title: Chromatin remodeling by antisense Pol II primes efficient Pol III transcription

status: Public on Dec 24 2022

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

summary: The packaging of the genetic material into chromatin imposes the remodeling of this barrier to allow efficient transcription. RNA polymerase II activity is associated with several histone modification complexes that enforce remodeling. How RNA polymerase III (Pol III) counteracts the inhibitory effect of chromatin is unknown. We report here that antisense RNA Polymerase II (Pol II) transcription is critical to prime and maintain nucleosome depletion at Pol III loci and allow efficient Pol III recruitment upon re-initiation of growth from stationary phase. Antisense Pol II is recruited by the Pcr1 transcription factor, which affects local histone occupancy through the associated SAGA complex and a Pol II phospho-S2 CTD / Mst2 pathway. These data expand the central role of Pol II in gene expression beyond mRNA synthesis.

overall_design: Gene expression and Pol III (Rpc1-TAP) occupancy in wild-type and Rpb1 CTD S2A mutant.

first: Damien

last: Hermand

first: Antonin

last: Morillon

first: Maxime

last: Wéry


title: Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules (lncRNAseq)

status: Public on Dec 20 2022

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

country: China

institute: School of Animal Science and Technology, Guangxi University

type: Non-coding RNA profiling by high throughput sequencing

summary: Mammary epithelial cells (MECs), the only cell type which could be capable of secreting milk in mammary gland, can be applied for the generation of transgenic mammary cell/gland bioreactor. However, continuously achieving large amount of high-quality goat MECs by non-invasion method, especially prepuberal MECs, in vitro has been a challenge. Here, we show that a small molecules cocktail enables the in vitro generation of chemically-induced mammary epithelial cells (CiMECs) with milk-secreting properties from goat ear fibroblasts. The properties of CiMECs were highly similar to those of naturally isolated MECs. Notably, the CiMECs lineage reprogramming process may partially imitate the MECs developmental process from embryonic to milk-secreting stages. Interestingly, fibroblasts were firstly reversed back to embryonic ectoderm/surface ectoderm-like state. Our findings constitute a substantial step toward further promoting the application of transgenic mammary bioreactors, moreover, also offer a new strategy for obtaining other cell types by reprogrammed fibroblasts.

overall_design: The six samples are analyzed. BERTV_0d are control group with three replicates. BFRTV_8d are treatment group with three replicates.

first: Dandan

last: Zhang

first: Ben

last: Huang


title: Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules (RNAseq)

type: Expression profiling by high throughput sequencing

overall_design: The twenty three samples are analyzed. BERTV0d and GMECs are control group with three replicates. BFRTV1d/2d/3d/6d are treatment group with three replicates.BFRTV4d, BFRTV8d and CiMECs are treatment group with three replicates.


title: Single-cell gene expression profiles of mouse macrophages stimulated with immune ligands

status: Public on Dec 19 2022

city: Los Angeles

first: Katherine

middle: M

last: Sheu

state: CA

address: 611 Charles E Young Dr E

country: USA

institute: UCLA

summary: Immune sentinel macrophages initiate responses to pathogens via hundreds of immune response genes. Each immune threat demands a tailored response, suggesting that the capacity for stimulus-specific gene expression is a key functional hallmark of healthy macrophages. To quantify this property, termed Response Specificity, we developed a single-cell experimental workflow and analytical approaches based on information theory and machine learning. We found that Response Specificity of macrophages is driven by combinations of specific immune genes that show low cell-to-cell heterogeneity and are targets of separate signaling pathways. The Response Specificity Profile, a systematic comparison of multiple stimulus response distributions, was distinctly altered by polarizing cytokines and enabled an assessment of the functional state of macrophages. Indeed, the Response Specificity Profile of peritoneal macrophages from old and obese mice showed characteristic differences, suggesting that Response Specificity may be a basis for measuring the functional state of innate immune cells.

overall_design: Macrophages were collected from the mouse peritoneum or differentiated from myeloid progenitors, and stimulated with a panel of immune ligands for 3hrs. Cells were collected into suspension and scRNAseq was performed using the BD Rhapsody platform.

first: Alexander

last: Hoffmann


title: Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules (scRNAseq)

overall_design: The eleven samples are analyzed. BERTV0d are control group with three replicates. BFRTV8d are treatment group with three replicates.


title: Predicting severity in COVID-19 disease using sepsis blood gene expression signatures

status: Public on Dec 18 2022

city: Vancouver

first: Robert

middle: E W

last: Hancock

state: British Columbia

address: Room 232 – 2259 Lower Mall Research Station

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

summary: Severely-afflicted COVID-19 patients can exhibit disease manifestations representative of sepsis, including acute respiratory distress syndrome and multiple organ failure. We hypothesized that diagnostic tools used in managing all-cause sepsis, such as clinical criteria, biomarkers, and gene expression signatures, should extend to COVID-19 patients. Here we analyzed the whole blood transcriptome of 124 early (1-5 days post-hospital admission) and late (6-20 days post-admission) sampled patients with confirmed COVID-19 infections from hospitals in Quebec, Canada. Mechanisms associated with COVID-19 severity were identified between severity groups (ranging from mild disease to the requirement for mechanical ventilation and mortality), and established sepsis signatures were assessed for dysregulation. Specifically, gene expression signatures representing pathophysiological events, namely cellular reprogramming, organ dysfunction, and mortality, were significantly enriched and predictive of severity and lethality in COVID-19 patients. Mechanistic endotypes reflective of distinct sepsis aetiologies and therapeutic opportunities were also identified in subsets of patients, enabling prediction of potentially-effective repurposed drugs. The expression of sepsis gene expression signatures in severely-afflicted COVID-19 patients indicates that these patients should be classified as having severe sepsis. Accordingly, in severe COVID-19 patients, these signatures should be strongly considered for the mechanistic characterization, diagnosis, and guidance of treatment using repurposed drugs.

overall_design: Gene expression analysis of whole blood from COVID-19 patients for endotype classification

first: Arjun

last: Baghela

first: Andy

last: An

first: Peter

first: Erica

last: Acton

first: Jeff

last: Gauthier

first: Elsa

last: Brunet-Ratnasingham

first: Travis

last: Blimkie

first: Gabriela

last: Cohen Freue

first: Daniel

last: Kaufmann

first: Amy

middle: H

last: Lee

first: Roger

last: Levesque

middle: E


title: Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis. [I]

city: Tucson

first: Bonnie

last: LaFleur

state: AZ

address: 4151 W Speedway Blvd

institute: University of Arizona

summary:
Here we used a pan-cytokeratin antibody to differentiate the epidermal from dermal compartment and assayed over 18,000 RNA probes from multiple regions of interest (ROI) comparing sun protected skin, and two regions (edge and center) from AK/sun damaged skin. This allows for a trajectory from sun protected to sun damaged within an individual.
Traditionally, cancer biology focusses on change within the tumor compartment for diagnosis and staging and current genetic profiling of actinic keratosis (the precursor lesion for cutaneous squamous cell carcinoma) has focused on analysis limited to whole skin or the epidermal compartment alone. Here we use spatial transcriptomics to compare and contrast the epidermal and stromal compartments from different regions of actinic keratosis and matched sun protected skin from six individuals. Our data show that the major changes in AK at the transcriptional level are evident in the dermal compartment.
Sun protected skin (n=5-6 from 6 individuals for a total of 34 ROI), the center of an AK lesion (n=3 for a total of 18 ROI) and edge of the AK lesion (n=2-3 for a total of 17 ROI) representing sun-damaged skin, from six unrelated individuals, the center of an AK lesion (n=3 for a total of 18 ROI) and edge of the AK lesion (n=2-3 for a total of 17 ROI) representing sun-damaged skin, from six unrelated individuals.

overall_design: We separate out the raw data from two different experiments done approximately 6 months apart and at two different laboratories, one was run at Nanostring (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_1.xlsx), Seattle, WA  and the other at Thomas Jefferson University (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_2.xlsx).  The innitial two samples were a pilot study to ensure that pan-cytokeratin antibodies on the Nanostring DSP assay would allow for evaluation of transcriptional changes in the dermal compartment of the skin in existing samples collected at the University of Arizona.  The second set of samples were run a the Core facility of Thomas Jefferson University after extramural funding (through a genomic supplement) had been obtained.

first: Andrew

last: South

first: Edgar

last: Tapia

first: H-H

middle: S

last: Chow

first: Joel

last: Parker

first: Lisa

last: White

first: Clara

last: Curiel-Lewandrowski


title: Investigating the role of cell adhesion molecule alpha-catenin during islet development

status: Public on Dec 15 2022

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary:
Purpose: Alpha catenin mediates cell-cell adhesion through the cadherin-catenin complex. It is important to maintain cell-cell adhesion and tissue organization. In this study we explore how cell-cell adhesion mediated by alpha catenin regulates islet aggregation and analyze the gene expression profiling related with islet adhesion, structure and function.
Methods: We selective ablate alpha catenin (Ctnna1) in endocrine cells of murine pancreas. Total RNA was extracted from pancreatic islets isolated from 8 weeks old mice of Ngn3-Cre; Ctnna1flox/flox and Wild-type controls. There were four animals for each group.
Results: We mapped about 60 million sequence reads per mouse sample. Our results showed that 245 genes were upregulated and 74 were downregulated by alpha catenin ablation.
Conclusions: Our results indicate that alpha catenin is required for normal islet aggregation and cellular composition.

