shows a stronger anti-correlation between epithelial and mesenchymal transcriptional programs and a better resolution of stages of EMT compared to the time-dependent progress. These properties enable more power to detect genes whose expressions are associated with EMT. Nonetheless, our analyses showed cell clusters unique to the time-dependent EMT, which correspond to en route cell populations that do not appear at steady states. Furthermore, combining dose- and time-dependent cell clusters gave rise to more accurate prognosis for cancer patients compared to individual EMT spectrum.

overall_design:
Normal human mammary epithelial cell MCF10A was stimulated with TGFbeta  at concentrations of 0, 12.5, 25, 50, 100, 200, 400, 800 pM for 14 days and all samples were pooled before loading into 10x Genomics. Single-cell 3'RNA-seq library was prepared according to the manufacturer's instructions.
RNA-Seq library was prepared using 10x Chromium Single Cell 3' –end Reagent Kits User Guide (v2 Chemistry).  Libraries were sequenced using paired-end sequencing (26bp Read 1 and 98bp Read 2) with a single sample index (8bp) on the Illumina HiSeq 2500. Two lanes were used to increase the sequencing depth. GBC tags were used to distinguish cells treated with the different TGFbeta doses.

first: Masataka

last: Takahashi

first: Nicholas

last: Panchy

first: Tian

last: Hong


title: A BDNF-TrkB autocrine loop enhances senescent cell viability [scRNA-seq]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: We used single cell RNA sequencing (scRNA-seq) to investigate the RNA expression correlation between BDNF and STAT3-associated targets in etoposide-treated human fibroblast cell populations.

overall_design: Proliferating human fibroblasts (WI-38 cells) were treated with etoposide to trigger senescent-like phenotypes. Cells were trypsinized, washed and then subjected to scRNA-seq experiment.

first: Carlos

last: Anerillas

first: Kwan-Wood

middle: G

last: Lam


title: Effect of depletion of Hmgcs2 on gene expression in neonatal mouse heart

city: Nanjing

first: Danyang

last: Chong

state: Jiangsu

address: 101 Longmian Avenue, Jiangning District, Nanjing

institute: Nanjing Medical University

summary: To investigate the role of ketone body in the transcriptome in neonatal mouse heart, we constructed Hmgcs2 knockout mice and performed gene expression profiling analysis using data obtained from RNA-seq of wild-type and Hmgcs2 knockout mouse hearts at postnatal 3rd day.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type and Hmgcs2 knockout mouse hearts at postnatal 3rd day.  Hmgcs2 is a gene involved in the regulation of ketone body production.


title: Single cell transcriptomic profiling of tau pathophysiology in a novel 3D neural-glial coculture model II

city: Boston

first: Christine

last: Cheng

state: Massachusetts

address: 24 Cummington Mall

department: Biology

institute: Boston University

summary: We report the development of a novel 3D human induced pluipotent stem cell derived neural-glial coculture model of tauopathy and identify pathways associated with pathogenesis by 10X 3' single cell RNA sequencing.

overall_design: 3D human induced pluripotent stem cell derived neurons exposed to oligomeric tau and glial cells were co-cultured with and without PU-H71 drug treatment. 10X 3' single-cell RNA sequencing was performed at 1, 2, and 3 week timepoints.

first: Hannah

middle: D

last: Rickner


title: Cannabidiol modulates type I IFN response genes and HIV infection in macrophages

city: Los Angeles

first: Anjie

last: Zhen

address: 615 Charles E Young Drive

department: Medicine- Hematology/ Oncology

institute: University of California, Los Angeles

summary: To understand the differential expression of CBD on monocytic cells and the mechanisms by which CBD interacts with our immune system and immune cell signaling.

overall_design: To examine the global effects of Cannabidiol (CBD) on transcriptome, we treated THP-1 (monocytic cell line) with either vehicle, CBD alone, 2'3cGAMP alone or CBD and 2'3'cGAMP for 8hrs.

first: Shallu

last: Tomer

first: Gajendra

last: Suryawanshi


title: Isolation of ferret astrocytes reveals their morphological, transcriptional, and functional differences from mouse astrocytes

city: Kanazawa City

first: Tsuyoshi

last: Hattori

state: Ishikawa

address: 13-1 Takara-Machi

department: Department of Neuroanatomy

institute: Kanazawa University

summary: To identify differently expressed genes between ferret and mouse astrocytes, we performed RNA-seq studies on primary ferret and mouse astrocytes cultured in serum free medium. We isolated primary astrocytes from mixed glial cultures which are prepared from the cortices of ferrets and mice at postnatal day 1. Each biological replicate was generated from 2 individuals of the same species. We detected substantial changes in the expression of genes associated with cell proliferation and migration, and identified ferret astrocyte-specific genes.

sample_organism:
Mustela putorius furo
Mus musculus

platform_organism:
Mustela putorius furo
Mus musculus

overall_design: We generated mRNA profiles of primary astrocytes which were prepared from ferret and mouse neonatal cortices using Illumina HiSeq 2000 platform.

first: Jureepon

last: Roboon

first: Takayuki

last: Kannon

first: Kazuyoshi

last: Hosomichi

first: Atsuhi

last: Tajima

first: Osamu

last: Hori


title: A BDNF-TrkB autocrine loop enhances senescent cell viability [RNA-seq]

summary: Cellular senescence is characterized by cell cycle arrest, resistance to apoptosis, and a senescence-associated secretory phenotype (SASP) whereby cells secrete pro-inflammatory and tissue-remodeling factors. Given that the SASP exacerbates age-associated pathologies, some aging interventions selectively eliminate senescent cells. In this study, a drug library screen uncovered TrkB (NTRK2) inhibitors as selectively capable of triggering apoptosis of senescent, but not proliferating, human fibroblasts. Senescent cells expressed high levels of TrkB, which supported senescent cell viability, and secreted the TrkB ligand BDNF. The reduced viability of senescent cells after ablating BDNF function supported an autocrine function for TrkB and BDNF, and the increased expression of BCL2L2 through ERK5, downstream of BDNF-TrkB, favored senescent cell survival. Strikingly, treatment with TrkB inhibitors reduced the accumulation of senescent cells in aged mouse organs. Our results suggest that the SASP factor BDNF promotes cell survival by activating TrkB and is a promising therapeutic target to reduce the senescent cell burden.

