title: RNA sequencing of Cal33 and SAS head and neck squamous cell carcinoma cell lines treated with GSK-J1 and radiation

status: Public on Feb 20 2024

city: Dresden

first: Claudia

last: Peitzsch

address: Fetscherstr. 105

institute: Center for Regenerative Therapies Dresden (CRTD)

summary: Background: The sensitivity of head and neck squamous cell carcinoma (HNSCC) to ionizing radiation, among others, is determined by the number of cells with high clonogenic potential and stem-like features. These cellular characteristics are dynamically regulated in response to treat-ment and may lead to an enrichment of radioresistant cells with a cancer stem cell (CSC) pheno-type. Epigenetic mechanisms, particularly DNA and histone methylation, are key regulators of gene-specific transcription and cellular plasticity. Therefore, we hypothesized that specific epi-genetic targeting may prevent irradiation-induced plasticity and may sensitize HNSCC cells to radiotherapy. Methods: We compared the DNA methylome and intracellular concentrations of tricarboxylic acid cycle metabolites in radioresistant FaDu and Cal33 cell lines with their parental controls, as well as aldehyde dehydrogenase (ALDH)-positive CSCs with negative controls. Moreover, we conducted a screen of a chemical library targeting enzymes in-volved in epigenetic regulation in combination with irradiation and analyzed the clonogenic potential, sphere formation, and DNA repair capacity to identify compounds with both radiosensi-tizing and CSC-targeting potential. Results: We identified the histone demethylase inhibitor GSK-J1, which targets UTX (KDM6A) and JMJD3 (KDM6B), leading to increased H3K27 tri-methylation, heterochromatin formation, and gene silencing. The clonogenic survival assay after siRNA-mediated knock-down of both genes radiosensitized Cal33 and SAS cell lines. Moreover, high KDM6A expression in tissue sections of patients with HNSCC was associated with improved locoregional control after primary (n = 137) and post-operative (n = 187) radio/chemotherapy. Conversely, high KDM6B expression was a prognostic factor for reduced overall survival. Conclusions: Within this study, we investigated cellular and molecular mechanisms underlying irradiation-induced cellular plasticity, a key inducer of radioresistance, with a focus on epigenetic alterations. We identified UTX (KDM6A) as a putative prognostic and therapeutic target for HNSCC patients treated with radiotherapy.

overall_design: The HNSCC cell lines SAS and Cal33 were treated with GSK-J1 (IC5, 4.5 µM) with or without a single 4 Gy x-ray irradiation. After 24 hours treatment, RNA was isolated using the RNeasy mini kit (Qiagen; #74104) according to the manufacturer’s recommendation, in triplicates. RNA concentrations were measured with the NanoDrop ND-1000 (Peqlab). RNA sequencing was performed at the Genomics and Proteomics Core Facility (GPCF, DKFZ, Heidelberg, Germany). Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit following the manufacturer’s instructions. Libraries concentration and quality control were performed using Qubit (Invitrogen) and Tapestation (Agilent). The samples were sequenced in a 2 × 100 bp paired-end setting on an Illumina HiSeq 4000 system according to the manufacturer’s protocol.

first: Iñaki

last: Schniewind

first: María

last: Besso

first: Wahyu

middle: W

last: Hadiwikarta

first: Ina

last: Kurth


title: Pharmacological HIF-1 activation synergically upregulated exosome production with adiponectin through induction and stabilization of T-cadherin

status: Public on Feb 21 2024

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

type: Expression profiling by high throughput sequencing

summary:
Purpose: Addition of HIF-PH inhibitor, Roxadustat upregulate and stabilize T-cadherin protein. The purpose is to investigate whether genes induced by HIF-PH inhibitors are involved in the regulation of T-cadherin.
Methods:  mRNA of F2T cells, murine endotherial cell line stably overexpressed T-cadhetin supplemented with or without Adiponectin and/or Roxadustat were sequenced on Illumina NovaSeq 6000 (Illumina). Total RNA qualities were analysised using RNA6000 pico kit (Agilent) and we confirmed that RNA integrity number of samples were 6.5 or more. Data analysis was performed using iDEP ve.1.1 or Biojupies on web application.
Results: We identified about 1,000 genes upregulated by addition of Roxadustat. In KEGG pathway analysis, we especially focused on cell adhesion and ECM-receptor interaction among upregulated genes.

overall_design: mRNA profiles of F2T cells, murine endotherial cell line stably overexpressed T-cadherin supplemented with or without Adiponectin and/or Roxadustat

first: Kohei

last: Fujii

first: Yuya

last: Fujishima

first: Shunbun

last: Kita


title: Developmental origin of oligodendrocytes determines their function in the adult brain

status: Public on Feb 23 2024

city: Solna

first: Bastien

last: Hervé

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: The functional importance of oligodendrocyte developmental heterogeneity is unknown. Using a genetic strategy to ablate dorsally-derived oligodendrocyte lineage cells (OLCs), we found that the areas in which dorsally-derived OLCs normally reside in the adult CNS become populated and myelinated by OLCs of ventral origin. These ectopic oligodendrocytes (eOLs) have a distinctive gene expression profile, as well as subtle myelination abnormalities. The failure of eOLs to assume the role of the original dorsally-derived cells result in locomotor and cognitive deficits in the adult animal. This study reveals the importance of developmental heterogeneity within the oligodendrocyte lineage, and its importance for homeostatic brain function.

overall_design: Sox10-loxP-eGFP-polyA-STOP-loxP-tdTomato (hereafter abbreviated as ‘Sox10-GFP-tdTom’ or ‘Tom’) reporter mice express enhanced GFP in all oligodendrocyte lineage cells (OLCs) in the absence of Cre activity. To differentially label ventrally- and dorsally-derived OLCs in the forebrain, Sox10-GFP-tdTom mice were crossed to Emx1-Cre mice (hereafter abbreviated as ‘Emx’). To study the functional importance of dorsally-derived OLCs in the adult brain, dorsally-derived, Emx1-positive OLCs were ablated by crossing the Emx1-Cre line to the Sox10-loxP-GFP-poly(A)-STOP-loxP-DTA (hereafter abbreviated as ‘Sox10-DTA’ or ‘DTA’) mouse line. To determine the ablation efficiency, all three mouse lines were crossed (hereafter abbreviated as ‘Emx/Tom/DTA’), allowing the visualization of the remaining dorsally-derived OLCs after ablation.  Mouse strains used for RNA-sequencing: Control: Emx/Tom, Ablated: Emx/Tom/DTA

first: Sarah

last: Foerster

first: Elisa

middle: M

last: Floriddia

first: David

last: van Bruggen

first: Petra

last: Kukanja

first: Shangli

last: Cheng

first: Eosu

last: Kim

first: Benjamin

middle: U

last: Phillips

first: Christopher

middle: J

last: Heath

first: Cody

last: Call

first: Theresa

last: Bartels

first: Katherine

last: Ridley

first: Björn

last: Neumann

first: Laura

last: López-Cruz

first: Abbe

middle: H

last: Crawford

first: Richa

middle: B

last: Tripathi

first: Cian

last: Lynch

first: Manuel

last: Serrano

first: Nicoletta

last: Kessaris

first: Lisa

last: Saksida

last: Rowitch

first: William

middle: D

last: Richardson

first: Wibke

last: Moebius

first: Klaus-Armin

last: Nave

first: Matthew

last: Rasband

first: Dwight

middle: E

last: Bergles

first: Timothy

last: Bussey

first: Chao

last: Zhao

first: Gonçalo

last: Castelo-Branco

first: Robin

last: Franklin


title: Gene expression profile at single cell levels of the cells from the controls and tau P251L Drosophila brain.

status: Public on Feb 26 2024

city: Boston

first: Hassan

last: Bukhari

state: MA

address: 77, Avenue Louise Pasteur

department: Pathology

country: USA

institute: Brigham and Womens hospital

summary: Tau protein has been implicated in the pathology of Alzheimer's disease and related disorders. We CRISPR engineered an endogenous model of tauopathy by knocking in a pathogenic human tau mutation, tau P301L, in Drosophila, tau P251L KI. We used single cell RNA sequencing to identify the differentially expressed genes or pathways.

overall_design: Control and  tau P251L KI brains were dissociated, cells were isolated and analyzed using scRNAseq.

first: Mel

last: Feany


title: Single-cell RNAseq analysis of wild type and Socs3 cKO retinal immune cells

status: Public on Feb 25 2024

first: Emil

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

summary: Myeloid SOCS3 deficiency leads to increased retinal neovascularization in an oxygen-induced retinopathy mouse model. To investigate the role of SOCS3 in the function of myeloid lineage cells, particular microglia during retinopathy, total immune cells were sorted from wildtype and myeloid Socs3 knockout mice with retinopathy applied for single-cell RNAseq analysis by 10X Genomics technology.

overall_design: scRNA-seq was performed for immune cells isolated from retinas of 6 KO and 6 sex-matched WT mice with or without oxygen-induced retinopathy (at postnatal day 13), using FACS. Total 1,200~2,500 cells were sequenced to an average of 65,00-118,000 reads/cell.

first: Tianxi

last: Wang

first: Petr

last: Baranov

first: Guishuai

last: Cai

first: Sun

last: Ye


title: Effect of dietary phosphorus deprivation during the dry period on the liver transcriptome of high yielding periparturient dairy cows

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

summary: While dietary phosphorus (P) deprivation extending from the dry period into early lactation impairs health and productivity of cows, restricting dietary P supply during the dry period not only appears to be innocuous but rather effectively mitigates hypocalcemia during the first wk of lactation. To investigate possible negative metabolic effects of P deprivation during the dry period, the present study tested the hypothesis that restarted dietary P supply during the dry period alters the liver transcriptome of dairy cows during the periparturient period. Thirty late-pregnant multiparous Holstein-Friesian dairy cows entering their 2nd, 3rd or 4th lactation were assigned to either a dry cow ration with low (LP, 0.16% P in DM) or adequate P content (AP, 0.35% in DM) during the last 4 wk of the dry period (n = 15/group). Liver transcriptomics, which was carried out in a subset of five 2nd parity cows of each group (n = 5), and determination of selected hormones and metabolites in blood of all cows, was performed approximately one wk before calving and on d 3 postpartum. Liver tissue specimens and blood samples were obtained by a micro-invasive biopsy technique from the right 10th intercostal space and puncture of a jugular vein, respectively. 175 hepatic transcripts were expressed differentially between LP vs. AP cows in late pregnancy, and 165 transcripts differed between LP vs. AP cows in early lactation (Fold change > 1.3 and < -1.3, P < 0.05). In late pregnancy, the enriched biological processes of the up-regulated and the down-regulated transcripts were mainly related to immune processes and signal transduction (P < 0.05), respectively. In early lactation, the enriched biological processes of the up-regulated and the down-regulated transcripts were involved in mineral transport and biotransformation (P < 0.05), respectively. The plasma concentrations of the hormones and acute phase proteins (progesterone, insulin-like growth factor 1, serum amyloid alpha, haptoglobin, and 17β-estradiol) determined were not affected by P supply. These results suggest that P deprivation during the dry period moderately affects the liver transcriptome of cows in late pregnancy and early lactation, and causes no effects on important plasma hormones and acute phase proteins indicating no obvious impairment of health or metabolism of the cows.

