title: Decreased estrogen level in ovariectomized mice causes an increase in oxidative stress in osteal macrophages leading to development of cellular senescence [scRNA-seq]

overall_design: scRNA-seq for osteal macrophages isolated from ovariectomized and control mice


title: BCR, not TCR, repertoire diversity is associated with favorable COVID-19 [GEX]

status: Public on Nov 26 2024

city: Bunkyo

first: Yoko

last: Tabe

state: Tokyo

address: 2 Chome-1-1 Hongo

department: Department of Clinical Laboratory Medicine

country: Japan

institute: Juntendo University

summary: The SARS-CoV-2 pandemic has had a widespread and severe impact on society, yet there have also been instances of remarkable recovery, even in critically ill patients. In this study, we used single-cell RNA sequencing to analyze the immune responses in recovered and deceased COVID-19 patients during moderate and critical stages. The study included three unvaccinated patients from each outcome category. Although expanded T cell receptor (TCR) clones were predominantly SARS-CoV-2-specific, they represented only a small fraction of the total repertoire in all patients. In contrast, while deceased patients exhibited monoclonal B cell receptor (BCR) expansions without COVID-19 specificity, survivors demonstrated diverse and specific BCR clones. These findings suggest that neither TCR diversity nor BCR monoclonal expansions are sufficient for viral clearance and subsequent recovery. Differential gene expression analysis revealed that protein biosynthetic processes were enriched in survivors, but that potentially damaging mitochondrial ATP metabolism was activated in the deceased. This study underscores that BCR repertoire diversity, but not TCR diversity, correlates with favorable outcomes in COVID-19.

overall_design: To investigate transcriptional and immunological differences between COVID-19 survivors and deceased patients, we performed scRNA-seq along with TCR and BCR analysis of samples from both response groups, in addition to healthy donors

first: Faith

middle: J

last: Paran

first: Rieko

last: Oyama

first: Abdullah

last: Khasawneh

first: Tomohiko

last: Ai

first: Hendra

middle: S

last: Ismanto

first: Aalaa

last: Sherif

first: Dianita

last: Saputri

first: Chikako

last: Ono

first: Mizue

last: Saita

first: Satomi

last: Takei

first: Yuki

last: Horiuchi

first: Ken

last: Yagi

first: Yoshiharu

last: Matsuura

first: Yasushi

last: Okazaki

first: Kazuhisa

last: Takahashi

first: Daron

middle: M

last: Standley

first: Toshio

last: Naito


title: Epigenetic Activation of TUSC3 Sensitizes Glioblastoma to Temozolomide Independent of MGMT Promoter Methylation Status

city: Tampa

first: Anders

last: Berglund

state: Florida

address: 12902 Magnolia Drive

department: Department of Biostatistics and Bioinformatics

country: USA

institute: Moffitt Cancer Center

type: Methylation profiling by genome tiling array

summary: Temozolomide (TMZ) is an important first-line treatment for glioblastoma (GBM), but there are limitations to TMZ response in terms of durability and dependence on the promoter methylation status of the DNA repair gene O6-methylguanine DNA methyltransferase (MGMT). MGMT-promoter-hypermethylated (MGMT-M) GBMs are more sensitive to TMZ than MGMT-promoter-hypomethylated (MGMT-UM) GBMs. Moreover, TMZ resistance is inevitable even in TMZ-sensitive MGMT-M GBMs. Hence, epigenetic reprogramming strategies are desperately needed in order to enhance TMZ response in both MGMT-M and MGMT-UM GBMs. In this study, we present novel evidence that the epigenetic reactivation of Tumor Suppressor Candidate 3 (TUSC3) can reprogram sensitivity of GBM stem cells (GSCs) to TMZ irrespective of MGMT promoter methylation status. Interrogation of TCGA patient GBM datasets confirmed TUSC3 promoter regulation of TUSC3 expression and also revealed a strong positive correlation between TUSC3 expression and GBM patient survival. Using a combination of loss-of-function, gain-of-function and rescue studies, we demonstrate that TUSC3 reactivation is associated with enhanced TMZ response in both MGMT-M and MGMT-UM GSCs. Further, we provide novel evidence that the demethylating agent 5-Azacitidine (5-Aza) reactivates TUSC3 expression in MGMT-M GSCs, whereas the combination of 5-Aza and MGMT inhibitor Lomeguatrib is necessary for TUSC3 reactivation in MGMT-UM GSCs. Lastly, we propose a pharmacological epigenetic reactivation strategy involving TUSC3 that leads to significantly prolonged survival in MGMT-M and MGMT-UM orthotopic GSCs models. Collectively, our findings provide a framework and rationale to further explore TUSC3-mediated epigenetic reprogramming strategies that could enhance TMZ sensitivity and outcomes in GBM. Mechanistic and translational evidence gained from such studies could contribute towards optimal design of impactful trials for MGMT-UM GBMs that currently do not have good treatment options.

overall_design: Bisulphite converted DNA from 16 GBM samples were hybridized to the Illumina Infinium HumanMethylationEPIC microarray

first: Qiong

last: Wu

middle: E

first: Robert

last: Macaulay

first: Arnold

middle: B

last: Etame


title: Kir6.1, a component of an ATP-sensitive potassium channel, regulates natural killer cell development [scRNA-Seq]

city: New York

first: William

last: Coetzee

state: United States

address: 550 First Ave

department: Pathology

institute: NYU School of Medicine

type: Expression profiling by high throughput sequencing

summary: Involved in immunity and reproduction, natural killer (NK) cells offer opportunities to develop new immunotherapies to treat infections and cancer or to alleviate pregnancy complications. Most current strategies use cytokines or antibodies to enhance NK-cell function, but none use ion channel modulators, which are widely used in clinical practice to treat hypertension, diabetes, epilepsy, and other conditions. Little is known about ion channels in NK cells. We show that Kcnj8, which codes for the Kir6.1 subunit of a certain type of ATP-sensitive potassium (KATP) channel, is highly expressed in murine splenic and uterine NK cells compared to other K+ channels previously identified in NK cells.  Kcnj8 expression is highest in the most mature subset of splenic NK cells (CD27-/CD11b+) and in NKG2A+ or Ly49C/I+ educated uterine NK cells. Using patch clamping, we show that a subset of NK cells expresses a current sensitive to the Kir6.1 blocker PNU-37883A. Kcnj8 does not participate in NK cell degranulation in response to tumor cells in vitro or rejection of tumor cells in vivo, or IFN-γ release. Transcriptomics show that genes previously implicated in NK cell development are amongst those differentially expressed in CD27-/CD11b+ NK cells deficient of Kcnj8. Indeed, we found that mice with NK-cell specific Kcnj8 gene ablation have fewer CD11b+CD27- and KLRG-1+ NK cells in the bone barrow and spleen. These results show that the KATP subunit Kir6.1 has a key role in NK-cell development.

overall_design: Splenic NK cells from wildtype mice were isolated via negative selection. Cells were lysed and RNA was obtained via PicoPure™ RNA Isolation Kit (Applied Biosystems). Lipid-based cell multiplexing was used in order to combine NK cells from different mcie.


title: Targeting the vulnerability of arachidonic acid metabolism to enhance immunotherapy efficacy in ARID1A-deficient colorectal cancer [RNA-Seq]

city: Harbin

first: Yanqiao

last: Zhang

address: No.150 Haping Road, Nangang District, Harbin, Heilongjiang, 150081, China

country: China

institute: Third Affiliated Hospital of Harbin Medical University

summary: ARID1A, a core constituent of SWI/SNF complex, is mutated in about 10% of colorectal cancer (CRC). This study demonstrates a synergistic effect of arachidonic acid metabolism inhibitors with immune checkpoint inhibitors (ICIs) by regulating functionality of CD8+ T cells and vasculogenic mimicry (VM) formation in ARID1A-deficient CRC. Mechanistically, ATAC-seq and ChIP-qPCR demonstrated that the lack of ARID1A results in reduced levels of the key enzymes PTGS1 and PTGS2, which control the arachidonic acid pathway. This reduction generated a reliance on the remaining functionality of arachidonic acid pathway in ARID1A-deficient cells.

overall_design: This study conducted RNA-seq analysis on ARID1A wild-type and mutant cell lines, and further enriched differentially expressed genes

first: Chao

last: Liu

first: Shuijie

last: Li

first: Luying

last: Cui


title: Evolutionarily guided transcription factor design programs novel T cell states [bulkRNA-seq]

city: Stanford

first: Andy

last: Chen

address: 240 Pasteur Dr.

institute: Stanford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Protein-coding genes in the human genome evolved via modular rearrangement of domains from ancestral genes. Here, we develop a scalable, evolutionarily guided method to assemble novel protein-coding genes from constituent domains within a protein family, termed DESynR (Domain Engineered via Synthesis and Recombination) factors. Using primary human chimeric antigen receptor-T cells as a model system, we find that the expression of DESynR Activator Protein-1 (AP-1) transcription factors (TFs) significantly outperforms the expression of natural AP-1 TFs in multiple functional assays in vitro and in vivo. Top DESynR AP-1 TFs exhibit non-intuitive architectures of constituent domains, including from TFs that are not canonically expressed in T cells. DESynR AP-1 TFs induce broad transcriptional and epigenetic reprogramming of T cells and in some cases, lead to the development of non-natural T cell states, engaging gene modules from disparate human cell types. Taken together, we demonstrate that novel configurations of existing protein domains may uncover non-evolved genes that program cell states with therapeutically-relevant functions.

overall_design: Live-sorted and human CD19-28z CAR T cells overexpressing various natural and engineered AP-1 TFs were analyzed by ATAC-seq following repetitive stimulation with Nalm6 targets in vitro.

first: Oliver

last: Takacsi-Nagy

first: Austin

last: Hartman

middle: Y


title: BCR, not TCR, repertoire diversity is associated with favorable COVID-19 [TCR-Seq]

first: Yoko

last: Tabe

first: Faith

last: Paran

first: Rieko

last: Oyama

first: Abdullah

last: Khasawneh

first: Tomohiko

last: Ai

first: Hendra

last: Ismanto

first: Aalaa

last: Sherif

first: Dianita

last: Saputri

first: Chikako

last: Ono

first: Mizue

last: Saita

first: Satomi

last: Takei

first: Yuki

last: Horiuchi

first: Ken

last: Yagi

first: Yoshiharu

last: Matsuura


title: Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and glioma progression

city: 上海

first: 润华

last: 杜

address: 上海市浦东新区

institute: 上海药物所

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

overall_design: Refer to individual Series


title: Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay

city: Mainz

first: Marie-Luise

last: Winz

address: Staudingerweg 5

country: Germany

institute: Johannes Gutenberg-University Mainz

summary: New1 is a homolog of fungal translation elongation factor 3 (eEF3) inSaccharomyces cerevisiae. Its absence has previously been described to lead to cold sensitivity, ribosome biogenesis defects, and ribosomal queues upstream of Stop codons on selected mRNAs. Here, we find that, especially in cold conditions, lack of New1 induces no-go decay (NGD) on specificmRNAs, leading, as a consequence, to decreased mRNA and protein levels of such genes.The effect correlates with the presence of specific Lysine and Arginine codons just upstream of the Stop codon. In total, more than 10% of yeast coding sequences end with the affected codons. We have confirmed NGD and subsequent downregulation at the protein level for the metabolic enzymes Pgk1, Gpm1, and Adh1, translation elongation factors EF-1 alpha and EF-1 beta (gamma-subunit), ribosomal protein Rps5, as well as ribosome biogenesis factor Nop1 and adenosine kinase Ado1.