overall_design: We sequenced the mRNA present in WI-38 senescent cells in which either TrkB or BDNF were silenced (siNTRK2 and siBDNF, respectively) compared to siCtrl siRNA, and included siCtrl-transfected proliferating cells as well.

first: Allison

middle: B

last: Herman

first: Rachel

last: Munk

first: Matthew

last: Payea

first: Martina

last: Rossi

first: Dimitrios

last: Tsitsipatis

first: Jennifer

middle: L

last: Martindale

first: Yulan

last: Piao

first: Krystyna

last: Mazan-Mamczarz

first: Jinshui

last: Fan

first: Chang

middle: Y

last: Cui

first: Kotb

last: Abdelmohsen

first: Rafael

last: de Cabo

first: Myriam

last: Gorospe


title: An LKB1-mitochondria axis controls Th17 effector function [ATAC-Seq]

status: Public on Sep 19 2022

first: Immunometabolism

last: Department

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: T helper 17 (Th17) cells are a distinct subset of CD4+ T cells necessary for maintaining gut homeostasis and have prominent roles in autoimmunity and inflammation1. Th17 cells have unique metabolic features, including a stem cell-like signature2,3 and reliance on mitochondrial respiratory chain function and tricarboxylic acid (TCA) cycle to coordinate metabolic and epigenetic remodeling4,5. Dynamic changes in mitochondrial membrane morphology are key to sustain organelle function6. However, it remains unclear whether mitochondrial membrane remodeling orchestrates metabolic and differentiation events in Th17 cells. Here we demonstrate that mitochondrial membrane fusion and tight cristae organization are required for Th17 cell function (i.e. cytokine expression) but dispensable in other T cell subsets. We find that Th17 cells rely on mitochondrial fusion as a result of their low metabolic activity. Thus, lowering metabolic activity in other T cell subsets by nutrient restriction was sufficient to increase reliance on mitochondrial fusion for effector function. Transcriptional, proteomic, and metabolomic profiling identified the serine/threonine kinase liver associated kinase B1 (LKB1) as an essential node coupling mitochondrial function to cytokine expression in T cells. By genetic and metabolomic approaches, we demonstrate that LKB1 regulates IL-17A expression by controlling TCA cycle metabolites and transcriptional remodeling. Th-17 cell-specific deletion of optic atrophy 1 (OPA1), a protein involved in mitochondrial inner membrane fusion and cristae organization, reduced autoimmune pathogenesis in a mouse model of multiple sclerosis, while additional deletion of LKB1 restored disease. Our findings highlight distinct mitochondrial requirements in CD4+ T cells, identify mitochondrial membrane fusion as a major determinant of Th17 responses, and reveal LKB1 as a sensor of mitochondrial integrity that links mitochondrial cues to effector programs in Th17 cells.

overall_design: CD4+ T cells were isolated from cell suspensions from spleen and peripheral lymph nodes (LN) from wild type and Opa1 conditional floxed mice crossed with CD4Cre to generate Opa1 deficient CD4 T cells. Isolated CD4s were then polarized to Th17 using TGF-β (5 ng ml-1), IL-6 (10 ng ml-1), IL-1β (10 ng ml-1), anti-mouse IFN-γ (10 μg ml-1) and anti-mouse IL-4 (10 μg ml-1). 3 biological replicates were isolated, processed and analyzed.

first: Francesc

last: Baixauli

first: David

last: Sanin

first: Erika

last: Pearce


title: The effect of CD153 engagement on the activation of senescence-associated (SA) T cells

city: Kyoto

first: Yuji

last: Fukushima

address: 53 Shogoin Kawahara-cho

institute: Kyoto University

summary: Advancing age is associated with the increase and accumulation of unique lymphocyte populations. Among them, CD153+ PD-1+ CD4+ T cells (SA-T cells) may underlie the pathogenesis of autoimmune and chronic inflammatory diseases. To assess the possible involvement of CD153 in regulating the cellular function, we performed bulk RNA-seq analysis.

overall_design: Enriched CD153+ SA-T cells were stimulated in vitro for 16 hours with anti-CD3/CD28 antibodies (Abs) in the presence of either plate-bound anti-CD153 Ab (RM153) or control IgG. The CD153-engaged and control cells were compared by RNA-seq analysis with three biological replicates.

first: Y

first: M

last: Hattori


title: Individual and combinatorial contribution of type I, II and III interferons in limiting SARS-CoV-2 replication, disease progression and age-related mortality [RN21189]

city: London

first: Andreas

last: Wack

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Using a mouse-adapted SARS-CoV-2 variant (SARS-CoV-2 MA20), newly generated in our lab, we found that endogenous type I and type III IFNs synergize to limit SARS-CoV-2 replication and to expedite virus clearance and that enhanced disease progression in aged mice depends on impaired type II IFN immunity

overall_design: Adult 8‐12‐week‐old mice and aged 16‐24 week‐old C57BL/6  wild-type mice mice were either mock infected or  infected with 300 PFU SARS‐CoV‐2 MA20 in a 40 μl volume. Lungs were harvested at 3, 4 and 5 days post infection.

