title: PAX6 promotes neuroendocrine phenotypes of prostate cancer via enhancing MET/STAT5A-mediated chromatin accessibility

city: shanghai

first: jing

state: shanghai

address: Rm 1515, Bldg 17, 160 Pujian Rd, Shanghai 200127, China

institute: Shanghai jiaotong university

summary: Neuroendocrine prostate cancer (NEPC) is a highly aggressive form of prostate cancer characterized by the loss of androgen receptor (AR) signaling and the acquisition of neuroendocrine (NE) characteristics. However, the underlying molecular mechanism, especially related to the drivers or the determinants responsible for NE transdifferentiation, remains unclear. In this study, we compared gene expression profiling of NEPC and non-NEPC specimens and paid a particular attention to those transcriptional factors affecting neural differentiation during development. We identified that Paired box 6 (Pax6) expression was significantly elevated in NEPC and negatively regulated by AR signaling. While knock-down of Pax6 in NEPC cells inhibited NEPC phenotypes, over-expression of Pax6 in non-NEPC cells led to development of NEPC. Mechanistically, loss of AR resulted in an enhanced expression of Pax6, which reprogramed the lineage plasticity of prostate cancer cells to develop NE phenotypes through the c-Met/Stat5a signaling. By performing ATAC-seq, we found that high expression level of Pax6 elicited enhanced chromatin accessibility mainly through attenuation of H4K20me3 that usually causes chromatin silence in cancer cells. Taken together, these findings highlight PAX6 as a novel molecule to drive NEPC progression and suggest that it might serve as a potential target for the management of NEPC.

overall_design:
To investigate the role of PAX6 in the differentiation of LNCaP cell line from androgen-sensitive to androgen-insensitive, we established an androgen-insensitive cell line similar to NEPC by treating LNCaP cells with enzalutamide for 30 days. Morever, we overexpressed PAX6 in LNCaP cells. Besides, we established DU145_shPAX6 cell lines to investigate whether PAX6 knockdown could repress the neuroendocrine transdifferentiation of NE-like cells.
We then performed gene expression profiling analyzing data obtained from RNA-seq of  LNCAP, LNCAP_ENZ, DU145-shCon and DU145_shPAX6 cells. We also performed ATAC seq to explore  the chromatin accessibility in LNCaP_oePAX6, LNCaP_oeSTAT5A compared with LNCaP_con cells.

last: Jing

first: Xinxing

last: Du

first: Yu

last: Liang


title: DMS-MapSeq Analysis of Antisense Oligonucleotide Binding to lncRNA PANDA

status: Public on Jan 09 2024

city: Boston

first: Gabriel

middle: A

last: Romero Agosto

address: 77 Avenue Louis Pasteur

country: USA

institute: Harvard Medical School

summary: While various methods exist for examining and visualizing the structure of RNA molecules, dimethyl sulfate-mutational profiling and sequencing (DMS-MaPseq) stands out for its simplicity and versatility. This technique has proven effective for studying RNA structures both in vitro and in complex biological settings. We've updated the protocol for using DMS-MaPseq, and it can also be employed to identify the binding of antisense oligonucleotides (ASOs) to RNA. By applying this updated protocol, we successfully characterized the structural ensemble of the HIV1 Rev Response Element (RRE), along with its two alternative structures. The findings align with previously published research. Additionally, we resolved the structure of the long non-coding RNA PANDA, which was previously unknown. Moreover, we used PANDA as a basis for designing ASOs and confirmed their binding through a substantial decrease in DMS-reactivities at the anticipated ASO binding locations.

overall_design: DMS-MaPseq was performed on a set of in-vitro refolded RNAs to validate it. It was also used on a set of in-vitro refolded RNAs along with ASOs to cause misfolding detected bt DMS-MaPseq


title: Time of Day Bias for Biological Sampling in Studies of Mammary Cancer

city: Morgantown

first: James

last: Walton

state: West Virginia

address: 108 Biomedical Road

department: Neuroscience

institute: West Virginia University

summary: Despite its demonstrated biological significance, time of day is a broadly overlooked biological variable in preclinical and clinical studies. How time of day affects the influence of peripheral tumors on central (brain) function remains unspecified. Thus, we tested the hypothesis that peripheral mammary cancer tumors alter the transcriptome of immune responses in the brain and that these responses vary based on time of day; we predicted that time of day sampling bias would alter the interpretation of the results. Brain tissues collected at mid dark and mid light from mammary tumor-bearing and vehicle injected mice were analyzed using the Nanostring nCounter Mouse Neuroinflammation Panel V1. Peripheral mammary tumors significantly affected expression within the brain of over 100 unique genes of the 770 represented in the panel, and fewer than 25% of these genes were affected similarly across the day. Indeed, between 65-75% of GO biological processes represented by the differentially expressed genes were dependent upon time of day of sampling. The implications of time-of-day sampling bias in interpretation of research studies cannot be understated. We encourage considering time of day as a significant biological variable in studies and to appropriately control for it and clearly report time of day in findings.

overall_design: Mammary tumor or vehicle injected female mice; brains collected at two times of day (mid day, mid dark); n=5 for each tumor condition and time of day; 3 brain regions dissected; total RNA extracted from each region resulting in 60 samples for simultaneous gene expression analysis of of 770 neuroinflammation-related genes.

middle: C

first: William

middle: H

last: Walker 2nd

first: Randy

middle: J

last: Nelson

first: A

last: DeVries


title: Comparative transcriptome of cancer cells cultured in a conventional manner

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

country: Japan

institute: Kanazawa Medical University Hospital

type: Expression profiling by high throughput sequencing

summary: Comparative gene expression analysis of PC9 versus PC9-BrM4 versus PC9-AMG human lung cancer cells cultured in a conventional manner.

overall_design: Total RNAs extracted from PC9, PC9-BrM4 and PC9-AMG human lung cancer cells cultured in a conventional manner were sequenced by NextSeq 500/550 High Output Kit v2.5.

first: Kojiro

last: Ishibashi

first: Yo

last: Niida

first: Eishu

last: Hirata


title: Comparative transcriptome of astrocytes in MGS

summary: Comparative gene expression analysis of astrocytes cultured with conventional method or in MGS.

overall_design: Total RNAs extracted from astrocytes cultured with conventional method and astrocytes in MGS were sequenced on the Illumina NextSeq.


title: LITAF PROMOTES MEMBRANE REPAIR AGAINST PORE-FORMING PROTEINS

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: U2OS cells were co-transfected with PiggyBac (PB) transposon plasmid pPB-SB-CMV-puro-SD3 and the transposase p-hyPBASE. The modified PiggyBac (PB) transposon, which has a constitutively active CMV promoter which can stimulate or disrupt expression of neighboring genes, depending on insertional orientation. For each library, between 10e7-10e8 cells were transfected, cultured with the addition of 3 µg/ml puromycin for one week to select cells that had incorporated the transposon, and then used for screens of resistance to alpha-toxin-induced cell death with minimal further expansion. Mutagenized cells were treated twice with alpha-toxin (500 ng/ml) for 48h to ensure the selection of only highly resistant cells. Genomic DNA (gDNA) was isolated from 5-10 X 10e6 cells and transposon insertion sites were mapped using high throughput sequencing.

overall_design: Eight individual libraries were created and were combined for common insertion site analysis (CIS).

first: Caroline

last: Stefani

first: Adam

last: Lacy-Hulbert


title: RNA sequencing of sorted P17 murine endothelial cells from the OIR model with OSM or PBS intravitreal injection at P12

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

country: Germany

institute: University Medical Center Freiburg

summary: IL-6 family cytokines as OSM modify angiogenesis to different degree. This study investigates the influence of intravitreal injection of OSM on the formation of neovascularization in the mice model of Oxygen-induced retinopathy (OIR). Mice at P12 were injected OSM or PBS , retinal cells isolated at P17 via sort and the transcriptome analyzed by RNA sequencing.

overall_design: C57BL/6 mice were used for the established OIR model. Data consists of 5 OSM (Oncostatin M) and 6 PBS treated mice from three independent litters and OIR runs. M1-4, M5-8 and M9-11 are each from one litter and OIR run.

first: Felicitas

last: Bucher


title: DIDO is necessary for adipogenesis promoting diet-induced obesity [I]

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

summary: Rates of overweight and obesity continue to rise in the population worldwide. Obesity reduces life expectancy because it is an important predisposing factor for cancer, cardiovascular diseases and diabetes mellitus. Adipose tissue (AT), the main organ for fat storage with endocrine capacity, plays fundamental roles in systemic metabolism and in obesity-related diseases. Adiposity and lipodystrophy are associated with metabolic disorders, indicating that normal AT function is required for metabolic health. Dido1 is a marker gene for stemness and gene-targeting experiments compromised several functions from cell division to embryonic stem cell differentiation, in vivo and in vitro. Using animals carrying a DIDO mutant without the N-terminal, we report that these mice display a lean phenotype with reduced adipose tissue and hypolipidemia even when fed with an obesogenic diet. The phenotype related to impaired adipogenesis, partially corrected by transcription factors C/EBPα or PPARγ expression and to hypothermia subsequent to dermal fat thinning. Deep sequencing of the epididymal white fat (Epi WAT) transcriptome shows the role of Dido1 in the control of cellular lipases. The molecular analysis involves Dido1 in orchestrating adipogenesis and altogether offers a model different from described lipodystrophies in mice and pioneers a new path to understand obesity and identify mechanism for obesity intervention.

overall_design: List of mRNA profiles of Dido1 wild type and mutants

first: María Ángeles

last: García-López

first: Carlos

last: Martinez-A

first: Thierry

last: Fischer


title: Molecular profiling of osteoprogenitor cells reveals FOS as a master regulator of bone non-union

city: Bern

first: Daniel

middle: Walter

last: Hanhart

state: Bern

address: Murtenstrasse 24

department: Department for BioMedical Research (DBMR)

country: Switzerland

institute: UroGenus

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

overall_design: Refer to individual Series


title: DIDO is necessary for the adipogenesis that promotes diet-induced obesity

summary: The prevalence of overweight and obesity continues to rise in the population worldwide. Because it is an important predisposing factor for cancer, cardiovascular diseases, diabetes mellitus, and COVID-19, obesity reduces life expectancy. Adipose tissue (AT), the main fat storage organ with endocrine capacity, plays fundamental roles in systemic metabolism and obesity-related diseases. Dysfunctional AT can induce excess or reduced body fat (lipodystrophy). Dido1 is a marker gene for stemness; gene-targeting experiments compromised several functions ranging from cell division to embryonic stem cell differentiation, both in vivo and in vitro. We report that mutant mice lacking the DIDO N terminus show a lean phenotype. This consists of reduced AT and hypolipidemia, even when mice are fed a high-nutrient diet. DIDO mutation caused hypothermia due to lipoatrophy of white adipose tissue (WAT) and dermal fat thinning. Deep sequencing of the epididymal white fat (Epi WAT) transcriptome supported Dido1 control of the cellular lipid metabolic process. We found that, by controlling the expression of transcription factors such as C/EBPα or PPARγ, Dido1 is necessary for adipocyte differentiation, and that restoring their expression reestablished adipogenesis capacity in Dido1 mutants. Our model differs from other lipodystrophic mice and could constitute a new system for the development of therapeutic intervention in obesity.