overall_design: The design of the underlying study has been described in detail elsewhere (Wächter et al., 2022a). Briefly, 30 late-pregnant multiparous Holstein-Friesian dairy cows entering their second, third or fourth lactation were randomly assigned to one of the 2 experimental groups, that were fed a dry cow ration with either low (LP, 0.16% P in DM) or adequate P content (AP, 0.35% P in DM) during the last 4 wk of the dry period. The study cows were part of the herd of a research farm with an average 305-d milk yield of 12,500 kg. Dry cows and fresh cows were kept in separated areas of a freestall. Cows with signs of imminent parturition were moved to individual calving pens and if deemed to be clinically healthy proceeded to the lactation group within 24 of calving. From the moment of calving both groups were fed the same standard lactating cow ration with adequate P content. Lactating cows were milked twice daily between 04.30 h and 05.30 h and between 15.30 h and 16.30 h.

first: Sophia

last: Wächter

first: Imke

last: Cohrs

first: Klaus

last: Eder

first: Walter

last: Grünberg


title: Transcriptome of lung endothelial cells in SARS-CoV-2 infection model

city: Sapporo

first: Kyoko

last: Hida

address: Kita-ku, N13W7

institute: Hokkaido University

summary: To investigate the pathophysiology of lung endothelial cells in SARS-CoV-2 mouse model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data using 4 types (uninfected/infected, young/mid-aged) of isolated lung endothelial cells.

first: Takuya

last: Tsumita

first: Ryo

last: Takeda


title: Three-dimensional chromatin landscapes in MLLr AML [Micro-C]

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

department: Molecular Medicine

institute: UT health San Antonio

summary: Rearrangements of the mixed lineage leukemia (MLLr) gene are frequently associated with both pediatric and adult leukemia. However, the treatment options for these aggressive MLLr leukemias are limited due to the genomic complexity and dynamics of 3D structure in oncogene transcription and leukemia development. Here, we use Micro-C and transcriptome profiling to examine the MLLr-driven aberrant 3D genome architecture in gene-edited MLL-AF9 AML samples with biologically matched healthy donors. Recurrent and MLLr-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing in the same AML samples also revealed extensive and recurrent MLLr-specific promoter–enhancer and promoter–silencer loops. Overall, this study highlights the critical regulatory elements and provides rational and effective targeting strategy in MLLr AML.

overall_design: Micro-C for normal hematopoietic stem progenitor cells (HSPCs, CD34+, n=2) and acute myeloid cells (MLL-AF9 AML, n=2).

first: Feng

last: Pan


title: Three-dimensional chromatin landscapes in MLLr AML [RNA-Seq]

overall_design: RNA-seq for normal hematopoietic stem progenitor cells (HSPCs, CD34+, n=2) and acute myeloid cells (MLL-AF9 AML, n=2).


title: RNA sequencing of tumors from mice fed diets excluding methionine/tryptophan/niacin (Part 4)

status: Public on Feb 19 2024

first: Daisuke

last: Motooka

summary: In the past, animal experiments with rats, by depleting various amino acids in the diet, have shown that a deficiency of methionine inhibits tumor growth at the individual level and that methionine is important in the development and progression of cancer. This methionine is one of the essential amino acids and is the initiation codon that initiates protein translation from mRNA. Methionine is known to be converted to SAM, which is required for nucleic acid synthesis in cancer. Tumors are underdeveloped in an environment deficient in methionine, which is known as the "Hoffman effect". In fact, past reports have shown that in the absence of methionine, tumor growth is suppressed, and methionine has recently been shown to be essential in cancer stem cells or "tumor initiating cells". In addition, the focus on methionine in cancer is said to influence tumor-cell metabolism, histone patterns, and T cell immunity in the cancer microenvironment. In cancer immunity, not only methionine but also its upstream pathways are said to be involved. Tryptophan/niacin, which is located upstream of the methionine cycle, is metabolized to form nicotinamide, and MNAM is formed from the SAM and nicotinamide via nicotinamide N-methyltransferase (NNMT). NNMT and MNAM have been reported to participate in the mechanism of inhibition of the apoptosis signal-regulated kinase 1-p38 MAPK pathway, resulting in increased colon cancer cell resistance to 5-FU. NNMTs promote nicotinamide adenine dinucleotide depletion and epigenetic reprogramming, which have been implicated in the development of metabolic plasticity, circumvention of the major tumor suppressive process of cellular senescence, acquisition of stem cell properties, and resistance to therapy and poor clinical outcomes. Also, MNAM synthesized in this methionine cycle is said to suppress T cells and promote cancer. Hence, we implanted the colon cancer cell line HT-29 cultured in normal medium with all nutrients into NOD SCID mice and kept them for 2 weeks on a diet without the aforementioned methionine/tryptophan/niacin. Afterwards, tumors were removed and RNA-sequencing was performed, and a marked increase in the expression of RN7SL1, a non-coding RNA, was observed.

overall_design: All experiments in the present study were approved by the Osaka University Animal Experiments Committee, the formal ethics committee for institutional animal study at Osaka University, Japan, under the approval No. 30-011, and the experiments were conducted in accordance with the Osaka University Regulations on Animal Experiments. Five-week-old wild-type NOD SCID mice, derived from a mouse strain with a naturally occurring mutant, exhibiting an autosomal recessive inheritance pattern, and showing severe immunodeficiency due to the absence of T and B cells, which results in minimal rejection of xenogeneic cells and tissues, were procured from Japan SLC, Inc. All mice were female. Mice were randomly divided into cages for each feeding condition described below. Given that not only methionine but also its upstream pathways are involved in cancer immunity. Tryptophan/niacin, which is located upstream of the methionine cycle, is metabolized to form nicotinamide, which is related to the methionine pathway, and 1-methyl-nicotinamide (MNAM) is formed from S-adenosylmethionine (SAM) synthesized from methionine, via nicotinamide N-methyltransferase, and thus MNAM synthesized in this methionine cycle is said to suppress T cells and promote cancer, we therefore subcutaneously implanted HT-29 cultured in regular medium containing all nutrients into the backs of 2 x 10⁵ NOD SCID mice, and the mice were then divided into four groups: those kept on normal food, those kept on food excluding methionine only, those kept on food excluding niacin/tryptophan, and those kept on food without methionine/tryptophan/niacin. And, they were reared for 2 weeks. Special diets for the mice were custom-ordered with as much appearance and taste as possible. Rearing conditions were such that the floor was changed daily to minimize the intake of excretory-derived amino acids. Room temperature was maintained around 23°C and lights were turned on in 12-hour cycles. Although our initial plan was to euthanize the mice if the tumor size exceeded 150 mm3 or if the mouse's body weight increased by more than 20% within a week, we in practice successfully completed the intended three-week experimental period without encountering any breaches of the restrictions pertaining to tumor size or body weight. At the conclusion of the animal experiment, we adhered to the following ethical guidelines: For mice weighing around 20g, the concentration of carbon dioxide used for scarification was 40%, with a flow rate of 0.5L/min for an inhalation time of 10 minutes; For smaller mice weighing 16g or less, the concentration of carbon dioxide was reduced within the range of 30% to 40%, with a lower flow rate between 0.2L/min to 0.5L/min for a shorter inhalation time between 5 to 10 minutes, to minimize the stress and pain to the mice during the procedure. Tumors were then removed and evaluated for RNA expression and type by RNA sequence. After confirming the cessation of mouse respiratory movements, the tumor was promptly excised within 30 minutes in a well-maintained environment with laboratory air conditioning and a clean experimental table in the laboratory. Subsequently, the tumor was immersed in RNA LATER reagent (Sigma-Aldrich), and RNA extraction was performed using RNeasy kit (Qiagen), followed by RNA sequencing analysis.

first: Hiromichi

last: Sato

first: Sikun

last: Meng

first: Kazuki

last: Sasaki

first: Shogo

last: Kobayashi

first: Kansuke

last: Kido

first: Yoshiko

last: Tsuji

first: Yasuko

last: Arao

last: Saito

first: Yoshifumi

last: Iwagami

first: Daisaku

last: Yamada

first: Yoshito

last: Tomimaru

first: Takehiro

last: Noda

first: Hidenori

last: Takahashi

first: Shizuka

last: Uchida

first: Ken

last: Ofusa

first: Taroh

last: Satoh

first: Yuichiro

last: Doki

first: Hidetoshi

last: Eguchi

first: Tomoaki

last: Hara

first: Hideshi

last: Ishii


title: Transient loss of Polycomb components induces an epigenetic cancer fate

status: Public on Feb 28 2024

city: Montpellier

first: Vincent

last: Loubiere

state: FRANCE

address: 141 rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: UMR9002; CNRS-UM

type: Genome binding/occupancy profiling by high throughput sequencing

type: Genome variation profiling by high throughput sequencing

summary: Although cancer initiation and progression are generally associated with the accumulation of somatic mutations, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility, suggesting that genetic mechanisms might not be the only drivers of malignant transformation. However, whether purely non-genetic mechanisms are sufficient to initiate tumorigenesis irrespective of mutations is unknown. Here, we show that a transient perturbation of transcriptional silencing mediated by Polycomb Group proteins is sufficient to induce an irreversible switch to a cancer cell fate in Drosophila. This is linked to the irreversible derepression of genes that can drive tumorigenesis, including members of the JAK-STAT signaling pathway and zfh1, the fly homolog of the ZEB1 oncogene, whose aberrant activation is required for Polycomb-induced tumorigenesis. These data show that a reversible perturbation of Polycomb Group protein levels can induce cancer in the absence of driver mutations, suggesting that tumors can emerge through epigenetic dysregulation leading to inheritance of altered cell fates.

overall_design: Characterization of ph-dependent tumors transcriptomes, chromatin accesibility (ATAC-Seq) and genomic DNA.