first: Daniel

last: Schnepf

first: Julius

last: Beer

first: Martin

last: Schwemmle


title: A BDNF-TrkB autocrine loop enhances senescent cell viability

first: Supriyo

last: De

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

overall_design: Refer to individual Series


title: Deciphering imprints of impaired memory B-cell maturation in germinal centers of patients with Common variable immunodeficiency

city: Leiden

first: Mirjam

last: van der Burg

address: Albinusdreef 2

institute: LUMC

summary: Common variable immunodeficiency (CVID), characterized by recurrent infections, low serum class-switched immunoglobulin isotypes and poor antigen specific antibody responses, comprises a heterogeneous patient population in terms of clinical presentation and underlying etiology. The diagnosis is regularly associated with a severe decrease of germinal center (GC) derived B-cell populations in peripheral blood. However, data from B-cell differentiation within GC is limited. We present a multiplex approach combining histology, flow cytometry and B-cell receptor repertoire analysis of sorted GC B-cell populations allowing the modelling of distinct disturbances in GCs of three CVID patients. Our results reflect pathophysiological heterogeneity underlying the reduced circulating pool of post-GC memory B cells and plasmablasts in the three patients. In patient 1, quantitative and qualitative B-cell development in GCs is relatively normal. In patient 2, irregular shaped GCs are associated with reduced somatic hypermutation (SHM), antigen selection and class-switching, while in patient 3, high SHM, impaired antigen selection and class-switching with large single clones imply increased re-cycling of cells within the irregular shaped GCs. In lymph nodes of patients 2 and 3, only limited numbers of memory B cells and plasma cells are formed. While reduced numbers of circulating post GC B cells is a general phenomenon in CVID, the integrated approach exemplified distinct defects during GC maturation ranging from near normal morphology and function to severe disturbances with different facets of impaired maturation of memory B cells and/or plasma cells. Integrated dissection of disturbed GC B-cell maturation by histology, flowcytometry and BCR repertoire analysis reveals essential steps during memory formation.

overall_design: B-cell subsets were sorted from secondary lympoid organs and peripheral blood of 3 patients with CVID and 3 healthy donors. Subsequently, IGH repertoire analysis was performed to get insight in the maturation processes in the germinal center

first: Pauline

last: van Schouwenburg

first: Susanne

last: Unger

first: Kathryn

last: Payne

first: Fabian

last: Kaiser

first: Ingrid

last: Pico-Knijnenburg

first: Jens

last: Pfeiffer

first: Oliver

last: Hausmann

last: Friedmann

first: Michelle

last: Erbel

first: Maximilian

last: Seidl

last: van Zessen

first: Andrew

last: Stubbs

first: Klaus

last: Warnatz


title: Individual and combinatorial contribution of type I, II and III interferons in limiting SARS-CoV-2 replication, disease progression and age-related mortality [RN21061]

first: Andreas

last: Wack

summary: Using a mouse-adapted SARS-CoV-2 variant (SARS-CoV-2 MA), we found that endogenous type I and type III IFNs synergize to limit SARS-CoV-2 replication and to expedite virus clearance and that enhanced disease progression in aged mice depends on impaired type II IFN immunity

overall_design: Adult 8‐12‐week‐old mice and aged 16‐24 week‐old Ifnar1‐/‐ mice on a C57BL/6 background, were either mock infected or  infected with 10^5 PFU SARS‐CoV‐2 MA in a 40 μl volume. Lungs were harvested at 3 days post infection.

last: Schnepf

last: Beer


title: A transcriptional cross species map of pancreatic islet cells

city: Neuherberg

first: Sophie

last: Tritschler

address: Ingolstädter Landstrasse 1

country: Germany

institute: Helmholtz Zentrum Munich

summary: This dataset consists of single-cell RNA-seq (10X) data from healthy, adult human and pig pancreatic islets.  Pancreatic islets of Langerhans secrete hormones to regulate systemic glucose levels. Emerging evidence suggests that islet cells are functionally heterogeneous to allow a fine-tuned and efficient endocrine response to physiological changes. A precise description of the molecular basis of this heterogeneity, in particular linking animal models to human islets, is an important step towards identifying the factors critical for endocrine cell function in physiological and pathophysiological conditions.   In this study, we used single-cell RNA sequencing to profile more than 50’000 endocrine cells isolated from healthy human, porcine and murine pancreata and characterize transcriptional heterogeneity and evolutionary conservation of those cells across the three species. We systematically delineated endocrine cell types and α- and β-cell heterogeneity through prior knowledge- and data-driven gene sets shared across species, which altogether capture common and differential cellular properties, transcriptional dynamics and putative driving factors of state transitions.   We showed that global endocrine expression profiles correlate, and that critical identity and functional markers are shared between species, while only approximately 20% of cell-type enriched expression is conserved. We resolved distinct human α- and β-cell states that form continuous transcriptional landscapes. These states differentially activate maturation and hormone secretion programs, which are related to regulatory hormone receptor expression, signaling pathways and different types of cellular stress responses. Finally, we mapped mouse and pig cells to the human reference and observed that the spectrum of human α- and β-cell heterogeneity and aspects of such functional gene expression are better recapitulated in the pig than mouse data.   Here, we provide a high-resolution transcriptional map of healthy human islet cells and their murine and porcine counterparts, which is easily queryable via an online interface. This  comprehensive resource informs future efforts that focus on pancreatic endocrine function, failure and regeneration, and enables to assess molecular conservation in islet biology across species for translational purposes.

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design: Single cell RNA seq data of isolated pancreatic islets from adult human and pig donors was generated using the 10X Genomics technology.

first: Moritz

last: Thomas

first: Böttcher

last: Anika

first: Ludwig

last: Barbara

first: Kemter

last: Elisabeth

first: Eckhard

last: Wolf

first: Heiko

last: Lickert

last: Theis


title: RNA immunoprecipitation and next generation sequencing  (RIP-seq) specific for HAX1 protein

first: Krzysztof

last: Goryca

summary: RNA immunoprecipitation was performed to characterize RNA interactome specific to endogenous HAX1 protein

overall_design: 10 samples: 5 samples immunoprecipitated with anti-HAX1 antibody, 5 samples with IgG control