overall_design: We performed UV crosslinking and analysis of cDNA (CRAC) for the collision sensor and E3 ubiquitin ligase Hel2 and for New1, in presence or absence of the respective other player. To this end,in yeast Saccharomyces cerevisiae, BY4741, we genomically tagged Hel2 or New1 (only version in the genome, single copy) with a His-TEV-ProteinA tag in either a wildtype or new1-deleted (for Hel2) or hel2-deleted (for New1) strain background. Cells were cultured at 30°C or 20°C, as mentioned, and UV-crosslinked.  The tagged protein was purified along with crosslinked RNA and sequencing libraries were prepared in a total of 4 replicates (2 at 30°C, 2 at 20°C). For each replicate, a control experiment was conducted in which no protein was tagged (BY), in the wildtype background, to assess background signals.

first: Max

last: Müller

first: Lena

last: Tittel

first: Elisabeth

last: Petfalski

first: Kaushik

middle: V

last: Iyer

first: Tamer

last: Butto

first: Stefan

last: Pastore


title: Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and glioma progression [RNA-Seq]

summary: Histone lysine lactylation is a physiologically relevant epigenetic pathway that can be stimulated by the Warburg effect and L-lactate. Nevertheless, the mechanism by which cells use L-lactate to generate lactyl-CoA, the cofactor for the modification, and how this process is regulated remain unknown. Here we report identification of GTPSCS as a robust lactyl-CoA synthetase using biochemistry and cell biology approaches. The mechanism of this catalytic activity was elucidated using the crystallographic structure of GTPSCS in complex with L-lactate, followed by mutagenesis experiments. GTPSCS translocates into the nucleus and interacts with p300 to form a functional lactyltransferase to elevate histone lactylation, but not histone succinylation. This process is dependent on not only a nuclear localization signal in the GTPSCS G1 subunit, but also acetylation at G2 subunit residue K73 which mediates the interaction with p300. GTPSCS-p300 collaboration synergistically regulates histone H3K18la, subsequently enhancing the expression of GDF15. This process promotes the proliferation of glioma cells and facilitates tumor formation in mice. In addition, GTPSCS is upregulated in glioma and correlates with glioma malignancy, while histone H3K18la, and GDF15 levels are positively associated with glioma malignancy and poor prognosis in GBM patients. The GTPSCS-lactyltransferase-histone Kla axis thus represents an epigenetic pathway linking lactate metabolism with an oncogenic gene expression pattern in glioma.

overall_design: We carried out RNA-Seq analyses in either patient-derived SUCLG1-depleted rSUCLG1 WT UTSW63 cells or its rSUCLG1 K192R mutant counterpart.

first: Ruilong

last: Liu

first: He

last: Huang

first: Yingming

last: Zhao


title: Targeting the vulnerability of arachidonic acid metabolism to enhance immunotherapy efficacy in ARID1A-deficient colorectal cancer [ATAC-seq]

first: Yanqiao

last: Zhang

overall_design: This study conducted ATAC-seq analysis on ARID1A wild-type and mutant cell lines, and further enriched differentially expressed genes

first: Chao

first: Shuijie

last: Li

first: Luying

last: Cui


title: Vascular EC-derived factors promote DPC functions.

city: Kobe

first: Ken-ichi

last: Mizutani

state: Hyogo

address: 1-1-3 Minatojima, Chuo-ku

institute: Kobe Gakuin University

summary: To explore the underlying molecular mechanism of crosstalk between endothelial cells (ECs) and dermal papilla cells (DPCs), we used RNA sequencing to investigate the transcriptional changes in the human follicle dermal papilla cells (HFDPC) culture induced by conditioned medium (CM) treatment from human umbilical vein endothelial cell (HUVEC) (EC-CM).

overall_design: To prepare EC-CM, passage 4 (P4) HUVECs were cultured to 50%–60% confluency in a 100-mm cell culture dish in 10 mL of EGM-2 medium. Then, the medium was replaced with 10 mL of fresh EGM-2 medium for 24 h, and the EC-CM was harvested. After centrifugation at 3,000 rpm for 10 min to remove the cell debris, the EC-CM was filtered through a 0.22 μm filter (Millipore) and directly used for HFDPC culture (P4). The EGM-2 medium (10 mL) incubated for 24 h in a culture dish without cells was used as the control. After the culture of HFDPC in the EC-CM medium or control medium for 24 h, we used the Direct-Zol RNA miniprep kit (Zymo Research) and the Agilent 2200 TapeStation to extract total RNA and determine its quality, respectively.


title: Cellular Communication Network Factor 3 contributes to the pathological process of rheumatoid arthritis via osteoclastgenesis in the joint.

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

institute: Hokkaido University

summary: Cellular Communication Network Factor 3 (CCN3) is a secreted protein. It belongs to the CCN family of regulatory proteins, which play essential roles in various cellular processes. In this study, we investigated the functional characteristics of CCN3 in rheumatoid arthritis. We found CCN3 is involved in cellular senescence and osteoclastgenesis of macrophage in vitro. To understand this mechanism, CCN3 is were added to Macrophage and their responses were examined by bulk-RNA analysis.

overall_design: RNA-seq for human macrophage stimulated by CCN3

first: Taiki

last: Tokuhiro

first: Mohamad

middle: A

first: Norimasa

last: Iwasaki


title: Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and glioma progression [ChIP-seq]

first: 润华

last: 杜

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for L-Lactyl-Histone H3 (Lys18) in shSUCLG1 rSUCLG1 WT and K192R UTSW63 cells.


title: The role of cadherin-11 in Unx/AngII induced kidney injury

city: Nashville

first: Lance

last: Riley

state: TN

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University


title: Cellular Communication Network Factor 3 contributes to the pathological process of rheumatoid arthritis via promoting cell senescence in synovial cells

summary: Cellular Communication Network Factor 3 (CCN3) is a secreted protein. It belongs to the CCN family of regulatory proteins, which play essential roles in various cellular processes. In this study, we investigated the functional characteristics of CCN3 in rheumatoid arthritis. We found CCN3 is involved in cellular senescence and inflammation of fibroblast like synoviocyte (FLS) in vitro. To understand this mechanism, CCN3 is were added to FLS and their responses were examined by bulk-RNA analysis.

overall_design: RNA-seq for fibroblast like synoviocyte (FLS) stimulated by CCN3


title: The role of cadherin-11 in Unx/AngII induced kidney injury [Huffstater_Unx]

summary: The objective of this study was to understand the impact of losing cadherin-11 (CDH11) on kidney injury. CDH11 has previously been demonstrated to be associated with a number of fibrotic diseases, but its role in kidney injury remains unknown. In vivo models of kidney injury demonstrated improved renal function and reduced tubulointerstitial fibrosis with CDH11 inhibition. However, the mechanism by which CDH11 inhibition mitigates kidney injury is unknown. RNAseq analysis showed altered expression of over 50 genes in two models of kidney injury when CDH11-/- mice were compared with CDH11+/+ mice. These results together indicate that CDH11 deletion alters many genes and pathways that could contribute to kidney injury, including alpha-1 antitrypsin, which is increased in CDH11-/- mice and has been shown to be beneficial in kidney injury.

overall_design: 3 CDH11+/+ and 4 CDH11-/- mice were injured using uninephrectomy with angiotensin II (Unx/AngII) infusion. For the Unx/AngII model, one kidney was removed from each mouse, then had osmotic pumps implanted to secrete AngII at a rate of 800 ng/kg/min, and mice were sacrificed 4 weeks after the surgery.

first: Tessa

last: Huffstater

first: W

middle: D

last: Merryman


title: The role of cadherin-11 in Unx/AngII induced kidney injury [Huffstater_AA]

overall_design: 4 CDH11+/+ and 4 CDH11-/- mice were injured using the aristolochic acid nephropathy (AAN) model. Mice were injected with 3 mg/kg aristolochic acid every day for 5 days and then sacrificed 2 weeks after the final injection.


title: The effects of traditional Chinese medicine Yinqi Sanhuang Jiedu Decoction on gene expression in HepG2.2.15 cells

status: Public on Nov 25 2024

city: Beijing

state: Beijing

address: No 5 Bei Xiange Road

department: Clinical Laboratory

institute: Guang’anmen Hospital, China Academy of Chinese Medical Sciences

summary: Yinqi Sanhuang Jiedu Decoction (YQSHJD) is a clinically-proven formula for treating chronic hepatitis B and related fibrosis, demonstrating significant anti-HBV effects in clinical trials. However, its direct inhibitory effect on HBV and the underlying mechanisms remain unclear. The objective of this study is to elucidate the molecular mechanism through which YQSHJD inhibits HBV. HBV-replicating HepG2.2.15 cells were utilized as an in vitro HBV model to study the impact of YQSHJD on HBV replication. Network pharmacology and transcriptome analysis were used to research the targets for YQSHJD in inhibiting HBV replication. The results showed YQSHJD could inhibit HBV replication through regulation of the host antiviral targets.

overall_design: RNAs was extracted from HepG2.2.15 cells that were incubated with physiological saline and YQSHJD freeze-dried powder dilution for 3 days. The mRNA differential expression profile between the two groups was determined through RNA sequencing in Beijing, Novogene Co., Ltd, China.

first: Nannan

first: Cheng

last: An

first: Wenliang

last: Lv


title: BCR, not TCR, repertoire diversity is associated with favorable COVID-19 [BCR-Seq]

first: Yoko

last: Tabe

first: Faith

last: Paran

first: Rieko

last: Oyama

first: Abdullah

last: Khasawneh

first: Tomohiko

last: Ai

first: Hendra

last: Ismanto

first: Aalaa

last: Sherif

first: Dianita

last: Saputri

first: Chikako

last: Ono

first: Mizue

last: Saita

first: Satomi

last: Takei

first: Yuki

last: Horiuchi

first: Ken

last: Yagi

first: Yoshiharu

last: Matsuura

first: Yasushi

last: Okazaki

first: Kazuhisa

last: Takahashi

first: Daron

last: Standley

first: Toshio

last: Naito


title: Transcriptomic analysis of Paenarthrobacter nicotinovorans ATCC 49919 nicotine metabolism [2]

city: Iași

first: Marius

last: Mihasan

state: Iași

address: Bulevardul Carol I, nr. 20 A

department: Biology

country: Romania

institute: Alexandru Ioan Cuza University of Iasi

summary: Paenarthrobacter nicotinovorans pAO1 is a nicotine degrading microorganism that shows promising applications in converting nicotine-containing waste into useful green chemicals. Its biotechnological applications are nevertheless hampered by the lack of knowledge and tools to perform genetic and metabolic engineering. The objective of the work is to provide the first transcriptome of the strain and is a second step in our envisioned complete omics characterization of nicotine metabolism in P. nicotinovorans ATCC 49919. Acknowledgements. This work was supported by a grant of the Romanian Ministry of Education and Research, CNCS - UEFISCDI, project number PN-III-P4-ID-PCE-2020-0656, within PNCDI III.