overall_design: Pancreas mRNA profiles of 8-weeks old wild type (WT) and Ngn3-Cre; Ctnna1 flox/flox mice

first: Wilma

last: Tixi

first: Hung-Ping

last: Shih


title: Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity

status: Public on Dec 14 2022

city: Seattle

middle: Moreda

last: Tresenrider

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: With a critical need for more complete in vitro models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA-seq multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10x methods produce highly concordant cell type compositions and then expand sci-Plex to analyze the cell type composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell types up to six weeks later. Our data show sci-Plex’s potential to dramatically scale-up the analysis of treatment conditions on relevant human models.

overall_design: Day 28, Day 78, and Day 185 retinal organoids were subjected to both 10x and sci-RNA-seq. Individual D28 (314) and D63 (96) organoids were labeled and subjected to sci-RNA-seq3.

first: Cole

last: Trapnell

first: Thomas

middle: A

last: Reh

first: Kiara

middle: C

last: Eldred

first: Akshayalakshmi

last: Sridhar


title: Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis. II[

overall_design: We separate out the raw data from two different experiments done approximately 6 months apart and at two different laboratories, one was run at Nanostring (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_txt), Seattle, WA  and the other at Thomas Jefferson University (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement2.txt).  The initial two samples were a pilot study to ensure that pan-cytokeratin antibodies on the Nanostring DSP assay would allow for evaluation of transcriptional changes in the dermal compartment of the skin in existing samples collected at the University of Arizona.  The second set of samples were run a the Core facility of Thomas Jefferson University after extramural funding (through a genomic supplement) had been obtained.


title: Mechanisms of IRF2BPL-related Disorders and Identification of a Potential Therapeutic Strategy

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: NEDAMSS is a recently discovered neurological disorder caused by heterozygous truncations in the intron-less transcriptional regulator, IRF2BPL. Here, we reprogram patient skin fibroblasts to astrocytes and neurons to study mechanisms of this newly described disease. While full-length wild-type IRF2BPL is primarily localized to the nucleus, we find that truncated patient variants sequester the wild-type protein to the cytoplasm and cause aggregation. Moreover, patient astrocytes fail to support neuronal survival in co-culture assays and exhibit aberrant mitochondria and respiratory dysfunction. Treatment with small molecule Copper ATSM rescues neuronal survival and restores mitochondrial function. Importantly, the in vitro findings are recapitulated in vivo, where co-expression of full-length and truncated IRF2BPL in Drosophila results in cytoplasmic accumulation of full-length IRF2BPL. Moreover, flies harboring heterozygous truncations of the IRF2BPL ortholog (Pits) display progressive motor defects that are ameliorated by CuATSM treatment. Our findings provide insights into mechanisms involved in NEDAMSS and reveal a promising treatment for this severe disorder.

overall_design: Induced astrocytes (iAst) from patients and healthy controls were subject to CuATSM treatment and sequenced. Four patients, four healthy controls, treated and untreated samples, three biological and two technical replicates each, 96 RNA-seq libraries in total.

first: Shresth

last: Ray

first: Debdeep

last: Dutta

first: Cassandra

last: Dennys

first: Samantha

last: Powers

first: Florence

last: Roussel

first: Pawel

last: Lisowski

last: Glažar

first: Xiaojin

last: Zhang

first: Pipasha

last: Biswas

first: Joe

last: Carporale

first: Marc

last: Bickle

first: Rajewsky

last: Nicolaus

first: Nicholas

last: Wein

first: Hugo

last: Bellen

first: Shibi

last: Likhite

first: Paul

last: Marcogliese

first: Kathrin

last: Meyer


title: Transcriptome analysis of targeted RNA-knockdown using CRISPR-Csm in HEK293T cells

status: Public on Dec 12 2022

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

summary: To investigate the efficacy of CRISPR-Csm complexes for RNA-  knockdown in eukaryotes, we quantified transcript abundance in HEK293T cells after targeting several nuclear or cytoplasmic RNAs. RNA-seq demonstrates efficient and specific knockdown of CRISPR-Csm compared to Cas13 and shRNA knockdown.

overall_design: Transcriptome profiling folllowing three RNA-knockdown techniques (CRISPR-Csm, shRNA and Cas13) for multiple targets (XIST, SMARCA1, MALAT1, CKB) in HEK293T cells. RNA-seq was performed in singlicate and transcript abundances were compared to HEK293T cells transfected with an empty-vector control.

first: Trinidad

last: Marena

first: Colognori

last: David

first: Doudna

last: Jennifer


title: Effect of reduced glucocorticoid receptor-RNA affinity on dexamethasone treatment

status: Public on Dec 17 2022

city: Boulder

first: Nickolaus

middle: Charles

last: Lammer

state: Colorado

address: 3415 Colorado Ave

department: Biochemistry

institute: University of Colorado, Boulder

summary: The RNA binding ability of the glucocorticoid receptor (GR) remains an understudied area of GR regulation. Through in vitro binding assays, we identified a separation-of-function mutation (SoF) in the DNA-binding domain that greatly reduces RNA affinity with a slight reduction in DNA affinity. To study the effects of RNA binding on GR function, we first generated stable U2OS cells expressing wild-type GR-HaloTag, the SoF mutant, or a control (Ctrl) mutant that mimics the SoF's reduction in DNA affinity without impairing RNA affinity. We then treated the cells with dexamethsone every hour over three hours with 4-thiouridine labeling, isolated the labeled RNAs, and used deep sequencing to measure changes in the dexamethasone-driven transcriptome.

overall_design: 4sU-seq to measure differences in the transcriptome between glucocorticoid receptor constructs in U2OS over 3 hours of 100 nM dexamethasone treatment.

first: Mary

last: Allen

first: Deborah

last: Wuttke

first: Robert

middle: T

last: Batey


title: Changes in lipid metabolism driven by steroid signalling modulate proteostasis in C. elegans

city: Valencia

first: Carlos

last: Mora-Martínez

state: Comunidad Valenciana

address: Emilio Lluch 4Dup 16

country: Spain

institute: Universidad Internacional de Valencia

summary: Alzheimer’s, Parkinson’s or Huntington’s disease can be caused by mutations that enhance protein aggregation, but we still do not know enough about the molecular players of these pathways to develop treatments for these devastating diseases. Here, we screen for mutations that might enhance aggregation and to investigate the mechanisms that protect against dysregulated homeostasis. We report that the protein UNC-1 activates neurohormonal signalling from the sulfotransferase SSU-1 in ASJ sensory/endocrine neurons. This hormone targets the nuclear receptor NHR-1, which acts cell-autonomously in the muscles to protect against aggregation. A second nuclear receptor, DAF-12, functions oppositely to NHR-1 to maintain protein homeostasis. Transcriptomics analyses of unc-1 mutants revealed changes in the expression of genes involved in fat metabolism, suggesting for the first time that fat metabolism changes, controlled by neurohormonal signalling, contribute to protein homeostasis. Furthermore, the enzymes involved in the identified signalling pathway are potential targets for treating neurodegenerative diseases caused by disrupted protein homeostasis.

overall_design: Comparative expression analysis of wildtype, unc-1(vlt10), nhr-1(vlt16) and unc-1(vlt10); nhr-1(vlt16) C. elegans young adults carrying a transgene containing a 40-glutamine repeat fused to a yellow fluorescent protein (40Q::YFP). 6 replicates per genotype.

first: A

middle: P

last: Gómez-Escribano

first: C

first: M

last: Roca

first: D

last: Walker

first: J

last: Panadero

middle: D

last: Sequedo

first: R

last: Saini

first: H

middle: J

last: Knölker

last: Blanca

last: Burguera

last: Lahoz

last: Cañizares

last: Millán

first: N

middle: O

last: Burton

first: W

middle: R

last: Schafer

last: Vázquez-Manrique


title: iPSC-derived macrophages: the differentiation protocol affects cell immune and metabolic characteristics and differentiation trajectories

status: Public on Dec 10 2022

city: Moscow

first: Irina

last: Lyadova

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

summary: The generation of human macrophages from induced pluripotent stem cells (iMacs) is a rapidly developing approach used to create disease models, screen drugs, study macrophage-pathogen interactions and develop macrophage-based cell therapy. To generate iMacs, different types of protocols have been suggested, all thought to result in the generation of similar iMac populations. However, direct comparison of iMacs generated using different protocols has not been performed. We have compared the productivity, the differentiation trajectories and the characteristics of iMacs generated using two widely used protocols and found significant differences in: (i) protocol productivity; (ii) dynamic changes in the expression of genes related to inflammation and lipid homeostasis following iMac differentiation; and (iii) the transcriptomic profiles of terminally differentiated iMacs, including the expression of genes involved in inflammatory response (e.g., CCL2, CCL8, NLRP2), antigen presentation (e.g., HLA class II, CD74, CFSF) and lipid homeostasis (e.g., LDRL, MSR1, OLR1, RETN). The results document for the first time the dependence of fine iMac characteristics on the type of differentiation protocol, which is important for further development of the field and various iMac applications.

overall_design: We analyzed gene expression using RNA-seq in iPSC-derived macrophages obtained with two protocols of differentiation (EBS and 2DF) and two cell lines (iMA and K7). Both resulting iMacs and dynamics of differentiation were compared between protocols.