title: Identification of endogenous small peptides involved in rice immunity through transcriptomics- and proteomics-based screening

status: Public on Jan 08 2024

city: Kurashiki

first: Yoji

last: Kawano

state: Okayama

department: Institute of Plant Science and Resources

institute: Okayama University

summary: Small signalling peptides, generated from larger protein precursors, are important components to orchestrate various plant processes such as development and immune responses. However, small signalling peptides involved in plant immunity remain largely unknown. Here, we developed a pipeline using transcriptomics- and proteomics-based screening to identify putative precursors of small signalling peptides: small secreted proteins (SSPs) in rice, induced by rice blast fungus Magnaporthe oryzae and its elicitor, chitin. We identified 236 SSPs including members of two known small signalling peptide families, namely rapid alkalinization factors and phytosulfokines, as well as many other protein families that are known to be involved in immunity, such as proteinase inhibitors and pathogenesis-related protein families. We also isolated 52 unannotated SSPs and among them, we found one gene which we named immune response peptide (IRP) that appeared to encode the precursor of a small signalling peptide regulating rice immunity. In rice suspension cells, the expression of IRP was induced by bacterial peptidoglycan and fungal chitin. Overexpression of IRP enhanced the expression of a defence gene, PAL1 and induced the activation of the MAPKs in rice suspension cells. Moreover, the IRP protein level increased in suspension cell medium after chitin treatment. Collectively, we established a simple and efficient pipeline to discover SSP candidates that probably play important roles in rice immunity and identified 52 unannotated SSPs that may be useful for further elucidation of rice immunity. Our method can be applied to identify SSPs that are involved not only in immunity but also in other plant functions.


title: DIDO is necessary for the adipogenesis that promotes diet-induced obesity [II]

summary: The prevalence of overweight and obesity continues to rise in the population worldwide. Because it is an important predisposing factor for cancer, cardiovascular diseases, diabetes mellitus, and COVID-19, obesity reduces life expectancy. Adipose tissue (AT), the main fat storage organ with endocrine capacity, plays fundamental roles in systemic metabolism and obesity-related diseases. Dysfunctional AT can induce excess or reduced body fat (lipodystrophy). Dido1 is a marker gene for stemness; gene-targeting experiments compromised several functions ranging from cell division to embryonic stem cell differentiation, both in vivo and in vitro. We report that mutant mice lacking the DIDO N terminus show a lean phenotype. This consists of reduced AT and hypolipidemia, even when mice are fed a high nutrient diet. DIDO mutation caused hypothermia due to lipoatrophy of white adipose tissue (WAT) and dermal fat thinning. Deep sequencing of the epididymal white fat (Epi WAT) transcriptome supported Dido1 control of the lipid metabolic process. We found that, by controlling expression of transcription factors such as C/EBPα or PPARγ, Dido1 is necessary for adipocyte differentiation, and that restoring their expression reestablished adipogenesis capacity in Dido1 mutants. Our model differs from other lipodystrophic mice and could constitute a new system for the development of therapeutic intervention in obesity.


title: SRSF1 is crucial for male meiosis through alternative splicing during homologous pairing and synapsis in mice [RNA-seq]

city: Beijing

first: Jiali

last: Liu

address: 2 West Yuanmingyuan Road

country: China

institute: China Agricultural University

summary: Homologous pairing and synapsis are essential in meiotic prophase I during spermatogenesis. However, the underlying mechanisms of how alternative splicing (AS) functions in homologous pairing and synapsis remain largely unclear. We reveal that SRSF1 is essential for gene expression and AS in homologous pairing and synapsis. Conditional knockout (cKO) of Srsf1 in mouse germ cells impaired homologous pairing and synapsis, leading to non-obstructive azoospermia (NOA). SRSF1 was required for initial homology recognition, telomere-led chromosome movement, and synaptonemal complex (SC) assembly. Moreover, SRSF1 interacted with TRA2B and U2AF2, directly binding and regulating the expression of Dmc1, Sycp1, Sun1, and Majin via AS to implement homologous pairing and synapsis during the meiotic prophase I program. Altogether, our data reveal the critical role of an SRSF1-mediated post-transcriptional regulatory mechanism in homologous pairing and synapsis during meiotic prophase I, providing a framework for elucidating the molecular mechanisms underlying the post-transcriptional network of male meiosis.

overall_design: STRA8+ cell suspensions were isolated and prepared from mouse testes. Total RNA was extracted from STRA8+ cells.

first: Longjie

last: Sun

first: Juan

last: Chen

first: Rong

last: Ye

first: Zheng

last: Lv


overall_design: Reference: Wang et al., Plant Biotechnol J. 2020 Feb;18(2):415-428.  doi: 10.1111/pbi.13208.  We present a refined framework for isolating secreted signaling peptides involved in rice immunity by combining transcriptome and proteome analyses with functional assays using rice suspension cells. Three different materials were analyzed: 1) rice plants infected with rice blast fungus, 2) rice suspension cells treated with fungal elicitor chitin, and 3) media from the rice suspension samples. Two omic approaches were performed to identify differentially expressed genes identified by transcriptome and proteins detected exclusively in rice blast- and/or chitin-treated samples by proteome.

first: Pingyu

last: Wang

first: Yuanyuan

last: Zhang


title: Salmonella manipulates the host to drive pathogenicity via induction of interleukin 1β

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

sample_organism:
Bacteria
Mus musculus

platform_organism:
Bacteria
Mus musculus


title: Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression (RNA-Seq)

city: University Park

first: James

last: Lee

state: PA

address: 406 South Frear Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the function of these TF condensates in 3D genome organization and gene regulation remains elusive. In response to methionine (met) starvation in budding yeast, Met4 and a few sequence-specific co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form puncta-like structures that significantly overlap in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro. In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes are clustered in 3D in a Met4-dependent manner. A MET3pr-GFP reporter inserted near several native Met4 binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4 binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to met depletion (-met).

overall_design: RNA-seq of cells in MET active (-met) and inactive (+met) conditions in S.cere.

first: Lu

last: Bai

first: Leman

last: Simpson

first: Yi

last: Li


title: The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae

city: Leiden

first: Ron

middle: P

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

summary: Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum (M. marinum) is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen, we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma-like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week after infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis.

overall_design:
To study the effect of Mycobacterium tuberculosis (Mtb) infection on gene expression in zebrafish larvae, early embryos were robotically injected into the yolk with Mtb H37rv (Berlin strain) in PVP or with PVP alone.
Embryos/larvae were harvested at 0, 1, 2, 3, 4, 5, 6, 8 and 9 days post fertilization (dpf) and used for total RNA extraction. RNA samples derived from 0, 3, 4, 5, 6, and 8 dpf samples were used for Illumina RNA sequencing.
Differential gene expression analysis was performed by comparing Mtb-infected samples with PVP-infected control samples (in triplo; except for 8 dpf, which was in duplo).

first: Herman

last: Spaink


title: CRISPR screens identify candidate host factors for SARS and MERS coronavirus infection

city: SAN FRANCISCO

first: Andreas

middle: S

last: Puschnik

state: CA

address: 499 Illinois St, 4th floor

institute: Chan Zuckerberg Biohub

summary: Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are zoonotic pathogens that can cause severe respiratory disease in humans. Identification of the host factors that are necessary for viral infection and virus-induced cell death is critical to our understanding of the viral life cycle and can potentially aid the development of new treatment options. Here, we report CRISPR screen results of both SARS-CoV and MERS-CoV infections in derivatives of the human hepatoma cell line Huh7. Our screens identified the known entry receptors ACE2 for SARS-CoV and DPP4 for MERS-CoV. Additionally, the SARS-CoV screen uncovered several components of the NF-κB signaling pathway (CARD10, BCL10, MALT1, MAP3K7, IKBKG), while the MERS-CoV screen revealed the polypyrimidine tract-binding protein PTBP1, the ER scramblase TMEM41B, furin protease and several transcriptional and chromatin regulators as candidate factors for viral replication and/or virus-induced cell death. Together, we present several known and unknown coronavirus host factors that are of interest for further investigation.

overall_design:
All experiments were performed under required biosafety conditions. For the SARS-CoV screen, a genome-wide knockout gene library using the human GeCKOv2 library (Addgene, #1000000049, gift from Feng Zhang) (PMID: 25075903) was generated in clonal Huh7.5.1-Cas9 cells expressing ACE2-IRES-TMPRSS2 (PMID: 33333024). 144 million cells were infected with SARS-CoV at an MOI of 0.0001. Surviving cells were harvested at 12 days post-infection in RLT buffer and genomic DNA was extracted with AllPrep DNA/RNA spin columns (Qiagen). Eluted DNA was irradiated for biosafety reasons. Library cells at day 0 were extracted as baseline control.
For the MERS-CoV screen, Huh7.5.1-Cas9 cells transduced with the human GeCKOv2 library were infected with MERS-CoV at an MOI of 0.0001. The furin inhibitor Decanoyl-RVKR-CMK was added to the media at 5 μM throughout the experiment to prevent excessive syncytia formation. Surviving cells were harvested in DNA/RNA Shield (Zymo) at 8 days post-infection and genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo). Uninfected, Decanoyl-RVKR-CMK-treated library cells were cultured in parallel and harvested for comparison. Library cells at day 0 were extracted as baseline control.
The sgRNA expression cassettes were amplified from genomic DNA in a two-step nested PCR using KAPA HiFi HotStart ReadyMixPCR Kit (Kapa Biosystems) and sequenced on an Illumina NextSeq 500 using a custom sequencing primer, as previously described (PMID: 33333024).
Demultiplexed FASTQ files were processed using MaGeCK (PMID: 25476604). First, FASTQ files were aligned to a reference table containing sgRNA sequences to determine the counts of each sgRNA in each control and selected cell population. Then, count tables for GeCKO sublibraries A and B were combined and gene enrichment was calculated from sgRNA count tables using the total norm-method.