first: Ewa

middle: A

last: Grzybowska

first: Anna

last: Balcerak

first: Małgorzata

last: Rydzanicz


title: Leptin treatment has vasculo-protective effects in lipodystrophic mice

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisalle 30

department: Klinik und Poliklinik für Kardiologie

institute: Universitätsklinikum Leipzig

summary: Lipodystrophy syndromes (LD) are characterized by loss of adipose tissue, metabolic complications such as dyslipidemia, insulin resistance and fatty liver disease, as well as accelerated atherosclerosis. As a result of adipose tissue deficiency, the systemic concentration of the adipokine leptin is reduced. A current promising therapeutic option for patients with LD is treatment with recombinant leptin (metreleptin) resulting in reduced risk of mortality. Here, we investigate the effects of leptin on endothelial-to-mesenchymal transition (EndMT), which impairs the functional properties of endothelial cells and promotes atherogenesis in LD. Leptin treatment reduced inflammation, TGF-β2-induced expression of mesenchymal genes and prevented impairment of endothelial barrier function. Treatment of lipodystrophic and atherosclerosis prone animals (Ldlr-/-; aP2-nSrebp1c-Tg) with leptin reduced macrophage accumulation in atherosclerotic lesions, vascular plaque protrusion and the number of endothelial cells with mesenchymal gene expression, confirming a reduction in EndMT in LD after leptin treatment. Treatment with leptin inhibited LD-mediated induction of the pro-atherosclerotic cytokine growth/differentiation factor 15 (GDF15). Inhibition of GDF15 reduced EndMT induction triggered by plasma from LD patients. Our study reveals that in addition to the effects on adipose tissue function, leptin treatment exerts beneficial effects protecting endothelial function and identity in LD by reducing GDF15.

overall_design: Human umbilical vein endothelial cells were treated with TGF-β2 or additionally with leptin, and afterwards analyzed using scRNAseq.

first: Paulina

last: Stürzebecher

first: Susan

last: Kralisch

first: Stephan

last: Erbe


title: SpyCLIP sequencing of BUD31 in ovarian cancer cells

city: Jinan

first: Zixiang

last: Wang

state: Shandong

address: No.44 Wenhuaxi Road

department: Cheeloo College of Medicine

institute: Shandong University

summary: Mis-regulation of splicing factors are thought to activate cancer specific splicing programs that contribute to cancer development and progression. However, it remains a major challenge to identify the key splicing variants caused by aberrant expression of splicing factors in cancer. Here we report that splicing factor BUD31 is commonly overexpressed in high-grade serous ovarian carcinoma (HGSOC) and high level of BUD31 is associated with poor prognosis. RNA-seq analysis reveals that BUD31 inhibition predominantly results in alternation of exon skipping and intron retention.  We further identify binding motif and preferred genome-wide binding pattern of BUD31 by CLIP-seq analysis. Our data indicate that BUD31 is a critical oncogenic splicing factor in ovarian cancer and might act as a potential therapeutic target.

overall_design: Examination RNA binding sites of splicing factor BUD31 in ovarian cancer cells with two replicates.

first: Zhaojian

last: Liu


title: mTOR- and LARP1-dependent regulation of TOP mRNA poly(A) tail and ribosome loading [LARP1 KD, Torin1]

city: Nagoya

first: Koichi

last: Ogami

address: 65 Tsurumai-cho, Showa-ku

institute: Nagoya University

summary: Translation of TOP mRNAs encoding protein synthesis machinery is strictly regulated by an amino acid sensing mTOR pathway.  However, its regulatory mechanism remains elusive.  Here, we demonstrate that TOP mRNA translation positively correlates with its poly(A) tail length under mTOR active/amino acid-rich condition, suggesting that TOP mRNAs are post-transcriptionally controlled by poly(A) tail length regulation.  Consistent with this, tail length of TOP mRNAs dynamically fluctuates in response to amino acid availability.  Poly(A) tail shortens under mTOR active/ amino acid-rich condition, whereas the long-tailed TOP mRNAs accumulate under mTOR inactive/amino acid-starved (AAS) condition.  An RNA-binding protein LARP1 that specifically binds to TOP mRNAs is indispensable for the process.  We also show that LARP1 interacts with non-canonical poly(A) polymerases, PAPD4, PAPD5 and PAPD7 and induces post-transcriptional polyadenylation of the target when tethered to the mRNA.  Our findings illustrate that LARP1 contributes to the selective accumulation of TOP mRNAs with long poly(A) tail under AAS, resulting in accelerated ribosomal loading onto TOP mRNAs for the resumption of translation after AAS.

overall_design: 5’ capped polyA RNAs purified from HEK293T cells were analyzed by direct RNA-sequencing using the Oxford Nanopore’s MinION.


title: An LKB1-mitochondria axis controls Th17 effector function [RNA-Seq 1]

first: Immunometabolism

last: Department

overall_design: CD4+ T cells were isolated from cell suspensions from spleen and peripheral lymph nodes (LN) from mice from the indicated genotypes. Isolated CD4s were then polarized to Th17 using TGF-β (5 ng ml-1), IL-6 (10 ng ml-1), IL-1β (10 ng ml-1), anti-mouse IFN-γ (10 μg ml-1) and anti-mouse IL-4 (10 μg ml-1). RNA was extracted from polarized cells and then sequenced.

first: Francesc

last: Baixauli

first: Klara

last: Piletic

first: Daniel

last: Puleston

first: Cameron

last: Field

first: Lea

last: Flachsmann

first: Matteo

last: Villa

first: David

last: Sanin

first: Andrea

last: Quintana

first: Nisha

last: Rana

first: Joy

last: Edwards-Hicks

first: Michal

last: Stanczak

first: Katarzyna

last: Grzes

first: Agnieska

last: Kabat

first: Mario

last: Fabri

first: Mai

last: Azuma

first: George

last: Caputa

first: Mauro

last: Corrado

first: Yarub

last: Musa

last: Duda

first: Thoma

last: Jenuwein

first: Gerhard

last: Mittler

first: Joerg

middle: M

last: Buesscher

last: O’Sullivan

first: Edward

last: Pearce

first: Erika


title: Transcriptional profiling of osteogenic medium calcified human primary coronary artery smooth muscle cells.

status: Public on Sep 18 2022

city: Aachen

first: Claudia

last: Goettsch

address: Pauwelsstr. 30

institute: RWTH Aachen

summary:
Transcriptomics analysis of human coronary artery smooth muscle cells cultured in osteogenic medium (OM)  to induce a mineralized extracellular matrix.
To study the underlying molecular mechanisms driving vascular calcification, we analyzed the transcriptome of osteogenic medium (OM)-calcified human coronary artery smooth muscle cells on day  7.