first: V

last: Parreno

first: B

last: Schuettengruber

first: L

last: Fritsch

first: C

last: Rawal C

first: M

last: Erokhin

last: Gyorffy

first: D

last: Normanno

last: Di Stefano

first: J

last: Moreaux

first: N

last: Butova

first: I

last: Chiolo

last: Chetverina

first: A-M

last: Martinez

first: G

last: Cavalli


title: RNA sequencing of tumors from mice fed diets excluding methionine/tryptophan/niacin (Part 3.2, miRNA-Seq)

first: Daisuke

last: Motooka

type: Non-coding RNA profiling by high throughput sequencing

overall_design: All experiments in the present study were approved by the Osaka University Animal Experiments Committee, the formal ethics committee for institutional animal study at Osaka University, Japan, under the approval No. 30-011, and the experiments were conducted in accordance with the Osaka University Regulations on Animal Experiments. Five-week-old wild-type NOD SCID mice, derived from a mouse strain with a naturally occurring mutant, exhibiting an autosomal recessive inheritance pattern, and showing severe immunodeficiency due to the absence of T and B cells, which results in minimal rejection of xenogeneic cells and tissues, were procured from Japan SLC, Inc. All mice were female. Mice were randomly divided into cages for each feeding condition described below. Given that not only methionine but also its upstream pathways are involved in cancer immunity. Tryptophan/niacin, which is located upstream of the methionine cycle, is metabolized to form nicotinamide, which is related to the methionine pathway, and 1-methyl-nicotinamide (MNAM) is formed from S-adenosylmethionine (SAM) synthesized from methionine, via nicotinamide N-methyltransferase, and thus MNAM synthesized in this methionine cycle is said to suppress T cells and promote cancer, we therefore subcutaneously implanted HT-29 cultured in regular medium containing all nutrients into the backs of 2 x 10⁵ NOD SCID mice, and the mice were then divided into two groups: those kept on normal food and those kept on mice without methionine/tryptophan/niacin. And, they were reared for 2 weeks. Special diets for the mice were custom-ordered with as much appearance and taste as possible. Rearing conditions were such that the floor was changed daily to minimize the intake of excretory-derived amino acids. Room temperature was maintained around 23°C and lights were turned on in 12-hour cycles. Although our initial plan was to euthanize the mice if the tumor size exceeded 150 mm3 or if the mouse's body weight increased by more than 20% within a week, we in practice successfully completed the intended three-week experimental period without encountering any breaches of the restrictions pertaining to tumor size or body weight. At the conclusion of the animal experiment, we adhered to the following ethical guidelines: For mice weighing around 20g, the concentration of carbon dioxide used for scarification was 40%, with a flow rate of 0.5L/min for an inhalation time of 10 minutes; For smaller mice weighing 16g or less, the concentration of carbon dioxide was reduced within the range of 30% to 40%, with a lower flow rate between 0.2L/min to 0.5L/min for a shorter inhalation time between 5 to 10 minutes, to minimize the stress and pain to the mice during the procedure. Tumors were then removed and evaluated for RNA expression and type by RNA sequence. After confirming the cessation of mouse respiratory movements, the tumor was promptly excised within 30 minutes in a well-maintained environment with laboratory air conditioning and a clean experimental table in the laboratory. Subsequently, the tumor was immersed in RNA LATER reagent (Sigma-Aldrich), and RNA extraction was performed using RNeasy kit (Qiagen), followed by RNA sequencing analysis.

first: Hiromichi

last: Sato

first: Sikun

last: Meng

first: Kazuki

last: Sasaki

first: Shogo

last: Kobayashi

first: Kansuke

last: Kido

first: Yoshiko

last: Tsuji

first: Yasuko

last: Arao

last: Saito

first: Yoshifumi

last: Iwagami

first: Daisaku

last: Yamada

first: Yoshito

last: Tomimaru

first: Takehiro

last: Noda

first: Hidenori

last: Takahashi

first: Shizuka

last: Uchida

first: Ken

last: Ofusa

first: Taroh

last: Satoh

last: Doki

last: Eguchi

last: Hara


title: Methylomic trajectories in the developing human pancreas

city: Exeter

first: Ailsa

last: MacCalman

address: Barrack Road

country: United Kingdom

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary: Epigenetic processes such as DNA methylation play a key role in regulating tissue-specific and temporally-appropriate patterns of gene expression during development. Our knowledge about temporal changes to the epigenome in the developing human pancreas is limited. In this study we quantified levels of DNA methylation at over 800,000 sites in 112 human fetal pancreatic samples (51 male and 61 female) spanning from 6 to 21 post conception weeks (pcw). We found dramatic changes in DNA methylation across human pancreas development, with >22% of all methylation sites displaying significant changes across developmental age, with the majority of these sites showing stable levels of DNA methylation in the mature pancreas. Sites associated with developmental changes in DNA methylation during fetal pancreas development were significantly underrepresented in promoter regulatory regions but significantly overrepresented in regions flanking CpG islands (shores and shelves) and gene bodies. Highly significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small number of regions showing sex-specific DNA methylation trajectories across pancreas development. Weighted gene correlation network analysis (WGCNA) revealed modules of co-methylated loci associated with developmental age were enriched for genes involved in maturity onset diabetes of the young (MODY)  and other metabolic phenotypes. A comparison with developmentally-dynamic patterns of DNA methylation in the developing human brain revealed significant tissue specific differences between the fetal pancreas and the fetal brain. Our data confirms the prenatal period to be a time of dynamic epigenetic changes. To our knowledge, this is the most extensive study of DNA methylation patterns in human fetal pancreatic development.

overall_design: Quantified DNA methylation across the genome in 99 human fetal and 23 human adult pancreas samples

first: Elisa

last: De Franco

first: Joe

last: Burrage

first: Emma

last: Walker

first: Eilis

last: Hannon

last: Dempster

first: Alice

last: Franklin

first: Nick

last: Owens

first: Aaron

last: Jeffries

first: Andrew

last: Hattersley

first: Jonathan

last: Mill


title: Transcriptome analysis of CNS and splenic FOXP3+ Tregs vs. exFOXP3 T cells during EAE

status: Public on Feb 16 2024

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

country: Belgium

summary: EAE was induced in female FOXP3 fate mapping mice. At peak of disease, immune cells were isolated from brain and spinal cord (pooled as CNS) and spleen. Next, FOXP3+ and exFOXP3 T cells were FACS-sorted based on RFP and GFP expression.

overall_design: FOXP3+ Tregs are sorted as GFP+RFP+ and exFOXP3 T cells as GFP-RFP+.

first: Baeten

last: Paulien

last: Hamad

first: Broux

last: Bieke


title: Oncostatin M is a Master Regulator of an Inflammatory Network in Dnmt3a-Mutant Hematopoietic Stem Cells

status: Public on Feb 18 2024

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Age-associated clonal hematopoiesis (CH) occurs due to somatic mutations accrued in hematopoietic stem cells (HSCs) that confer a selective advantage in the context of aging. The mechanisms by which CH-mutant HSCs gain this advantage with aging are not comprehensively understood. Using unbiased transcriptomic approaches, we identify Oncostatin M (OSM) signaling as a candidate contributor to aging-driven Dnmt3a-mutant CH. We find that Dnmt3a-mutant HSCs from young mice do not functionally respond to acute OSM stimulation with respect to proliferation, apoptosis, hematopoietic engraftment, or myeloid differentiation. However, young Dnmt3a-mutant HSCs transcriptionally upregulate an inflammatory cytokine network in response to acute OSM including genes encoding IL-6, IL-1b and TNFa. In addition, OSM-stimulated Dnmt3a-mutant HSCs upregulate the anti-inflammatory genes Socs3 and Nr4a1, creating a negative feedback loop limiting sustained activation of the inflammatory network. In the context of an aged BM microenvironment with chronically elevated levels of OSM, Dnmt3a-mutant HSCs upregulate pro-inflammatory genes but do not upregulate Socs3 and Nr4a1. Together, our work suggests that chronic inflammation with aging exhausts the regulatory mechanisms in young CH-mutant HSCs that resolve inflammatory states, and that OSM is a master regulator of an inflammatory network that contributes to age-associated CH.

overall_design: We sought to test the transcriptional consequences of OSM-STAT3 signaling in a more purified control and R878H/+ HSC population. We prospectively isolated control and R878H/+ HSCs from young adult mice, stimulated ex vivo with 500ng/mL of recombinant murine OSM or vehicle control for 60min and immediately flash froze cell pellets for RNA extraction and RNA-seq. We identified significantly differentially expressed genes comparing OSM- vs. vehicle-treated control HSCs, and OSM- vs. vehicle-treated R878H/+ HSCs, using P < 0.05 and fold change (FC) ± 1.5 cutoffs. Differential gene expression of 1 hour stimulation vehicle vs. OSM in 1000 control HSCs or R878H/+ HSCs respectively. N= 6 mice per group, experiment done two independent times.

first: Logan

middle: S

last: Schwartz

first: Kira

middle: A

last: Young

first: Timothy

last: Stearns


title: Lipocalin-2 expression identifies an immuno-regulatory intestinal neutrophil population during GVHD

city: Freiburg

first: Nina

last: Peltokangas

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Acute graft-versus-host disease (aGVHD) is a life-threatening complication of allogeneic hematopoietic cell transplantation (allo-HCT). Strategies to promote intestinal tissue tolerance during aGVHD may improve patient outcomes. Using single-cell RNA-sequencing, we identified a Lipocalin-2 (LCN2)-expressing neutrophil population in mice with intestinal aGVHD. Transfer of LCN2-overexpressing neutrophils or treatment with recombinant LCN2 reduced aGVHD-severity, while the lack of epithelial or hematopoietic LCN2 enhanced aGVHD severity and caused microbiome alterations. Mechanistically, LCN2 induced IGF-1R signaling in macrophages via the LCN2 receptor Slc22A17, which increased IL-10 production while reducing MHC-II expression. Transfer of LCN2-pretreated macrophages reduced aGVHD severity. LCN2-treatment did not reduce graft-versus-leukemia effects. In aGVHD patients LCN2 expression correlated with IL-10 expression in intestinal biopsies. We identified a novel intestinal LCN2+ neutrophil population that reduces aGVHD-severity by decreasing MHC-II expression while increasing IL-10 production in macrophages. Administration of LCN2 presents a novel approach against aGVHD to be tested in clinical trials.