first: Rebecca

middle: M

last: Broeckel

first: Dylan

last: Flather


title: A pairwise cytokine code explains the organism-wide response to sepsis [Spatial transcriptomics by Array-seq]

city: Chicago

first: Michihiro

last: Takahama

state: Illinois

department: Pritzker School of Molecular Engineering

institute: University of Chicago

summary: Sepsis is a systemic response to infection with life-threatening consequences. Our understanding of the molecular and cellular impact of sepsis across organs remains rudimentary. Here, we characterize the pathogenesis of sepsis by measuring dynamic changes in gene expression across organs. To pinpoint molecules controlling organ states in sepsis, we compare the effects of sepsis on organ gene expression to those of 6 singles and 15 pairs of recombinant cytokines. Strikingly, we find that the pairwise effects of tumor necrosis factor plus interleukin (IL)-18, interferon-gamma or IL-1   suffice to mirror the impact of sepsis across tissues. Mechanistically, we map the cellular effects of sepsis and cytokines by computing changes in the abundance of 195 cell types across 9 organs, which we validate by whole-mouse spatial profiling. Our work decodes the cytokine cacophony in sepsis into a pairwise cytokine message capturing the gene, cell and tissue responses of the host to the disease.

overall_design: We performed whole-mouse spatial transcriptomics. Overall, 4 datasets (2 datasets/condition) were genenrated from the following experiments and samples: (1) whole-body section from naive mice, (2) whole-body section from LPS-injected mice (5 mg/kg, 24 hours).

first: Nicolas

last: Chevrier

first: Denis

last: Cipurko


title: Comparative transcriptome of cancer cells cultured in MGS

first: Hiroki

last: Ura

summary: Comparative gene expression analysis of PC9 versus PC9-BrM4 versus PC9-AMG human lung cancer cells cultured in MGS

overall_design: Total RNAs extracted from PC9, PC9-BrM4 and PC9-AMG human lung cancer cells cultured in MGS were sequenced by NextSeq 500/550 High Output Kit v2.5.

first: Kojiro

last: Ishibashi

first: Yo

last: Niida

first: Eishu

last: Hirata


title: Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression (ChIP-Seq)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP of TAP tagged Met4, Met28, Met32, Cbf1 in MET active (-met) and inactive (+met) conditions in S.cere.


title: Salmonella manipulates the host to drive pathogenicity via induction of interleukin 1β [16S]

first: Shai

last: Bel

summary: Acute gastrointestinal infection with intracellular pathogens like Salmonella Typhimurium triggers the release of the proinflammatory cytokine interleukin 1β (IL-1β). However, the role of IL-1β in intestinal defense against Salmonella remains unclear. Here, we show that IL-1b production is detrimental during Salmonella infection. Mice lacking IL-1b (IL-1b -/-) failed to recruit neutrophils to the gut during infection, which reduced tissue damage and prevented depletion of short-chain fatty acid-producing commensals. Changes in epithelial cell metabolism that typically support pathogen expansion, such as switching energy production from fatty acid oxidation to fermentation, were absent in infected IL-1b -/- mice which inhibited Salmonella expansion. Additionally, we found that IL-1b induces expression of complement anaphylatoxins and suppresses the complement-inactivator Carboxypeptidase N (CPN1). Disrupting this process via IL-1b loss prevented mortality in Salmonella-infected IL-1b -/- mice. Finally, we found that IL-1b expression correlates with expression of the complement receptor in patients suffering from sepsis, but not uninfected patients and healthy individuals. Thus, Salmonella exploits IL-1b signaling to outcompete commensal microbes and establish gut colonization. Moreover, our findings identify the intersection of IL-1b signaling and the complement system as key host factors involved in controlling mortality during invasive Salmonellosis.

overall_design: WT and IL-1b-/- C57BL/6 mice were orally infected with 10^7 CFU of Salmonella typhimurium SL1334. Feces were collected 4 days post-infection and DNA was extracted.


title: Chromatin targeting of the RNF12/RLIM E3 ubiquitin ligase controls transcriptional responses

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

institute: Erasmus MC

summary: Protein ubiquitylation regulates key biological processes including transcription. This is exemplified by the E3 ubiquitin ligase RNF12/RLIM, which controls developmental gene expression by ubiquitylating the REX1 transcription factor and is mutated in an X-linked intellectual disability disorder. However, the precise mechanisms by which ubiquitylation drives specific transcriptional responses are not known. Here, we show that RNF12 is recruited to specific genomic locations via a consensus sequence motif, which enables co-localisation with REX1 substrate at gene promoters. Surprisingly, RNF12 chromatin recruitment is achieved via a non-catalytic basic region and comprises a previously unappreciated N-terminal autoinhibitory mechanism. Furthermore, RNF12 chromatin targeting is critical for REX1 ubiquitylation and downstream RNF12-dependent gene regulation. Our results demonstrate a key role for chromatin in regulation of the RNF12-REX1 axis and provide insight into mechanisms by which protein ubiquitylation enables programming of gene expression.

overall_design: ChIP-seq for REX1, RNF12, RNF12(H569A,C572A) in mESCs.

middle: F

first: Cristina

last: Gontan

first: Joost

last: Gribnau


title: A pairwise cytokine code explains the organism-wide response to sepsis [spatial transcriptomics by Visium]

overall_design: We performed spatial transcriptomics of mouse kidney. Overall, 4 datasets (2 datasets/condition) were genenrated from the following experiments and samples: (1) kidney from naive mice, (2) kidney from LPS-injected mice (5 mg/kg, 24 hours).


title: Lack of cyclic stretch disturbs endothelial cell transcriptomic profile

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary: Cyclic circumferential stretch (CCS) induced by pulsatile blood pressure affects endothelial cell (EC) gene expression and regulates vascular mechanical properties. Although alterations in EC gene expression in response to increased CCS as observed in hypertensive patients is widely studied, the EC response to low or lack of CCS as observed in intracranial aneurysm (IA) disease has been poorly investigated. In this project we explored how exposure of ECs to low CCS may contribute to IA disease.

overall_design: HUVECS were seeded at 300’000 cells/well on pre-coated Collagen I BioFlex culture plates® (Flexcell International, USA) and grown until confluence. Then, the cells were submitted to cyclic stretch of 6% or not (0%) for 48-hours using the Flexcell strain unit FX-5000T (Flexcell International, USA) according to the manufacturers’ instructions. Thus, the cells were stretched over a 25mm loading station or maintain under static condition (0%) by placing a Flexstop beneath the well of the BioFlex culture plate. The mechanical stretch was applied following the pulse heart waveform with a frequency of 1Hz (Figure 1D). After 48-hours, we collected the cells that received a uniform strain.

first: Mannekomba

middle: R

last: Diagbouga

first: Brenda

last: Kwak


title: The effect of berberine upon 3T3L1 preadipocytes differentiation

city: Hong Kong

first: Jiawen

last: SHOU

address: Shatin

country: Hong Kong

institute: the Chinese University of Hong Kong

summary: Berberin has been shown to inhibit 3T3L1 preadipocytes differentiation. This study aims to determine the genes regulated by berberine and clarify the possible molecular mechanism underlying the action.

overall_design: MDI (including Isobutylmethylxanthine, dexamethasone and insulin) was added to induce 3T3L1 preadipocytes differentiation. And berberine was added to treated 3T3L1 preadipocytes during MDI-induced differentiaiton period.

first: J

middle: W

last: Shou

first: P

last: Shaw


title: Bulk transcriptomics analysis of SIX2+CITED1+ cells from Wilms Tumor

city: Los Angeles

first: Brendan

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

summary:
Purpose: Bulk transcriptomics analysis of Wilms tumor SIX2+CITED1+ cells to compare and identify unique nephron progenitor transcriptome profiling (RNA-seq) signature between unfavorable and favorable Wilms Tumors and against human fetal kidney
Methods: Wilms tumor samples were collected and transported on ice at 4°C in RPMI-1640 and a single cell suspensions were prepared following mechanical and enzymatic dissociation as previously publication. Enzymatic dissociation was performed with 125 U/ml collagenase I in RPMI-1640 at 37 °C for 35 min. The digested cells were then passed through a 100-μm cell strainer and a 40-μm cell strainer with washes of 1x PBS. The cell suspension was than centrifuged at 1500 rpm for 5 min and erythrocytes were eliminated using a red blood cell lysis kit.  WT SIX2+CITED1+ cells were isolated using SIX2-Cy5 and CITED1-Cy3 Smartflare RNA probes following manufacturer’s instructions and previous publication. Briefly, cells were incubated over night at 37 °C with both RNA probes diluted at 1:20 in PBS and 25ul/ml in RPMI-1640 supplemented with 5% FBS, and 0.2% antimicrobial agent Primocin. After 16-18 h, cells were dissociation using TrypLE 1x for 5 min, cells were centrifuged at 1500 rpm for 5 min and prepared for FACS. RNA extraction was performed immediately after FACS  using the RNeasy Micro Kit following manufacturer’s recommendations. After cDNA production and construction of DNA libraries, the samples were run on an Illumina NextSep500 (Illumina). Differential gene expression was analyzed using ERCC ExFold probes with the Remove Unwanted Variation R/Bioconductor software package  combined with edgeR
Results: Transcriptomics analysis of Wilms Tumor SIX2+CITED1+ cells in comparison to different tumor types and human fetal kidneys confirmed the nephrogenic signature of hFK-SIX2+CITED1+ and WT-SIX2+CITED1+ cells but highlighted differences in expression of pluripotency and self renewal-related genes like OCT4, FOXO1, SALL, NANOG along with a lower expression of β-catenin, TCF, and other growth factors known to promote differentiation (BMPs, FGFs). Hierarchical clustering of gene expression showed shared similarities between Wilms tumor samples against human fetal kidney samples however, with major differences in gene expression between tumor-to-tumor type was also present.
Conclusion: Our study represents the first transcriptomic characterization of Wilms Tumor cancer stem cells (SIX2+CITED1+) against human fetal kidney SIX2+CITED1+ cells. Identifying specify gene expression and signaling pathway profiles across different subtypes of Wilms Tumor and against human fetal kidney SIX2+CITED1+ cells.

overall_design: Wilms Tumor mRNA profiles of anaplastic, non-anaplastic, and non-anaplastic chemotreated SIX2+CITED1+ cells.

first: Laura

last: Perin

first: Stefano

last: Da Sacco

first: Astgik

last: Petrosyan

first: Matthew

middle: E

last: Thornton


title: A pairwise cytokine code explains the organism-wide response to sepsis

first: Michihiro

last: Takahama


title: The effect of berberine upon HepG2 cell viability

summary: Berberin has been shown to inhibit HepG2 cell viability. This study aims to determine the genes regulated by berberine and clarify the possible molecular mechanism underlying the action.

overall_design: Berberine was added to treated HepG2 cells for 24 hours.


title: Harnessing Bronchoalveolar Lavage Metagenomics for Distinguishing Lung Cancer from Pulmonary Infectious Diseases

city: Guangzhou

first: Bin

last: Yang

address: Guangzhou 510700

institute: Vision Medicals Co., Ltd.