relation:
Reanalysis of: GSM7688421
Reanalysis of: GSM7688422
Reanalysis of: GSM7688423
Reanalysis of: GSM7688424
Reanalysis of: GSM7688425
Reanalysis of: GSM7688426
Reanalysis of: GSM7688427
Reanalysis of: GSM7688428
Reanalysis of: GSM7688429
Reanalysis of: GSM7688430
Reanalysis of: GSM7688431
Reanalysis of: GSM7688432
Reanalysis of: GSM7688433
Reanalysis of: GSM7688434
Reanalysis of: GSM7688435
Reanalysis of: GSM7688436
Reanalysis of: GSM7688437
Reanalysis of: GSM7688438
Reanalysis of: GSM7688439
Reanalysis of: GSM7688440
Reanalysis of: GSM7688441

overall_design:
The strain was grown on citrate medium with and without nicotine. Cells were harvested at three different timepoints correlated with cellular growth and nicotine catabolism. The first timepoint (T1) was set at ~5 hours after inoculation (and nicotine-supplementation), representing the start of the exponential phase (and of nicotine catabolism). The second timepoint (T2), at ~10 HAI, captures the transition from the exponential to stationary phase: the on-going degradation of nicotine and its depletion from the growth medium. The third timepoint (T3), at 24 HAI, represents the stationary phase, when nicotine has been depleted from the growth medium. Total RNA was isolated, poly-adenylated, and directly sequenced using the Oxford Nanopore Technology (ONT) MinION Mk1B device coupled to a Flongle adapter. Basecalling was performed using Guppy_6.3.2 and high accuracy. Basecalled data was analysed using the nf-core/nanoseq pipeline for quality assessment, mapping to the reference genome, transcriptome assembly, transcript quantification and differential gene expression.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Amada

last: El-Sabeh


title: NPR1 promotes blue light–induced plant photomorphogenesis by ubiquitinating and degrading PIF4

city: Peking

first: Zhou

last: yangyang

state: Peking

address: West Campus of China Agricultural University, Haidian District, Beijing

institute: China Agriculture University

summary: Light is a major determinant of plant growth and survival. NONEXPRESSER OF PATHOGENESIS-RELATED GENES 1 (NPR1) acts as a receptor for salicylic acid (SA) and serves as the key regulator of SA-mediated immune responses. However, the mechanisms by which plants integrate light and SA signals in response to environmental changes, as well as the role of NPR1 in regulating plant photomorphogenesis, remain poorly understood. This study shows that SA promotes plant photomorphogenesis by regulating PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Specifically, NPR1 promotes photomorphogenesis under blue light by facilitating the degradation of PIF4 through light-induced polyubiquitination. NPR1 acts as a substrate adaptor for the CULLIN3-based E3 ligase, which ubiquitinates PIF4 at Lys129, Lys252, and Lys428, and leading to PIF4 degradation via the 26S proteasome pathway. Genetically, PIF4 is epistatic to NPR1 in the regulation of  blue light-–induced photomorphogenesis, suggesting it acts downstream of NPR1. Furthermore, cryptochromes mediate the polyubiquitination of PIF4 by NPR1 in response to blue light by promoting the interaction and ubiquitination between NPR1 and PIF4. Transcriptome analysis revealed that, under blue light, NPR1 and PIF4 coordinately regulate numerous downstream genes related to light and auxin signaling pathways. Overall, these findings unveil a role for NPR1 in photomorphogenesis, highlighting a mechanism for post-translational regulation of PIF4 in response to blue light. This mechanism plays a pivotal role in the fine-tuning of plant development, enabling plants to adapt to complex environmental changes.

overall_design: Total RNA was extracted from 4-day-old seedlings grown in continuous blue or red light using using the TaKaRa MiniBEST Plant RNA Extraction Kit

first: Yangyang

last: Zhou

first: Pengtao

last: Liu


title: Evaluating the effect of secreted ribonucleases from Ustilago maydis on the extracellular RNA profile/repertoire of Zea mays during corn smut disease [miRNA-seq]

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

type: Non-coding RNA profiling by high throughput sequencing

summary: The apoplast of host plants serves as a dynamic interface during invasion and subsequent establishment of disease by a microbial pathogen. In the recent past, host plant apoplasts have been demonstrated to harbour small membrane bound vesicles called extracellular vesicles (EVs) that contain both RNA and protein. EVs are considered to play a significant role in cell-cell communication between the host and the pathogen during infection. In this study the RNAs associated with EVs from the host plant Zea mays under infected and uninfected conditions were sequenced. Besides EV bound RNA, plant apoplasts also contain free RNA that are equally important for host pathogen interaction. We have also detected a pool of extracellular RNA (exRNA) in Z. mays located on leaf surfaces. In this experiment, we sequenced both the free apoplastic RNA and leaf surface RNA from Z. mays during U. maydis infection and under control uninfected conditions. The U. maydis genome codes for a number of secreted ribonucleases that are essential for the pathogenesis of the fungus. For three of these ribonucleases, we have also investigated their role in the regulation of cell:cell communication between Z. mays and U. maydis. Accordingly, this study includes comparative transcript profiling of all the three different forms of exRNA between Z. mays plants infected with either wild type U. maydis or U. maydis strains lacking one or more secreted ribonucleases.

overall_design: Z. mays plants of the variety B73 were infected at 7 days seedling stage with U. maydis strains SG200 WT, SG200Δnuc1Δnuc2 or SG200Δnuc3. The infected leaf samples were harvested at 5 days post infection (5 dpi). For isolation of leaf surface RNA, the leaf surfaces were sprayed   with vesicle isolation buffer (VIB) followed by RNA precipitation from the rinse buffer collected through centrifugation of the leaves. For isolating EV associated and free apoplastic RNAs, the harvested leaf samples were infiltrated with VIB followed by centrifugation to collect the apoplastic wash fluid (AWF). EVs were collected from the AWF by centrifugation at 40,000g for one hour and EV associated RNAs were isolated from the pellet. The supernatant was used for the isolation of the free apoplastic RNA. For uninfected samples, the seedlings were left uninfected and leaves were harvested at 12 days post sowing for RNA isolation. Thus, three different sets of RNAs were isolated and sequenced from four different conditions including one control uninfected and three infection conditions. Three biological replicates of the samples were sequenced.

first: Anupama

last: Ghosh

first: Roger

last: Innes

first: Madison

last: McGregor

first: Lucia

last: Borniego

first: Meenu

last: Singla-Rastogi

first: Megha

last: Hastantram Sampangiramaiah

last: Baldrich


title: Small molecule oxybutynin rescues proliferative capacity of complex III-defective MPCs

city: Ithaca

first: Joeva

last: Barrow

state: New York

address: 244 Garden Ave

institute: Cornell University

summary: Mitochondrial disease encompasses a group of genetically inherited disorders hallmarked by an inability of the respiratory chain to produce sufficient ATP. These disorders present with multisystemic pathologies that predominantly impact highly energetic tissues such as skeletal muscle. There is no cure or effective treatment for mitochondrial disease. We have discovered a small molecule known as oxybutynin that can bypass Complex III mitochondrial dysfunction in primary murine and human skeletal muscle progenitor cells (MPCs). Oxybutynin administration improves MPC proliferative capacity, enhances cellular glycolytic function, and improves myotube formation. Mechanistically, results from our isothermal shift assay indicates that oxybutynin interacts with a suite of proteins involved in mRNA processing which then trigger the upregulation biological pathways to circumvent CIII mitochondrial dysfunction. Taken together, we provide evidence for the small molecule oxybutynin as a potential therapeutic candidate for the future treatment of CIII mitochondrial dysfunction.

overall_design:
To uncover small molecules that can improve proliferation of complex III defective skeletal muscle myoblasts a small molecule screen of 50 compounds was performed in sol8 cells (treated with antimycin to inhibit complex III).
Since oxybutynin showed significant improvements in the proliferation of these cells we then validated its efficacy in murine primary myoblasts from uqcrfs1 floxed mice. Experimental groups included floxed (uqcrfs1+/+) and KO (uqcrfs1-/-)
Comparative gene expression profiling was conducted on Uqcrfs1 -/- primary myoblasts that were treated with 7.5uM of oxybutynin for 5 days

first: Kaydine

last: Edwards

first: Muying

last: Li


title: Comparative Analysis of MiRNA Expression Profiles of Yak Milk-derived Exosomes at Different Altitudes

city: lanzhou

first: Wenwen

last: Ren

address: xiaoxihu

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

summary: Yaks are a rare and unique animal species inhabiting the Qinghai-Tibet Plateau, known for their remarkable resilience. Milk-derived exosomes, tiny vesicles containing various biological molecules, play crucial roles in numerous pathological and physiological processes, including cell growth, development, and immune regulation. This study conducted small RNA sequencing to characterize the miRNA expression profiles of yak milk-derived exosomes from high and low altitudes, aiming to identify differentially expressed miRNAs. Our findings revealed that these differentially expressed miRNAs are involved in mammary gland inflammation, virus infection regulation, and heat stress response. Through GO and KEGG enrichment analyses, we discovered that the target genes of these differentially expressed miRNAs are enriched in signaling pathways related to Th17 cell differentiation and the Ras-MAPK signaling pathway. In conclusion, this research sheds light on the differential expression of miRNAs in yak milk-derived exosomes under varying environmental conditions. This new knowledge provides a theoretical foundation for further exploring yak resilience and the potential role of milk-derived exosomes in disease and immune modulation.