first: Anna

last: Klepikova


title: CHRM3 is a novel prognostic factor of poor prognosis and promotes GBM progression via activation of oncogenic invasive growth factors

city: Jining

first: Wei

last: Meng

address: 89 Guhuai Road

department: Affiliated Hospital of Jining Medical University

institute: Jining Medical University

summary: Glioblastoma (GBM) is the most aggressive cancer in brain and contains a high mortality ratedue to lack of effective treatment strategy. Molecular mechanisms of GBM characteristic invasive growth are urgently need to improve the poor prognosis. Via single nuclear-sequences of primary and recurrent GBM samples, level of the M3 muscarinic acetylcholine receptor (CHRM3) was significantly higher in recurrent samples. Moreover, immunohistochemical staining of an array of glioma samples showed that high levels of CHRM3 is correlated to poor prognosis of glioma, consistent with The Cancer Genome Atlas (TCGA) database. Knockdown of CHRM3 retarded glioma cell growth and invasion. In vivo assay of orthotopic glioma animal model indicated that inhibition of CHRM3 significantly suppressed glioma progression with prolonged survival time. Transcriptome analysis revealed that CHRM3 knockdown significantly reduced array of classic factors involved in cancer invasive growth including MMP1/MMP3/MMP10/MMP12 and CXCL1/CXCL5/CXCL8. Taken together, our study identified that CHRM3 is a new and important factor of GBM progression via regulation of multiple oncogenic genes and these results provide a new biomarker for prognosis and therapy of GBM patients.

overall_design: Glioblastoma (GBM) is the most aggressive cancer in brain and contains a high mortality ratedue to lack of effective treatment strategy. Molecular mechanisms of GBM characteristic invasive growth are urgently need to improve the poor prognosis. Via single nuclear-sequences of primary and recurrent GBM samples, level of the M3 muscarinic acetylcholine receptor (CHRM3) was significantly higher in recurrent samples. Moreover, immunohistochemical staining of an array of glioma samples showed that high levels of CHRM3 is correlated to poor prognosis of glioma, consistent with The Cancer Genome Atlas (TCGA) database. Knockdown of CHRM3 retarded glioma cell growth and invasion. In vivo assay of orthotopic glioma animal model indicated that inhibition of CHRM3 significantly suppressed glioma progression with prolonged survival time. Transcriptome analysis revealed that CHRM3 knockdown significantly reduced array of classic factors involved in canc  er invasive growth including MMP1/MMP3/MMP10/MMP12 and CXCL1/CXCL5/CXCL8. Taken together, our study identified that CHRM3 is a new and important factor of GBM progression via regulation of multiple oncogenic genes and these results provide a new biomarker for prognosis and therapy of GBM patients.

first: Bin

last: Zhang

first: Hua

last: Xu

first: Yongzhi

last: Wang

first: Guangning

first: Bo

last: Gao

first: Jianyi

last: Zhao

last: Han

first: Guohong

last: Song

first: Junchen


title: Tissue resident memory T cells trigger rapid exudation and local antibody accumulation

status: Public on Dec 09 2022

city: Lebanon

first: Pamela

last: Rosato

state: NH

address: 1 Medical Center Dr, Rubin fl 7-30

institute: Dartmouth College

summary:
Adaptive immunity is didactically partitioned into humoral and cell-mediated effector mechanisms, which may imply that each arm is separate and does not function together. Here, we report that the activation of CD8+ resident memory T cells in nonlymphoid tissues triggers vascular permeability, which facilitates rapid distribution of serum antibodies into local tissues. TRM reactivation was associated with transcriptional upregulation of antiviral signaling pathways as well as Fc receptors and components of the complement cascade. Effects were local, but evidence is presented that TRM in brain and reproductive mucosa are both competent to induce rapid antibody exudation. TRM reactivation in the mouse female genital tract increased local concentrations of virus-specific neutralizing antibodies including anti-vesicular stomatitis virus and passively transferred anti-HIV antibodies. We showed that this response was sufficient to increase the efficacy of ex vivo vesicular stomatitis virus neutralization. These results indicate that CD8+ TRM antigen recognition can enhance local humoral immunity.
Microarray data comparing RNA isolated from murine female reproductive tract tissue from control tissue (SIIN) versus tissues where resident memory T cells were reactivated 9 hours prior (GP33). Control mice (SIIN) received the irrelevant peptide SIINFEKL transcervically. Experimental mice (GP33) recieved the peptide gp33, which P14 resident memory T cells specifically recognize, transcervically.

overall_design: female reproductive tract tissue from 3 mice per condition (control and Trm reactivated) were processed for total RNA 9 hours following treatment

first: Sathi

last: Wijeyesinghe


title: Pharmacological inhibition of lipid import and transport proteins in ovarian cancer

status: Public on Dec 05 2022

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

summary: Ovarian cancer (OC) is still the most fatal gynecological cancer due to late diagnosis when peritoneal metastasis has already occurred. OC progression requires lipid nutrients that are either synthesized endogenously in the cancer cells or imported from the surrounding host tissue. Accordingly, blockade of lipid synthesis has been shown to be a powerful strategy against OC. However, direct evidence of the role of lipid import and transport for OC growth is still largely missing. Therefore, we exposed OC cells to inhibitors of lipid uptake and transport proteins, which are typically overexpressed in OC. Our data reveal that pharmacological inhibition of these lipid handling proteins caused drug-specific, dose- and time-dependent decline of lipid-uptake, which was associated with cell growth reduction, cell cycle arrest and apoptosis indicating that OC cells are exquisitely sensitive to lipid deficiency. This dependency provides the rationale for the development of novel lipid-antimetabolic strategies against OC.

overall_design: RNA-seq experiments; gene expression differences between ovarian cancer cell lines treated with BMS309403, HTS01037, NAV2729, SB-FI-26 or sulfosuccinimidyl-oleate (SSO) were analysed in biological triplicates.

first: Thomas

last: Grunt


title: The effect of background noise and its removal on the analysis of single-cell expression data

city: Planegg

first: Ines

last: Hellmann

address: Großhaderner Straße 2

department: Anthropology and Human Genomics, Faculty of Biology

institute: Ludwig-Maximilians-Universität München

summary: BACKGROUND: In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage from cell-free ambient RNA or barcode swappingevents. Here, we characterize this background noise exemplified by three single-cell RNA-seq(scRNA-seq) and two single-nucleus RNA-seq (snRNA-seq) replicates of mouse kidney cells. For each experiment, kidney cells from two mouse subspecies were pooled, allowing to identify cross-genotype contaminating molecules and estimate the levels of background noise.  RESULTS: We find that background noise is highly variable across replicates and individual cells, making up on average 3-35% of the total counts (UMIs) per cell and show that this has a considerable impact on the specificity and detectability of marker genes. In search of the source of the background noise, we find that expression profiles of cell-free droplets are very similar to expression profiles of cross-genotype contamination profiles and hence that the majority of background molecules originates from ambient RNA. Finally, we use our genotype-based estimates to evaluate the performance of three methods (CellBender, DecontX, SoupX) that are designed to quantify and remove background noise. We find that CellBender provides the most precise estimates of background noise levels and also yields the highest improvement for marker gene detection. By contrast, clustering and classification of cells are fairly robust towards background noise and only small improvements can be achieved by background removal that may come at the cost of distortions in fine structure.  CONCLUSION: Our findings help to better understand the extent, sources and impact of background noise in single-cell experiments and provide guidance on how to deal with it.

overall_design: Three scRNA-seq (rep1-3) and two snRNA-seq (nuc2, nuc3) replicates were generated from mouse kidney cells. In each experiment, cells from dissociated kidneys of three mice from different strains (C57BL/6, CAST/EiJ and 129S1/SvImJ) were pooled. The replicates rep2 & nuc2 and rep3 & nuc3 were generated from the same set of mice each.

first: Philipp

last: Janssen

first: Zane

last: Kliesmete

first: Beate

last: Vieth

first: Xian

last: Adiconis

first: Sean

last: Simmons

first: Jamie

last: Marshall

first: Cristin

last: McCabe

first: Holger

last: Heyn

first: Joshua

middle: Z

last: Levin

first: Wolfgang

last: Enard


title: Arsenic exposure induces enterocyte lipid accumulation, resulting in the accelerated tissue growth and maturation during the suckling period

status: Public on Nov 30 2022

city: San Diego

first: Xiaojing

last: Yang

address: 9500 Gilman Drive, La Jolla

department: Pharmacology

institute: University of California San Diego

summary: People with early life exposure to inorganic arsenic (iAs) have been associated with adverse health outcomes manifesting during both adolescence and adulthood, but the underlying mechanism is not fully understood. We found that acute oral iAs treatment to neonatal mice induces rapid accumulation of dietary fat in enterocytes, accelerating intestinal growth and enterocyte maturation. As gene regulation study underlines dysregulated lipid absorption pathways and apolipoprotein gene expressions, plasma lipoprotein abnormalities and atherogenic dyslipidemia were identified, highlighted by hypertriglyceridemia, and decreased HDL cholesterol. This pathological condition aggravates to early stages of NAFLD. In loss-of-function genetic models, these pathophysiological alterations induced by acute oral iAs exposure illustrates critical metabolic networks entailing LXR- and ATF4- regulatory schemes. Our findings demonstrate a cooperation between the intestinal tract and liver with the overproduction of serum and tissue TGs, early signs of metabolic syndrome. We anticipate an exacerbated condition if exposure is continued. This study provides a novel pathological reason for iAs exposure induced medical conditions related to metabolic syndromes.