summary: Recent progress in unbiased metagenomic next-generation sequencing (mNGS) allows simultaneous examination of microbial and host genetic material in a single test. Leveraging affordable bronchoalveolar lavage fluid (BALF) mNGS data, we employed machine learning to create a diagnostic approach distinguishing lung cancer from pulmonary infections, conditions prone to misdiagnosis in clinical settings. This prospective study analyzed BALF-mNGS data from lung cancer and pulmonary infection patients, delineating differences in DNA/RNA microbial composition, bacteriophage abundances, and host responses, including gene expression, transposable element levels, immune cell composition, and tumor fraction derived from copy number variation (CNV). Integrating these metrics into a host/microbe metagenomics-driven machine learning model (Model VI) demonstrated robustness, achieving an AUC of 0.87 (95% CI = 0.857-0.883), sensitivity = 73.8%, and specificity = 84.5% in the training cohort, and an AUC of 0.831 (95% CI = 0.819-0.843), sensitivity = 67.1%, and specificity = 94.4% in the validation cohort for distinguishing lung cancer from pulmonary infections. The application of a rule-in and rule-out strategy-based composite predictive model significantly enhances accuracy (ACC) in distinguishing between lung cancer and tuberculosis (ACC=0.913), fungal infection (ACC=0.955), and bacterial infection (ACC=0.836). These findings highlight the potential of cost-effective mNGS-based analysis as a valuable tool for early differentiation between lung cancer and pulmonary infections, offering significant benefits through a single comprehensive testing.

overall_design: This observational study assessed adults admitted to the First Affiliated Hospital, Zhejiang University School of Medicine, suspected of lung cancer or pulmonary infections. Enrollment occurred between March 8, 2020, and May 27, 2023, for patients aged ≥18, requiring BALF samples within 72 hours of intubation to establish the etiology. Exclusions involved cases with underlying leukemia, no definitive diagnosis post-extensive follow-up, or lacking matching DNA and RNA mNGS data from BALF samples. A total of 123 lung cancer, 279 pulmonary infections including tuberculosis, fungal, and bacterial infections. The diagnosis of lung cancer relies on clinical suspicion and positive laboratory results from tests cytology, flow cytometry and/or tissue biopsy. The diagnosis of pulmonary infections is based on clinical suspicion and determination of the causative pathogen through standard microbiological diagnostics (cultures, antigen/antibody tests, PCR, sequencing).

first: Dongsheng

last: Han


title: A pairwise cytokine code explains the organism-wide response to sepsis [Whole-tissue RNA-seq]

overall_design: We performed the experiments and 11 datasets were generated from the following experiments and samples: (1) LPS time course , (2) Cecal Ligation and Puncture (sham, severe, moderate, mild; d0.5), (3) Cytokine injection (6 singles and 14 pairs), (4) Cytokine injection (1 pair), (5) Plasma transfer, (6) Neutralizing antibody and 2 knockout mice, (7) Combination of neutralizing antibodies and knockout mice, (8) Cecal Ligation and Puncture (sham, severe, moderate, mild; d0.25 and d1), (9) Cecal Ligation and Puncture (severe; d0.5; Combination of neutralizing antibody and IFNg/IL18 knockout mice), (10) Cecal Ligation and Puncture (severe; d0.5; Combination of neutralizing antibody and IL1b knockout mice), (11) Cecal Ligation and Puncture (severe; d0.5; TNF neutralizing antibody and TNF knockout mice).

first: Nicolas

last: Chevrier


title: Single cell analysis of tumor-infiltrating CD4+ T cell from Tc1- and Tc9- treated mouse

status: Public on Jan 07 2024

city: Houston

first: Liuling

last: Xiao

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

summary: To conduct a comprehensive analysis, we performed scRNA-seq and paired T-cell receptor sequencing (scTCR-seq) on tumor-infiltrating CD4+ T cells.

overall_design: Thy1.1+ Pmel-1 Tc1 or Tc9 cells were transferred into Thy1.2+ B6 mice bearing chimeric tumor. Tumor tissues pooled from three mice for each group were harvested on day 30 after tumor inoculation and CD4+ T cells were isolated for scRNA-seq and scTCR-seq analyses.

first: Wendao

last: Liu

first: Qing

last: Yi


title: Salmonella manipulates the host to drive pathogenicity via induction of interleukin 1β [RNA-Seq]

first: Shai

last: Bel

overall_design: WT and IL-1b-/- C57BL/6 mice were orally infected with 10^7 CFU of Salmonella typhimurium SL1334. Colonic tissues were removed at 2 and 6 days post infection and RNA was exptracted and sequenced.


title: DRAIC mediates hnRNPA2B1 stability and m6A-modified IGF1R instability to inhibit tumor progression [m6A-seq]

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

summary: Both N6-methyladenosine (m6A) mediates RNA fates and ubiquitin mediates protein fates play an important role in either physiology or pathology including cancer, yet how long noncoding RNAs (lncRNAs) are involved in a link of molecular fate between m6A and ubiquitin remains unknown. Here, we reveal a role for a lncRNA Downregulated RNA in Cancer (DRAIC) to suppress tumor growth and metastasis in clear cell Renal Carcinoma (ccRCC). Mechanistically, DRAIC physically interacts with heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1) and enhances its protein stability by blocking E3 ligase F-box protein 11 (FBXO11)-mediated ubiquitin and proteasome-dependent degradation. Subsequently, hnRNPA2B1 destabilizes m6A modified-type 1 insulin-like growth factor receptor (IGF1R) to lead to inhibition of ccRCC progression. Moreover, four m6A modification sites of IGF1R are identified and results in its mRNA degradation. Collectively, our findings reveal that DRAIC/hnRNPA2B1 axis regulates IGF1R mRNA expression in an m6A-dependent manner and highlights an important mechanism of IGF1R fate. These findings shed light on DRAIC/hnRNPA2B1/FBXO11/IGF1R axis as potential therapeutic targets in ccRCC and build a link of molecular fate between m6A-modified RNA and ubiquitin-modified protein.

overall_design: RIP assay was performed using m6A antibody in HepG2 cells and the enriched RNA was sequenced with input sample

first: Ya

last: Wen

first: Xiwang

first: Yifei

last: Li

first: Xueqing

last: Zhao

first: Liqiang

last: Duan

first: Shuwen

last: Chenge

first: Xiaofeng

last: Zhua

first: Xiaoli

last: Chang

first: Chang

last: Zhang

first: Tianyou

last: Cheng

first: He

last: Wang

first: Yibi


title: Host and Microbe Blood Metagenomics Reveals Key Pathways Characterizing Critical Illness Phenotypes

city: San Francisco

first: Lucile

middle: P A

last: Neyton

address: 505 Parnassus Ave

institute: UCSF

summary:
Two molecular phenotypes of sepsis and acute respiratory distress syndrome, termed hyperinflammatory and hypoinflammatory, have been consistently identified by latent class analysis in numerous cohorts, with widely divergent clinical outcomes and differential responses to some treatments; however, the key biological differences between these phenotypes remain poorly understood.
We used host and microbe metagenomic sequencing data from blood to deepen our understanding of biological differences between latent class analysis-derived phenotypes and to assess concordance between the latent class analysis-derived phenotypes and phenotypes reported by other investigative groups (e.g., SRS1-2, MARS1-4, reactive/uninflamed).
We analyzed data from 113 hypoinflammatory and 76 hyperinflammatory sepsis patients enrolled in a two-hospital prospective cohort study. Molecular phenotypes had been previously assigned using latent class analysis.
The hyperinflammatory and hypoinflammatory phenotypes of sepsis had distinct gene expression signatures, with 5,755 genes (31%) differentially expressed. The hyperinflammatory phenotype was associated with elevated expression of innate immune response genes, while the hypoinflammatory phenotype was associated with elevated expression of adaptive immune response genes, and notably, T-cell response genes. Plasma metagenomic analysis identified differences in prevalence of bacteremia, bacterial DNA abundance and composition between the phenotypes, with an increased presence and abundance of Enterobacteriaceae in the hyperinflammatory phenotype. Significant overlap was observed between these phenotypes and previously identified transcriptional subtypes of acute respiratory distress syndrome (reactive/uninflamed) and sepsis (SRS1-2). Analysis of data from the VANISH trial indicated that corticosteroids might have a detrimental effect in hypoinflammatory patients.
The hyperinflammatory and hypoinflammatory phenotypes have distinct transcriptional and metagenomic features that could be leveraged for precision treatment strategies.

overall_design:
Gene expression patterns comparison for hypoinflammatory and hyperinflammatory sepsis patients
*** Raw data not provided due to patient privacy concerns with making the raw data fully public in GEO. ***

first: Carolyn

last: Calfee


title: Fungicide-tolerant persister formation during cryptococcal pulmonary infection

first: hao

last: ding

state: Beijing

address: BeiChen Road

institute: institute of microbiology

summary: Bacterial persisters, a subpopulation of genetically susceptible cells that are normally dormant and tolerant to bactericides, have been studied extensively because of their clinical importance. In comparison, much less is known about the determinants underlying fungicide-tolerant fungal persister formation in vivo. Here, we report that during mouse lung infection, Cryptococcus neoformans forms persisters that are highly tolerant to amphotericin B (AmB), the standard of care for treating cryptococcosis. By exploring stationary-phase indicator molecules and developing single-cell tracking strategies, we show that in the lung, AmB persisters are enriched in cryptococcal cells that abundantly produce stationary-phase molecules. The antioxidant ergothioneine plays a specific and key role in AmB persistence, which is conserved in phylogenetically distant fungi. Furthermore, the antidepressant sertraline shows potent activity specifically against cryptococcal AmB persisters. Our results provide evidence for and the determinant of AmB-tolerant persister formation in pulmonary cryptococcosis, which has potential clinical significance.

overall_design: Cryptococcus cells were cultured for 12 h at 30°C with shaking at 220 rpm in YPD liquid medium and then transferred to fresh YPD liquid medium and incubated for 6, 12, 18, 24, 36, 48, 72, 96 and 120 h. Cells were harvested for RNA extraction at each time point. The concentration and integrity of RNA in each sample were assessed by a Qubit RNA Assay Kit on a Qubit 2.0 Fluorometer (Life Technologies, CA, USA) and RNA Nano 6000 Assay Kit with the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively. RNA purity was determined using a Nano Photometer spectrophotometer (IMPLEN, CA, USA). The transcriptome libraries were constructed using the VAHTS mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) according to the manufacturer’s instructions. RNA-seq was performed by Annoroad Gene Technology Co., Ltd (Beijing, China). The samples were clustered using VAHRS RNA adapters set1/set2 and sequenced on an Illumina platform.