overall_design: small RNA sequence of yak milk-derived exosomes at dDifferent altitudes

first: Chunnian

last: Liang

first: Xianyong

last: Lan


title: Cross-species conserved miRNA as biomarker of radiation injury and to predict fatality risk

status: Public on Nov 27 2024

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: Multiple accidents in nuclear power plants and growing concerns in misuse of radiation exposure in warfare have called for rapid determination of radiation exposure and the chances to survive. Latest findings about circulating microRNA (miRNAs) using several animal models revealed considerable promises, although translating this knowledge to clinics remains a major challenge. To address this issue, we randomly divided 36 non-human primates (NHPs) into six equal groups and each group was exposed to six radiation doses from 6 Gy to 8.5 Gy with 0.5 Gy incremental order. Serum samples were collected pre-total body irradiation (TBI) and three timepoints afterwards namely, day 1, 2 and 6 post-TBI. Global microRNA (miRNA) reads were generated from deep sequencing platform and to increase the translational potential, we diligently aligned the miRNA sequences and functional responses of NHPs to human following an in silico routine. Those miRNAs, which were sequentially and functionally conserved between human and NHPs were curated to meet two primary objectives. First to find the molecular dynamics correlated to radiation dosimetry and second to find putative markers to predict the risk to radiation-induced fatality (RRiF). Multi-variate differential analysis identified dosimetry-miRNA markers that consistently regulated with increasing dose but independent of the time since irradiation (TSI). Likewise, a set of potential TSI-markers were identified that consistently shifted their regulations with increasing TSI, but independent of dosimetry. Functional analysis found a considerable gender bias in low range of dosimetry, but at high dose, when the RRiF increased, the bionetworks across the sexes operated in sync. Bionetworks linked to cell quantity and cell invasion significantly altered between the survived and decedent cohort. Proprietary algorithm identified candidate models with a few miRNAs that can predict RRiF with >80% AUC. An assay could be conceptualized from this putative RRiF panel supplemented with the dose-/TSI-markers to predict RRiF with high confidence.

overall_design: Non Human Primates were exposed to different doses of radiation, and serum samples were collected at different timepoints for each organism.

first: Nabarun

last: Chakraborty

first: George

last: Dimitrov

first: Swapna

last: Kannan

first: Alexander

last: Lawrence

first: Oluseyi

middle: O

last: Fatanmi

first: Stephen

last: Wise

first: Alana

last: Carpenter

first: Rasha

last: Hammamieh

first: Vijay

middle: K

last: Singh


title: Single-Cell Transcriptomic Analysis Reveals Differential Cell Subpopulations and Distinct Phenotype Transition in Normal and Acute Dissected Ascending Aorta

city: Shanghai

first: Jing

last: Zhang

address: No.241, west huaihai road, Xuhui district

department: Department of Cardiovascular Surgery

institute: Shanghai Chest Hospital, Shanghai Jiao Tong University

summary:
Background: Acute thoracic aortic dissection (ATAD) is a fatal condition characterized by tear of intima and formation of false lumen whereby leading to the rupture of aorta. To better understand the potential mechanism of ATAD, we analyzed characterization of different cell types between ATAD and control group and predicted interactions among different cell types which might promote the progression of ATAD.
Methods: Single-cell RNA sequencing (scRNA-seq) was performed including 5 patients with ATAD and 4 healthy controls. Cells were digested from ascending aortic tissues and subpopulations of most cell types were identified on the basis of scRNA-seq data. The gene expression profiles of each cell type and related changes between ATAD and control group were analyzed via bioinformatic analysis. We also predicted potential interaction among different cell types and verified the results by immunohistochemistry (IHC) and immunofluorescence (IF).
Results: We got 8 cell types from human ascending aorta and 50 subpopulations were identified after re-clustering including vascular smooth muscle cells (VSMCs), endothelial cells, fibroblasts, neutrophils, monocytes and macrophages. Higher proportion of synthetic VSMCs, dysfunctional neutrophils and monocytes were seen in ATAD group compared with control group. Next, we predicted cell differentiation trajectory of VSMCs, fibroblasts and neutrophils via CytoTRACE, then identified subpopulations with higher differentiation potential. Moreover, the hub genes of VSMCs, fibroblasts and neutrophils were examined by weighted gene co-expression network analysis. Further analysis revealed that six transmembrane epithelial antigen of prostate 4 metalloreductase (STEAP4) might be a new marker for isolation of synthetic VSMCs by verification with IHC and IF. We also found synthetic VSMCs-derived C-X-C motif chemokine ligand 12 (CXCL12) might interact with neutrophils and fibroblasts via combination with C-X-C motif chemokine receptor 4 (CXCR4) and atypical chemokine receptor 3 (ACKR3), respectively, which might recruit neutrophils and induce transdifferentitation of FBs into synthetic VSMCs.
Conclusion: In this study, we demonstrated integrative composition of different cell types in normal and dissected human ascending aorta and identified a new marker favorable to isolation of synthetic VSMCs. Furthermore, we also proposed a potential mechanism that synthetic VSMCs could interact with neutrophils and fibroblasts via CXCL12-CXCR4/ACKR3 axis whereby deteriorating the progression of ATAD. In total, these findings in our study might provide new insights to better understand the development and progression of ATAD.

overall_design: Examination of transcriptomic characteristics of normal and acute dissected ascending aortas

first: Yubin

last: He

first: Haizhen

last: Jin

first: Guanxin

first: Chong

last: Wang

first: Busheng

first: Wenrui

last: Ma

first: Jianfeng

first: Jie

last: Xing

first: Xiaobin

first: Yangyang

first: Huangdong

last: Dai

first: Naishi

last: Zhao

first: Dan

last: Zhu


title: New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

country: United Kingdom

institute: UCL

summary: The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression.

overall_design: To assess the effect of heavy metal exposure on Bombus impatiens, versus control individuals

first: Rick

last: Masonbrink

first: Amy

last: Toth

first: Katie

last: Geist


title: The effect of ethanolamine phosphate phosphorylase knockout on hepatic gene expression

city: Edmonton

first: René

last: Jacobs

state: Alberta

address: Room 4002E, Li Ka Shing Building, 11300 87 Ave NW

department: Department of Agricultural, Food and Nutritional Science

country: Canada

institute: University of Alberta

summary: Ethanolamine phosphate phospholyase (ETNPPL) is an enzyme that irreversibly degrades phospho-ethanolamine (p-ETN), an intermediate in the Kennedy pathway of phosphatidylethanolamine (PE) biosynthesis. PE is the second most abundant phospholipid in mammalian membranes. Disturbance of hepatic phospholipid homeostasis has been linked to the development of metabolic dysfunction-associated steatotic liver disease (MASLD). We generated whole-body Etnppl knockout mice to investigate the impact of genetic deletion of Etnppl on hepatic lipid metabolism. Female Etnppl+/+ and Etnppl-/- mice were fed either a chow diet for 20 weeks and livers were harvested for lipds, proteins, and gene expression studies.

overall_design: Full body Etnppl knockout (KO) and wild type (WT) female mice were fed a chow diet for 20 week. Livers were harvested, total RNA extracted, and poly-A selected mRNA was processed for paired-end sequencing. Differentially expressed genes were identified and affected metabolic pathways were identified by ontological analysis using DAVID.

first: Kholoud

last: Elmihi

first: Kelly-Ann

last: Leonard

first: Randy

last: Nelson

first: Aducio

last: Thiesen

first: Robin

last: Clugston

middle: L


title: ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements

city: Pasadena

first: Isabel

last: Goronzy

address: 1200 E California Blvd

department: Biology and Biological Engineering

institute: California Institute of Technology

summary: Gene expression is controlled by dynamic localization of thousands of regulatory proteins to precise genomic regions. Understanding this cell-type specific process has been a longstanding goal yet remains challenging because DNA-protein mapping methods generally study one protein at a time. To address this, we developed ChIP-DIP (ChIP Done In Parallel) to generate genome-wide maps of hundreds of diverse regulatory proteins in a single experiment. ChIP-DIP produces highly accurate maps within large pools (>160 proteins), for all classes of DNA-associated proteins, including histone modifications, chromatin regulators, and transcription factors, and across multiple conditions simultaneously. First, we used ChIP-DIP to measure temporal chromatin dynamics in primary dendritic cells following stimulation. Next, we explored quantitative histone combinations that define distinct classes of regulatory elements and characterized their functional activity in human and mouse cell lines. Overall, ChIP-DIP generates context-specific, protein localization maps at consortium scale within any molecular biology lab and experimental system.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-DIP was used to simultaneously map DNA-associated proteins in human K562 cells,  mouse embryonic stem cells and primary mouse dendritic cells.

first: Andrew

last: Perez

first: Mitchell

last: Guttman


title: Manipulation of NR3C1 on the expression of inflammatory transcription factors and their alternative splicing patterns

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: NR3C1-encoding glucocorticoid receptors have dual roles as RNA-binding protein and transcription factor. Recent studies revealed that NR3C1 might play an important role in the pathogenesis of PTSD (Post-traumatic stress disorder). However, its molecular mechanism remained unclear. In the present study, a neuronal cell model was constructed by transfecting a NR3C1-overexpressing plasmid pIRES-hrGFP-1a-NR3C1 or empty vector into HT22 cells. The changes in global transcription levels and alternative splicing events in HT22 cells after NR3C1 overexpression were analyzed by RNA sequencing. Compared with the empty vector control, the expression of inflammatory factors were differentially regulated by NR3C1, including genes involved in chemokine signal pathway, PI3K-Akt signal pathway, cytokine receptor interaction, neural ligand-receptor interaction and so on. In addition, NR3C1 regulated the alternative splicing of many genes involved in immune response, axon formation, stress response and inflammation. This study was the first to perform a transcriptome analysis of differential gene expression and alternative splicing in a NR3C1-overexpressing HT22 cell model. Our results suggested that NR3C1 could manipulate the expression of inflammatory transcription factors and their alternative splicing patterns, subsequently affecting the expression of downstream targets, leading to the onset of PTSD. This study will provide new insights in the NR3C1-mediated gene regulation in relation to PTSD.

overall_design: A neuronal cell model of NR3C1-overexpression in HT22 cells

first: Linfeng

last: Li

first: Wenlong

last: Xing

first: Liang

last: Jiang

first: Dong

last: Chen


title: Toxicity of glyphosate on planarian Dugesia japonica: Potential molecular mechanisms based on transcriptome analysis

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

summary: Glyphosate (GLY) is one of the most applied agrochemicals in the world, and its exposure has aroused the public health concern. Freshwater planarian is an ideal test organism for examining toxicity of pollutants and has become an emerging animal model for toxicology studies. However, potential toxicity mechanism of GLY in planarian has not been comprehensively studied. To explore the toxicity effects and molecular mechanism involved in GLY exposure of planarian, we analyzed the acute toxicity, histological change, DNA damage and transcriptional responses of freshwater planarian Dugesia japonica subjected to GLY. Results indicated that morphological malformation, histopathological change and genome DNA damage were observed after GLY exposure for different time. Transcriptomic analysis showed that numerous differentially expressed genes (DEGs) were obtained at 1, 3 and 5 d after exposure. GO and KEGG enrichment analysis of these DEGs was carried out and a dynamic and global view was obtained in planarian after GLY exposure at the transcriptomic level. Furthermore, qRT-PCR was performed on nine DEGs associated with detoxification, apoptosis, stress response, DNA repair, etc. The expression patterns were well consistent with the RNA-seq results at different timepoints, which confirmed the accuracy and reliability of the transcriptome data. Collectively, our results established that GLY could pose adverse effects on the morphology, histoarchitecture as well as genome DNA of D. japonica, and the planarians are capable of responding to the disadvantageous GLY stress by dysregulating the related genes and their participated in pathways concerning immune response, detoxification, energy metabolism, DNA damage repair, etc. To the best of our knowledge, this is the first report of transcriptomic analysis of freshwater planarian exposed to environmental pollutant, and it provided detailed sequencing data deriving from transcriptome profiling to deepen our understanding of the molecular toxicity mechanism of GLY on planarians.