overall_design: Single-cell RNA sequencing was performed on neutrophils (CD45+H2kb+CD11b+Ly6G+) residing in the terminal ileum on day 21 after allogeneic hematopoietic cell transplantation. BALB/c mice receiving 5 x 10ˆ6 BM cells with 4 x 10ˆ5 T cells from C57BL/6 donor mice developed acute GVHD, while BALB/c mice receiving only 5 x 10ˆ6 BM cells from C57BL/6 serve as a control.

first: Dominic

last: Grün

first: Jan

last: Hülsdünker

first: Robert

last: Zeiser


title: Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage

status: Public on Feb 17 2024

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University

summary: Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike’s interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.

overall_design: Genomically engineered HEK293T cells with amplicons derived from exogenous DNA that has recombined using the Bxb1 bacteriophage integrase and various complementary Bxb1 attP and attB sites

first: Nidhi

last: Shukla


title: RNA sequencing of tumors from mice fed diets excluding methionine/tryptophan/niacin (Part 3.1, RNA-Seq)

first: Daisuke

last: Motooka

overall_design: All experiments in the present study were approved by the Osaka University Animal Experiments Committee, the formal ethics committee for institutional animal study at Osaka University, Japan, under the approval No. 30-011, and the experiments were conducted in accordance with the Osaka University Regulations on Animal Experiments. Five-week-old wild-type NOD SCID mice, derived from a mouse strain with a naturally occurring mutant, exhibiting an autosomal recessive inheritance pattern, and showing severe immunodeficiency due to the absence of T and B cells, which results in minimal rejection of xenogeneic cells and tissues, were procured from Japan SLC, Inc. All mice were female. Mice were randomly divided into cages for each feeding condition described below. Given that not only methionine but also its upstream pathways are involved in cancer immunity. Tryptophan/niacin, which is located upstream of the methionine cycle, is metabolized to form nicotinamide, which is related to the methionine pathway, and 1-methyl-nicotinamide (MNAM) is formed from S-adenosylmethionine (SAM) synthesized from methionine, via nicotinamide N-methyltransferase, and thus MNAM synthesized in this methionine cycle is said to suppress T cells and promote cancer, we therefore subcutaneously implanted HT-29 cultured in regular medium containing all nutrients into the backs of 2 x 10^5 NOD SCID mice, and the mice were then divided into two groups: those kept on normal food and those kept on mice without methionine/tryptophan/niacin. And, they were reared for 2 weeks. Special diets for the mice were custom-ordered with as much appearance and taste as possible. Rearing conditions were such that the floor was changed daily to minimize the intake of excretory-derived amino acids. Room temperature was maintained around 23°C and lights were turned on in 12-hour cycles. Although our initial plan was to euthanize the mice if the tumor size exceeded 150 mm3 or if the mouse's body weight increased by more than 20% within a week, we in practice successfully completed the intended three-week experimental period without encountering any breaches of the restrictions pertaining to tumor size or body weight. At the conclusion of the animal experiment, we adhered to the following ethical guidelines: For mice weighing around 20g, the concentration of carbon dioxide used for scarification was 40%, with a flow rate of 0.5L/min for an inhalation time of 10 minutes; For smaller mice weighing 16g or less, the concentration of carbon dioxide was reduced within the range of 30% to 40%, with a lower flow rate between 0.2L/min to 0.5L/min for a shorter inhalation time between 5 to 10 minutes, to minimize the stress and pain to the mice during the procedure. Tumors were then removed and evaluated for RNA expression and type by RNA sequence. After confirming the cessation of mouse respiratory movements, the tumor was promptly excised within 30 minutes in a well-maintained environment with laboratory air conditioning and a clean experimental table in the laboratory. Subsequently, the tumor was immersed in RNA LATER reagent (Sigma-Aldrich), and RNA extraction was performed using RNeasy kit (Qiagen), followed by RNA sequencing analysis.

first: Hiromichi

last: Sato

first: Sikun

last: Meng

first: Kazuki

last: Sasaki

first: Shogo

last: Kobayashi

first: Kansuke

last: Kido

first: Yoshiko

last: Tsuji

first: Yasuko

last: Arao

last: Saito

first: Yoshifumi

last: Iwagami

first: Daisaku

last: Yamada

first: Yoshito

last: Tomimaru

first: Takehiro

last: Noda

first: Hidenori

last: Takahashi

first: Shizuka

last: Uchida

first: Ken

last: Ofusa

first: Taroh

last: Satoh

first: Yuichiro

last: Doki

first: Hidetoshi

last: Eguchi

first: Tomoaki

last: Hara

first: Hideshi

last: Ishii


title: A di-acetyl-decorated chromatin signature couples liquid condensation to suppress DNA end synapsis

city: TianJin

first: Kaiwen

last: Bao

country: China

institute: Tianjin Medical University

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

overall_design: Refer to individual Series


title: Direct comparison of mass cytometry and single-cell RNA sequencing of human peripheral blood mononuclear cells

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

summary: Single-cell methods offer a high-resolution approach for characterizing cell populations. Many studies rely on single-cell transcriptomics to draw conclusions regarding cell state and behavior, with the underlying assumption that transcriptomic readouts largely parallel their protein counterparts and subsequent activity. However, the relationship between transcriptomic and proteomic measurements is imprecise, and thus datasets that probe the extent of their concordance will be useful to refine such conclusions. Additionally, novel single-cell analysis tools often lack appropriate gold standard datasets for the purposes of assessment. Integrative (combining the two data modalities) and predictive (using one modality to improve results from the other) approaches in particular, would benefit from transcriptomic and proteomic data from the same sample of cells. For these reasons, we performed single-cell RNA sequencing, mass cytometry, and flow cytometry on a split-sample of human peripheral blood mononuclear cells. We directly compare the proportions of specific cell types resolved by each technique, and further describe the extent to which protein and mRNA measurements correlate within distinct cell types.

overall_design: We perform single-cell RNA-sequencing on a split-sample of human peripheral blood mononuclear cells.

first: Emily

middle: Y

last: Su

first: Kristen

last: Fread

first: Sarah

last: Goggin

first: Eli

middle: R

last: Zunder


title: A unified single cell atlas of the mouse retina

status: Public on Feb 15 2024

city: Houston

first: Jin

last: Li

state: Texas

address: 1 Baylor Plaza

department: Department of Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Single cell RNA sequencing (scRNA-seq) has advanced the assessment of cellular heterogeneity at the single-cell resolution by identifying transcriptional similarities and differences. Data resources of scRNA-seq have been largely produced and extensively studied for the mouse retina. They serve as a powerful tool to study cellular components, transcriptome relationships, and regulatory mechanisms underlying various retinal diseases and biological processes. The large volume of mouse retinal scRNA-seq data has been released in separate repositories, limiting their widespread use in mouse retina communities. In this work, we are presenting a unified single-cell atlas for adult wild-type mouse retina using our in-house generated single-cell RNA-seq data complementing public datasets. The collected data account for over 323,000 single cells. After data integration, cell clustering, and cell type annotation, we have annotated 11 major classes and over 120 retinal cell types to form a unified single-cell reference for the mouse retina. To facilitate the public use of the reference, we have deposited it on CELLxGENE, UCSC Cell Browser, and Single Cell Portal for visualization and gene expression exploration. The unified atlas is also released to annotate new mouse retinal cells using scArches utilities. This unified reference serves an easy-to-use data resource of mouse retina communities.

overall_design: 16 samples were dissociated retinal cells with no enrichment method and 2 samples were enriched for neuronal cells using CD73 and CD90.2 markers using FACS.

first: Xuesen

last: Cheng

first: Jongsu

last: Choi

first: Yumei

first: Rui

last: Chen


title: Deciphering the spatio-temporal transcriptional and chromatin accessibility of human retinal organoid development at the single cell level [scRNA-Seq]

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

institute: Newcastle University

summary: Molecular information on the very early stages of human retinal development remains scarce due to limitations in obtaining human eye samples of less than six weeks old. Pluripotent stem cell derived retinal organoids  provide an unprecedented opportunity for studying human retinal development; however their ability to fully recapitulate early retinal development has not been assessed as yet. Using a combination of scRNA-Seq and ST approaches, we present for the first time a genome wide, single cell spatio-temporal transcriptome of retinal organoid development. Our data demonstrate that retinal organoids recapitulate key events of retinogenesis including optic vesicle/cup formation, formation of a putative ciliary margin zone, emergence of RPCs and their precise and orderly differentiation to various types of retinal neurons. Combining the scRNA- with scATAC-Seq data, we were able to reveal cell type specific transcription factor binding motifs on accessible chromatin at each stage of organoid development and to show that chromatin accessibility is highly correlated to the developing human retina, but with some differences in the temporal emergence and abundance of some of the retinal cell types. Our work provides the first integrated molecular and spatial atlas of human retinal organoid development that could be used to identify novel genes and key pathways that underpin human retinal development and function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data during retinal development  using 8 samples (day10, 20, 35, 45, 60, 90, 150 and 210) of hiPSC-derived retinal organoids

first: Birthe

last: Dorgau

first: Joseph

last: Collin

first: Agata

last: Rozanska

first: Veronika

last: Boczonadi

first: Marina

last: MoyaMolina

first: Rafiqul

last: Hussain

first: Tamilvendhan

last: Dhanaseelan

first: Jonathan

last: Coxhead

first: Rachel

last: Queen


title: Mutation-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

status: Public on Feb 14 2024

city: Lausanne

first: Frédéric

last: Schütz

address: Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with de novo variants in the AFF3 degron , a sequence involved in its binding to ubiquitin ligase. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative (DN) mode-of-action, wherein an increased level of AFF3 resulted in pathological effects.  In line with this hypothesis, we describe an individual presenting a KINSSHIP-like phenotype carrying a partial duplication of AFF3. Further screening of intellectual disability cohorts revealed nine individuals with heterozygous and three with homozygous loss-of-function (LoF) variants, as well as two probands with compound LoF/missense and six with biallelic missense mutations in AFF3, who displayed a milder syndrome. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human AFF3 mRNA confirming their association with the ablation of aff3. Conversely, the missense isoforms did not complement demonstrating the deleteriousness of the variants identified in affected individuals.  To assess the different effect of these variants, we profiled the transcriptome of fibroblasts of affected individuals and isogenic cells harboring DN/DN, LoF/+, LoF/LoF or DN/LoF AFF3 genotypes. While the same pathways are affected, only one-third of the differentially expressed genes are common to both homozygote datasets, indicating that AFF3 LoF and DN mutations largely modulate transcriptomes differently. In particular, the apical junction and DNA repair pathways displayed opposite modulation.  Our results and the high pleiotropy shown by this locus in GWASes suggest that even slight changes in the AFF3 function might be deleterious.