overall_design: Human primary coronary artery smooth muscle cells from three independent donors were cultured in control medium or calcified in osteogenic medium (OM).

first: Marina

last: Heuschkel

first: Anne

last: Babler

first: Jonas

last: Heyn

first: Emiel

last: van der Vorst

first: Marja

last: Steenman

first: Maren

last: Gesper

first: Ben

last: Kappel

first: David

last: Magne

first: Yann

last: Goueffic

first: Rafael

last: Kramann

first: Willi

last: Jahnen-Dechent

first: Nikolaus

last: Marx

first: Thibaut

last: Quillard


title: Transcriptional profiling of calcium-phosphate calcified human primary coronary artery smooth muscle cells.

summary:
Transcriptomics analysis of human coronary artery smooth muscle cells cultured in calcium-phosphate medium (CaP) to induce a mineralized extracellular matrix.
To study the underlying molecular mechanisms driving vascular calcification, we analyzed the transcriptome of calcium-phosphate calcified human cronary aortic smooth muscle cells on day  3.

overall_design: Human primary coronary artery smooth muscle cells from three independent donors were cultured in control medium or calcified in calcium-phosphate medium (CaP).


title: Proteome-wide effects of single gene perturbations in a eukaryotic cell

city: Mainz

first: Falk

last: Butter

state: Germany

address: Ackermannweg 4

department: Quantitative Proteomics

institute: Institute of Molecular Biology gGmbH

summary: Eukaryotic gene expression is controlled at the transcriptional, translational and protein degradation level and its principles are starting to emerge. While transcriptional outcomes, which are commonly also used as a proxy for protein abundance, have been investigated on a larger scale, the study of translational output requires large-scale proteomics data. However, data for proteome alterations by systematic assessment of knockouts genome-wide is not available yet. We here determined the individual proteome changes for  3,308 non-essential genes in the yeast S. pombe (www.butterlab.org/SpProtQuant). We observed that genes with high proteome remodeling are predominantly involved in gene expression regulation, in particular acting as translational regulators. Focusing on those knockout strains with a large number of altered proteins, we performed paired transcriptome/proteome measurements to uncover translational regulators and features of translational regulation. Furthermore, by similarity clustering of these proteome changes, we infer gene functionality that can be extended to other species such as human or baker’s yeast.

overall_design: Overall 94 knockout strains were sequenced in quadruplicates. The data also includes 2 biological wt replicates for comparison.

first: Merve

last: Öztürk

first: Michal

last: Levin


title: An LKB1-mitochondria axis controls Th17 effector function

first: Immunometabolism

last: Department


title: Therapeutic Intervention with Anti-Complement Component 5 Antibody Does Not Reduce NASH but Does Attenuate Atherosclerosis and MIF Concentrations in Ldlr-/-.Leiden Mice.

first: Florine

last: Seidel

address: Zernikedreef 9

institute: TNO Innovation for Life

summary:
Background: Chronic inflammation is an important driver in the progression of non-alcoholic steatohepatitis (NASH) and atherosclerosis. The complement system, one of the first lines of defense in innate immunity, has been implicated in both diseases. However, the potential therapeutic value of complement inhibition in the ongoing disease remains unclear.
Methods: After 20 weeks of high-fat diet (HFD) feeding, obese Ldlr-/-.Leiden mice were treated twice a week with an established anti-C5 antibody (BB5.1) or vehicle control. A separate group of mice was kept on a chow diet as a healthy reference. After 12 weeks of treatment, NASH was analyzed histopathologically, and genome-wide hepatic gene expression was analyzed by next-generation sequencing and pathway analysis. Atherosclerotic lesion area and severity were quantified histopathologically in the aortic roots.
Results: Anti-C5 treatment considerably reduced complement system activity in plasma and
MAC deposition in the liver but did not affect NASH. Anti-C5 did, however, reduce the development of atherosclerosis, limiting the total lesion size and severity independently of an effect on plasma cholesterol but with reductions in oxidized LDL (oxLDL) and macrophage migration inhibitory factor (MIF).
Conclusion: We show, for the first time, that treatment with an anti-C5 antibody in advanced stages of NASH is not sufficient to reduce the disease, while therapeutic intervention against established atherosclerosis is beneficial to limit further progression.

overall_design: In this study we investigated the potential health effect of therapeutic inhibition of complement component 5 (C5). After 20 weeks of high-fat diet (HFD)-feeding, obese Ldlr-/-.Leiden mice were treated with an anti-C5 antibody or vehicle control and a separate group of mice was kept on chow diet as a healthy reference.

first: Robert

last: Kleemann

first: Wim

last: van Duyvenvoorde

first: Nikki

last: van Trigt

first: Nanda

last: Keijzer

first: Sandra

last: van der Kooij

first: Cees

last: van Kooten

first: Lars

last: Verschuren

first: Aswin

last: Menke

first: Amanda

last: Kiliaan

first: Johnathan

last: Winter

first: Timothy

middle: R

last: Hughes

first: B

last: Morgan

first: Frank

last: Baas

first: Kees

last: Fluiter

first: Martine

middle: C

last: Morrison


title: Comparison of intimal and medial calcification in vitro

first: Claudia

last: Goettsch


title: An LKB1-mitochondria axis controls Th17 effector function [RNA-Seq 2]

first: Immunometabolism

last: Department

overall_design: CD4+ T cells were isolated from cell suspensions from spleen and peripheral lymph nodes (LN) from wild type and Opa1 conditional floxed mice crossed with CD4Cre to generate Opa1 deficient CD4 T cells. CRISPR-Cas9 deletion of LKB1 was performed with Alt-R™ CRISPR-Cas9 System (IDT) and 4D-Nucleofector™ technology (Lonza) in freshly isolated CD4+ T cells. Isolated CD4s were then polarized to Th17 using TGF-β (5 ng ml-1), IL-6 (10 ng ml-1), IL-1β (10 ng ml-1), anti-mouse IFN-γ (10 μg ml-1) and anti-mouse IL-4 (10 μg ml-1). RNA was extracted from polarized cells and then sequenced. 3 biological replicates were isolated, processed and analyzed.