overall_design: There are 12 samples in total. One control (CK) and three treatments (T1, T3 and T5), and three replicates for the control and each treatment.

first: He-Cai

last: Zhang

first: Chang-Ying

last: Shi

first: Wen-Jing

last: Zhao

first: Guang-Wen


title: Aberrant Neuronal Connectivity and Network Activity of Neurons Derived from Patients with Idiopathic Schizophrenia

city: Munich

first: Moritz

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

summary: Schizophrenia (SCZ) is a psychiatric disorder with a strong genetic determinant. A major hypothesis to explain disease aetiology comprises synaptic dysfunction associated with excitatory-inhibitory imbalance of synaptic transmission, ultimately contributing to impaired network oscillation and cognitive deficits associated with the disease. Here, we studied the morphological and functional properties of a highly defined co-culture of GABAergic and glutamatergic neurons derived from induced pluripotent stem cells (iPSC) from patients with idiopathic SCZ. Our results indicate upregulation of synaptic genes and increased excitatory synapse formation on GABAergic neurons in co-cultures. In parallel, we observed decreased lengths of axon initial segments, concordant with data from postmortem brains from patients with SCZ. Patch-clamp analyses revealed differential processing of excitatory input with markedly increased spontaneous excitatory postsynaptic currents (EPSC) recorded from GABAergic SCZ neurons and decreased spontaneous EPSC from glutamatergic SCZ neurons. Likewise, we observed decreased amplitudes of calcium signals selectively in GABAergic neurons while frequency was increased in both neuronal populations. Finally, MEA recordings from neuronal networks indicate increased synchronization of network activity. In conclusion, our results suggest selective deregulation of neuronal activity and synaptic transmission in SCZ samples, providing evidence for differential signal processing in GABAergic and glutamatergic neurons as a potential base for aberrant network synchronization.

overall_design: NGN2 & AD2 Neurons generated from Schizophrenia and Control lines

first: Johanna

last: Heider

first: Emilio

middle: P

last: Gonzalez

first: Sophia-Marie

last: Hartmann

first: Nirmal

last: Kannaiyan

first: Sabrina

last: Vogel

first: Richard

last: Wüst

first: Andreas

last: Fallgatter

first: Udo

last: Kraushaar

first: Hansjürgen

last: Volkmer


title: NAD+ depletion drives impaired endothelial cell proliferation and age-related vascular decline

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Aging is accompanied by a decline in neovascularisation potential and increased susceptibility to ischemic injury. Here, we confirm the age-related impaired neovascularization following ischemic leg injury and impaired angiogenesis. The age-related deficits in angiogenesis arose primarily from diminished EC proliferation capacity, but not migration or VEGF sensitivity. Aged EC harvested from the mouse hindlimb displayed a pro-angiogenic gene expression phenotype, along with considerable changes in metabolic genes. Metabolomics analysis and 13C glucose tracing revealed that late passage HUVECs display impaired ATP production and altered glycolysis and TCA cycle intermediates, with significant shifts occurring at nicotinamide adenine dinucleotide (NAD⁺)-dependent steps along with NAD+ depletion, suggestive of compromised NAD⁺ metabolism. Supplementation with nicotinamide mononucleotide (NMN), a precursor of NAD⁺, enhances enhanced late-passage EC proliferation and sprouting angiogenesis from aged mice aortas. Taken together, our study illustrates the centrality of NAD+-dependent metabolism in the maintenance of EC proliferation capacity with age.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for young and old mouse muscle endothelial cells

first: Kevin

last: Kiesworo

first: Thomas

last: Agius

first: Michael

middle: R

last: Macarthur

first: Martine

last: Lambelet

first: Arnaud

last: Lyon

first: Jing

first: Sebastian

last: Déglise

first: Katrien

last: De Bock

first: Sarah

last: Mitchell

first: Alejandro

last: Ocampo

first: Florent

last: Allagnat

first: Alban

last: Longchamp


title: Creation and Validation of the First Infinium DNA Methylation Array for the Human Imprintome [brain]

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

summary:
Differentially methylated imprint control regions (ICRs) regulate the monoallelic expression of imprinted genes. Their epigenetic dysregulation by environmental exposures throughout life results in the formation of common chronic diseases. Unfortunately, existing Infinium methylation arrays lack the ability to profile these regions adequately. Whole genome bisulfite sequencing (WGBS) is the unique method able to profile these regions, but it is very expensive and it requires not only a high coverage but it is also computationally intensive to assess those
To address this deficiency, we developed a custom methylation array containing 22,819 probes. Among them, 9,757 probes map to 1,088 out of the 1,488 candidate ICRs recently described. To assess the performance of the array, we created matched samples processed with the Human Imprintome array and WGBS, which is the current standard method for assessing the methylation of the Human Imprintome. We compared the methylation levels from the shared CpG sites and obtained a mean R2 = 0.569. We also created matched samples processed with the Human Imprintome array and the Infinium Methylation EPIC v2 array and obtained a mean R2 = 0.796. Furthermore, replication experiments demonstrated high reliability (ICC: 0.799-0.945).

overall_design: 16 brain samples analyzed with the Human Imprintome array. No replicates.

first: Natalia

last: Carreras-Gallo

first: Varun

last: Dwaraka

first: David

last: Skaar

first: Tavis

last: Mendez

first: Antonio

last: Planchart

first: Wanding

last: Zhou

first: Randy

last: Jirtle

first: Ryan

last: Smith

first: Cathrine

last: Hoyo


title: Creation and Validation of the First Infinium DNA Methylation Array for the Human Imprintome [blood_imprintome]

overall_design: 17 whole blood samples analyzed with the Human Imprintome array with 2 replicates each


title: Creation and Validation of the First Infinium DNA Methylation Array for the Human Imprintome [blood_epic]

overall_design: 3 whole blood samples analyzed with the EPICv2 custom array. No replicates.


title: Salinomycin treatment of Alisertib induced senescent A549 cells

city: Amsterdam

first: gabriele

last: casagrande raffi

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands cancer institute

summary: Bulk RNA-seq data of alisertib induced senescent cells treated with Salinomycin vs. Untreated

overall_design: Cells were seeded with a density on 1mln/plate (in 15cm dish) then treated with alisertib for one week to induce senescence refreshing the drug twice. Then cells were treated for 48 hrs with salinomycin 2.5 µM and harvested for RNA extraction


title: RUNX2 promotes pulmonary fibrosis through the conversion of alveolar fibroblasts into pathological fibroblasts

city: San Diego

first: Le

last: Xu

address: 8018 Regents Road Atp. 301

department: Pediatrics

institute: University of California, San Diego

summary: A hallmark of pulmonary fibrosis is aberrant activation of lung fibroblasts into pathological fibroblasts producing excessive extracellular matrix (ECM). Thus, identification of key regulator(s) driving the generation of pathological fibroblasts can inform effective countermeasures against disease progression. In this study, we show that Leptin Receptor (Lepr)+ fibroblasts arising during alveologenesis include Signal Peptide-CUB-EGF Domain-containing Protein 2 (Scube2)+ alveolar fibroblasts as a major constituent significantly contributing to collagen triple helix repeat containing 1 (Cthrc1)+ Periostin (Postn)+ pathological fibroblasts in two mouse models of pulmonary fibrosis. Genetic ablation of the Postn+ pathological fibroblasts attenuates fibrosis. Comprehensive analysis of single cell RNA sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) reveal Runt related transcription factor 2 (RUNX2) as a key regulator of fibrotic genes. Consistently, conditional deletion of Runx2 with Lepr-CreERT2 or Scube2-CreERT2 reduces the generation of pathological fibroblasts, ECM deposition, and pulmonary fibrosis. Therefore, Lepr+ derived fibroblasts which include Scube2+ alveolar fibroblasts are a key source of pathological fibroblasts, and targeting Runx2 provides a potential treatment option for pulmonary fibrosis.

overall_design: Single cell ATAC-seq from sorted adult lung mesenchymal cells (Epcam-CD31-CD45-) of saline control and Bleomycin (BLM) treated mice. Bleomycin sample are from wild type B6 male, single dose bleo (1.0U/kg). Control sample are from wild type B6 male. Lungs are harvested at Day 14 post administration.

first: Yohei

last: Korogi

first: Rongbo

last: Li

first: Xin

last: Sun


title: Transcriptomic profile of Arabidopsis thaliana treated with exogenous Riboflavin

city: Athens

first: Gerasimos

last: Daras

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

summary: Riboflavin, also known as vitamin B2, is crucial for cell function as it is the central component of FMN and FAD cofactors. These flavocoenzymes are essential for various cellular processes including the control of flavoproteins activity. Flavins are vital for growth and cellular metabolism of plants, supporting functions like photosynthesis, mitochondrial electron transport, and fatty acid oxidation. Further, previous studies have shown that exogenous application of riboflavin enhances plant defenses against abiotic and biotic stresses. In this study, to identify and implicate genes and signaling pathways involved in these processes, a holistic transcriptome analysis was conducted on Arabidopsis wild-type plants treated with Riboflavin and the mutant called “melin” which accumulates Riboflavin at exceptionally high levels.

overall_design: Total RNA was extracted using the Direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer’s instructions from six days-old Col-0 (wild-type) and fmn/fhy (mos) seedlings grown under standard conditions: 16 hours of light and 8 hours of darkness per day, with a light intensity of 100 μmol m–2 s–1. Additionally,  RNA was extracted from Col -0 (wild-type) (CR) seedlings treated with 0.6 mM Riboflavin for 8 hours during the dark cycle. The quantity and integrity of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA, USA) and agarose gel electrophoresis. RNA-seq libraries were generated using the polyA Strand-Specific Transcriptome Library method of BGI  for DNBSEQ platform. Sequencing was performed on DNBSEQ platform instrument at BGI (Beijing Genomics Institute) in three biological replicates for each sample. Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10). RNA-seq data were analyzed using SOAPnuke (version 1.5.2) with parameters “-l 15 -q 0.2 -n 0.05" and the HISAT2 pipeline (version 2.0.4) with parameters “--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8".