overall_design: Intestinal RNA was prepared from vehicle and iAs treated mice at 14-day-old (n=12), RNA from three mice were pooled, and a total four samples per group were used for RNA-sequencing.

first: Andre

last: Weber

first: Elvira

last: Mennillo

first: Patrick

last: Secrest

first: Philip

last: Gordts

first: Max

last: Chang

first: Christopher

middle: W

last: Benner

first: Junlai

last: Liu

first: Michael

last: Karin

first: Robert

last: Tukey

first: Shujuan

last: Chen


title: Co-option of the transcription factor SALL1 in mole ovotestis formation [ChIP-seq]

status: Public on Dec 04 2022

first: Francisca

last: Martinez Real

address: Ihnestrasse 73

institute: Max Planck Institute for Molecular Genetics

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Changes in gene expression represent an important source for phenotypical innovation. Yet, how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing comparative analyses of epigenetic and transcriptional data in mole and mouse, we identified SALL1 as a co-opted gene for the formation of testicular tissue in mole ovotestes. Chromosome conformation capture analyses highlight a striking conservation of the 3D organization at the SALL1 locus, but a prominent evolutionary turnover of enhancer elements. Interspecies reporter assays support the capability of mole-specific enhancers to activate transcription in urogenital tissues. Through overexpression experiments in transgenic mice, we further demonstrate the capability of SALL1 to induce the ectopic gene expression programs that are a signature of mole ovotestes. Our results highlight the co-option of gene expression, through changes in enhancer activity, as a prominent mechanism for the evolution of traits.
We used ChIP-seq for three histone modifications, H3K4me1, H3K4me3 and H3K27ac to identify regulatory elements in developing gonads

sample_organism:
Mus musculus
Talpa occidentalis

platform_organism:
Mus musculus
Talpa occidentalis

overall_design: We performed enhancer identification analyses using the software CRUP and combining the three histone marks

first: Magdalena

last: Schindler

middle: M

last: Real


title: RNAseq of ST6GAL1-wild type and ST6GAL1-knock out cells of MDA-MB-231 cells.

status: Public on Dec 01 2022

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

summary: Dynamic change of glycosylation is found in various cancers; however, the precise role of glycosylation in metastasis is remained largely unknown. Current study show that α2,6-sialylation or β-galactoside α2,6-sialyltransferase (ST6Gal1) inhibits circulating tumor cell aggregation and depletion or restoration of α2,6-sialylation in patient derived xenograft model amplified or diminished cell aggregation and lung metastasis.

overall_design: ST6GAL1 was knocked out using CRISPR/Cas9 technology in MDA-MB-231 cells. To obtain differnt clones of ST6KO and ST6WT cells, single cells were sorted into 96 well/plate. Cells were checked using western blotting, and flow cytometry analysis. Cells were lysed for total RNA isolation using Trizol. Samples were sent to Northwestern University’s Center for Genetic Medicine Sequencing core facility for deep sequencing analysis.

first: Nurmaa

middle: K

last: Dashzeveg

first: Huiping


title: Alteration in m6A methylome of goat lung under PPRV infection

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

country: India

institute: ICAR-NBAGR

summary: We report the application of  MeRIP-seq (m6A-specific methylated RNA immunoprecipitation) for m6A site profiling of lung tissue under Peste des petits ruminants virus (PPRV) infection.

overall_design: Lung was collected from the PPRV infected goat.  For this comparative study, the lung of apparently healthy goats of the same age group was obtained. m6A-sequencing of the RNA isolated from both the infected and control samples.

first: RAJA

middle: I

last: NABI KHAN

first: MANAS

last: PRAHARAJ

first: WASEEM

last: MALLA

first: NEELIMA

last: HOSAMANI

first: BEENA

last: MISHRA

first: KAUSHAL

last: R RAJAK

first: BASAVARAJ

last: SAJJANAR

first: B

first: RAVI

last: GANDHAM

first: Muthuchelvan

last: Dhanavelu


title: The cellular landscape of breast cancer associated malignant pleural effusions

city: Heidelberg

first: Delphine

last: Merino

state: Victoria

address: Level 5, ONJ Centre, 145 Studley Rd, Heidelberg

department: Translational Breast Cancer Program

country: Australia

institute: Olivia Newton-John Cancer Research Institute

summary: Malignant pleural effusions (MPE) are a common complication of advanced cancers, particularly those adjacent to the pleura such as lung and breast cancer and are a  frequent complication in metastatic disease. The pathophysiology of MPE formation in advanced breast cancer remains poorly understood, and their composition and  biology are understudied. To characterise the phenotypic diversity of malignant pleural effusion, we performed single-cell RNA sequencing on 10 MPEs from 7  metastatic breast cancer patients with diverse molecular subtypes: two triple negative (TNBC) patients, three luminal B patients including one with a rare inflammatory  subtype, and two luminal A patients. For all patients, we sequenced cells from the entire MPE, without performing any enrichment or selection, in order to ascertain  the cellular composition and molecular phenotypes in an unbiased manner. Our dataset presents the first unbiased and unselected assessment of breast cancer associated MPEs at single cell resolution,  providing the community with a vital resource for the study of MPEs. Our work highlights the molecular and cellular diversity captured in MPEs and advances the use  of these clinically relevant biopsies both in monitoring disease progression and in the development of targeted therapeutics for patients with advanced breast cancer.

overall_design:
Single-cell RNA-sequencing data of 10 whole MPEs from 7 metastatic breast cancer patients. Patients have diverse molecular subtypes, including: two triple negative (TNBC) patients, three luminal B patients including one with a rare inflammatory subtype (BCB-0020), and two luminal A patients.
*** Submitter declares that raw data are unavailable due to patient privacy concerns. ***

first: Holly

last: Whitfield

first: Jean

last: Berthelet

first: Stefano

last: Mangiola

first: Caroline

last: Bell

first: Robin

middle: L

last: Anderson

first: Bhupinder

last: Pal

first: Belinda

last: Yeo

first: Anthony

last: Papenfuss

first: Melissa

last: Davis


title: Ribosome biogenesis disruption mediated chromatin structure changes in C. elegans larvae revealed by SRAtac, an integrated, customizable end to end analysis pipeline for ATAC-seq

status: Public on Nov 29 2022

city: Austin

first: Elif

last: Sarinay Cenik

state: TX

address: NHB 2.606, Stop A5000 100 East 24th St.

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Nucleolus is the largest nuclear body and the site of ribosome biogenesis. Recent studies implicated an important role for nucleolus as an organizer of chromatin architecture. However, lack of genetic tools to disrupt nucleolar ribosome biogenesis limited our understanding of the causal link between chromatin architecture and nucleolar ribosome assembly. Here, we introduce SRAlign, a reproducible, configurable, and extensible NGS data processing workflow as well as SRAtac, a customizable and end to end analysis pipeline for ATAC-seq analysis. We apply these methods to determine the changes in chromatin accessibility upon specific depletion of an RNA polymerase I subunit, RPOA-2, a ribosome biogenesis components RRB-1 in Caenorhabditis elegans. We found highly comparable changes in chromatin accessibility in response to these two perturbations. However, the identified chromatin accessibility changes are weakly correlated with gene expression changes. Our results support feedback from nucleolar ribosome biogenesis to chromatin structure during the L1 stage in C. elegans but question the significance of these changes on gene expression.

overall_design: Comparative chromatin structure studies analysis of ATAC-seq data in Caenorhabditis elegans specifically depleted of nucleolus and translation components RPOA-2 and RRB-1.

first: Trevor

middle: F

last: Freeman

first: Qiuxia

last: Zhao

first: Ayesha

last: Rahman


title: Co-option of the transcription factor SALL1 in mole ovotestis formation

first: Francisca

last: Martinez Real

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

overall_design: Refer to individual Series


title: Single-cell RNA-seq analysis of the T-cell lymphoproliferative and inflammatory disorders triggered by defective LAT signalosome

city: Marseille

first: Rudy

last: AUSSEL

address: Parc Scientifique et Technologique de Luminy

country: France

institute: CIML

summary: LatY136F mice in which tyrosine 136 of the LAT adaptor is mutated accumulate CD4+ T cells that trigger a fast-onset autoimmune and inflammatory condition called LAT signaling pathology (LSP). Its histopathological manifestations resemble those of human IgG4-related disease (IgG4-RD), an inflammatory condition unifying a constellation of clinical entities leading to multi-organ damage. Using single-cell RNA sequencing, we analyzed 5,030 CD4+ T cells isolated from the spleen of LatY136F mice over the period that leads to LSP installation. It charted the trajectory leading to full-fledged LSP and demonstrated that LSP involved T follicular helper (Tfh) cells, CD4+ cytotoxic T cells, and IgG1+ plasma cells. These cell types were also identified in the massive infiltrates found in LatY136F lung. Therefore, the LatY136F LSP entails all the cell types postulated to trigger human IgG4-RD. It offers the unique possibility to disentangle their pathological cross-talk as illustrated here using B cell-deficient LatY136F mice.

overall_design: 53448 T cells were isolated from 44 spleen from 44 C57BL/6Rj mice and processed using the Chromium Single Cell 3’ kit from 10X genomics (California, USA) for the library preparation and the Illumina HiSeq4000 . FASTQ raw files were processed using Cell Ranger software (v3.0.1, default parameters), which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads were aligned to the mouse mm10 genome.