first: Weixin

last: Ke

first: Yingying

last: Chen

first: Yuyan

last: Xie

first: Linqi


title: Effects of lifelong exercise and age on transcriptome dynamics in MHC I and MHC IIa muscle fibers at baseline and in response to resistance exercise

city: Manhattan

first: Aliza

last: Rubenstein

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

summary: RNA-Seq was used for the first time to investigate the effects of resistance exercise on transcriptome dynamics in slow myosin heavy chain (MHC) I and fast MHC IIa muscle fibers among 3 groups of men. Vastus lateralis muscle biopsies were obtained before and 4 hours after resistance exercise.

overall_design: A total of 25 males were included in this investigation. The participants included 8 lifelong exercisers (74±1y), 9 old healthy non-exercisers (75±1y), and 8 young exercisers (25±1y). Vastus lateralis biopsies were obtained in conjunction with a resistance exercise bout (bilateral knee extensions with 3x10 reps at 70% of 1-RM) and included a basal biopsy and another biopsy 4 hours after the exercise session. From each biopsy sample, individual muscle fibers were isolated. After myosin isoform identification of isolated fibers via SDS-PAGE, RNA extraction of MHC I and MHC IIa muscle fibers was performed. Thus, each resulting sample contained total RNA from either MHC I or MHC IIa muscle fibers. A total of 100 samples were analyzed using RNA-Seq.  The study design allowed us to examine the acute effects of resistance exercise on transcriptome dynamics in MHC I and MHC IIa muscle fibers with age and exercise.

first: Ulrika

last: Raue

first: Gwénaëlle

last: Begue

first: Kiril

last: Minchev

first: Bozena

last: Jemiolo

first: Kevin

last: Gries

first: Toby

middle: L

last: Chambers

middle: B

first: Elena

last: Zaslavsky

first: Stuart

last: Sealfon

first: Todd

last: Trappe

first: Scott


title: YOD1 promotes renal fibrosis by stabilizing JAK2 through deubiquitination

status: Public on Jan 06 2024

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

summary: Renal fibrosis is an important pathological change in the development of progressive kidney diseases. Ubiquitination is a post-translational modification of proteins involved in the regulation of various pathophysiological processes. In this study, we found that the deubiquitinating enzyme YOD1 is significantly upregulated in the kidney tissues of Ang II-challenged mice and Ang II upregulates YOD1 expression in renal tubular epithelial cells. YOD1 deficiency significantly alleviated renal injury and fibrosis induced by Ang II infusion in mice. Mechanistically, RNA-seq and co-immunoprecipitation analysis showed a pro-fibrotic protein, JAK2, as a YOD1-binding protein. We identify that JAK2 interacts with the C-terminal Znf domain of YOD1. YOD1 removed K48-linked ubiquitination of JAK2 at residue K970 via its active site C155, which stabilizes JAK2 and then maintains JAK2/STAT3 signaling pathway activation to induce pro-fibrotic gene expression in renal tubular epithelial cells. JAK2 inhibitors reversed the renal fibrosis promoted by YOD1 in mice. We also show increased levels of YOD1 and JAK2 in the kidney tissues of patients with renal fibrosis. In addition, YOD1 knockout significantly prevents unilateral ureteral ligation (UUO)-induced renal fibrosis in mice. Collectively, these findings identify YOD1 as a novel regulator in renal fibrosis via deubiquitinating JAK2.

overall_design: We utilized transcriptome sequencing (RNA-seq) to identify candidate pathways regulated by YOD1 in Ang II-treated TCMK1 cells.

first: Ying

last: Zhao

first: Guang

last: Liang


title: Awakening and Eliminating Dormant Cancer Cells: A Foundation for Resistance Removal and Recurrence-Free Recovery [RNA-seq]

city: Hangzhou

first: Yao-Shun

last: Yang

state: Zhejiang Province

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: Tumor therapy mainly targets the tumor bulk, but tends to fail to eradicate the small resistant population of dormant cancer cells (DCCs) that enable relapse and/or metastasis beyond therapy. Using chemoradiotherapy resistant assay and SETD4 expression of a histone lysine methyltransferase, DCCs with high capacity of tumor-initiation and tumorsphere formation were isolated from three types of breast tumors. Exogenous DEK, a nuclear protein, activated the DCCs by binding to open chromatin which decreased SETD4, up-regulated the MYC and down-regulated the P53 signaling pathways. DEK-containing exosomes in blood highly correlate with tumor progress and exosomal DEK promotes tumor relapse and metastasis beyond chemoradiotherapy. Beyond activation, these formerly dormant cancer cells lost their chemoradiotherapy resistance. In treatment of DEK-containing exosomes plus chemoradiotherapy in mice, three types of breast tumors were eliminated without recurrence. Prior DCCs reactivation, as triggered by exogenous DEK may provide treatment options that eliminate both metastasis and recurrence potential.

overall_design: mRNA profiles of DCCs and A-DCCs in MCF7

first: Xi-Zheng

last: Jia

first: Qian-Yun

last: Lu

first: Sun-Li

last: Cai


title: Demultiplexing Ig repertoires by parallel mRNA/DNA sequencing shows major differential alterations in severe COVID-19

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

summary: To in-depth analyze the anti-SARS-CoV-2 humoral response and find elements that can lead or prevent acute respiratory distress syndrome (ARDS), we dissected the multiple layers of B cell responses by NGS immunoglobulin repertoires on RNA template from peripheral blood cell of severe COVID-19 patients.

overall_design: Blood samples from 19 Intensive Care Unit patients infected with SARS-CoV-2 were included in this study (12 with ARDS and 7 without ARDS) and were followed over multiple time points (D0, D7 and 4 months after admission). Samples from healthy volunteers (24 samples), recruited between the ages of 18 and 75 and free from any pathology were used as controls.

first: Virginie

last: Pascal

first: Paco

last: Derouaul

first: Michel

last: Cogne


title: Awakening and Eliminating Dormant Cancer Cells: A Foundation for Resistance Removal and Recurrence-Free Recovery [ATAC-seq]

overall_design: Accessible chromatin profiles of DCCs and A-DCCs in MCF7


title: MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomics (RNA-Seq)

city: Seattle

first: Karol

last: Bomsztyk

address: 850 Republican St

department: Medicine

institute: University of Washington

summary: Integration of ChIP, MeDIP, MeRIP, and RT Seq for multiomics analysis of frozen and FFPE tissue

overall_design: Mouse frozen and FFPE tissue from 4 organs (brain, heart, kidney, and liver) were obtained and analyzed using ChIP, MeDIP, MeRIP, and RT PCR and Sequencing. Data was compared using correlation scatterplots, differential expression, IGV (sequencing read profile snapshots), PCA, PCR Crunch (expression and epigenetic mark levels), and Venn diagrams.

first: Daniel

last: Mar

first: Ilona

last: Babenko

first: Ran

last: Zhang

first: William

last: Noble

first: Oleg

last: Denisenko

first: Tomas

last: Vaisar


title: MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomics (MeDIP-Seq)

type: Methylation profiling by high throughput sequencing


title: Fibroblasts:  Normal fibroblasts vs. Carcinoma-associated fibroblasts

city: Chengdu

first: Jin

state: Sichuan

address: West China Hospital of Stomatology, Chengdu

institute: sichuan university

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Transcriptional profiling of human carcinoma-associated fibroblasts (CAFs) comparing control normal fibroblasts (NFs). NFs derived from normal tissues and CAFs derived from the patients with oral cancer were identified by immunocytochemistry. Goal was to determine differentially expressed lncRNAs between NFs and CAFs.

overall_design: NFs vs. CAFs cells (both in passage 3) . Biological replicates: 3 control replicates, 3 CAFs replicates.

first: Hongmei

last: Zhou


title: The effect of berberine upon AAPH-damaged C17.2 neural stem cells

first: Jiawen

last: SHOU

summary: Berberine shows protective effect against AAPH-damaged C17.2 neural stem cells. This study aims to determine the genes regulated by berberine and clarify the possible molecular mechanism underlying the action.

overall_design: AAPH (7.38 mM) was used to induce oxidative damage to C17.2 neural stem cells. Berberine (1.69 uM) was added to treat AAPH-damaged C17.2 neural stem cells for 12 hours.

first: J

last: Shou

first: P

last: Shaw


title: DRAIC mediates hnRNPA2B1 stability and m6A-modified IGF1R instability to inhibit tumor progression [RNA-seq]

first: Shan

last: Gao

overall_design: To identify the potential lncRNAs as a prognostic biomarker in cancer, we performed the cox single factor analysis in four cancer types, including lung squamous cell carcinoma, lung adenocarcinoma, ccRCC and adrenocortical cancer that our laboratory focused on, based on the Cancer Genome Atlas (TCGA) data, which showed that 14 lncRNAs were potential prognostic biomarkers in these four cancer types. There was only one lncRNA DRAIC that had the same prognostic trend in these four cancer types, which has been characterized as a tumor suppressor or oncogene in previous studies

first: Ya

last: Wen

first: Xiwang

last: Yang

first: Yifei

last: Li

first: Xueqing

last: Zhao

first: Liqiang

last: Duan

first: Shuwen

last: Chenge

first: Xiaofeng

last: Zhua

first: Xiaoli

last: Chang

first: Chang

first: Tianyou

last: Cheng

first: He

last: Wang

first: Yibi


title: Gene expression in Tc1 vs Tc9 cell at day 5 polarization

first: Liuling

last: Xiao

summary:
T cells from spleen and lymphnode were isolated with EasySep Mouse CD8+ T Cell Isolation kit. Isolated CD8+ T cells were stimulated and cultured with plate-bound anti-CD3 and soluble anti CD28 antiboies in Tc1 or Tc9 cell polarizing conditios. After 3-day of polarization, cell were transferred into a new well and culture for another 2-day. on day 5 after seeding, Tc1 and Tc9 cells were collected and sequenced.
We used microarrays to detail the global programme of gene expression of Tc1 and Tc9 cells at day 5 polarization.

overall_design: In vitro polarized Tc1 and Tc9 cells were colletected at day 5 for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain genes selected highly expressed in Tc9 cells as cmpared with Tc1 cells.

first: Qing

last: Yi


title: Transcriptome profiling of mRNAs  in cortex of normal rats

city: Shanghai

first: Ming-Shu

last: Xu

address: No. 650 South Wanping Road, Xuhui District

department: Shanghai Research Institute of Acupuncture and Meridian

institute: Shanghai University of Traditional Chinese Medicine

summary: We analyzed transcriptomic characteristic of motor cortex from Sprague-Dawley rat brain.

overall_design: We selected 3 normal Sprague-Dawley rats. The motor cortex was stripped from brain tissue, and total RNAs were extracted according to the manufacturer’s instructions. Qualified total RNA was further purified. We complete the construction of sequencing sample library. The number of fragments of each gene was counted, and then normalized. Finally, the FPKM value of each gene was calculated by Perl script.