first: Stamatis

last: Rigas


title: ACSL4 and polyunsaturated lipids support metastatic extravasation and colonization

city: Hangzhou

first: yilong

last: Zou

state: Zhejiang

address: 18 Shilongshan Street, Xihu District

institute: Westlake University

summary: Metastasis is the leading cause of the cancer-related death. To systemically study the dependent factors impacting cancer metastasis, we conducted serial transplantation to obtain ES-2-MC2-Liver cells, a cell line with high metastatic efficiency. We then performed in vivo CRISPR screen using phosphatase and metabolism-focused sgRNA library and ranked differential targeting genes. For further validating the identified gene essentialities in previous results, we generated a mini-library targeting the top-depleted and -enriched genes in metastatic organs and performed in vivo CRISPR screen on ES-2-MC2-Liver cells and SKHEP1 cells. Notably, polyunsaturated lipids synthase, ACSL4, displayed as the top perturbed hits among the lung-specific metastatic mediators. We also evaluated enzymes involved in unsaturated fatty acids degradation were dispensable for metastatic tumor colonization. Taken together, our results systemically study the mediators of cancer metastasis and established the dual functions of PUFA-lipids in tumor progression and metastasis that may be exploitable for therapeutic development.

overall_design: 1. We infected the ES-2-MC2-Liver cells with sgRNA from phosphatase- and metabolism-focused CRISPR library. Cells collected before intraperitoneal implantion served as the baseline (n=1). Comparative analyses were then conducted between cancer cells isolated from the metastatic livers (n=5) or lungs (n=3 for the phosphatase library and n=5 for the metabolism library) and subcutaneous tumors. 2. ES-2-MC2-Liver and SKHEP-1cells were utilized to perform in vivo pooled mini-CRISPR screens for validation. Cells collected before implantation served as the baseline (n=4). Comparative analyses were conducted between cancer cells isolated from the metastatic livers (n=4 for ES-2-MC2-Liver cells) or lungs (n=4) and subcutaneous tumors (n=4).

first: Yilong

first: Yuqi

last: Wang


title: Comparing the transcriptome of small intestinal epithelial cells in CD1d-KO vs WT mice

first: Patricia

last: Barral

address: Great Maze Pond

department: CIBCI

institute: King's College London

summary: Intestinal homeostasis is maintained through the combined functions of epithelial and immune cells that collaborate to preserve the integrity of the intestinal barrier. However, the mechanisms by which immune cell populations regulate intestinal epithelial cell (IEC) homeostasis remain unclear. Here, we use a multi-omics approach to study the immune-epithelial crosstalk and identify CD1d-restricted Natural Killer T (NKT) cells as regulators of IEC biology. We find that NKT cells are abundant in the proximal small intestine and show hallmarks of activation at steady state. Subsequently, NKT cells regulate the survival and the transcriptional and cellular composition landscapes of IECs in intestinal organoids, through mechanisms dependent on IFN-γ and IL-4 secretion by NKT cells but independent of the expression of CD1d on IECs. In vivo, lack of NKT cells results in an increase in IEC turnover, while NKT cell activation leads to IFN-γ-dependent epithelial apoptosis. Our findings propose NKT cells as potent producers of cytokines that contribute to the regulation of IEC homeostasis.

overall_design: To investigate the effect of the lack of CD1d/NKT cells on the transcriptome of small intestine IECs, we compared the gene expression profile of IECs in CD1d-KO and WT animals. 8 samples were sequenced; replicates of four samples from CD1d-/- and WT animals were obtained from 2 individual experiments. 150,000 small intestinal epithelial cells were isolated per sample according to the described protocol and sorted directly on RLT buffer supplemented with 2-mercaptoethanol on a BD FACSAriaTM Fusion flow. Samples were frozen at –80°C before RNA extraction

first: Marta

last: Lebrusant-Fernandez


title: Creation and Validation of the First Infinium DNA Methylation Array for the Human Imprintome [cord_blood]

first: Dereje

last: Jima

overall_design: 8 oord blood samples analyzed with the Human Imprintome array with two replicates each.

first: Natalia

last: Carreras-Gallo

first: Varun

last: Dwaraka

first: David

last: Skaar

first: Tavis

last: Mendez

first: Antonio


title: RNA-seq of low osteogenic ASCs that were transfected with the pAcGFP1-C1 control vector and pAcGFP1-C1_GSTT1 vector

city: Goyang

first: JAE YEON

last: MOON

address: Dongguk-ro 32

country: South Korea

institute: Dongguk university

summary: To elucidate the mechanism of action of GSTT1, RNA-seq analysis was performed to determine genes and signaling pathways influenced by GSTT1 in ASCs.

overall_design:
Three replicates were analyzed for three different patient groups
The hASCs were established from lipoaspirates from three different donors. A statement of consent was informed to all donors. All experiments were performed according to the relevant guidelines and regulations


title: Small intestine lamina propia iNKT cells in comparison to iNKT cells residing in lymphoid tissues

overall_design: 4 samples were sequenced across 2 individual experiments. Small intestinal lamina propia iNKT cells were sorted in a BD FACS Aria Fusion into RLT buffer before proceeding to mRNA isolation. Samples were frozen at –80°C before RNA extraction.

first: Rebeca

last: Jimeno


title: Local thermal ablation breaks immune tolerance in pacreatic cancer [RNA-seq 1]

city: Verona

first: Francesco

last: De Sanctis

address: Piazzale L.A. Scuro, 10

department: Department of Medicine

country: Italy

institute: University and Hospital Trust of Verona

summary: Pancreatic cancer (PC) is a devastating disease characterised by late diagnosis, genetic neoplastic heterogeneity, poor T-cell infiltration, a highly immunosuppressive tumour microenvironment, and metastatic spreading which results in poor clinical outcomes. Surgery remains the most effective treatment, although it is limited to a few patients. Local ablative techniques, such as radiofrequency ablation (RFA), have been proposed to control PC progression in patients with nonresectable tumours. However, the impact of these therapies on promoting the activation of the immune system and eliciting an effective anti-tumour immune response remains elusive. Whether local ablative techniques could overcome resistance to immunotherapy in PC is unknown.   We enrolled a cohort of patients with non-resectable locally advanced pancreatic cancer and longitudinally evaluated the impact of local thermal ablation on circulating immunological parameters. Additionally, we used cancer cell lines derived from PC transgenic mouse models to establish a preclinical platform that recapitulates systemic and localised inflammation induced by RFA in vivo. Finally, we employed this preclinical experimental platform to evaluate the efficacy of the therapeutic treatments.   Thermal ablation induced a short-term inflammatory process resulting in a systemic increase in myeloid cells as well as increased plasma levels of high mobility group box 1 molecule, which correlates with a better patient outcome. We performed thermal ablative procedures in mice bearing orthotopic PC and evaluated the therapeutic efficacy of thermal treatment alone or in combination with immune checkpoint-based immunotherapy through activation of a T lymphocyte-dependent anti-tumour immune response. We demonstrated that RFA synergises with immunotherapy to restrict tumour progression, significantly improving the overall survival of PC-bearing mice. Tumour immune landscape characterisation confirmed that RFA in combination with immunotherapy supported the sculpting of an immune hostile milieu towards an effective anti-tumour milieu characterised by an increased infiltration of cytotoxic T lymphocytes in spite of CD206-expressing tumour-associated macrophages.   Our study confirmed that RFA enhances immunotherapy effectiveness by breaking tumour immune tolerance and unleashing the full cytotoxic abilities of tumour-specific T-cells. Thus, RFA can circumvent the current limitations of immunotherapy in patients with pancreatic cancer.

overall_design: Comparison of gene expression profile of KPC-derived PDAC treated with RFA, immunotherapy and RFA + immunotherapy compared to untreated control. Tumor samples were collected at sacrifice.


title: Local ablation disrupts immune evasion in pancreatic cancer [RNA-seq 2]

overall_design: Comparison of gene expression profile of KPC-derived PDAC treated with RFA compared to untreated control. Tumor samples were collected 48h after treatment.


title: Single-cell RNA-seq reveals the midkine-mediated immune microenvironment dysfunction in human keloids fibrotic niche

city: Guangzhou

first: Jingting

address: No 1, Zhongshan 2 Road, 12th Floor

department: Institue of Precision Medicine

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: A keloid scar is recognized as the most intractable skin pathological scar due to its continuous overgrowth, invasion of adjacent boundary and high recurrence rate. Heterogeneity of fibroblasts or vascular endothelial cells was previously characterized, while the immune microenvironment within this fibrotic niche remains largely unknown.

overall_design: we profiled over 100,987 single cells from 3 samples of human keloid scars, perilesional keloid skin, normal skin scar and normal skin each, in order to investigate the cellular heterogeneity of various cell types possibly associated with the unique characteristics of keloid scar.

first: Peng

first: Shaohai

last: Qi


title: CD4+ T cell-innate immune crosstalk is critical during Staphylococcus aureus biofilm infection.

city: White/Caucasian

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

institute: UNMC

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

overall_design: Refer to individual Series


title: Comparing the transcriptome of small intestinal epithelial cells in organoids after co-culture with NKT cells

overall_design: 8 samples were sequenced; replicates of four samples from WT organoids co-cultured with NKT cells or alone for 3 days were obtained from 2 individual experiments. After co-culture, media was removed and organoids were washed with 1mL pre-warmed ADEMEM+++ to remove NKT cells before proceeding to mRNA isolation. Samples were frozen at —80°C before RNA extraction.


title: Optic nerve head-neural progenitor cells inhibit neuronal stress and glaucoma

status: Public on Nov 24 2024

city: Ann Arbor

first: Thanh

last: Hoang

state: MI

address: 1000 Wall St, Brehm Building , Room 7426

department: Ophthalmology

institute: University of Michigan

summary: This study provides single-cell RNA-Seq data from 20 day old rat optic nerve head

overall_design: scRNA-seq were prepared on dissociated Optic nerve heads using the 10X Genomics Chromium Single Cell 3’ Reagents Kit v3.1 (10X Genomics, Pleasanton, CA). Libraries were constructed following the manufacturer’s instructions and were sequenced using Illumina NextSeq. Sequencing data were processed through the Cell Ranger 6.1.1 pipeline (10X Genomics) using default parameters.

first: Steven

last: Bernstein

first: Zara

last: Mehrabian

first: Yan

last: Guo

first: Jean

last: Jouffroy

first: Esmahan

last: Durmaz

first: Ben

last: Mead

first: Stanislav

last: Tomarev

first: Jonathan

last: Epstein

first: Adam

last: Kronk

first: Seth

last: Blackshaw


title: Investigating the role of Paf1 in transcription by RNA polymerase I

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

summary: Polymerase-associated factor 1 complex (Paf1C) has been identified to promote transcription by Pols I and II and is conserved across eukaryotes. This transcription factor has been well-studied for Pol II, but its role in transcription by Pol I has not been fully characterized. Therefore, the goal of this study was to use a high-resolution technique, native elongating transcript sequencing (NET-seq), to investigate the effect of the loss of two of the five Paf1C subunits (Paf1 and Cdc73) on Pol I occupancy in yeast. Most notably, we found that in both paf1D and cdc73D mutants, there was a significant reduction in Pol I occupancy at the 5’ end of the rDNA template as compared to WT yeast. Overall, our results suggest that Paf1C is an important transcription elongation factor for Pol I.

overall_design: NET-seq libraries were prepared for two replicates each of WT, cdc73△, and paf1△ yeast.