first: Francesc

last: Baixauli

first: David

middle: E

last: Sanin

first: Erika

last: Pearce


title: Porphyromonas gingivalis leads to dysplasia of normal esophageal epithelial cells via Sonic hedgehog pathway

city: Beijing

first: Xueting

last: Jia

address: No. 95 Yong'an Road, Xicheng District

institute: Beijing Friendship Hospital, Capital Medical University

summary:
Purpose: To investigate the pathogenic effect of P. gingivalis on normal esophagus and the mechanism behind
Methods: Total mRNA  was extracted to determine the transcriptional dysregulation of Het-1A  cells after treated with P. gingivalis supernatant.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Het-1A cells in P. gingivalis supernatant-free medium and  P. gingivalis supernatant-present medium.

first: Xiaofeng

last: Huang


title: Individual and combinatorial contribution of type I, II and III interferons in limiting SARS-CoV-2 replication, disease progression and age-related mortality

first: Andreas

last: Wack


title: Identification of four immune subtypes in locally advanced rectal cancer treated with neoadjuvant chemotherapy for predicting the efficacy of subsequent immune checkpoint blockade

status: Public on Sep 17 2022

city: Chongqing

first: He

last: Xiao

state: Chongqing

address: No. 10, Changjiang Branch Road, Yuzhong District, Chongqing 400042, China

department: Department of Cancer Center

institute: Daping Hospital, Army Medical University

summary: Introduction: Neoadjuvant chemoradiotherapy (nCRT) was the foundation treatment for locally advanced rectal cancer (LARC). The nCRT can improve the efficacy of immunotherapy on account of its in-situ vaccine effect.   Objective: The aim is to identify stable and reliable transcriptome signatures to predict the efficacy of immune checkpoint blockade (ICB) in patients with LARC.   Methods: Immunophenotyping was established by using xCell immune cell infiltration abundance and consistent clustering in GSE39582 and verified in several data sets. The effects of immunophenotyping, follicular regulatory T cells, tumor associated fibroblasts (CAF) and tertiary lymphoid structures (TLS) signatures on the efficacy of ICB were analyzed by using IMvigor210, GSE91061 and an independent Daping Hospital (DPH) cohort.   Results: There are four stable and repeatable immune subtypes in rectal cancer, among which C1 is low immune infiltration type, C2 is high interstitial infiltration type, C3 is high immune infiltration type and C4 is ion channel type. C2 is mainly characterized by high infiltration CAF, C3 is characterized by high infiltration of cytotoxic T lymphocytes, high expression of PD-L1 and TLS. In rectal cancer patients receiving nCRT, immunophenotyping was not significantly associated with pathological remission rate, but immunophenotyping was an independent prognostic factor of RFS. In IMvigor210 patients treatment with atezolizumab, the pathological remission rates of C1, C2, C3 and C4 were 23.86%, 10.94%, 33.33% and 23.08% respectively (χ2 = 8.981, P = 0.029), which were 11.76%, 50.00%, 42.86% and 0.0% respectively in the GSE91061 patients treatment with nivolumab (Fisher's exact probability, P = 0.018). Both follicular regulatory T cells and CAF showed a further impact on the ICB therapeutic efficacy of C2 and C3 subtype. In addition, both GSE91404 and DPH cohorts showed that nCRT treatment induced a significant increase in the expression of TNFRSF9 and abundance of macrophages in C3 subtype.  Conclusion: Our data suggest that there are four immune types of rectal cancer, which are related to the prognosis of patients. Among them, C3 and some C2 subtypes represents the patients who may benefit from ICB after nCRT treatment.

overall_design:
Daping Hospital (DPH) cohort was comprised of resected tissues from nine LARC patients with complete pathological response (pCR), nine without pathological response (npCR) and biopsy tissues from nine LARC patients prior nCRT.
The raw fastq files containing sequence information are not permitted to be submitted according to Chinese law.

first: Le

last: He

first: Min

last: Jin

first: Dan

last: Jian

first: Bo

last: Yang

last: Dai

first: Yan

last: Feng

first: Dong

last: Wang


title: Vdelta2+ TCR sequencing of Vgamma9Vdelta2 T cells from adults and newborns

status: Public on Sep 16 2022

city: Hamburg

first: Immo

last: Prinz

address: Falkenried 94

department: Institute of Systems Immunology

institute: University medical center Hamburg Eppendorf

overall_design: We have isolated Vgamma9Vdelta2 T cells from 3 healthy adult donors and 5 neonates. RNA was extracted and Vdelta2 TCR cDNA library was amplified for illumina Miseq

first: Anna

last: Harms

first: Sarina

last: Ravens

first: Lihua

last: Deng

first: Likai

last: Tan


title: RNA-seq analysis in human adipose tissue and jejunum in subjects with morbidly obesity

city: Madrid

first: Jose Maria

middle: Moreno

last: Navarrete

state: (None)

address: Calle de Monforte de Lemos nº 5

country: Spain

institute: CIBER

summary: To investigate total RNA in subcutaneous and visceral adipose tissue and in jejunum in subjects with morbidly obesity.

first: José

last: Moreno-Navarrete

last: Fernandez-Real


title: Cancer-associated fibroblast-specific lncRNA LINC01614 enhances glutamine uptake in lung adenocarcinoma

city: Nanjing

first: Rong

last: Yin

address: Baiziting 42

department: Thoracic Surgery

institute: Nanjing Medical University Affiliated Jiangsu Cancer Hospital

summary: To investigate the mechanism of CAF-exosome-packaged LINC01614 in the regulation of the glutamine metabolism of cancer cells.

overall_design: The transfer and functional role of LINC01614 in lung adenocarcinoma (LUAD) and CAFs were investigated using  4-Thiouracil labeled RNA transfer and gain-and loss-of function approaches. RNA pull-down, RNA  immunoprecipitation, dual-luciferase assay, gene expression microarray, and bioinformatics  analysis were performed to investigate the underlying mechanisms involved.