overall_design:
To assess the effect of AFF3  biallelic missense variants we established primary fibroblasts lines of four healthy controls and two affected individuals carrying biallelic missense variants in AFF3, i.e. patient B1 who is homozygous for the p.(Lys528Arg) variants and patient B7 who is compound heterozygote for the p.(Val1036Ile) and p.(Arg1186Gln) variants.
We profiled the transcriptome of primary fibroblasts of the two affected individuals carrying biallelic missense variants in AFF3 and compared them to those of fibroblasts of three of the healthy controls (the fourth one was removed due to QC issues). The transcriptome profile of each line was analyzed in biological triplicate.

first: Sissy

last: Bassani

first: Jacqueline

last: Chrast

first: Giovanna

last: Ambrosini

first: Norine

last: Voisin

first: Fabio

last: Sirchia

first: Lydia

last: Turban

first: Susanna

last: Schubert

first: Abou

last: Rami

first: Jan-Ulrich

last: Schlump

first: Desiree

last: DeMille

first: Pinar

last: Bayrak-Todemir

first: Gary

last: Nelson

first: Kristen

middle: N

last: Wong

first: Laura

last: Duncan

first: Mackenzie

last: Mosera

first: Christian

last: Gilissen

first: Lisenka

last: Vissers

first: Rolph

last: Pfundt

first: Rogier

last: Kersseboom

first: Hilde

last: Yttervik

first: Geir

last: Hansen

first: Christoffer

last: Jonsrud

first: Marie

middle: F

last: Smeland

first: Michael

last: Lyons

first: Claudia

last: Carvalho

first: Chaofan

last: Zhang

first: James

last: Lupski

first: Lorraine

last: Potocki

first: Leticia

last: Flores-Gallegos

first: Rodrigo

last: Morales-Toquero

first: Florence

last: Petit

first: Binnaz

last: Yalcin

first: Annabelle

last: Tuttle

first: Lane

last: Mccormick

first: Mary

last: Kukolich

first: Marcello

last: Scala

first: Michele

last: Iacomino

first: Federico

last: Zara

first: Karin

last: Writzl

first: Ales

last: Maver

last: Iseli

first: Nicolas


title: Deciphering the spatio-temporal transcriptional and chromatin accessibility of human retinal organoid development at the single cell level [scATAC-Seq]

first: Majlinda

last: Lako

first: Birthe

last: Dorgau

first: Joseph

last: Collin

first: Agata

last: Rozanska

first: Veronika

last: Boczonadi

first: Marina

last: MoyaMolina

first: Rafiqul

last: Hussain

first: Tamilvendhan

last: Dhanaseelan

first: Jonathan

last: Coxhead

first: Rachel

last: Queen


title: Transcriptome analysis after BBB-EC migration

status: Public on Feb 11 2024

first: Ibrahim

last: HAMAD

summary: A monolayer of hCMEC/D3 (BBB-EC) was grown in an insert. After reaching confluency, BBB-EC were treated with TNFa and IFNg for 24h. Next, BBB-EC were washed. Tregs were isolated from human blood (both healthy donors (HD)and untreated RRMS patients) and added to the upper chamber of the insert or were cultured in the BBB-EC medium as control (untouched_1). They were let to migrate for 24h and the upper fraction (non-migrated_2) and lower fraction (migrated_3) were collected.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of untouched, non-migrated and migrated Tregs from healthy donors and untreated RRMS patients.

first: Baeten

last: Paulien

last: Hamad

first: Broux

last: Bieke


title: Mitochondrial transfer mediates endothelial cell engraftment through mitophagy

first: Yonglin

last: Zhu

address: 300 Longwood Ave

department: Cardiac Surgery

institute: Boston Children's Hospital

summary: One of the downstream effects of mitophagy is the transient activation of mitochondrial biogenesis and, in turn, enhanced mitochondrial respiration. To gain insights into the transcriptional changes produced in ECs by incorporating exogenous mitochondria through either co-culture with MSCs (mitoT-ECs) or artificial transplantation (mitoAT-ECs), we performed RNA-seq analysis.

overall_design:
Comparison the transcriptomic difference among three groups of ECs corresponding to (1) ECs that received exogenous mitochondria by artificial transplantation (mitoAT-ECs), (2) ECs that received exogenous mitochondria (from MSCs) by coculture with MSCs (mitoT-ECs), and (3) ECs that were co-cultured with MSCs but did not receive exogenous mitochondria (unprimed-ECs), served as control.

[UPDATE] 05-09-2024: The Sample titles were updated. The old titles are in the Sample description field.

first: Juan

last: Melero-Martin

first: Ruei-Zeng

last: Lin


title: Deciphering the spatio-temporal transcriptional and chromatin accessibility of human retinal organoid development at the single cell level [Spatial Transcriptomics]

last: Lako


title: Hypoxia inducible factor prolyl hydroxylase inhibition compromises development and progression of acute myeloid leukaemia

city: Edinburgh

first: Yuka

last: Kabayama

address: 5 Little France Drive

institute: University of Edinburgh

summary: Acute myeloid leukaemia (AML) is a largely incurable haematological disease, for which new efficient therapeutic strategies are urgently needed. While leukaemogenesis occurs under hypoxic conditions of the bone marrow, the therapeutic tractability of the hypoxia inducible factor (HIF) system in AML is elusive. Given that inactivation of HIF-1α and HIF-2α promotes leukaemic transformation, a possible therapeutic strategy for AML treatment is to constitutively stabilise HIF- α proteins. This can be achieved by targeting the HIF-prolyl hydroxylases (PHDs), the catalysis of which promotes HIF-1α and HIF-2α degradation. Here, we demonstrate that genetic inactivation of Phd1 or Phd2 compromises initiation and progression of AML, without impacting normal haematopoiesis, thus implying the immense therapeutic potential of targeting PHDs in AML. To pharmacologically inactivate PHDs, we employed clinical grade PHD inhibitors as well as a new selective PHD inhibitor (IOX5), which stabilises HIF-α through a novel mechanism of action. Pharmacological PHD inhibition compromises AML cells in a HIF-α dependent manner to disable pro-leukaemogenic pathways in AML cells, re-program their metabolism, and induce cell death, at least in part via pro-apoptotic BNIP3. Importantly, concurrent inhibition of anti-apoptotic BCL-2 by clinically used Venetoclax potentiates the anti-leukaemic effect of PHD inhibition. Thus PHD inhibition with consequent HIF-α stabilisation is a promising new non-toxic strategy for AML treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iMLL-AF9 preleukaemic cells treated with PHD2 inhibitor.

first: Hannah

last: Lawson


title: Myelin plasticity in ventral tegmental area is required for opioid reward

status: Public on Feb 10 2024

city: Stanford

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive, SIM1 G3035

department: Neurology

institute: Stanford University

summary: All drugs of abuse induce long-lasting changes in synaptic transmission and neural circuit function that underlie substance use disorders. Another recently appreciated mechanism of neural circuit plasticity is mediated through activity-regulated changes in myelin that can tune circuit function and influence cognitive behavior1. Here, we explored the role of myelin plasticity in dopaminergic circuity and reward learning. We demonstrate that dopaminergic neuronal activity-regulated myelin plasticity is a key modulator of dopaminergic circuit function and opioid reward. Oligodendroglial lineage cells respond to dopaminergic neuronal activity evoked by either optogenetic stimulation of dopaminergic neurons, optogenetic inhibition of GABAergic neurons, or administration of morphine or cocaine. These oligodendroglial changes are evident selectively within the ventral tegmental area (VTA), but not along the axonal projections in the medial forebrain bundle nor within the target nucleus accumbens (NAc). Genetic blockade of oligodendrogenesis dampens dopamine release dynamics in nucleus accumbens and impairs behavioral conditioning to morphine. Taken together, these findings underscore a critical role for oligodendrogenesis in reward learning and identify dopaminergic neuronal activity-regulated myelin plasticity as an important circuit modification that is required for opioid reward.

overall_design: To study interactions between neuronal and glial cell populations in the Ventral tegmental area (VTA) and how are they affected by morphine, mice (saline control, n=3; 10 mg/kg morphine, n=3) were subjected to Conditioned Place Preference test. The nuclei from flash frozen tissue were FACS sorted and processed for single-nucleous RNA-sequencing.

first: Kiarash

last: Shamardani

first: Karen

last: Malacon

first: Belgin

last: Yalcin


title: Effect of genetic deletion of TREM1 on gene expression of brain primary microglia during aging and in 5XFAD Alzhiemer mice

status: Public on Feb 09 2024

first: Edward

middle: N.

last: Wilson

address: 1201 Welch Road MSLS P254

summary:
To investigate the function of TREM1 in the regulation of innate immune cell function, we established mice in which TREM1 target gene has been genetically deleted.
We then performed gene expression profiling analysis using data obtained from RNA-seq of microglia from young and old WT and TREM1-/-mice and from 5XFAD and 5XFADxTREM1+/- mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TREM1+/- microglia

first: Katrin

last: Andreasson


title: Effect of genetic deletion of TREM1 on gene expression during aging of primary peritoneal macrophage cells

summary:
To investigate the function of TREM1 in the regulation of innate immune cell metabolism, we established mice in which TREM1 target gene has been genetically deleted.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 500,000 different cells from young and old WT and TREM1-/-mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TREM1 KO macrophages.


title: Inflammation causes insulin resistance via IRF3-mediated reduction in FAHFA levels

city: Boston

first: NORC

last: Boston

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

summary: Obesity-induced inflammation metabolic dysfunction, but the mechanisms remain elusive. Here we showed that the innate immune factor IRF3 is a direct transcriptional regulator of glucose homeostasis through induction of endogenous FAHFA hydrolase Aig1 in adipocytes. Adipocyte-specific knockout IRF3 protects mice against high-fat diet-induced insulin resistance, whereas overexpression of IRF3 in adipocytes promotes insulin resistance on a high-fat diet. Furthermore, pharmacological inhibition of AIG1 reversed obesity-induced insulin resistance and restored glucose homeostasis in the setting of adipocyte IRF3 overexpression. We therefore, identify the adipocyte IRF3/AIG1 axis as a crucial link between obesity-induced inflammation and insulin resistance and suggest an approach for limiting the metabolic dysfunction accompanying obesity.