first: Anais

last: Joachim

last: Aussel

first: Léna

last: Gélard

first: Marie

last: Malissen

first: Bernard


title: Single cell Hi-C deconvolutes proliferation and differentiation of chromosome conformation in embryonic mesoderm, ectoderm and blood

status: Public on Nov 25 2022

city: Rehovot

first: Nimrod

last: Rappoport

state: Shfela

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Embryonic development involves massive proliferation and differentiation of cell lineages. This must be supported by chromosome replication and epigenetic reprogramming, but how proliferation and cell fate acquisition are balanced in this process is not well understood. Here we use single cell Hi-C to map chromosomal conformations in post-gastrulation mouse embryo cells and study their distributions and correlations with matching embryonic transcriptional atlases. We find that embryonic chromosomes show a remarkably strong cell cycle signature. Despite that, replication timing, chromosome compartment structure, topological associated domains (TADs) and promoter-enhancer loops are sufficiently heterogeneous to support de-novo clustering of single nuclei into distinct epigenetic states. About 10% of the nuclei are identified as primitive erythrocytes, showing exceptionally compact and organized compartment structure. The remaining cells are broadly associated with ectoderm and mesoderm identities, showing only mild differentiation of TADs and compartment structures, but more specific localized contacts in hundreds of ectoderm and mesoderm promoter-enhancer pairs. The data distinguish the chromosome folding of fully committed cells from those in plastic and continuously differentiating embryo cells, suggesting localized regulatory contacts in embryos are established prior to differentiation of compartment structure and TAD localization.

overall_design: Hi-C: 10 plates analyzed overall. scRNA-seq: 15 plates analyzed overall.

first: Elad

last: Chomsky

first: Takashi

last: Nagano

first: Charlie

last: Seibert

first: Yaniv

last: Lubling

first: Yael

last: Baran

first: Aviezer

last: Lifshitz

first: Wing

last: Leung

first: Zohar

last: Mukamel

first: Ron

last: Shamir

first: Peter

last: Fraser

first: Amos

last: Tanay


title: Effect of global or hypodermal depletion of RPOA-2

first: Qiuxia

last: Zhao

state: Texas

address: 2415 Speedway

summary: To investigate the contributions of hypodermal ribosome biogenesis to organism-wide growth, we established C.elegans strains where RPOA-2 can be depleted globally or particularly in hypodermis using auxin-inducible degradation (AID) system. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different strains at 2 time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for global RPOA-2 depleted strains (degron::GFP::rpoa-2; eft-3p::TIR1, embryo, +IAA), hypodermal RPOA-2 depleted strains (degron::GFP::rpoa-2; col-10p::TIR1, embryo, +IAA),  and control strains (degron::GFP::rpoa-2, embryo, -IAA).


title: Revealing the Key Regulators of Cell Identity in the Human Adult Pancreas

status: Public on Nov 24 2022

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

institute: KU Leuven


title: Co-option of the transcription factor SALL1 in mole ovotestis formation [4C]

status: Public on Nov 22 2022

city: Berlin

first: Francisca

last: Martinez Real

summary: Changes in gene expression represent an important source for phenotypical innovation. Yet, how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing comparative analyses of epigenetic and transcriptional data in mole and mouse, we identified SALL1 as a co-opted gene for the formation of testicular tissue in mole ovotestes. Chromosome conformation capture analyses highlight a striking conservation of the 3D organization at the SALL1 locus, but a prominent evolutionary turnover of enhancer elements. Interspecies reporter assays support the capability of mole-specific enhancers to activate transcription in urogenital tissues. Through overexpression experiments in transgenic mice, we further demonstrate the capability of SALL1 to induce the ectopic gene expression programs that are a signature of mole ovotestes. Our results highlight the co-option of gene expression, through changes in enhancer activity, as a prominent mechanism for the evolution of traits.

overall_design: We used 4C-seq with the viewpoint in the Sall1 promoter to measure the interacctions of the gene with its regulatory landscape

first: Magdalena

last: Schindler

last: Real


title: High-speed live cell interferometry for screening bioprinted organoids

status: Public on Nov 26 2022

city: Los Angeles

first: Peyton

last: Tebon

address: 615 Charles E Young Dr S

department: Orthopaedic Surgery

institute: UCLA

summary: We developed bioprinted tumor organoids linked to real-time growth pattern quantitation via high-speed live cell interferometry (HSLCI). We demonstrate that bioprinting gives rise to 3D organoid structures that preserve histology and gene expression.

overall_design: Evaluation of RNA-profiles of manually- and automatic seeded tumor organoids.

first: Bowen

last: Wang

first: Alexander

last: Markowitz

first: Ardalan

last: Davarifar

first: Brandon

last: Tsai

first: Patrycja

last: Krawczuk

first: Alfredo

middle: E

last: Gonzalez

first: Sara

last: Sartini

first: Graeme

last: Murray

first: Huyen

last: Nguyen

first: Nasrin

last: Tavanie

first: Thang

first: Paul

last: Boutros

first: Michael

middle: A

last: Teitell

first: Alice

last: Soragni


title: Co-option of the transcription factor SALL1 in mole ovotestis formation [RNA-seq]

status: Public on Nov 23 2022

first: Francisca

last: Martinez Real

summary:
Changes in gene expression represent an important source for phenotypical innovation. Yet, how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing comparative analyses of epigenetic and transcriptional data in mole and mouse, we identified SALL1 as a co-opted gene for the formation of testicular tissue in mole ovotestes. Chromosome conformation capture analyses highlight a striking conservation of the 3D organization at the SALL1 locus, but a prominent evolutionary turnover of enhancer elements. Interspecies reporter assays support the capability of mole-specific enhancers to activate transcription in urogenital tissues. Through overexpression experiments in transgenic mice, we further demonstrate the capability of SALL1 to induce the ectopic gene expression programs that are a signature of mole ovotestes. Our results highlight the co-option of gene expression, through changes in enhancer activity, as a prominent mechanism for the evolution of traits.
We performed RNAseq on mouse mutant ovaries overexpressing Sall1 and compared them to wildtype ovaries at E13.5

overall_design: We applied differential expression analyses using DEseq2 between mutant and wt ovaries


title: Three-way contact analysis characterizes the higher-order organization of the Tcra locus

status: Public on Nov 28 2022

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

summary: The generation of highly diverse antigen receptors in T and B lymphocytes relies on V(D)J recombination. The enhancer Eα has been implicated in regulating the accessibility of Vα and Jα genes through long-range interactions during T cell antigen receptor gene Tcra rearrangements. However, direct evidence for Eα physically mediating the interaction of Vα and Jα genes is still lacking. In this study, we utilized the 3C-HTGTS assay, a chromatin interaction technique based on 3C, to analyze the higher-order chromatin structure of the Tcra locus. Our analysis revealed the presence of sufficient information in the 3C-HTGTS data to detect multi-way contacts. Three-way contact analysis of the Tcra locus demonstrated the co-occurrence of the proximal Jα genes, Vα genes, and Eα in CD4+CD8+ double-positive thymocytes. Notably, the INT2-TEAp loop emerged as a prominent structure likely responsible for bringing the proximal Jα genes and the Vα genes into proximity. Moreover, the enhancer Eα utilizes this loop to establish physical proximity with the proximal Vα gene region. This study provides insights into the higher-order chromatin structure of the Tcra locus, shedding light on the spatial organization of chromatin and its impact on V(D)J recombination.

overall_design: Examination of 3C-HTGTS or 4C-seq NGS data involving pair-wise or/and three-way chromatin interactions from different viewpoints respectively before or/and after EACBE knock out (duplicates).

first: Ranran

last: Dai

first: Yongchang

last: Zhu

first: Zhaoqiang

last: Li


title: The insulating activity of the Drosophila BX-C chromatin boundary Fub-1 is parasegmentally regulated by lncRNA read-through

status: Public on Nov 16 2022

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

summary: Though long non-coding RNAs (lncRNAs) represent a substantial fraction of the Pol II transcripts in multicellular animals, only a few have known functions. Here we report that the blocking activity of the Bithorax complex (BX-C) Fub-1 boundary is segmentally regulated by its own lncRNA. The Fub-1 boundary is located between the Ultrabithorax (Ubx) gene and the bxd/pbx regulatory domain, which is responsible for regulating Ubx expression in parasegment PS6/segment A1. Fub-1 consists of two hypersensitive sites, HS1 and HS2. HS1 is an insulator while HS2 functions primarily as a lncRNA promoter. To activate Ubx expression in PS6/A1 enhancers in the bxd/pbx domain must be able to bypass Fub-1 blocking activity. We show that expression of the Fub-1 lncRNAs in PS6/A1 from the HS2 promoter inactivates Fub-1 insulating activity. Inactivation is due to readthrough as the HS2 promoter must be directed towards HS1 to disrupt blocking.

overall_design: MicroC experiments were conducted on done in biological duplicates. The control lines were matching staged embryos from another experiment, where transgenes were inserted at eve locus and do not impact topology at BX-C.