first: Tongyan

last: Liu

first: Zhibin

last: Hu

first: Lin

last: Xu


title: Clinical and pathological findings in neurolymphomatosis: preliminary association with gene expression profiles in sural nerves.

city: Milan

first: Nilo

last: Riva

address: via Olgettina 60

department: Neuroscience

country: Italy

institute: IRCCS San Raffaele

summary: Although inflammation appears to play a role in neurolymphomatosis (NL), the mechanisms leading to degeneration in the peripheral nervous system are poorly understood. The purpose of this exploratory study was to identify molecular pathways underlying NL pathogenesis, combining clinical and neuropathological investigation with gene expression (GE) studies. Based on the neuropathic symptoms and signs, NL patients were classified into three forms of neuropathy: chronic symmetrical sensorimotor polyneuropathy (SMPN, n=3), multiple mononeuropathy (MN, n=4) and acute motor-sensory axonal neuropathy (AMSAN, n=1). Predominantly diffuse malignant cells infiltration of epineurium was present in chronic SMPN, whereas endoneurial perivascular cells invasion was observed in MN. In contrast, diffuse endoneurium malignant cells localization occurred in AMSAN. We identified alterations in the expression of 1266 genes, with 115 up-regulated and 1151 down-regulated genes, which were mainly associated with ribosomal proteins (RP) and olfactory receptors (OR) signaling pathways, respectively. Among the top up-regulated genes were actin alpha 1 skeletal muscle (ACTA1) and desmin (DES). Similarly, in NL nerves ACTA1, DES and several RPs were highly expressed, associated with endothelial cells and pericytes abnormalities. Peripheral nerve involvement may be due to conversion towards a more aggressive phenotype, potentially explaining the poor prognosis. The candidate genes reported in this study may be a source of clinical biomarkers for NL.

overall_design: The purpose of this exploratory study was to identify molecular pathways underlying NL pathogenesis, combining clinical and neuropathological investigation with gene expression (GE) studies. We characterized the clinical and pathological features of eight patients with NL. We further analysed GE changes in sural nerve biopsies obtained from a subgroup of NL patients (n=3) and thirteen patients with inflammatory neuropathies as neuropathic controls.

first: Ferdinando

last: Clarelli

first: Teuta

last: Domi

first: Federica

last: Cerri

first: Silvia

last: Santoro

first: Riva

last: Nilo

first: Angelo

last: Quattrini


title: Deterministic programming of human pluripotent stem cells into microglia facilitates studying their role in health and disease

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

summary:
Microglia, the resident immune cells of the central nervous system (CNS), are derived from yolk-sac macrophages that populate the developing CNS during early embryonic development. Once established, the microglia population is self-maintained throughout life by local proliferation. As a scalable source of microglia-like cells (MGLs), we here present a forward programming protocol for their generation from human pluripotent stem cells (hPSCs). The transient overexpression of PU.1 and C/EBPβ in hPSCs led to a homogenous population of mature microglia within 16 d. MGLs met microglia characteristics on a morphological, transcriptional, and functional level. MGLs facilitated the investigation of a human tauopathy model in cortical neuron–microglia cocultures, revealing a secondary dystrophic microglia phenotype. Single-cell RNA sequencing of microglia integrated into hPSC-derived cortical brain organoids demonstrated a shift of microglia signatures toward a more-developmental in vivo–like phenotype, inducing intercellular interactions promoting neurogenesis and arborization. Taken together, our microglia forward programming platform represents a tool for both reductionist studies
in monocultures and complex coculture systems, including 3D brain organoids for the study of cellular interactions in healthy or diseased environments.

overall_design: Single-cell RNA sequencing of 2D microglia monocolture (MGL), organoids without microglia (Organoid) and organoids cocultured with microglia (COC).

first: Anna

last: Speicher

first: Lisanne

last: Korn

first: Julia

last: Csatari

first: Matthias

last: Pawlowski


title: The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site selection in Arabidopsis

city: Valencia

first: Jaime

last: Pérez

address: Calle del Ingeniero Fausto Elio, s/n

institute: IBMCP

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

overall_design: Refer to individual Series


title: Knockout of the DNA binding domains in human-specific lncRNAs causes changed expression of target genes

city: Guangzhou

first: Jie

last: Lin

address: Shatai Road

institute: Southern Medical University

summary: To demonstrate proof of concept and validate the prediction of lncRNAs’ target genes, we performed three cases of genome editing to knock out the short sequences that contain the predicted DNA binding domains (DBD) of human-specific lncRNAs in three cancer cell lines. The knockout of a 157 bp sequence (containing the DBD of RP13-516M14.1) in the HeLa cell line, a 202 bp sequence (containing the DBD of RP11-426L16.8) in the RKO cell line, and a 198 bp sequence (containing the DBD of SNORA59B) in the SK-MES-1 cell line, all caused the significantly changed expression of target genes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the knockout of  three human-specific lncRNAs (RP13-516M14.1, RP11-426L16.8 and SNORA59B),and their controls (wild types).

first: Zhu

last: Hao


title: Single-cell sequencing reveals effects of chemotherapy on the immune landscape and TCR/BCR clonal expansion in a relapsed ovarian cancer patient

status: Public on Sep 15 2022

first: Yunshan

last: Ning

state: Guangdong

address: No.1023-1063, Shatai South Road, Baiyun District

department: School of Laboratory Medicine and Biotechnology

summary: Cancer recurrence and chemoresistance are the leading causes of death in high-grade serous ovarian cancer (HGSOC) patients. However, the unique role of the immune environment in tumor progression for relapsed chemo-resistant patients remains elusive. In single-cell resolution, we characterized a comprehensive multi-dimensional cellular and immunological atlas from tumor, ascites, and peripheral blood of a chemo-resistant patient at different stages of treatment. Our results highlight a role in recurrence and chemoresistance of the immunosuppressive microenvironment in ascites, including MDSC-like myeloid and hypo-metabolic γδT cells, and of peripheral CD8+ effector T cells with chemotherapy-induced senescent/exhaustive. Importantly, paired TCR/BCR sequencing demonstrated relative conservation of TCR clonal expansion in hyper-expanded CD8+ T cells and extensive BCR clonal expansion without usage bias of V(D)J genes after chemotherapy. Thus, our study suggests strategies for ameliorating chemotherapy-induced immune impairment to improve the clinical outcome of HGSOC.