overall_design: To identify the downstream genes of IRF3 in adipocytes, we performed two RNA-sequencing experiments: 1) we defined the transcriptional profiles of adipocytes using translating ribosome afﬁnity puriﬁcation (TRAP) from eWAT of Ad-NuTRAP and FI3KO-Ad-NuTRAP mice after 8 weeks of HFD feeding at thermoneutrality; 2) WT and FI3OE SVF-derived adipocytes by RNA-sequencing.

first: Shuai

last: Yan

first: Evan

last: Rosen


title: 5hmC and m6a modification and Translatomes of monocytes and macrophages

status: Public on Feb 07 2024

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute


first: Giovanna

last: Ambrosini

address: Station 19

institute: EPFL

summary:
We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with de novo variants in the AFF3 degron , a sequence involved in its binding to ubiquitin ligase. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative (DN) mode-of-action, wherein an increased level of AFF3 resulted in pathological effects.
In line with this hypothesis, we describe an individual presenting a KINSSHIP-like phenotype carrying a partial duplication of AFF3. Further screening of intellectual disability cohorts revealed nine individuals with heterozygous and three with homozygous loss-of-function (LoF) variants, as well as two probands with compound LoF/missense and six with biallelic missense mutations in AFF3, who displayed a milder syndrome. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human AFF3 mRNA confirming their association with the ablation of aff3. Conversely, the missense isoforms did not complement demonstrating the deleteriousness of the variants identified in affected individuals.
To assess the different effect of these variants, we profiled the transcriptome of fibroblasts of affected individuals and isogenic cells harboring DN/DN, LoF/+, LoF/LoF or DN/LoF AFF3 genotypes. While the same pathways are affected, only one-third of the differentially expressed genes are common to both homozygote datasets, indicating that AFF3 LoF and DN mutations largely modulate transcriptomes differently. In particular, the apical junction and DNA repair pathways displayed opposite modulation.
Our results and the high pleiotropy shown by this locus in GWASes suggest that even slight changes in the AFF3 function might be deleterious.

overall_design:
To assess the effect of dominant negative (KINSSHIP) and loss of function variants in AFF3 we engineered  knock-in Ala233Thr (named DN), and knock-out (named LoF) isogenic HEK293T cell models with CRISPR-Cas9. The analyzed cell lines present different genotypic configurations: DN/DN (line No. 54 and 90), LoF/+ (No. 1) , LoF/LoF (No. 216, 98, 20,15 and 4), and DN/LoF(No. 51 and 86).
We profiled the transcriptome of AFF3 DN and LoF models and compared them with three wildtype HEK293T controls.
The transcriptome profile of each line was analyzed in biological triplicate.

first: Sissy

last: Bassani

first: Jacqueline

last: Chrast

first: Norine

last: Voisin

first: Fabio

last: Sirchia

first: Lydia

last: Turban

first: Susanna

last: Schubert

first: Abou

last: Rami

first: Jan-Ulrich

last: Schlump

first: Desiree

last: DeMille

first: Pinar

last: Bayrak-Todemir

first: Gary

last: Nelson

first: Kristen

last: Wong

first: Laura

last: Duncan

first: Mackenzie

last: Mosera

first: Christian

last: Gilissen

first: Lisenka

last: Vissers

first: Rolph

last: Pfundt

first: Rogier

last: Kersseboom

first: Hilde

last: Yttervik

first: Geir

last: Hansen

first: Christoffer

last: Jonsrud

first: Marie

last: Smeland

first: Michael

last: Lyons

first: Claudia

last: Carvalho

first: Chaofan

last: Zhang

first: James

last: Lupski

first: Lorraine

last: Potocki

first: Leticia

last: Flores-Gallegos

first: Rodrigo

last: Morales-Toquero

first: Florence

last: Petit

first: Binnaz

first: Annabelle

last: Tuttle

first: Lane

last: Mccormick

first: Mary

last: Kukolich

first: Marcello

last: Scala

first: Michele

last: Iacomino

first: Federico

last: Zara

first: Karin

last: Writzl

first: Ales

last: Maver

last: Iseli

first: Nicolas

last: Guex

first: Alexandre


title: Deciphering the spatio-temporal transcriptional and chromatin accessibility of human retinal organoid development at the single cell level

first: Majlinda

last: Lako


title: Translatomes of monocytes and macrophages

first: RENHUA

last: SONG

summary:
RNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications control the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear.
We profile translatomes of monocytes and macrophages at resting, pro- and anti-inflammatory states.

overall_design: Polyribo-Seq sample preparation and uHPLC Size Exclusion Chromatography (SEC) were performed as described by Yoshikawa et al.,.

first: Natalia

last: Pinello

first: Renhua

last: Song

first: Quintin

last: Lee

first: Justin

last: Wong


title: Circulating Cell-Free RNA in Blood as a Host Response Biomarker for the Detection of Tuberculosis [test_data]

status: Public on Feb 06 2024

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: Tuberculosis (TB) remains a leading cause of death from an infectious disease worldwide. This is partly due to a lack of tools to effectively screen and triage individuals with potential TB. Whole blood RNA signatures have been extensively studied as potential biomarkers for TB, but they have failed to meet the World Health Organization's (WHOs) optimal target product profiles (TPPs) for a non-sputum triage or diagnostic test. In this study, we investigated the utility of plasma cell-free RNA (cfRNA) as a host response biomarker for TB. We used RNA profiling by sequencing to analyze plasma samples from individuals with a cough lasting at least two weeks, who were seen at outpatient TB clinics in Uganda, Vietnam, and the Philippines. We split the samples into a discovery set for model training and testing, and reserved a validation set from a separate cohort to validate the model performance. We trained 15 machine learning classification models and developed a 6-gene signature that has a high performance in differentiating TB positive and negative individuals (Area Under the Curve, AUC = 0.95, 0.92, 0.95 for the test, training and validation sets respectively). This 6-gene signature exceeds the optimal WHO TPPs for a TB triage test (sensitivity: 97.1% [95% CI: 80.9-100%], specificity: 85.2% [95% CI: 72.4-100%]) and was robust to differences in geographic location, sample collection, and HIV status. Analysis of matched whole blood samples from the validation cohort highlighted the differences in origin of plasma and whole blood RNA. Overall, our results demonstrate the utility of plasma cfRNA for the detection of TB and suggest the potential for a point-of-care, gene expression-based assay to aid in early detection of TB.

overall_design:
In the study presented here 251 patients who presented with a cough >= 2 weeks were identified in three separate cohorts, across three different countries (Uganda, Vietnam, Philippines). Patients were identified as TB positive or negative at clinics (tb status indicated in the “tb” column of the metadata). We extracted the cell-free RNA from the plasma of patients and conducted RNA sequencing. We split these samples into discovery (cohort 1 and 2) and validation (cohort 3). And then further split the discovery into 70% for machine learning model training and 30% for model testing. The validation cohort was evaluated independently. The data shown here are the gene transcript counts from the test data samples.
Please note that the records have been updated with raw sequencing data on Mar 27, 2024.

first: Adrienne

last: Chang

first: Conor

last: Loy

first: Daniel

last: Eweis-LaBolle

first: Joan

last: Lenz

first: Amy

last: Steadman

first: Alfred

last: Andama

first: Nguyen

last: Viet Nhung

first: Charles

last: Yu

first: William

last: Worodria

first: Claudia

last: Denkinger

first: Payam

last: Nahid

first: Adithya

last: Cattamanchi


title: 5hmC modification of monocytes and macrophages

first: RENHUA

last: SONG

summary:
RNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications control the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear.
We profile 5hmC epitranscriptomes of monocytes and macrophages at resting, pro- and anti-inflammatory states.

overall_design: 5hmC-IP-Seq was performed as described by Delatte, et al.,  and Lan et al.,.

first: Natalia

last: Pinello


title: Circulating Cell-Free RNA in Blood as a Host Response Biomarker for the Detection of Tuberculosis [training_data]

overall_design:
In the study presented here 251 patients who presented with a cough >= 2 weeks were identified in three separate cohorts, across three different countries (Uganda, Vietnam, Philippines). Patients were identified as TB positive or negative at clinics (tb status indicated in the “tb” column of the metadata). We extracted the cell-free RNA from the plasma of patients and conducted RNA sequencing. We split these samples into discovery (cohort 1 and 2) and validation (cohort 3). And then further split the discovery into 70% for machine learning model training and 30% for model testing. The validation cohort was evaluated independently. The data shown here are the gene transcript counts from the training data samples.
Please note that the records have been updated with raw sequencing data on Mar 27, 2024.


title: m6A modification of monocytes and macrophages

summary:
RNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications control the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear.
We profile m6A epitranscriptomes of monocytes and macrophages at resting, pro- and anti-inflammatory states.

overall_design: m6A-IP-Seq was performed as previously described by refined RIP-seq protocol for epitranscriptome analysis with low input materials.

first: Renhua

last: Song

first: Quintin

last: Lee


title: Positional cues underlie cell fate specification during branching morphogenesis of the embryonic mammary epithelium

status: Public on Feb 05 2024

city: Paris

first: Silvia

last: Fre

address: 26 rue d’Ulm

department: Genetics and Developmental Biology

institute: Institut Curie

summary: By single-cell RNA-sequencing across 4 stages of embryonic development, we reconstructed the differentiation trajectories of multipotent mammary stem cells towards basal and luminal fate. Our data revealed that MaSCs can already be resolved into distinct populations exhibiting lineage commitment at the time coinciding with the first sprouting events of mammary branching morphogenesis (E15.5). Through an interactive web tool for the visualization of gene expression across our developmental atlas, we provide novel molecular markers for committed and multipotent MaSCs, and define their spatial distribution within the developing tissue. Furthermore, we show that the mammary embryonic mesenchyme is composed of two spatially-restricted cell populations, representing the sub-epithelial and dermal mesenchyme.

overall_design: Embryonic mammary gland cells were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of EpCAM signal (epithelial or mesenchymal cells, respectively) and analyzed by scRNAseq using the 10x Chromium system.

last: Carabaña Garcia

first: Wenjie

last: Sun

first: Bethan

last: Lloyd-Lewis


title: DDX5 inhibits hyaline cartilage fibrosis and degradation in osteoarthritis via alternative splicing and G-quadruplex unwinding