first: Jinger

last: Yang

first: David

last: Schneider


title: Leucine zipper-based sorting system enables generation of multi-functional CAR T cells

city: New York

first: Scott

middle: Edward

last: James

state: NY

address: 408 E 69th Street

institute: Memorial Sloan Kettering Cancer Center

summary: Resistance to chimeric antigen receptor (CAR) T cell therapy develops through multiple mechanisms including antigen-loss escape and tumor-induced immune suppression. Expression of multiple CARs may overcome multi-antigen-loss escape. Similarly, expression of switch receptors that convert inhibitory immune checkpoint signals into positive costimulatory signals may enhance CAR T cell activity in the tumor microenvironment.  Engineering multiple features into one cell product, however, is limited by transgene packaging constraints of current vector systems. Here, we describe a leucine zipper-based cell sorting methodology that enables selective single-step immunomagnetic purification of cells co-transduced with two vectors, designed to potentially double the number of incorporated transgenes. This “Zip-sorting” system facilitated generation of T cells simultaneously expressing up to four CARs and co-expressing up to three switch receptors. These multi-CAR multi-Switch receptor arrays enabled T cells to eliminate antigenically heterogeneous syngeneic leukemia populations co-expressing multiple inhibitory ligands. Zip-sorted multi-CAR multi-Switch receptor T cells represent a combinatorial therapeutic strategy to overcome multiple mechanisms of CAR T cell resistance.

overall_design: Single cell RNAseq profiles of combined CD4+ and CD8+ CAR T cells sorted 24h after stimulation: dual-CAR, dual-CAR dual-Switch, dual-CAR triple-Switch

first: Sophia

last: Chen

first: Brandon

last: Ng

first: Jacob

last: Fischman

first: Lorenz

last: Jahn

first: Alexander

last: Boardman

first: Adhithi

last: Rajagopalan

first: Harold

last: Elias

first: Alyssa

last: Massa

first: Dylan

last: Manuele

first: Katherine

last: Nichols

first: Amina

last: Lazrak

first: Nicole

last: Lee

first: Aoife

last: Roche

first: Alex

last: McFarland

first: Angelina

last: Petrichenko

first: John

last: Everett

first: Frederic

last: Bushman

first: Teng

last: Fei

first: Anastasia

middle: I

last: Kousa

first: Andri

last: Lemarquis

first: Susan

last: DeWolf

middle: U

last: Peled

first: Santosha

last: Vardhana

first: Christopher

last: Klebanoff

first: Marcel

last: van den Brink


title: The effect of NKT cell activation on the transcriptome of intestinal epithelial cells

city: London

first: Patricia

last: Barral

overall_design:
To investigate the effect of NKT cell activation on intestinal epithelial cell (IEC) function, we intraperitonally injected mice with the prototypical lipid antigen α-Galactosylceramide (αGal) or with PBS (control).
IECs from the proximal small intestine were harvested at two timepoints (18h or 72h) for bulk RNA-seq analysis.
IECs from three mice were used for each of the three treatment groups.

first: Tom

last: ap Rees


title: Identifying therapeutic vulnerability in ataxia telangiectasia and Rad3-related protein (ATR) inhibitor resistant splicing factor mutant myeloid malignancies

city: Charlestown

first: Timothy

last: Graubert

state: Massachusetts

address: 149, 13th Street, Navy Yard

department: Cancer Center

institute: Massachusetts General Hospital

summary: The goal of this study is to undertake splicing analysis to validate clones derived from K562 cell lines which have been CRISPR engineered to carry mutations frequently observed in hematologic cancers on splicing factor U2af1.

overall_design:
U2af1 specific guide RNAs which harbored specific mutations were used to target the nucleotides that code for Serine and Glutamine at amino acid positions 34 (S34) and 157 (Q157), respectively.
Two different mutations each at U2af1S34 and U2af1Q157 loci were introduced individually in different K562 clones. While Serine at position 34 was converted to Phenylalanine or Tyrosine, Glutamine at position 157 was altered to Proline or Arginine.
Subsequently, RNA-sequencing was carried out from individual clones.

first: Sumit

last: Rai

first: Vineet

last: Sharma


title: CD4+ T cell-innate immune crosstalk is critical during Staphylococcus aureus biofilm infection [RAG KO scRNA-seq]

first: Tammy

last: Kielian

summary: Access to the brain for treating neurological sequalae requires a craniotomy, which can be complicated by infection. T cells preferentially home to the brain, but not other tissue sites, during Staphylococcus aureus (S. aureus) craniotomy infection; however, their functional importance is unknown. CD4+ T cells were critical for bacterial containment during craniotomy infection as Rag1-/- mice and WT animals treated with anti-CD4 or VLA-4 and LFA-1 antibodies exhibited elevated bacterial burdens. scRNA-seq revealed transcriptional heterogeneity in brain CD3+ infiltrates, with CD4+ cells most prominent and typified by both Th1 and Th17 signatures, and adoptive transfer of either subset in Rag1-/- mice prevented S. aureus outgrowth. scRNA-seq revealed a profound IFN-γ signature in innate immune cells from Rag1-/- mice during craniotomy infection, supporting extensive T cell-innate immune crosstalk that was validated by immunostaining in the brain parenchyma. A cooperative role for Th1 and Th17 driven responses was demonstrated by treatment of Ifng-/- mice with IL-17A/F neutralizing Ab that recapitulated phenotypes observed in Rag1-/- animals, which were not observed following the loss of either cytokine alone. Collectively, these results implicate a critical role for CD4+ T cells in S. aureus containment during craniotomy infection by shaping the innate immune landscape.

overall_design: To better understand the function of t cells on other immune cells during craniotomy infection, we collected immune cells from a mouse model of craniotomy infection to perform scRNA-seq. CD45+ immune cells were sorted from brain homogenates of wildtype (WT; C57BL/6) or RAG1 KO (KO) mice subjected to craniotomy infection at days 3 and 7 post-craniotomy infection.

first: Gunjan

last: Kak

first: Zachary

last: van Roy

first: Rachel

last: Fallet

first: Lee

last: Korshoj


title: The Role of Mediator Subunit MED30 in Licensing the c-Myc Oncogenic Program [PRO-seq]

city: La Jolla

first: Chunyu

last: Jin

address: 9500 Gilman Dr. MC0648

summary: Despite extensive functional and structural investigation of the Mediator complex, the basis for selective functional requirements for specific Mediator subunits for the actions of specific DNA binding transcription factors remain incompletely understood.  Here, we report the MED30 subunit of Mediator, one of the core subunits maintaining the complex, plays a critical role in regulating the MYC transcription program in cancer cells. This is consequent to MED30 being required for stabilizing Mediator complex and MYC binding on the genome, involving low-affinity hydrophobic interaction functions of the MYC N-terminal Intrinsic Disordered Region (IDR). A mutational screen reveals that mutations in critical residues in the MYC coiled-coil domain structurally adjacent to the IDR of MED30 strongly inhibit tumor growth, even in the presence of wild-type MED30, mimicking the effects of MED30 deletion. This study provides new insights into the principles governing the Mediator complex actions MYC-related biological processes.

overall_design: Dox-induced shMED30 Mia PaCa-2 stable cell line were treated or untreated with 0.5μg/ml doxycycline for 3 days before nuclei isolation. 1/50 number of drosophila S2 cells were spike-in for overall input control. Each condition has two replicates.

first: Wei

last: Yuan

first: Michael

middle: G

last: Rosenfeld


title: ATR/CHK1/WEE1 dependency in SRSF2-mutated myeloid malignancies

summary: The aim of this experiment is to characterize mRNA splicing in clones derived from the K562 cell line, which have been genetically engineered using CRISPR/Cas9 to carry SRSF2 mutations frequently observed in myeloid malignancies

overall_design:
SRSF2 specific guide RNAs which harbored substitution mutations were used to target the nucleotides that code for Proline at amino acid position 95 (P95).
Mutations that replace amino acid Proline (P) at position 95 (P95) on SRSF2 were introduced individually in different K562 clones. Proline was substituted with arginine (P95R), leucine (P95L) or histidine(P95H).
Subsequently, RNA-sequencing was carried out from individual clones.

first: Samuli

last: Eldfors


title: The Role of Mediator Subunit MED30 in Licensing the c-Myc Oncogenic Program


title: Profiling the cancer-prone microenvironment in a zebrafish model for MPNST

first: Dereje

last: Jima

summary: Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined, particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by (1) the difficulty in discriminating between microenvironmental, precancerous, and cancer cells; and (2) the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental, precancerous, and cancerous cell populations by fluorescence-activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor (MPNST), a type of soft tissue sarcoma that exhibits rapid, aggressive growth. Using RNA-seq, we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune-associated signaling networks and significant upregulation of tumor-promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand-receptor pairs that may promote sarcomagenesis.  This work provides insight into how the microenvironment may promote MPNST initiation and progression.

overall_design:
N = 3-4 SAMPLES PER TREATMENT GROUP:
Pre Cancerous Sox10 High
Pre Cancerous Sox10 Low
Control Sox10 Low
Cancer Sox10 High
Cancer Sox10 Low

first: Heather

last: Shive

first: John

middle: S

last: House

first: Jordan

last: Ferguson

first: Aubrie

last: Selmek

first: Dillon

middle: T

last: Lloyd


title: Whole transcriptome sequencing explored the toxic effect of cadmiun on Caenorhabditis elegans [RNA-seq]

city: Zhengzhou

first: Panpan

last: Wang

address: 郑州市高新区科学大道100号郑州大学

department: College of Public Health

institute: 郑州大学

summary:
Purpose: Cadmium (Cd) is detrimental to environment and human health, but the specific mechanism of the regulatory network is still remained unclear. Caenorhabditis elegans (C. elegans) is selected as the ideal model organism to investigate the effect of Cd exposure.
Methods: We employed the phosphoproteomic technologies, high-throughput sequencing method and bioinformatic tools (RNAhybrid, Risearch2 and Targetscan) to investigate the phosphorylated change and the regulatory networks of circRNA, lncRNA, microRNA (miRNA) and mRNA after Cd exposure in C. elegans. The Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis (GSEA) were also employed. The relationship between transcriptional factors (TFs) and kinases, and the kinase-substrate were predicted using Jaspar database and iGPS, respectively.
Results:26 differentially expressed circRNAs (DEcircRNAs), 143 lncRNAs (DElncRNAs), 69 miRNAs (DEmiRNAs) and 6209 mRNAs (DEmRNAs) were identified. According to qRCR, four DEcircRNAs and three DElncRNAs were found and confirmed the different expression levels between the treated and control group. 23 miRNAs and six miRNAs were the potential targets of the confirmed circRNAs and lncRNAs respectively using the predictive tools of RNAhybrid, RIsearch and Targetscan. Similarly, the target mRNAs of miRNAs were identified. Next, the regulatory network of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA were established. Furthermore, five protein-coding genes might be regulated by DElnRNAs through cis-acting and 114 by trans-acting. The GO and KEGG analysis were performing on the parents’ genes of the mRNAs. GSEA was performed on all protein-coding genes, and the correlation between these genes and validated lncRNAs were used for pre-ranking. For the phosphopromotics, 42 differentially regulative phosphopeptides were identified. In this work, four novel pairs of TFs-kinases-substrate which might be influenced by Cd exposure were firstly constructed.
Conclusions: Cd might mainly influence the reproductive function and aging of C. elegans through regulating the circRNAs and lncRNAs. Also, it might inhibit the expression of TFs to reduce the phosphorylated level of corresponding protein.