title: Single-cell RNA sequencing of total lung cells from Atg14f/f,Atg14f/f-CD11c-cre, Atg14f/f-LysM-cre mice

city: Beijing

first: Siwei

last: Feng

address: No.30,Shuangqing street

institute: Siwei Feng

summary: We found that several autophagy genes in myeloid cells are required to protect against high-dose Mtb (~1000cfu) infection. To understand the immune cell population in these mice after high-dose Mtb infection and what may contribute to the susceptibility, we did scRNAseq on naïve mice and mice infected with high-dose of Mtb strain Erdman.

overall_design: Lung cells from naive Atg14f/f,Atg14f/f-CD11c-cre, Atg14f/f-LysM-cre and 21dpi Atg14f/f,Atg14f/f-CD11c-cre, Atg14f/f-LysM-cre mice. Cells pooled from 4 mice each, age 8-10 wks.


title: Evaluating the microbiota shift caused by Msc knock-out in wild type and DSS-induced colitis mice

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: The Msc (musculin) is responsible in vitro for the low responsiveness of human Th17 cells to the growth factor IL-2, providing an explanation for Th17 cells rarity in inflammatory tissue. Through this analysis, it has been evaluated the shift in microbiota composition caused by the knock-out of the Msc gene in two diffent mice models (wild-type and DSS-induced colitis)

overall_design: Total DNA was extracted from the stool of the mice, amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

first: Amedeo

last: Amedei

first: Edda

last: Russo

first: Leandro

last: Di Gloria

first: Francesco

last: Annunziato


title: scRNA-seq analysis of SHH medulloblastomas in Math1-Cre/SmoM2 mice with homozygous or heterozygous co-deletion of Bcl2l1 (aka Bcl-xL)

status: Public on Jan 05 2024

city: Atlanta

first: Timothy

last: Gershon

state: Georgia

address: 201 Dowman Dr

institute: Emory University

summary: We found that medulloblastomas that form in Smo mutant mice grow more slowly when the animals are genetically engineered so that the gene Bcl2l1 is conditionally deleted in the tumor cells. We undertook this study to define changes in cellular heterogeneity and gene expression patterns in the Bcl2l1-deleted medulloblastomas, compared to medulloblastomas with an intact Bcl2l1 allele.

overall_design: We generated replicate mice that developed medulloblastoma by interbreeding Math1-Cre,  SmoM2 and Bcl2l1 f/f mouse lines to generate Math1-Cre/SmoM2/Bcl2l1 f/f and Math1-Cre/SmoM2/Bcl2l1 f/+ mouse pups. We harvested tumors from replicate mice of each genotype at either P12 or P20. We then subjected the tumors to Drop-seq analysis using our previously published methods

first: Daniel

last: Malawsky


title: Intersectional genetic tracing reveals the origin of alveolar stem cells during lung repair and regeneration

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

institute: Center for Excellence in Molecular Cell Science

summary: Alveolar type 2 (AT2) cells are stem cells of the alveolar epithelia. Previous genetic lineage tracing studies reported multiple cellular origins for AT2 cells after injury. However, conventional lineage tracing based on Cre-loxP has the limitation of non-specific labeling. Thus, the exact contribution of various epithelial cells to the pools of AT2 cells under different conditions remains unclear. Here, we used dual recombinases-mediated intersectional genetic lineage tracing to investigate the cellular origins of AT2 cells during lung homeostasis, injury and repair. In contrast to previous studies, we found AT1 cells were terminally differentiated cells and did not contribute to AT2 cells after lung injury and repair. Distinctive, but simultaneous, labeling of club cells, bronchioalveolar stem cells (BASCs), and AT2 cells revealed the exact contribution of each to AT2 cells after lung injury. Moreover, we found that club cells have the potential to rebuild virtually all alveoli in some severely injured lung regions. Mechanistically, Notch signaling promotes a BASCs-to-AT2 cell transition, but it inhibits club cell-to-AT2 cell conversion during lung repair. This intersectional genetic lineage tracing strategy with enhanced precision allowed us to elucidate the physiological role of AT1, club, BASCs, and AT2 cells to alveolar regeneration after injury.

overall_design: tdT+, ZsG+, tdT+ZsG+ lung epithelial cell of the Scgb1a1-CreER;Sftpc-DreER;R26-TLR mice at 4 weeks after bleomycin injury were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Kuo

last: Liu

first: Xinfeng

last: Meng

first: Zixin

first: Muxue

last: Tang

first: Zan

last: Lv

first: Xiuzhen

last: Huang

first: Hengwei

last: Jin

first: Xinmeng

last: Han

first: Xiuxiu

first: Wenjuan

last: Pu

first: Huan

last: Zhu

first: Bin

last: Zhou


title: VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification [scRNA-Seq]

city: guangzhou

last: Li

state: 广东

address: UCAS

department: GIBH

institute: UCAS

summary: In contrast to rodents, the mechanisms underlying human trophectoderm and early placenta specification are understudied due to ethical barriers and the scarcity of embryos. Recent reports have shown that human pluripotent stem cells (PSCs) can differentiate into trophectoderm (TE)-like cells (TELCs) and trophoblast stem cells (TSCs), offering a valuable in vitro model to study early placenta specification. Here, we demonstrate that the VGLL1 (vestigial-likefamilymember1), which is highly expressed during human and non-human primate TE specification in vivo but is negligibly expressed in mouse, is a critical regulator of cell fate determination and self-renewal in human TELCs and TSCs derived from naïve PSCs. Mechanistically, VGLL1 partners with the transcription factor TEAD4 (TEA domain transcription factor 4) to regulate chromatin accessibility at target gene loci through histone acetylation and acts in cooperation with GATA3 and TFAP2C. Our work is relevant to understand primate early embryogenesis and how it differs from other mammalian species.

overall_design: Human naïve PSCs were dissociated into single cells with a 1:1 mixture of 0.5 mM EDTA and TrypLE Express and plated at a density of 100,000 cell/well of 6-well plate on Geltrex in TE induction medium (1:1 mix of Neurobasal medium (Gibco) and DMEM/F12 (HyClone) supplemented with N2 (Gibco) and B27 (Gibco), penicillin-streptomycin (HyClone), Glutamax (Gibco), β-mercaptoethanol (Sigma), 1 µM PD0325901 (Axon) and 1 µM A83-01 (Selleck)) for five days. TELCs at day 5 were used for downstream analysis throughout this study. For generating expandable TSCs, TELCs at day 5 were dissociated into single cells with TrypLE and plated on Geltrex-coated six-well plates at a 1:4-1:8 split ratio in TSC medium (DMEM/F12 supplemented with N2 and B27, penicillin-streptomycin, Glutamax, β-mercaptoethanol, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF (PeproTech), 0.5 µM A83-01 (Selleck), 1 µM SB431542 (Selleck), 2 µM CHIR99021 (Axon), 0.8 mM VPA (Vetec) and 5 µM Y-27632 (Axon)) supplemented with 10 µM Y-27632.


title: Awakening and Eliminating Dormant Cancer Cells: A Foundation for Resistance Removal and Recurrence-Free Recovery [ChIP-seq]

first: Yao-Shun

last: Yang

overall_design: Analysis of binding sites of DEK in MCF7 A-DCCs

first: Xi-Zheng

last: Jia

first: Qian-Yun

last: Lu

first: Sun-Li

last: Cai


title: 3' RACE-seq of reporter and endogenous LINE-1 mRNA's 3' non-templated ends in 293T and PA-1 cells under permanent (genomic knock-out) or temporal (RNAi) depletions of XRN1, DCP2, (DIS3L2) and control conditions

city: Poznan

first: Zbigniew

last: Warkocki

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

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

Publication: D Janecki, R Sen, N Szóstak, A Kajdasz, M Kordys, K Plawgo, D Pandakov, A Philips, Z Warkocki (2024): LINE-1 mRNA 3’ end dynamics shape its biology and retrotransposition potential. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad1251

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Awakening and Eliminating Dormant Cancer Cells: A Foundation for Resistance Removal and Recurrence-Free Recovery

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


title: Targeting tumor-stromal interactions in triple negative breast cancer using a human vascularized micro-tumor model

city: Irvine

first: Christopher

last: Hatch

address: 2400 Biological Sciences III

institute: University of California, Irvine

summary: Background: Triple-negative breast cancer (TNBC) is characterized by its highly aggressive pathology and limited number of approved targeted therapies. Emerging evidence suggests that stromal cells within the tumor microenvironment (TME) play a crucial role in TNBC progression, making them potential therapeutic targets. Yet the molecular basis of stromal cell activation and tumor-stromal crosstalk in TNBC is poorly understood, limiting the development of therapies targeted to this axis. Methods: To explore potential therapeutic targets within the stromal niche of TNBC, we employed an advanced human in vitro microphysiological system model – the vascularized microtumor (VMT) – in which perfused vascular networks within a microfluidic platform self-assemble in a complex extracellular matrix (ECM) and supply nutrients and drugs to growing tumors. By leveraging single-cell RNA sequencing (scRNA-seq), we investigated gene expression patterns, cellular heterogeneity, and intercellular communication within TNBCs. Results: Our analysis revealed that histopathologically-normal human breast tissue-derived stromal cells activate neoplastic signaling pathways when exposed to the TNBC TME. Through a comparison of these interactions in VMTs with scRNA-seq data obtained from clinical specimens, we successfully identified therapeutic targets situated at the tumor-stromal interface that hold potential clinical significance. Promising results were observed in TNBC VMTs when combining treatments that target Tie2 signaling, thereby normalizing vasculature, with tumor-targeted paclitaxel. Furthermore, dual inhibition of Her3 and Akt also demonstrated efficacy against TNBC. Conclusions: By using an organotypic in vitro VMT model to recapitulate key components of the TNBC TME, we demonstrate the potential of inducing a favorable tumor microenvironment as a targeted therapeutic approach in TNBC.

overall_design: To explore potential therapeutic targets within the stromal niche of triple-negative breast cancer (TNBC), we employed an advanced human in vitro microphysiological system model – the vascularized microtumor (VMT) – in which perfused vascular networks within a microfluidic platform self-assemble in a complex extracellular matrix (ECM) and supply nutrients and drugs to growing tumors. By leveraging single-cell RNA sequencing (scRNA-seq), we investigated gene expression patterns, cellular heterogeneity, and intercellular communication within TNBCs.