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

summary: Hyaloid cartilage fibrosis is one of the important reasons for the poor prognosis of advanced osteoarthritis (OA), and is the main factor leading to joint stiffness and deformity. However, the mechanism of hyaline cartilage fibrosis remains largely unclear. Here we report that DDX5, one of the founding members of the DEAD-box RNA helicase family, was dramatically down-regulated in the degenerated articular cartilage of aged mice, and patients with OA, mouse destabilization of the medial meniscus (DMM) models，and cytokine (Interleukin (IL)-1β and tumor necrosis factor (TNF)-α) stimulation.In vitro and in vivo experimental findings that inhibition of DDX5 expression increases the fibrocartilage phenotype by reduction collagen type I (COL I) protein expression and up-regulate collagen type II (COL II) protein expression. In addition, The reduction of DDX5 aggravate cartilage degradation by induce the production of cartilage degrading enzymes. In addition, DDX5 induced exon 25 skip of FN1-AS and exon 14 skip of PLOD2-AS produced a transcript (termed FN1-AS1-SE25 and PLOD2-AS-SE14). The reduction in DDX5 results in an increase in the FN1-AS-WT and PLOD2-AS-WT variants.

overall_design: By comparing the RNA-seq analysis of ATDC5 under the condition of cytokine treatment, explore the alternative splicing in osteoarthritis

first: Yang

first: Qianqian

last: Liu

first: Mingrui

last: Han

first: Zhigui

last: Wu


title: Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog, NIPAL1, and the MAPK signaling pathway

status: Public on Jan 31 2024

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

summary: Naturally occurring canine invasive urinary carcinoma (iUC) closely mimics human high grade iUC in terms of age of onset, pathology, cellular and molecular features, metastatic profiles, and treatment response . Shetland sheepdogs (Shelties), the focus of this study, are a small herding breed and popular family pet. Multiple studies demonstrate their extraordinary disease risk, with one survey reporting that of 3359 Shelties, iUC comprised 12% of all Sheltie cancer diagnoses, which is six times the expected rate of 2% for all dogs. In this study we analyze one hundred Shelties and 55 dogs from closely related breeds and identify a single major risk locus associated with iUC, featuring NIPA-like domain containing 1 (NIPAL1), a strong candidate gene, and associated mutations. By segregating samples according to genotype, we identify six additional loci that modify individual disease risk when combined with a putative pathogenic protein altering mutation in NIPAL1. Merging the GWAS loci with tumor sequence identifies the mitogen activated protein kinase (MAPK) signaling pathway as a key component of canine iUC genetic susceptibility.

overall_design: ChIP-Seq for 3 histone modifications H3K4me1, H3K4me3, and K3K27ac in 2 canine invasive urinary carcinoma cell line samples.

first: Heidi

middle: G

last: Parker

middle: C

first: Jocelyn

last: Plassais

first: Deepika

last: Dhawan

first: Erika

last: Kim

first: Deborash

last: Knapp

first: Elaine

last: Ostrander


title: Nanopore long-read RNA sequencing shows region-specific sex differences in wild-type mouse brain mRNA isoform expression and usage

city: Birmingham

first: Brittany

last: Lasseigne

state: AL

address: 1900 University Boulevard

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

summary: To address differences in splicing across brain regions (cerebellum, cortex, hippocampus, and striatum) and sexes, we used long-read Oxford Nanopore Technologies (ONT) RNA sequencing to sequence 40 wild-type mouse brain cDNA libraries from 10 mice and calculated differential expression and transcript usage. We found that there is differential gene expression, differential transcript expression, and differential transcript usage across all brain regions. We found that the brain region with the most differential expression and transcript usage is the cerebellum, potentially driven by differences in cell type composition. Additionally, our findings suggest there is much differential splicing across brain regions and to a lesser extent, within brain regions across sexes.

overall_design: We obtained flash-frozen hippocampus, striatum, cerebellum, and cortex wild-type C57BL/6J mouse brain tissues from The Jackson Laboratory (JAX #000664, age = 20 weeks) from five male and five female mice. We loaded 11 μl of each pooled library with 1 μl Rapid Adapter T (12 μl total) each onto 12 R9.4 flow cells (FLO-MIN106D). Because the Oxford Nanopore Technologies GRIDion (GRD-MK1) sequencing device can only hold five flow cells at a time, we sequenced these libraries in three separate sequencing runs (2, 5, and 5 flow cells at a time) for 72 hours each.

first: Emma

last: Jones

first: Timothy

last: Howton


title: The placenta has an active role in maintaining fetal homeostasis following maternal immune activation

status: Public on Feb 01 2024

city: Gentofte

first: Albin

last: Sandelin

address: Markvangen 26

country: Denmark

institute: University of Copenhagen

summary: Activation of the maternal immune system during pregnancy affects fetal development, which can increase in postnatal susceptibility to a range of diseases, including cardiovascular, metabolic and psychiatric disorders. During maternal immune activation (MIA), the maternal body must balance its ressources between mounting an immune response and investing resources into continued metabolism and growth, essentials for survival of the fetus and a successful pregnancy. How the placenta responds to MIA over time and how it can protect the fetus is not well understood, and neither are the fetal consequences of MIA. Here, we characterised the response to acute maternal lung inflammation across time in maternal and fetal organs, using a combination of omics, imaging and integrative computational analyses. We found that the placenta, unlike other maternal organs, did not react by a typical innate immune response, but instead induced genes associated with increased tissue integrity,  likely to prevent fetal exposure to potential infections, and simultaneously reduced expression of growth-associated genes. Subsequently, a return to homeostasis was observed, with heightened expression of biosynthesis and endoplasmic reticulum (ER) stress genes. These responses likely protect the fetus from inflammation, as we observed no immune response in the fetal liver transcriptome. Instead, we observed metabolic adaptations in the fetus, including a release of docosahexaenoic acid (DHA) carrying metabolites, including triglyceride and phosphatidylcholine. Notably, DHA is crucial for fetal brain development. This metabolic response is likely a combination of the placental MIA response and temporary maternal fasting, caused by MIA-induced fever and lack of nutrient intake. Our study shows, for the first time, the integrated temporal and systemic response to LPS in lungs across maternal and fetal organs

overall_design: RNA-seq time course analysis of pregnant mice and fetus tissues  following LPS or H20 instillation in maternal lungs

first: Signe

last: Schmidt Kjølner Hansen

first: Daria

last: Rago

first: Karin

last: Sørig Hougaard


title: Transcriptome Analysis Reveals the Biocontrol Mechanism of Endophytic Bacteria AM201, Rhodococcus sp., against Root Rot Disease of Atractylodes macrocephala

status: Public on Jan 30 2024

city: HangZhou

first: Xiaoqi

last: Gao

address: 548 Binwen Road, Binjiang District, Hangzhou City, Zhejiang Province

institute: zhejiang chinese medical university

summary: Transcriptome analysis was performed on the rhizome tissues of Atractylodes macrocephala under different treatments. The four treatments were: sterile water irrigation alone, FS root irrigation, FS and AM201 root irrigation, and FS combined with methyltobuzin (TM) root irrigation. And the differential genes between AM201 and FO groups were identified and compared, which helps to reveal the resistance mechanism of AM201 to Atractylodes macrocephala root rot disease

overall_design: Gene expression profiling analysis of transcriptome data from rhizome tissues of Atractylodes macrocephala under four different treatments


title: Sexually Dimorphic Response to Hepatic Injury in Newborn Suffering from Intrauterine Growth Restriction

city: Hangzhou

first: yusen

last: wei

institute: Zhejiang University

summary: Intrauterine growth restriction (IUGR) is associated with increased relative liver weight at birth, hepatic function decline, and a higher risk for chronic liver and cardiovascular diseases in adults. Precise mechanisms of early developmental plasticity to intervene in poor fetal programming and adult disease remain largely elusive and warrant extensive research. Selecting natural piglets’ model of IUGR, using the liver as a readout and combining previous transcriptome findings, a map of cellular landscape was created to reveal a sex-dependent manner in IUGR-induced hepatic injury and its long-term functional repercussions.Here, we show data on the transcriptional profiles of 41,969 high-quality cells from normal birthweight (NBWs) and IUGR piglets (IUGRs) from hepatic tissue and demonstrated strong homology with human using human-derived liver single-cell dataset. We discovered that male liver was much more severely damaged and inflammation by IUGR than female liver at the one-week postnatal node.

overall_design: Liver single-cell mRNA profiles of IUGR and normal piglets (female n=2, male n=6) were generated by deep transcriptome sequencing using Illumina NovaSeq 6000 platform.

first: Wei

last: Yu sen


title: Quantitative live-cell imaging of secretion activity reveals dynamic immune responses

city: Bunkyo-ku

first: Yoshitaka

last: Shirasaki

state: Tokyo

address: Hongo 7-3-1

department: Graduate School of Pharmaceutical Science

institute: The University of Tokyo

summary: Quantification of cytokine secretion has facilitated advances in the field of immunology, yet the dynamic and varied secretion profiles of individual cells, particularly those obtained from limited human samples, remain obscure. Herein, we introduce a new technology for quantitative live-cell imaging of secretion activity (qLCI-S) that enables high-throughput and dual-color monitoring of secretion activity at the single-cell level over several days, followed by transcriptome analysis of individual cells based on their phenotype. The efficacy of qLCI-S was demonstrated by visualizing the characteristic temporal pattern of cytokine secretion of group 2 innate lymphoid cells, which constitute less than 0.01% of human peripheral blood mononuclear cells, and by revealing minor subpopulations with enhanced cytokine production. The underlying mechanism of this feature was linked to the gene expression of stimuli receptors. This new technology paves the way for exploring gene expression signatures linked to the spatiotemporal dynamic nature of various secretory functions.

overall_design: After 5-days of qLCI-S for the ILC2s stimulated with IL-2/IL-33/TSLPs, hyperactive and silent phenotypes were harvested as individual clones and single cells, respectively, and applied to RNA-Seq analysis.

first: Mai

last: Yamagishi

first: Kaede

last: Miyata

first: Yumiko

last: Tanaka

first: Osamu

last: Ohara

first: Koichi

last: Fukunaga

first: Kazuyo

last: Moro

first: Sotaro

last: Uemura


overall_design: mRNA profiles of HepG2 and APOA4 KO cell line (n=3) with different treatments of hypoxia were generated by deep transcriptome sequencing using Illumina NovaSeq 6000 platform.