overall_design: Tumor leison, ascites and peripheral blood of a HGSOC patient were isolated and analyzed using scRNA-seq and scTCR/BCR-seq.

first: Runrong

last: Li

first: Yanyu

last: Ren

first: Hanxiao

last: Feng

first: Yan

first: Fanliang

last: Meng


title: The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site selection in Arabidopsis [MNase-seq]

summary: In eukaryotes, DNA is associated with histones to form nucleosomes, the basic component of the chromatin. This structure presents a physical barrier for nuclear proteins to access DNA and, therefore, its plays a critical role in multiple processes such as transcription, replication and repair. Eukaryotes have evolved multiple chromatin remodelers to control nucleosome position and composition like the SWI/SNF family, which has been studied in detailed in diverse model organisms. We recently uncovered an evolutionarily conserved SWI/SNF complex in plants reminiscent of the mammalian BAF subclass, which incorporates the ATPases MINU and signature subunits TPF. In this study we characterize the impact of TPF depletion in the model plant Arabidopsis and we explore the genomic targets of the BAF complex, as well as its impact on nucleosome position and gene expression. Our results show that TPF mutants have strong developmental phenotypes, suggesting an important role in the complex function. TPF and MINU genomic targets show change in the position of the +1 nucleosome towards the promoter when the complex is mutated. While there is little correlation between this shift and changes in gene expression levels, we find a strong correlation between +1 nucleosome shift and the presence of extended 5´ regions towards the promoter in hundreds of BAF targets, suggesting a change in TSS usage. These additional 5´ UTR regions might alter RNA function and be responsible for the strong developmental phenotypes observed in the TPF and MINU mutants.

overall_design: Chromatin from inflorescences of Col-0, minu1-2 minu2-1, and tpf1-1 tpf2-1(2 biological replicates per background) were digested with Micrococcal Nuclease and mononucleosomal DNA was purified and used for libraries contruction at BGI following the BGISEQ-500 ChIP-Seq library preparation protocol. Libraries were sequenced at 100PE.

first: Javier

last: Gallego-Bartolomé

first: Borja

last: Diego-Martin

last: Perez-Alemany


title: Transcriptome Profiling of Leukemia Initiating Cells in Acute Precursor B Lymphoblastic Leukemia

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Background: In leukemia, a distinct subpopulation of cancer-initiating cells called leukemia stem cells (LSCs) are believed to drive population expansion and tumor growth. Failing to eliminate LSCs may result in disease relapse regardless of the amount of non-LSCs destroyed. The first step in targeting and eliminating LSCs is to identify and characterize them. Methods: Acute precursor B lymphoblastic leukemia (B-ALL) cells were incubated with fluorescent glucose analog 2-(N-(7-Nitrobenz-2-oxa-1, 3-diazol-4-yl) Amino)-2-Deoxyglucose (NBDG) and sorted based on NBDG uptake. Cell subpopulations defined by glucose uptake were then serially transplanted into mice and evaluated for leukemia initiating capacity. Gene expression profiles of these cells were characterized using RNA-Sequencing (RNA-Seq). Results: A distinct population of NBDG-low cells was identified in patient B-ALL samples. These cells are a small population (1.92% of the entire leukemia population), have lower HLA expression, and are smaller in size (4.0 to 7.0 μm) than NBDG-high cells. All mice transplanted with NBDG-low cells developed leukemia between 5 and 14 weeks, while those transplanted with NBDG-high cells did not develop leukemia (p≤0.0001-0.002). Serial transplantation of the NBDG-low mouse model resulted in successful leukemia development. NBDG-medium (NBDG-med) populations also developed leukemia. Interestingly, comprehensive molecular characterization of NBDG-low and -med cells from patient-derived xenograft models using RNA-Seq revealed a distinct profile of 2,162 differentially-expressed transcripts (DETs) (p<0.05) with 70.6% down-regulated in the NBDG-low cells. Hierarchical clustering of DETs showed distinct segregation of NBDG-low from the NBDG-med and -high groups with a number of marked transcription expression alterations in the NBDG-low group consistent with cancer survival. Conclusions: A unique subpopulation of cells with low glucose uptake (NBDG-low) in B-ALL was discovered. These cells, despite their quiescence characteristics, once transplanted in mice, showed potent leukemia initiating capacity. Although NBDG-med cells also showed leukemia initiating capacity, gene expression profiling revealed a distinct signature that clearly distinguishes NBDG-low cells from NBDG-med and the rest of the leukemia populations. These results suggest that NBDG-low cells may represent quiescent LSCs. These cells can be activated in the appropriate environment in vivo, showing leukemia initiating capacity. Our study provides insight into the biologic mechanisms of B-ALL initiation and/or survival.

overall_design: Human B-cell acute lymphoblastic leukemia (B-ALL) patient-derived xenograft (PDX) models were created by intratibial injection in NSG mice. A total of 18 samples consisting of six different PDX samples, with two different passages from two samples grown in separate mice as biological replicates, were analyzed by RNA-Sequencing (RNA-Seq) in this study. Leukemia cells were harvested from each mouse and characterized and sorted on the basis of glucose uptake using the fluorescent glucose analog 2-[N-(7-Nitrobenz-2-oxa-1, 3-diazol-4-yl) Amino)-2-Deoxyglucose] (NBDG) with fluorescence-activated cell sorting (FACS). Cells were sorted into three populations as NBDG-low (low-fluorescing/low glucose uptake),  NBDG-medium (medium-fluorescing/medium glucose uptake), and NBDG-high (high-fluorescing/high glucose uptake). Each cell sample was then snap-frozen and subsequently used for library preparation and RNA-Seq analysis.

first: Noriko

last: Satake