first: Xin

middle: Y

last: Bing

first: Airat

last: Ibragimov

last: Schedl


title: Widespread genomic/molecular alterations of DNA helicases and their clinical/therapeutic implications across human cancer

status: Public on Nov 11 2022

city: jinan

last: Qin

state: Shandong Province

address: Wenhuaxi Road

institute: Qilu hospital of Shandong University

summary: DNA helicases are essential to genomic stability by regulating DNA metabolisms and their loss-of-function mutations lead to genomic instability and predisposition to cancer. Paradoxically, overexpression of DNA helicases is observed in several cancers, but systemic analyses of their alterations and biological or clinical implications in human cancer have not been reported. Here we analyzed genomic and molecular alterations in 12 important DNA helicases across 33 cancer types from the TCGA dataset to provide an overview of their aberrations. Significant expression heterogeneity of 12 DNA helicases was observed. We calculated DNA helicase score (DHS) based on their expression, and categorized tumors into high, low and intermediate subtypes. High DHS subtypes were robustly associated with stemness, proliferation, hyperactivated oncogenic signaling, longer telomeres, total mutation burden, copy number alterations (CNAs) and shorter survival. Importantly, tumors with high DHSs exhibited stronger expression of alternative end-join (alt-EJ) factors, indicative of sensitivity to chemo- and radio-therapies. Several drugs are identified to inhibit DNA helicases, with the Auror A kinase inhibitor Danusertib as the strongest candidate. The aberrant expression of DNA helicases was associated with CNAs, DNA methylation and m6A regulators. Our findings thus reveal widespread dysregulation of DNA helicases and their broad connection with featured oncogenic aberrations across human cancer. The close association of DHS with the alt-EJ pathway and cellular proliferation suggests that tumors with higher DHS are sensitive to chemotherapy and radiotherapy; The Auror A kinase inhibitor Danusertib may also inhibit DNA helicases. These findings thus contribute to DNA helicase-based cancer therapy.

overall_design: mRNA expression profile in 10 pairs of clear cell renal cell carcinoma tissues and adjacent non-neoplastic tissues.

first: Jing

last: Wang

first: Xing

first: Tao

last: Huang

first: Zhiqing

last: Fang

first: Lei

last: Yan

first: Yidong

last: Fan

first: Dawei

last: Xu


title: Effect of depletion of MIB1 in HCT116 cells

city: Seoul

first: Junyoung

last: Park

address: 84, Heukseok-ro

department: Department of Life Science

country: South Korea

institute: Chung-Ang University

summary: To investigate gene regulation by MIB1 in HCT116 cells, we established stable knockdown HCT116 cell lines.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq with control (shNC) and MIB1 knockdown (shMIB1) HCT116 cells.

first: Sangbeom

last: Seo


title: Transcriptional Profiling Provides New Insights into Organ Culture-Induced Changes in Human Donor Corneas

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary: Corneal transplantation is one of the most common forms of tissue transplantation worldwide. Donor corneal tissue used in transplantation is provided by eye banks, which store the tissue in culture medium after procurement. To date, the effects of cell culture on human corneal tissue have not been fully elucidated. Using the 3’ RNA sequencing method for massive analysis of cDNA ends (MACE), we show that cultivation of corneal tissue leads to significant changes in a variety of molecular processes in human corneal tissue that go well beyond aspects of previously known culture effects. Functionally grouped network analysis revealed nine major groups of biological processes that were affected by corneal organ culture, among them keratinization, hypoxia, and angiogenesis, with genes from each group being affected by culture time. A cell type deconvolution analysis revealed significant modulations of the corneal immune cell profile in a time dependent manner. The results suggest that current culture conditions should be further refined and that prolonged cultivation may be detrimental. Recently, we showed that MACE enables transcrip-tional profiling of formalin-fixed and paraffin-embedded (FFPE) conjunctival tissue with high accuracy even after more than 10 years of storage. Here we demonstrate that MACE provides comparable results for native and FFPE corneal tissue, confirming that the technology is suitable for transcriptome analysis of a wide range of archived diseased corneal samples stored in histo-logical archives. Finally, our data underscore the feasibility of bioinformatics cell-type enrich-ment analysis in bulk RNA-seq data to profile immune cell composition in fixed and archived corneal tissue samples, for which RNA-seq analysis of individual cells is often not possible.

overall_design: RNA sequencing of 7 cultured and 3 control human corneas.

first: Julian

last: Wolf

first: Paola

last: Kammrath Betancor

first: Philip

last: Maier

first: Sonja

last: Ute Heinzelmann

first: Jana

last: Jiang

first: Thomas

last: Reinhard

first: Günther

last: Schlunck

first: Thabo

last: Lapp


title: Effect of depletion of Gli1 on gene expression  of primary rat nucleus pulposus cells

status: Public on Nov 10 2022

city: Chongqing

first: Libangxi

last: Liu

address: 183 Xinqiao Main Street Shapingba, Chongqing 400037, People’s  Republic of China

institute: Department of Orthopedics Xinqiao Hospital, Army Medical University

summary: To investigate the synergistic effect of Gli1 on the regulation of nucleus pulposus cells, we obtained primary SD rat nucleus pulposus cells and knocked down Gli1 by shRNA.We then used the data obtained from RNA-seq from three different biorepeating cells for gene expression profiling analysis.

overall_design: Comparison of gene expression profiles of RNA-seq data from nucleus pulposus cells treated with sh-Gli1 and sh-NC

first: Liabangxi

first: Chencheng

last: Feng


title: FUS-ERG induces late-onset azacitidine resistance in AML cells

status: Public on Nov 21 2022

city: Otsu

first: Ai

last: Asai

state: Shiga

address: setatsukinowacho

department: hematology

country: Japan

institute: Shiga university of medical science JAPAN

summary: Stable Ba/F3 transfectants with FUS-ERG were repeatedly exposed with Aza in a clinical administration manner of 7-days treatment and 21-days interval to investigate Aza sensitivity. RNA-seq was performed when Aza susceptibility began to change and identified genes with altered expression or transcript variants.

overall_design: Comparative analysis of gene expression profiling and transcript variants of RNA-seq data for FUS-ERG vector transduced cell and empty vector transduced cells

first: Masahiro

last: Kawahara

first: Akira

last: Andoh

first: Makoto

last: Murata


title: Toxin-mediated downregulation of absorptive ion transporters NHE3, DRA, and SGLT1 in the colon contributes to diarrhea associated with Clostridioides difficile infection.

status: Public on Nov 12 2022

city: Nashville

first: Christopher

last: Peritore-Galve

state: Tennessee

address: 1161 21st Avenue South, MCN A4208

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

summary: We defined global differences in transcriptome profiles between mice inoculated with toxin mutant strains of Clostridioides difficile. These data were mined to study differences in expression of ion transporters that may be implicated in diarrhea during disease.

overall_design: The distal colon, defined as the final third of the mouse colon, was excised from euthanized mice two days post-inoculation with vehicle control (PBS) or mutant and wildtype C. difficile strains. Three biological replicates for each strain or control treatment were used to test differences in expression.


title: Genome analysis and elucidation of the biosynthetic pathway for the cRAS inhibitor rasfonin in Cephalotrichum gorgonifer

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

institute: Universität f. Bodenkultur Wien

summary: Background: Fungi are important sources for bioactive compounds that find their applications in many important sectors like in the pharma-, food- or agricultural industries. In an environmental monitoring project for fungi involved in soil nitrogen cycling we also isolated Cephalotrichum gorgonifer (strain NG_p51). In the course of strain characterization work we found that this strain is able to produce high amounts of rasfonin, a polyketide inducing autophagy, apoptosis, necroptosis in human cell lines and shows anti-tumor activity in RAS-dependent cancer cells. Results: In order to elucidate the biosynthetic pathway of rasfonin, the strain was genome sequenced, annotated, submitted to transcriptome analysis and genetic transformation was established. Biosynthetic gene cluster (BGC) prediction revealed the existence of 22 BGCs of which the majority was not expressed under our experimental conditions. In silico prediction revealed two BGCs with a suite of enzymes possibly involved in rasfonin biosynthesis. Experimental verification by gene-knock out of the key enzyme genes showed that one of the predicted BGCs is s indeed responsible for rasfonin biosynthesis. Conclusions: The results of this study lay the ground for molecular biology focused research in Cephalotrichum gorgonifer. Furthermore, strain engineering and heterologous expression of the rasfonin BGC is now possible which facilitates the construction of high producing strains or the synthesis of rasfonin derivates for diverse applications.

overall_design: Cephalotrichum gorgonifer was grown for 24 or 48 hours on AMM; each sample was replicated

first: Andreas

last: Schüller

first: Lena

last: Studt-Reinhold

first: Lucia

last: Silvestrini

first: Markus

last: Gorfer

first: Ulrich

last: Güldener

first: Roman

last: Labuda

last: Bacher

first: Maria

last: Doppler

first: Erika

last: Gasparotto

first: Arianna

last: Gattesco

first: Michael

last: Sulyok

first: Joseph

last: Strauss


title: A Novel mode of half site binding in budding yeast II

status: Public on Nov 04 2022

city: St. Louis

first: Pamela

last: Recio

state: MO

address: 4523 Clayton Avenue

department: Genetics

institute: Washington University in St Louis

summary: Despite decades of research, predicting where a transcription factor (TF) binds using its sequences alone continues to be an outstanding problem. Here, our thermodynamic model of Gal4p-DNA binding revealed a new mechanism of binding site selection in which Gal4p can bind to promoters that lacks it consensus site. Further investigation revealed that these sequences that Gal4p unexpectedly binds to have a high density of its half site, CGG. Analyses showed the ability of CGG half sites to predict zinc cluster TF in vivo binding and exposed a clear relationship between CGG half sites and zinc cluster binding in multiple binding datasets. To dissect the molecular logic of this half site mode of binding we designed a Sort-seq library containing 6,798 yeast promoter sequences and measured their expression. We learned that there is a linear relationship between CGG half site density and zinc cluster driven expression in vivo. Additionally, we found that promoters encoding 10 half sites have the same transcriptional output as a single consensus site and found no clear effects of half site orientation and spacing on strength of activation. Our experiments demonstrate that this novel mode of half site binding is widespread across the yeast genome and expands our knowledge about TF binding specificity that can be applied to higher eukaryotes.