overall_design: Examination of the change of RNA and protein after cadmium exposure in Caenorhabditis elegans.

first: Zhi

last: Qu

first: Peisen

last: Guo


title: Real-time quantitative PCR analysis of Lentinula edodes mycelium face on different stress treatments.

city: wuhan

first: jiaxin

last: song

address: No. 1, Shizishan Street, Hongshan District, Wuhan City, Hubei Province

department: College of Plant Science & Technology

institute: Huazhong Agricultural University

summary: L. edodes strain w1 was cultured at 25°C in MYG medium (containing 1% malt  extract, 0.1% peptone, 0.1% yeast extract, and 2% glucose). Fresh mycelium blocks  were cultured in a 9cm petri dish containing MYG medium. After 8-day dark cul-  ture, and they were divided into different treatment groups (group A,B,C,D,E).  Group A was treated with 8mm-diameter L. edodes mycelium block on MYG  medium for seven days and then treated at 37 °C for 30 min. 3. Group B was  treated with 8mm-diameter L. edodes mycelium block on MYG medium for seven  days and then treated at 4 °C for 60 min. Group C was treated with 8mm-diameter  L. edodes mycelium block on MYG medium for seven days and then under 3500  lx light for 1 h. In group D, 8mm-diameter fresh L. edodes mycelium block were  inoculated into MYG medium containing cadmium ions. In group E, 8mm-diameter L. edodes mycelium block was inoculated at 10 mm from the edge of the petri dish,  and cultured at 25 ° C for 7 days. Afterwards, an activated 8-mm diameter tricho-  derma mycelium block was inoculated at 1 cm from the edge of the petri dish at  one end of the petri dish diameter (corresponding to the other end where L. edodes  mycelium block was inoculated)

overall_design: qPCR gene expression profiling.  Lentinula edodes mycelium were used and treated separately as indicated in the summary.

first: Ruiping

last: Xu


title: Rising from the dead: A novel mechanism involving pyroptosis and pathologic neovascularization in retinopathy of prematurity

city: Guangzhou，China

first: sen

middle: da

last: XIE

state: Guangdong

address: 54 Xianlie Road

institute: Zhongshan ophthemology center

summary: To elucidate the changes in retinal angiogenesis, we performed single-cell RNA sequencing on OIR model isolated retinal cells.We found the specific expression of AIP1 gene in endothelial cells, which is related to the formation and development of retinal blood vessels, and the expression of AIP1 gene may play a protective role in the progression of disease.

overall_design: Six samples from the retinas of murine, each of which was taken from two murine.

last: Chi

first: Yonghaoo

last: Li

first: Dasen

last: Xie

first: Hui

last: Chen


title: The Role of Mediator Subunit MED30 in Licensing the c-Myc Oncogenic Program [ChIP-seq]

first: Chunyu

last: Jin

overall_design: To map the binding sites of Mediator component MED17, MED30 and MYC, these factors ChIP-seq were performed in Mia PaCa-2 cells with antibodies MED17 (invitrogen PA5-30314), MED30 (from Dr. Thomas G. Boyer, UT health San Antonio, homemade) and Myc (CST #9402), respectively. To test the effect of MED30 knockdown in Myc's binding, MYC ChIP-seq was perform with or without three days 0.5ug/ml Dox treatment in Dox-induced shMED30 Mia PaCa-2 cells. To test the domain/motif contribution to binding for Myc,  letivrus vector expressing HA-tagged Myc fragment and WT in Dox-induced manner were intergrated into Mia PaCa-2 cells, and 0.5ug/ml Dox was administrated for 1 day, another WT sample was not treated with Dox, serving as negative control.

first: Guofeng

last: Zhao

first: Kenneth

last: Ohgi

first: Michael

last: Rosenfeld


title: RNA-seq and CUT&Tag analysis of the effects of lncRNA LOC105378662 knockdown in gastric cancer cells

city: Shanghai

first: Lu

last: Zang

address: No.197, Ruijin 2nd rd. Shanghai, China

department: Department of General Surgery

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: To elucidate whether lncRNA LOC105378662 plays a role in gastric cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of LOC105378662 siRNA and control siRNA transfectants. And we found LOC105378662 interact with BRD7 ( bromodomain containing 7), which usually acted as a co-factor in gene transcription. Therefore, we compared the enrichment of BRD7 in MGC803 cells with LOC105378662 siRNA and control siRNA transfectants through CUT&Tag sequencing.

overall_design: Refer to individual Series. RNA-seq and CUT&Tag were performed in MGC803 gastric cancer cells after lncRNA LOC105378662 knock down. BRD7 Ab (abcam, ab56036) was used in CUT&Tag assay.

first: Shuchun


title: The Role of Mediator Subunit MED30 in Licensing the c-Myc Oncogenic Program [RNA-seq]

overall_design: To examine the transcriptome influence of depleting difference mediator subunit, shRNAs target MED1,MED20, MED30 or non-target Ctrl were packaged into lenti-virus and infected into Mia PaCa-2 cells, and total RNAs were extracted two days post infection. MED30 wild-type or mutant overexpression comparing to knockdown RNA seq in Mia PaCa-2 was performed with 0.5ug/ml doxycycline-induced teton shRNA or cDNA overexpression, and total RNAs were extracted two days post Dox induction. All shRNAs were packaged in lentivirus and infected into cells.


title: Cold-blooded vertebrate utilizes behavioral fever to alleviate T-cell apoptosis and optimize antimicrobial immunity

first: Haiyou

last: Gao

state: 上海市

address: State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai, China

institute: 华东师范大学

summary: Fever confers significant survival benefits on endotherms by optimizing both innate and adaptive immunity. Ectotherms achieve thermoregulation using behavioral strategies, but existing evidence supports its enhancement effect on innate immunity only. Therefore, it remains unknown whether the coordination between fever and adaptive immunity was independently acquired by endotherms or instead represents a gradually evolved function common to vertebrates. In the present study, we reported that Nile tilapia developed behavioral fever to enhance the immune response against Edwardsiella piscicida infection. Behavioral fever lasted five days, and the immune potential was optimized at 4–6 days post infection, indicating a potential correlation between fever events and T-cell immunity. Further investigation suggested that fever did not affect T-cell activation or proliferation but improved the ability of T cells to produce IFN- and Granzyme B and enhanced cytotoxicity, thereby eliminating the infection more effectively. Notably, we identified a previously unknown advantage conferred by fever during infection: alleviation of T-cell apoptosis to maintain a considerable T-cell pool. Mechanistically, fever induced the expression of HSP70, which in turn entered the nucleus and bound to and promoted the phosphorylation of ERK1/2, thereby inhibiting the cleavage of caspase-8/caspase-3 and preventing T-cell apoptosis. Our findings elucidate the detailed mechanism by which behavioral fever optimizes T-cell immunity in a cold-blooded vertebrate and propose that integrating fever with adaptive immunity to gain survival advantages is an ancient strategy acquired before the emergence of tetrapod.

overall_design: RNA-seq profiling of spleen lymphocytes in behavioral fever group and normal group on Day4 post infection

first: Xiumei

last: Wei

first: Kang

first: Yi

last: Cao

first: Wenzhuo

last: Rao

first: Jiansong

last: Zhang

first: Jialong

last: Yang


title: RNA sequencing of wild type or calcineurin-deficient mouse bone marrow-derived dendritic cells stimulated with or without lipoarabinomannan (LAM) from Mycobacterium tuberculosis Aoyama-B

city: Suita

first: Daisuke

last: Motooka

address: Yamadaoka

institute: Osaka University

summary: To elucidate the function of calcineurin in dendritic cells (DCs) downstream of C-type lectin receptor, we established mouse model that has DC-specific calcineurin deficiency. We stimulated the bone marrow-derived DCs from these mice with lipoarabinomannan (LAM), a ligand of Dectin-2, and performed RNA sequencing. From multiple genes that showed altered expression pattern in calcineurin-deficient DCs, we found that Il10 transcription increased in the absence of calcineurin. Our further study elucidated the mechanism by which calcineurin regulates Il10 transcription in LAM activated DCs.

overall_design: Bone marrow-derived DCs from wild type and calcineurin-deficient mice were stimulated with lipoarabinomannan (LAM) for 0, 2, 4, 8, or 12 h and used for RNA sequencing.

first: Xiuyuan

last: Lu

first: Masatsugu

last: Oh-hora

last: Okuzaki

first: Sho

last: Yamasaki


title: NPC-derived exosome-mediated effects on macrophages

status: Public on Nov 23 2024

city: Taoyuan

first: Tzu-Tung

last: Liu

address: Zhongda Rd,. Zhongli District

country: Taiwan

institute: National central university

summary: Transcriptomic analysis delineated the interactions between NPC cells and macrophages through exosome cargos. The findings revealed that NPC cells modulated macrophage polarization via exosomes, thereby promoting tumor progression

overall_design: Exosome-mediated effects on macrophages were evaluated using bulk RNA sequencing.

first: Shu-Chen


title: Plasma-Derived Exosomes in Chronic Spontaneous Urticaria Induce the Release of Inflammatory Mediators from Mast cell through miRNA-619-5p/SOCS4 Pathway

first: Ruixiang

last: Li

address: 56 Hengfu Road

institute: Guangzhou Institute of Dermatology

summary: This study aims to explore the critical role of exosomes derived from plasma of patients in the progression of CSU.

overall_design: miRNA analysis of health donor vs Chronic Spontaneous Urticaria

first: Runxiang


title: CUT&RUN to map WT1 binding in M15 cell lines that are genome edited for the KTS isoforms.

city: Edinburgh

first: Silvia

last: Peluso

state: Midlothian

address: Western General Hospital, Crewe Road

institute: MRC HGU at the University of Edinburgh

summary: throughput profiling of WT1 in M15 mouse mesonephric cells and M15 genome edited for the KTS isoforms. The genome-edited lines were derived from the M15 cells by transfection and puromycin selection of cells with the guide RNA expressing plasmids. Briefly, the guide RNAs were designed against the splice site that is essential for KTS isoform. Out of the designed guide RNAs, some of them were cloned into the pX601 vector with the Sa Cas9 variant, and clone confirmation was done using sequencing.    Isoform-specific lines were established by providing oligos for repair which represented the region corresponding to the codons coding for KTS or not.

overall_design: Wilms Tumor 1 profiling by high throughput sequencing

first: Ruthrotha

last: Bharathavikru