first: Stephanie

last: Hachey

first: Daniela

last: Gaebler

first: Aneela

last: Mocherla

first: Kevin

last: Nee

first: Kai

last: Kessenbrock

last: Hughes


title: Identification of a Notch transcriptomic signature for breast cancer [dataset1]

city: Stockholm

first: Eike-Benjamin

last: Braune

address: Nobels väg 6

department: CMB

country: Sweden

institute: Karolinska Institutet

summary: Dysregulated Notch signalling contributes to breast cancer development and progression, but validated tools to measure the level of Notch signalling in breast cancer subtypes and in response to systemic therapy are largely lacking. A transcriptomic signature of Notch signalling would thus be warranted, and in this report, we have established such a classifier. To generate the signature, we first identified Notch-regulated genes from six basal-like breast cancer cell lines subjected to elevated and reduced Notch signalling by culturing on immobilized Notch ligand Jagged1 or blockade of Notch by -secretase inhibitors, respectively. From this cadre of Notch-regulated genes, we developed candidate transcriptomic signatures that were trained on a breast cancer patient dataset (the TCGA-BRCA cohort) and an optimal 20-gene signature was selected from analysis of the transcriptomes of a broader breast cancer cell line cohort. We validated the signature on two independent patient datasets (METABRIC and Oslo2) and it showed an improved coherence score and tumour specificity compared with previously published signatures. Furthermore, the signature score was particularly high for basal-like breast cancer, indicating an enhanced level of Notch signalling in this subtype. The signature score was increased after neoadjuvant treatment in the PROMIX and BEAUTY patient cohorts, and a lower signature score generally correlated with better clinical outcome. Collectively, the 20-gene transcriptional signature has the potential to better stratify patients and to evaluate the response of future Notch-based therapies for breast cancer.

overall_design:
To generate the signature, we first identified Notch-regulated genes from six basal-like breast cancer cell lines subjected to elevated and reduced Notch signalling by culturing on immobilized Notch ligand Jagged1 or blockade of Notch by g-secretase inhibitors, respectively. From this cadre of Notch-regulated genes, we developed candidate transcriptomic signatures that were trained on a breast cancer patient dataset (the TCGA-BRCA cohort) and a broader breast cancer cell line cohort.
To explore the accuracy and robustness of the three signatures further, we generated a novel transcriptomic dataset using the same principal experimental set up for activation (Jagged1) and blockade (DAPT) of Notch signalling as described,but this time from a larger panel of  breast cancer cell lines from different subtypes of breast cancer. Untreated samples (FC) as well as additional control samples (Jag1+DAPT) were sequenced as well.
Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using None from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.  Library preparation, Sequencing; Data Processing
Validated under ISO accreditation 17025:2005
The authors would like to acknowledge support from Science for Life Laboratory, the National Genomics Infrastructure, NGI, and Uppmax for providing assistance in massive parallel sequencing and computational infrastructure.
MultiQC report, library info TPM and Limma R object analysis files ( (supplied as compressed files)

first: Felix

last: Geist

first: Xiaojia

last: Tang

first: Judy

last: Boughey

first: Liewei

last: Wang

first: Roberto

last: Leon-Ferre

first: Antonino

last: D’Assoro

first: James

middle: N

last: Ingle

first: Matthew

last: Goetz

first: Kang

first: Theodoros

last: Foukakis

first: Anita

last: Seshire

first: Dirk

last: Wienke

first: Urban

last: Lendahl

first: Krishna

last: Kalari


title: MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomics (MeRIP-Seq)

first: Karol

last: Bomsztyk

first: Daniel

last: Mar

first: Ilona

last: Babenko

first: Ran

last: Zhang

first: William

last: Noble

first: Oleg

last: Denisenko

first: Tomas

last: Vaisar


title: Identification of a Notch transcriptomic signature for breast cancer [dataset2]

first: Eike-Benjamin

last: Braune

overall_design:
To generate the signature, we first identified Notch-regulated genes from six basal-like breast cancer cell lines subjected to elevated and reduced Notch signalling by culturing on immobilized Notch ligand Jagged1 or blockade of Notch by g-secretase inhibitors, respectively. From this cadre of Notch-regulated genes, we developed candidate transcriptomic signatures that were trained on a breast cancer patient dataset (the TCGA-BRCA cohort) and a broader breast cancer cell line cohort.
RNA libraries of samples used for Notch signature gene determination were constructed as described above and samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with a 151nt(Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+. Three biological replicates were sequenced per condition.
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with a 151nt(Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Validated under ISO accreditation 17025
The authors would like to acknowledge support from Science for Life Laboratory, the National Genomics Infrastructure, NGI, and Uppmax for providing assistance in massive parallel sequencing and computational infrastructure.

first: Felix

last: Geist

first: Xiaojia

last: Tang

first: Judy

last: Boughey

first: Liewei

last: Wang

first: Roberto


title: MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomics (H3K4m3-Seq)


title: ABCC4 impacts megakaryopoiesis and protects megakaryocytes against 6-mercaptopurine induced cytotoxicity [RNA-seq Mouse]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: The role of ABCC4, an ATP-binding cassette transporter, in the process of platelet formation, megakaryopoiesis, is unknown. Here, we show that ABCC4 is highly expressed in megakaryocytes (MKs). Mining of public genomic data (ATAC-seq and genome wide chromatin interactions, Hi-C) revealed that key megakaryopoiesis transcription factors (TFs) interacted with ABCC4 regulatory elements and likely accounted for high ABCC4 expression in MKs. Importantly these genomic interactions for ABCC4 ranked higher than for genes with known roles in megakaryopoiesis suggesting a role for ABCC4 in megakaryopoiesis. We then demonstrate that ABCC4 is required for optimal platelet formation as in vitro differentiation of fetal liver derived MKs from Abcc4-/- mice exhibited impaired proplatelet formation and polyploidization, features required for optimal megakaryopoiesis. Likewise, a human megakaryoblastic cell line, MEG-01 showed that acute ABCC4 inhibition markedly suppressed key processes in megakaryopoiesis and that these effects were related to reduced cAMP export and enhanced dissociation of a negative regulator of megakaryopoiesis, protein kinase A (PKA) from ABCC4. PKA activity concomitantly increased after ABCC4 inhibition which was coupled with significantly reduced GATA-1 expression, a TF needed for optimal megakaryopoiesis. Further, ABCC4 protected MKs from 6-mercaptopurine (6-MP) as Abcc4-/- mice show a profound reduction in MKs after 6-MP treatment. In total, our studies show that ABCC4 not only protects the MKs but is also required for maximal platelet production from MKs, suggesting modulation of ABCC4 function might be a potential therapeutic strategy to regulate platelet production.

overall_design: We performed differential gene expression analysis using data obtained from RNA-seq of WT and Abcc4-/- mice (N=3 for each group).

first: Yao

first: Shibiao

first: Scott

last: Olsen

first: John

middle: D

last: Schuetz


title: MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomics (H3K27Ac-Seq)

first: Karol

overall_design: Mouse frozen and FFPE tissue from 4 organs (brain, heart, kidney, and liver) were obtained and analyzed using ChIP, MeDIP, MeRIP, and RT PCR and Sequencing. Data was compared using correlation scatterplots, differential expression, IGV (sequencing read profile snapshots), PCA, PCR Crunch (expression and epigenetic mark levels), and Venn diagrams.

first: Daniel


title: MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomics


title: ABCC4 impacts megakaryopoiesis and protects megakaryocytes against 6-mercaptopurine induced cytotoxicity [RNA-seq Human]

overall_design: We performed differential gene expression analysis using data obtained from RNA-seq of  MEG-01 cells differentiated with Phorbol 12-myristate 13-acetate in presence and absence of Ceefourin 2 (N=2 for each group).

first: Sabina

last: Ranjit


title: Gene expression signatures to the radiation attenuated Schistosome Vaccine

city: Salvador

first: Almiro

middle: Pires

last: Neto

state: Bahia

address: Waldemar Falcão Street

department: Immunology

country: Brazil

institute: Gonçalo Muniz Institute

summary: Despite several decades of research, an effective vaccine against schistosomiasis remains elusive. The radiation-attenuated (RA) cercarial vaccine is still the best model eliciting high protection levels, although the immune mechanisms have not yet been fully elucidated.Transcriptomic data of PBMC from vaccinated and infected C57BL/6 mice in three timepoints (Days 7 and 17 after infection or vaccination, and Day 7 post-challenge) were reanalyzed. In addition, we generated data on PBMC collected 35 days after a high dose infection of 500 cercariae. Gene co-expression networks and Over Representation Analysis (ORA) were performed using the CEMiTool package. Protein-protein interaction networks were constructed using STRING and the hub proteins for each module were identified using Cytoscape.Co-expression network analysis identified a module (M2) associated with the infection process, grouping genes related to Th2 immune response; and a module (M6) associated with the vaccination process, displaying pathways related to Th1 response, CD8+ T cells and NK cells. Within each module, five hub proteins were identified based on protein-protein interaction networks. The M2 infection module hub revealed Chil3, Il4, Cx3cr1, Emr1 and Ccl2; and the (M6) vaccination module presented Prf1, Klrc1, IFN-γ, Ncr1 and Tbx21. Our data point out to the potential role of NK cells that may contribute to the RA vaccine response through the production of IFN-γ orchestrated by the T-bet transcription factor (Tbx21).

overall_design: Mice were vaccinated with one dose (V1) or three doses (V3) of 500 attenuated cercariae, or infected (VC) with 500 normal cercariae. Then, gene expression in mice PBMC was measured in a time course manner at day 7 (7dpi) and 17 (17dpi) after vacination or day 7 (7dpi), 17 (17dpi) and 35 (35dpi) after infection. In addition, the vaccine groups (V1 and V3) and a challenge control (Chc) were challenge with 120 normal cercariae and PBMC gene expression was measured 7 days post-challenge (7dpc). PBMC from control (C) non-treated mice was used to generate the baseline of gene expression. Four to five independent biological replicates were assessed per group (V1, V3, VC and Chc) per time point, and 16 biological replicates from control group (C) were used to generate the baseline of expression for PBMC microarray analysis. All biological replicate consisted of a pool of PBMCs (containing equal amounts of total RNA) from three mice. Data is derived from one independent experiment.

first: Juliana

last: Vitoriano-Souza

first: Robert

middle: A

last: Wilson

first: Luciana

last: Leite

first: Pablo

middle: I

last: Ramos

first: Leonardo

last: Farias


title: Spermidine Induces Cytoprotective Autophagy of Female Germline Stem Cell in vitro

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: To uncover the mechanism of SPD-induced autophagy in FGSCs, we used RNA sequencing technology to compare the mRNA expression differences between the control groups and the SPD treated groups. FGSCs mRNA profiles of the control groups and the SPD treated groups were generated by deep sequencing, in two replicates. The library quality was determined using a Bioanalyzer 2100 (Agilent). The Illumina HiSeq 2500 platform was used for RNA sequencing. The quality of RNA-seq reads was examined using FastQC.

overall_design: SPD-treated and control FGSCs mRNA profiles of 4h were generated by deep sequencing, in two replicates.

first: Xiaoyan

last: Yuan


title: MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomics (PolII-Seq)

last: Bomsztyk

summary: Integration of ChIP, MeDIP, MeRIP, and RT Seq for multiomics analysis of frozen and FFPE tissue

last: Mar

first: Ilona

last: Babenko

first: Ran

last: Zhang

first: William

last: Noble

first: Oleg

last: Denisenko

first: Tomas

last: Vaisar


title: Identification of a Notch transcriptomic signature for breast cancer

first: Eike-Benjamin

last: Braune


title: 3' RACE-seq of endogenous LINE-1 mRNA's 3' non-templated ends in PA-1 control kd, XRN1 kd, DCP2 kd, and DIS3L2 kd (kd by RNAi for 48h = set 1, or 126h = set 2), and 293T wild-type and XRN1 KO.

first: Zbigniew

last: Warkocki

summary:
Human LINE-1 retrotransposons can mobilize in the human genome by a copy-and-paste machanism involving RNA intermediates. LINE-1 mRNA 3' ends play a major role in initiation of reverse transcription (a step retrotransposition).
To assess the impact of RNA 3’ end dynamics of LINE-1 mRNA on its retrotransposition potential in human cells we analyzed 3' non-templated ends on LINE-1 mRNA by 3' RACE-seq. RNA was retrieved from multiple clonal 293T and PA-1 cells wild-type or knock-out in either XRN1, DCP2, or DIS3L2.