overall_design: Genome binding /occupancy profiling by high throughput sequencing

middle: S

first: Nikhil

last: Mitra

first: David

last: Song

first: Xuhua

last: Chen

first: Grace

last: Jaramillo

first: Rob


title: Expression data from Mus musculus tumor stromal vascular fraction

status: Public on Nov 09 2022

city: Stockholm

first: Jieyu

last: Wu

address: Solnavagen 9

country: Sweden

institute: Karolinska institutet

summary: Subcutanesouly tumors from both Bmal1+/+ and Bmal1-/- mice were used to isolated stromal vascular fractions (SVF). Tumor cells with GFP+ signals were exclusive. Remain GFP- cells were collected to do RNAseq.

overall_design: Stromal vascular fractions (SVF) from subcutaneous tumor from Bmal1+/+ and Bmal1-/- mice (n = 4/group) were isolated by fluorescence-activated single cell sorting (FACS). GFP+ positive tumor cells were excluded, remaining GFP- cells were served for RNA extraction and hybridization o Affymetrix microarray. We try to find out different gene expression in tumor host with circadian rhythm gene knockout.

first: Xu

last: Jing

first: Xiaoting

last: Sun

first: Yihai

last: Cao


title: High fat diet induced dysregulation in adipose tissue microRNAs

status: Public on Nov 08 2022

city: Memphis

first: Udai

last: Singh

state: TN

address: 881 Madison Avenue

department: Pharmacy

institute: University of Tennessee Health Science Center

summary:
During obesity progression differential expression of microRNAs (miRs) play a role in effector (Teff) functions.
A set of  high fat diet adipose tissue derived immune cell miRs shows profound upregulation or downregulation in the expression profile as compared to normal diet.

overall_design: our preliminary data indicates that high fat diet  down-regulates adipose resident T cell miRs-10a, -125b, and -1247 and suggesting that mimicking these miRs might be of therapeutics for the obesity and metabolic syndrome.

first: Sonia

last: Kiran


title: Transcriptional changes between mono- and dual-species biofilms of Pseudomonas aeruginosa and Candida albicans, ± meropenem treatment

city: Canterbury

first: Rebecca

middle: Anne

last: Hall

address: Giles Lane

department: School of Biosciences

country: United Kingdom

institute: University of Kent

summary: The goals of this dual-seq experiment were to 1) identify transcriptional changes between mono-species and dual-species biofilms of Candida albicans and Pseudomonas aeruginosa and 2) identify transcriptional changes within mono- or dual-species P. aeruginosa biofilm cells in response to meropenem treatment.

sample_organism:
Pseudomonas aeruginosa
Candida albicans

platform_organism:
Pseudomonas aeruginosa
Candida albicans

overall_design: Mono- and dual-species biofilms of C. albicans and P. aeruginosa were grown in vitro, with or without meropenem treatment. Four biological replicates were included, with six samples per replicate. For transcriptional analyses, the reference genomes used were: P. aeruginosa PAO1 (https://www.ncbi.nlm.nih.gov/nuccore/NC_002516.2) and C. albicans SC5314 Assembly 21 (http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/current/).

first: Farhana

last: Alam

first: Jessica

last: Blair


title: A Novel mode of half site binding in budding yeast I


title: A Novel mode of half site binding in budding yeast

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

overall_design: Refer to individual Series


title: Five diatoms transcriptomes under iron limitation and oxidative stress

status: Public on Nov 07 2022

city: Seattle

first: Shiri

last: Graff van Creveld

state: WA

address: 616 NE Northlake Place

department: Oceanography

institute: University of Washingtom

summary: Divergent functions of two clades of flavodoxin in diatoms mitigate oxidative stress and iron limitation   Thalassiosira pseudonana and 4 open-ocean diatoms were subjected to iron limitation or short-term oxidative stress (hydrogen peroxide). mRNA profiles of T. pseudonana (CCMP1335), Thalassiosira oceanica (CCMP1005), Amphora coffeaeformis (CCMP1405), Chaetoceros sp. (CCMP199), and Cylindrotheca closterium (CCMP340).

sample_organism:
Cylindrotheca closterium
Thalassiosira pseudonana
Thalassiosira oceanica
Amphora coffeiformis
Chaetoceros sp. CCMP199

overall_design: mRNA profiles of five diatoms under control conditions, iron limitation, and oxidative stress conditions.

first: Sacha

last: Coesel

first: Stephen

last: Blaskowski

first: Ryan

last: Groussman

first: Megan

last: Schatz

first: E

middle: V

last: Armbrust


title: Gene expression profile at single cell level of Lin-Sca-1+c-Kit+ cells (LSKs) from miR-142 WT CML mice (CP LSC) and of LSKs from miR-142 KO CML mice (BC LSC). [scRNA-Seq]

status: Public on Nov 02 2022

city: Monrovia

first: Bin

last: Zhang

state: CA

address: 1218 S. Fifth Ave

department: Department of Hematological Malignancies Translational Science

institute: City of Hope Beckman Research Institute

summary: To assess how the miR-142 deficit affected the BM LSC-enriched LSK landscape, we conducted a single cell RNA-seq analysis of BM miR-142+/+ BCR-ABL (CP CML) and miR-142−/− BCR-ABL (BC CML) LSKs which were harvested from the respective mice, 2 weeks after BCR-ABL induction.

overall_design: ~8000 cells per sample were captured on a 10x Genomics Chromium using a Next GEM Single Cell 3' GEM kit V3.1 (10xGenomics). Using the Leiden clustering algorithm to identify groups of cells with similar transcriptomes, we identified 8 distinct LSK clusters. We annotated these clusters into distinct lineage-primed subsets using the expression levels of hematopoietic gene transcription factors and cluster differentiation (CD) antigens.

first: Shu

last: Tao


title: The helicase domain of Dicer ensures essential accuracy of miRNA biogenesis in mice

status: Public on Nov 03 2022

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

summary: Dicer ribonucleases, which generate small RNAs for the RNA interference (RNAi) and microRNA (miRNA) pathways, often have an N-terminal DExD helicase subdomain (also called HEL1). In the mammalian Dicer, HEL1 inhibits RNAi while it appears unnecessary for miRNA biogenesis. To determine its functional significance, we genetically eliminated HEL1 from Dicer in mice. We observed embryonic growth retardation, defects in the cardiopulmonary system, and perinatal lethality. HEL1 suppresses biogenesis of mirtrons, a non-canonical low-abundant class of miRNAs, and is required for high-fidelity cleavage and strand selection during biogenesis of canonical miRNAs. The HEL1 domain itself is essential rather than its helicase activity, because mutations of critical catalytic amino acids do not affect mouse viability or fertility and have minimal impact on miRNA biogenesis. Therefore, HEL1 is a critical structural component of the mammalian Dicer, supporting its role of a conserved structural “mold” that ensures high-fidelity processing and adaptive evolution of mammalian miRNA precursors.

overall_design: Bulk small RNA-seq of 9 mouse ESC samples:  - 3x WT transfected with MosIR  - 3x DicerX homozygotes transfected with MosIR  - 3x DicerX homozygotes & PKR null transfected with MosIR

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Eliska

last: Taborska


title: Effect of high-fat diet (HFD) and icosapent ethyl on the transcriptome of the adrenal cortex

status: Public on Oct 26 2022

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

summary:
We studied the effect of diet-induced obesity on the transcriptional profile of the adrenal cortex.
We also studied the effect of icosapent ethyl on the transcriptome of the adrenal cortex of obese mice.

overall_design: Mice were fed for 20 weeks a high-fat or a low-fat diet. Some HFD mice received the last 10 weeks HFD supplemented with icosapent ethyl. The adrenal cortex of the mice was isolated and RNASeq was performed.

first: VI

first: Anupam

last: Sinha

first: Anke

last: Witt


title: KLF6 alleviates hepatic ischemia-reperfusion injury by inhibiting autophagy

status: Public on Oct 30 2022

city: Zhengzhou

first: Jiye

last: Li

address: No. 1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: the First Affiliated Hospital of Zhengzhou University

summary:
To find the genes with significant expression changes after liver ischemia-reperfusion injury,we established a hypoxia-reoxygenation model using AML12 cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq under normoxia and hypoxia-reoxygenation conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of AML12 cells under normoxia (Control) and hypoxia-reoxygenation conditions(H/R).

first: Dongsheng

last: Yu


title: An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters [RNA-Seq]

status: Public on Oct 27 2022

city: Ithaca

first: B. Franklin

last: Pugh

state: NY

address: 465 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

summary: Genome-wide, little is understood about how proteins organize at inducible promoters before and after in-duction, and to what extent inducible and constitutive architectures depend on cofactors. We report that se-quence-specific transcription factors and their tethered cofactors (e.g., SAGA, Mediator, TUP, NuA4, SWI/SNF, RPD3-L) are already bound to promoters prior to induction (“poised”), rather than recruited upon induction, whereas induction recruits the pre-initiation complex (PIC). Through depletion and/or deletion ex-periments we show that SAGA does not function at constitutive promoters, although a SAGA-independent Gcn5 does acetylate +1 nucleosomes there. At poised promoters, SAGA catalyzes +1 nucleosome acetylation but not PIC assembly. At induced promoters, SAGA catalyzes acetylation, deubiquitylation, and PIC assembly. Surprisingly, SAGA mediates induction by creating a PIC that allows TFIID to stably associate, rather than creating a TFIID-independent PIC, as is generally thought. These findings suggest that inducible systems, where present, evolved on top of constitutive systems.