first: Yusen

last: Wei


title: The genome-wide dual-CRISPR screening identifies essential non-coding regulatory elements

status: Public on Jan 28 2024

city: Leiden

first: Minkang

last: Tan

address: Einthovenweg 20

department: Department of Cell and Chemical Biology

country: Netherlands

institute: Leiden University Medical Center

summary: Non-coding regulatory elements (NCRE) represent a major fraction of the human genome, play important roles in different biological pathways, and have the potential as genomic medicine targets. We developed a straightforward dual-CRISPR screening system capable of deleting thousands of NCREs genome-wide to study their functions in distinct biological contexts in K562 cells and 293T cells. We show that many NCREs, including ultraconserved elements (UCE), have silencer activity and play essential roles in cell growth and drug response. NCREs with redundant functions could also be identified from the screening data. This dual-CRISPR system is also compatible with single-cell sequencing. We identified that UCE PAX6_Tarzan might be critical in heart development, as removing it from human embryonic stem cells led to defects in cardiomyocyte differentiation. Our study provides further evidence that many NCREs have important biological functions contributing to human biology and diseases, and may serve as future drug targets.

overall_design: We have developed a new dual-CRISPR screening system that could delete thousands of NCREs in a systematic and genome-wide fashion. This dual CRISPR screening system is easy to construct and sequence, without the need for additional barcoding. As target regions of more than 200 bp in size are removed from the genome, NCREs could be studied irrespective of their specific biological functions. We designed dual-CRISPR libraries targeting 4,047 UCEs in the human genome from UCNEbase (Dimitrieva and Bucher, 2013), 1,527 in vivo-validated conserved enhancers from VISTA Enhancer Browser (Visel et al., 2007), and all 13,539 predicted enhancers in K562 cells from ENCODE (Yip et al., 2012). Using this system, we studied the biological functions of the UCEs in the human genome and identified regions that would affect cell survival and drug response in K562 and 293T cells.

first: Baoxu

last: Pang

first: Yufeng

last: Li

first: Almira

last: Akkari-Henić


title: Apolipoprotein E controls Dectin 1 dependent development of monocyte-derived alveolar macrophages upon pulmonal b-glucan induced inflammatory adaptation

status: Public on Jan 26 2024

city: Bonn

first: Jiangyan

last: Yu

address: Carl-Troll-Str. 31

institute: University of Bonn

summary: To investigate the impact of a non-pathological sterile environmental stimulus in a controlled manner

overall_design: scRNA-Seq of lung BALF from mouse treated with PBS or glucan

first: H

last: Theobald

first: D

last: Bejarano

first: J

last: Haub

first: N

last: Katzmarski

last: Schulte

first: K

last: Bassler

first: B

last: Ćirović

first: C

last: Osei

first: F

last: Piattini

first: L

last: Vornholz

first: X

first: A

last: Al

first: S

last: Chakarov

last: Haendler

first: G

last: Brown

last: Wiliams

last: Bosurgi

last: Ginhoux

last: Ruland

first: M

last: Beyer

last: Greter

last: Kopf

middle: L

last: Schultze

last: Schlitzer


title: The TaSnRK1-TabHLH489 module integrates brassinosteroid and sugar signaling to regulate grain length in bread wheat

status: Public on Feb 04 2024

city: Qingdao

first: Jinyang

last: Lyu

state: Shandong

address: BinHai road

department: School of Life Sciences

institute: Shandong University

summary: Regulation of grain size is a crucial strategy for improving crop yield and is also a fundamental aspect of developmental biology. However, the underlying molecular mechanisms governing grain development in wheat remain largely unknown. In this study, we identified a wheat atypical basic helix-loop-helix (bHLH) transcription factor, TabHLH489, which is tightly associated with grain length through genome-wide association study and map-based cloning. Knockout of TabHLH489 and its homologous genes resulted in increased grain length and weight, whereas overexpression led to decreased grain length and weight. TaSnRK1α1, the α-catalytic subunit of plant energy sensor SnRK1, interacted with and phosphorylated TabHLH489 to induce its degradation, thereby promoting wheat grain development. Sugar treatment induced TaSnRK1α1 protein accumulation while reducing TabHLH489 protein levels. Moreover, brassinosteroid (BR) promotes grain development by decreasing TabHLH489 expression through the transcription factor BRASSINAZOLE RESISTANT1 (BZR1). Importantly, natural variations in the promoter region of TabHLH489 affect the TaBZR1 binding ability, thereby influencing TabHLH489 expression. Taken together, our findings reveal that the TaSnRK1α1-TabHLH489 regulatory module integrates BR and sugar signaling to regulate grain length, presenting potential targets for enhancing grain size in wheat.

overall_design: To explore the functional mechanism of TabHLH489 in the development of wheat grains, we collected 5-day-post-anthesis (5-DPA) grains from Fielder and OE-TabHLH489, respectively. The plants were cultivated in a greenhouse under a 16-hour light (22 °C)/8-hour dark (16 °C) cycle, maintaining approximately 50% relative humidity. Each sample consisted of grains collected from five individuals, mixed to form a single biological repeat.

first: Dongzhi

last: Wang

last: Sun

first: Min

last: Fan

first: Jun

last: Xiao

first: Ming-Yi

last: Bai


title: B3GNT7 regulates mucin O-glycosylation to alleviate colonic inflammation

status: Public on Jan 22 2024

city: Huai'an

first: Honggang

address: No.1 Huanghe West Road

institute: The Affiliated Huai’an No.1 People’s Hospital of Nanjing Medical University

summary: B3GNT7, an important glycosyltransferase highly expressed in intestinal epithelial cells, is involved in physiological processes in the intestine. This study presents novel findings on the potential role and mechanism of B3GNT7 in ulcerative colitis (UC).   DSS-induced mouse model of colitis was established to investigate the expression of B3GNT7 in the colon using transcriptomics and immunohistochemistry. Bioinformatics analysis was conducted to explore the biological functions of B3GNT7. The correlation between the transcription levels of B3GNT7 in the colonic tissues of UC patients from the IBDMDB database was analyzed and the severity of colonic inflammation, along with potential mechanisms. The DSS-induced colitis mouse model was successfully established, and transcriptomic analysis revealed a significant downregulation of B3GNT7 expression in the colonic tissues compared to healthy mice. Functional enrichment analysis showed that the main biological function of B3GNT7 was to participate in the mucin O-glycosylation process. Protein interaction analysis indicates that the molecules showing strong interaction with B3GNT7 were members of the mucin MUC family, including MUC2, MUC3, and MUC6. In UC patients, the transcription levels of B3GNT7 were significantly decreased, particularly in patients with moderate to severe disease activity. The expression level of B3GNT7 was negatively correlated with the endoscopic severity of UC. Gene set enrichment analysis (GSEA) further revealed significant enrichment of B3GNT7 in the mucin O-glycosylation synthesis signaling pathway. The downregulation of B3GNT7 expression in the colonic tissues of UC may contribute to impaired mucin barrier function and the progression of colitis.

overall_design: To establish an experimental colitis mice model, we induced colitis in mice by administering 2.5% DSS in their drinking water. On the 8th day, we compared the changes in body weight and colon length between the DSS Group and the control group (CON group).  Colon tissue samples were collected for transcriptome sequencing (RNA-seq) analysis.

first: Peng

last: Shen

first: Yan

last: Li


title: The effect of LCN2 treatment on anti-inflammatory bone marrow derived macrophages

status: Public on Jan 24 2024

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Allogeneic hematopoietic stem cell transplantation remains the most efficacious treatment for many hematological malignancies. However, its therapeutic potential is affected by the most prominent side effect graft versus host disease. Despite advances in the treatment of graft versus host disease in recent years, morbidity and mortality remains high, which requires the development of new treatment approaches. We therefore implemented mouse models to assess potential treatment options for graft versus host disease. In in vivo experiments, we had observed a protective effect of LCN2 on graft versus host disease of the gastrointestinal tract. We also observed higher numbers of anti-inflammatory macrophages in the intestinal tissues of these animals. Therefore, we aimed to determine potentially regulated genes in these cells by using an in vitro approach of LCN2-treated macrophages.

overall_design: Bone marrow from healthy C57BL/6 mice was collected and seeded in cell culture dishes with complete media (10 % low endotoxin FCS, 1 % PenStrep, 20 ng/ml mCSF). Cells were cultured for seven days with or without supplementation of 150 ng/ml rmLCN2. On day 7, cells were stimulated with 20 ng/ml rmIL-4 towards an anti-inflammatory phenotype. A third group was treated with LCN2 at this time point. After 24 hours of stimulation, cells were harvested for further processing.

first: Robert

last: Zeiser

first: Nadia

last: El Khawanky

first: Melanie

last: Boerries


title: Arrestin domain containing 2 is highly induced in response to disuse in young and aged muscle and is sufficient to lower C2C12 myotube diameter

status: Public on Jan 23 2024

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

summary: Arrestin Domain Containing 2 and 3 (Arrdc2/3) are genes whose mRNA contents are decreased in young skeletal muscle following mechanical overload. Arrdc3 is linked to the regulation of signaling pathways in non-muscle cells that could influence skeletal muscle size. Despite a similar amino acid sequence, Arrdc2 function remains undefined. The purpose of this study was to further explore the relationship of Arrdc2/Arrdc3 expression with changes in mechanical load in young and aged muscle and define the effect of Arrdc2/3 expression on myotube diameter. In young and aged mice, mechanical load was decreased using hindlimb suspension while mechanical load was increased by reloading previously unloaded muscle or inducing high force contractions. Arrdc2 and Arrdc3 mRNAs were overexpressed in C2C12 myotubes using adenoviruses. Myotube diameter was determined 48 h post-transfection and RNA sequencing was performed on those samples. Arrdc2 and Arrdc3 mRNA content was higher in the unloaded muscle within 1 day of disuse and remained higher up through 10 days. The induction of Arrdc2 mRNA was more pronounced in aged muscle than young muscle in response to unloading. Reloading previously unloaded muscle of young and aged mice restored Arrdc2 and Arrdc3 levels to ambulatory levels. Increasing mechanical load beyond normal ambulatory levels lowered Arrdc2 but not Arrdc3 mRNA in young and aged muscle. Arrdc2, not Arrdc3, overexpression was sufficient to lower myotube diameter in C2C12 cells in part by altering the transcriptome favoring muscle atrophy. These data are consistent with Arrdc2 contributing to disuse atrophy, particularly in aged muscle.

overall_design: C2C12 myotubes were transfected 3 days post-differentiation using adenoviruses encoding Arrdc2+Gfp or only Gfp as a control. Forty-eight h post-transfection, C2C12 myotubes were harvested and RNA was extracted. RNA-Seq was used to compare differentially expressed genes between Arrdc2 overexpressing vs. Gfp only myotubes.

first: Grant

last: Laskin

first: Ana

last: Cabrera

first: Nicholas

middle: P

last: Greene

last: Tomko

first: Bradley

last: Gordon