Publication: D Janecki, R Sen, N Szóstak, A Kajdasz, M Kordys, K Plawgo, D Pandakov, A Philips, Z Warkocki (2024): LINE-1 mRNA 3’ end dynamics shape its biology and retrotransposition potential. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad1251

overall_design: 3’ RACE-seq on endogenous LINE-1 mRNA from a total of 7 clonal wild-type 293T cells, 7 clonal XRN1 KO cell lines in 293T, 1 clonal DCP2 KO cell line in 293T, 1 clonal DCP2 plus XRN1 KO cell line in 293T. Also sequencing of artificial spike-ins with a known number of 0, 8, 16, 32, 64, and 128 consecutive A residues. All RACE-seq libraries were performed in 3 technical replicates for each mRNA analyzed. Note a set of 4 cellular conditions: wild-type, XRN1 KO, DCP2 KO, and DCP2 plus XRN1 KO (based on cells obtained from dr Sarah Slavoff, Luo et al., 2020, 10.1021/acs.biochem.0c00069) was performed only for reporter LINE-1 and GAPDH, and not the other 2 mRNAs. Libraries generated as described in Warkocki et al., 2018 (https://doi.org/10.1016/j.cell.2018.07.022) but PCR was done using the TaKaRa GLX polymerase.

first: Dorota

last: Adamska

first: Natalia

last: Szóstak

first: Arkadiusz

last: Kajdasz


title: Circulating isomiRs May Be Superior Biomarkers Compared to Their Corresponding Canonical miRNAs: A Pilot Biomarker   Study of Using isomiR-ome to Detect Coronary Calcium-Based Cardiovascular Risk in Patients with NAFLD

city: Be'er Sheva

first: Nataly

last: Makarenkov

address: David Ben Gurion Blvd 1

institute: Ben Gurion University

type: Non-coding RNA profiling by high throughput sequencing

summary: Cardiovascular (CV) disease is the leading cause of morbidity and mortality in patients with non-alcoholic fatty liver disease (NAFLD).  Yet clinically, distinguishing between NAFLD patients with average CV risk from those at elevated risk is not easily achieved by traditional CV risk factors and clinically-based scoring systems. Here we hypothesize that in-depth analysis of circulating miRNAs can identify strong putative biomarkers for the degree of CV risk among patients with NAFLD

overall_design: Plasma miRNAs of 12 NAFLD patients were sequenced by next-generation sequencing (NGS).

first: Uri

last: Yoel

first: Yulia

last: Haim

first: Nikhil

last: Bhandarkar

first: Aryeh

last: Shalev

first: Ilan

last: Shelef

first: Idit

last: Liberty

first: Gal-Ben

last: Arie

first: David

last: Yardeni

first: Assaf

last: Rudich

first: Ohad

last: Etzion

first: Isana

last: Veksler-Lublinsky


title: PRMT5 inhibition by LLY-283 in HSJD-DIPG-007 DMG cells

city: Oxford

first: Elizabeth

middle: J

last: Brown

address: Roosevelt Drive

department: Centre for Medicines Discovery

country: United Kingdom

institute: University of Oxford

summary: H3K27-altered Diffuse Midline Glioma (DMG) is a universally fatal paediatric brainstem tumour. The prevalent driver mutation H3K27M creates a unique epigenetic landscape that may also establish therapeutic vulnerabilities to epigenetic inhibitors. From a wider screen of an epigenetic inhibitor library, we identified PRMT5 inhibitors as amongst the top hits reducing DMG cell viability. Here, we treated HSJD-DIPG-007 +/- the PRMT5 inhibitor LLY-283. RNA-sequencing was performed at 0, 1, 2, 3, 5, 7 and 10 days to assess the changes in gene expression following PRMT5 inhibition in DMG cells. This shows that PRMT5 inhibition changes expression in genes associated with multiple disease relevant phenotypes, including sterol metabolism, differentiation, and the extracellular matrix. By characterising the changes in the transcriptome following PRMT5 inhibition this provides crucial insights into the potential of PRMT5 inhibitors as a treatment for H3K27-altered DMG.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HSJD-DIPG-007 cells treated with LLY-283/vehicle for 0, 1, 2, 3, 5, 7 or 10 days

first: Adam

last: Cribbs

first: Martin

last: Philpott

first: Udo

last: Oppermann

first: Alex

last: Bullock

first: Gillian

last: Farnie


title: Gene expression data from precision cut lung slices (PCLS) of old and young mice infected with two strains of Pseudomonas aeruginosa

city: Hannover

first: Stella Marie

last: Reamon-Buettner

address: Nikolai-Fuchs Strasse1

department: Preclinical Pharmacology & In Vitro Toxicology

institute: Fraunhofer-ITEM

summary:
The study aimed to mimic inflamm-aging using ex vivo precision-cut lung slices (PCLS) from young and old mice, and to investigate the influence of aging on inflammation upon infection with the P. aeruginosa standard lab strain PAO1 and a clinical P. aeruginosa isolate, D61.
Genome-wide transcriptome analysis revealed that genes associated with processes of immune system were strongly regulated with aging upon P. aeruginosa infection. Very early events of pulmonary inflamm-aging can be mimicked ex vivo in tissue slices of distal lungs and aging promotes pulmonary inflammation upon P. aeruginosa infection

overall_design: Murine precision cut lung slices (mPCLS) were prepared from the strain C57BL/6NCrl  i.e. n=7 old, and n=8 young mice. PCLS were infected with two different strains of P .aeruginosa or uninfected (control). Two mPCLS samples were used for RNA isolation and gene expression analysis.

first: Stella

first: Monika

last: Niehof

first: Charline

last: Sommer


title: Comparative analysis of Olfactory bulb RNA obtained from control and odor stimulated mice

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Transcript profiling of OB from control and odor stimulated mice to determine the effect of odor enrichment

overall_design: Agilent one-color experiment,Organism: Mouse Agilent Microarray Gene Expression 8x60K Arrays AMADID: 74809

first: Smitha

last: Bhaskar

first: Jeevan

last: Gowda

first: Anujith

last: Kumar


title: Transcriptome analysis in transgenerational epigenetic inheritance

city: New Delhi

first: Abhay

last: Sharma

state: New Delhi

address: Sukhdev vihar

department: Molecular medicine

institute: CSIR Institute of genomics and integrative biology

summary: The study was performed towards understanding transgenerational epigenetic inheritance at transcriptome level.  The founder males of F0 generation (actin-GAL4/Pin; UASRNAi-mts/+), and the resulting, male-line derived F1 (Pin/+; +/+), and F2 (+/+; +/+) generation individuals were used as test lineage, and the wild-type w1118  progeny as control lineage flies. The fly strains used for generating founder F0 line included Pin/CyO-dYFP; UASRNAi-mts/MKRS, actin-GAL4/CyO; +/+, and w1118. Precursor strains, as appropriate, were outcrossed with w1118 to minimize genetic background differences.

overall_design: F0 males (actin-GAL4/Pin; UASRNAi-mts) were mated with w1118 females to obtain F1 progeny (Pin/+; +/+), and F1 males mated with w1118 females to obtain F2 progeny (+/+; +/+) in the test lineage. In parallel, w1118 flies were self-crossed, and the control lineage flies obtained. Three to five biological replicates were used.

first: Karunakar

last: Pinreddy


title: GATA Switch Enhancers Mark Dynamically Regulated Chromatin Interaction Nodes during Erythroid Maturation

city: Cambridge

first: Jonathan

last: Li

state: Massachusetts

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

summary: Erythropoiesis is among the best understood examples of cell differentiation.  In a required step, GATA1 replaces GATA2 at genomic loci, termed GATA switch enhancers.  Little is known about how this switch affects chromatin architecture.  Here, we show that cohesin binds GATA1 and occupies most GATA switch enhancers.  Cohesin-based chromatin interaction analysis  demonstrated that the most dynamic and interactive enhancers are enriched for GATA switch sites/TAL1 occupancy and frequently lack super-enhancer features.  A c-kit locus CRISPR/Cas9 screen identified GATA motifs within one such element as strongly impacting expression.  These data highlight the role of developmentally exchanged transcription factors in modulating genomic folding.

overall_design: Epigenetic profiling of erythroid differentiation

first: Alireza

last: Ghamari

first: Gabriela

last: Pregernig

first: Denes

last: Hnisz

first: Mitchel

last: Cole

first: Matthew

last: Canver

first: Quiming

last: Yao

first: Avik

last: Choudhuri

first: Luca

last: Pinello

first: Leonard

last: Zon

first: Daniel

last: Bauer

first: Richard

last: Young

first: Ernest

last: Fraenkel

first: Alan

last: Cantor


title: miRNA profile in mouse hepatocyte-derived exosomes

city: La Jolla

first: Wei

last: Ying

address: 9500 Gilman Dr, Stein Clinical Research Building, Room 225

institute: UC San Deigo

summary: This project was designed to understand the difference in miRNA components within hepatocyte-derived exosomes

overall_design: lean, 4wks HFD, and 16wks HFD

first: Jerrold

last: Olefsky


title: Effect of lnc-CEBPB-13 overexpression on miRNA and miRNA-targeted mRNA expression

city: Yantai

first: Xicheng

last: Song

address: No.20, Yuhuangding East Road, Zhifu District, Yantai City, Shandong Province

department: Department of Otorhinolaryngology, Head and Neck Surgery

institute: Qingdao University Affiliated Yantai Yuhuangding Hospital

summary: We performed transcriptome sequencing to identify differentially expressed miRNAs and identified signaling pathways for miRNA-targeted mRNA.

overall_design: Comparison of gene expression profiles of Jurkat cells with RNA-seq data from lnc-CEBPB-13 overexpression and control group