overall_design: Genome-wide analysis of yeast TFs under heat shcok and mock heat shock conditions using ChIP-exo

first: Chitvan

last: Mittal

first: Olivia

last: Lang

first: Alain

last: Bataille

first: William

last: Lai

first: B


title: Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

status: Public on Oct 25 2022

city: Norwich

first: Martin

last: Vickers

state: Norfolk

address: Colney Ln

institute: John Innes Centre

summary: Durum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of durum variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. Overall, we provide a valuable resource for studying endosperm development in this increasingly important crop species.

overall_design: RNA samples were extracted from endosperm tissue dissected from developing grains. We analysed 8 timepoints (6, 8, 10, 13, 15, 18, 20, 30 days post anthesis) throughout grain development, and three replicates (harvested from three separate plants) per timepoint.

first: Jiawen

last: Chen

first: Alexander

last: Watson-Lazowski

first: David

last: Seung


title: Gene profiling changes in BM Lin-Sca-1+c-Kit+ cells (LSKs) from miR-142-/- (KO), miR-142+/+ (WT), miR-142-/- BCR-ABL (BC CML) and miR-142+/+ BCR-ABL (CP CML) mice. [bulk RNA-Seq]

status: Public on Nov 01 2022

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary:
To gain insight into how miR-142 deficit drives a BC-like transformation, we performed RNA-seq on bone marrow (BM) Lin-Sca-1+c-Kit+ cells (LSKs) harvested from normal miR-142+/+ (wt) and miR-142−/− (miR-142 KO) mice, as well as from leukemic miR-142+/+ BCR-ABL (CP CML) and miR-142−/− BCR-ABL (BC CML) mice, two weeks after BCR-ABL induction.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 24 samples of LSK cells from 4 mouse strains (KO vs WT, KO CML vs CML).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BM LSK cells from miR-142+/+ BCR-ABL (CP CML) versus miR-142−/−BCR-ABL (BC CML) mice, and for BM LSKs from miR-142+/+ (WT) vs miR-142−/− (KO) mice.

first: Bin

last: Zhang

first: Min-Hsuan


title: Intermedin (Adrenomedullin 2) plays a protective role in sepsis by regulating T- and B-cell proliferation and activity

city: Chengdu

first: Feng

middle: Zhong

last: Xue

state: Sichuan

address: No. 2222, Frontier Medical Center, Xin Chuan Road, Zhong He Street

institute: Sichuan University

summary: Sepsis is a life-threatening condition caused by dysregulated host responses to infection. Intermedin (IMD), a calcitonin family peptide, has been shown to protect against sepsis by alleviating vascular leakage and inflammatory responses. Herein, by using transcriptome sequencing (RNA-Seq), we found that IMD-knockout mice exhibited a primary immunosuppression phenotype characterized by a marked decrease in the expression of T- and B-cell function-related genes. This immunosuppression made the IMD-KO mice more vulnerable to pathogenic invasion than normal mice, and even a mild infection killed nearly half of the IMD-KO mice. IMD is likely to directly promote T- and B-cell proliferation through ERK1/2 phosphorylation. In addition, IMD may regulate T-cell differentiation via Ilr7 and Rag1/2, which control T-cell receptor (TCR) recombination, and may regulate B-cell activity via Pax5, which may be the most multifunctional transcription factor for B cells, regulating at least 170 genes that activate genes necessary for B-cell functions. Exogenous supplementation with IMD restored the expression of T/B-cell-related genes and significantly reduced IMD-KO mouse mortality. Our study reveals for the first time that IMD may play an important role in the adaptive immune response by regulating T- and B-cell proliferation and differentiation and provides translational opportunities for the design of immunotherapies for sepsis or other diseases associated with primary immunodeficiency.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the  bone marrow cells in  wild-type (WT) and IMD knockout(KO) micee, 4 groups in total and  3 replicates  each group

first: Zhongxue

last: Feng


title: Chi3l1 is a modulator of glioma stem cell states and a therapeutic vulnerability for glioblastoma

status: Public on Oct 24 2022

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

address: 1300 Morris Park Avenue

department: Systems and Computational Biology

institute: Albert Einstein College of Medicine


title: Antibody blockade resets CHI3L1-induced glioma stem cell phenotypic transitions and reduces glioblastoma tumor burden

summary: CHI3L1 (Chitinase 3-like1) is one of the highest expressed genes in glioblastoma and is associated with therapy resistance and low survival of patients. Here, we show that exposure of glioma stem cells (GSCs) to CHI3L1 induces marked phenotypic and transcriptomic change from CD133+/SOX2+ pro-neural to CD44+/CHI3L1+ mesenchymal phenotype. CHI3L1 induces chromatin remodeling in GSCs and regulates accessibility of ZNF281, CTCFL, SOX9, and the OCT4-SOX2-TCF3-NANOG transcription factor complex that drive the CHI3L1-mediated mesenchymal “switch” and maintain GSC identity.

overall_design:
We performed ATAC-Seq on CHI3L1-treated and non-CHI3L1-treated (CTRL) glioma stem cells to determine changes in chromatin accessibility following exposure to CHI3L1. Annotation of the peaks showed that the CHI3L1-treated group has an increased proportion of its accessible regions occurring at promoters within 1000 bp of a TSS (36.86% in CHI3L1-treated vs. 32.90% in CTRL). Furthermore, the peak densities at the TSS showed increases in signal for the CHI3L1 treated group, indicating that the TSSs are comparatively more accessible.

Please note that each processed data was generated from both replicates and is linked to the corresponding rep1 sample records.

first: Nikos

last: Tapinos

first: J

first: Jia-Shu


title: Systemic Alterations in Type-2 Conventional Dendritic Cells Lead to Impaired Tumor Immunity in Pancreatic Cancer

status: Public on Oct 21 2022

last: DeNardo

email: johnbaer@wustl.edu, ddenardo@wustl.edu

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

summary: Intratumoral T-cell dysfunction is a hallmark of pancreatic tumors, and efforts to improve dendritic cell (DC)-mediated T-cell activation may be critical in treating these immune therapy unresponsive tumors. Recent evidence indicates that mechanisms that induce dysfunction of type 1 conventional DCs (cDC1) in pancreatic adenocarcinomas (PDAC) are drivers of the lack of responsiveness to checkpoint immunotherapy. However, the impact of PDAC on systemic type 2 cDC2 development and function has not been well studied. Herein, we report the analysis of 3 cohorts, totaling 106 samples, of human blood and bone marrow (BM) from patients with PDAC for changes in cDCs. We found that circulating cDC2s and their progenitors were significantly decreased in the blood of patients with PDAC, and repressed numbers of cDC2s were associated with poor prognosis. Serum cytokine analyses identified IL6 as significantly elevated in patients with PDAC and negatively correlated with cDC numbers. In vitro, IL6 impaired the differentiation of cDC1s and cDC2s from BM progenitors. Single-cell RNA sequencing analysis of human cDC progenitors in the BM and blood of patients with PDAC showed an upregulation of the IL6/STAT3 pathway and a corresponding impairment of antigen processing and presentation. These results suggested that cDC2s were systemically suppressed by inflammatory cytokines, which was linked to impaired antitumor immunity.

overall_design: Examination of antigen-presenting cells and progenitors from blood and bone marrow of healthy donors and PDAC patients

first: C

last: James

first: John

last: Baer


title: Mucosal exposure to non-tuberculous mycobacteria elicits B-cell mediated protection against pulmonary tuberculosis

status: Public on Oct 23 2022

city: Fort collins

first: Marcela

last: Henao-Tamayo

state: CO

address: 1682 Campus delivery, 200 W Lake street

department: Microbiology, Immunology, anad Pathology

institute: Colorado State University

summary: Bacille Calmette Guerin (BCG) is the only licensed vaccine against Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB) disease. However, BCG has limited efficacy, necessitating the development of better vaccines. Non-tuberculous mycobacteria (NTM), a distinct lineage from Mtb, are opportunistic pathogens present in the environment. TB endemic countries experience higher exposure to NTM, but previous studies have not elucidated the relationship between NTM exposure and BCG efficacy. Therefore, we developed a mouse model (BCG+NTM) that mimics human BCG vaccination at an early stage and continuous NTM exposure via the oral route, including during TB infection. Our results show that BCG+NTM mice had improved protection against pulmonary TB correlating with increased pulmonary influx of B-cells, higher titers of anti-Mtb IgA and IgG antibodies in serum and airways, compared to mice vaccinated with BCG alone. Notably, the lungs of BCG+NTM mice developed B-cell aggregates expressing markers of germinal center formation as determined by spatial transcriptomics. We conclude a direct correlation between NTM exposure and protection from TB, with B-cells playing a crucial role.

overall_design: This is a spatial transcriptomics dataset generated using 10X Visium kit for FFPE tisues. There are four groups: Saline (control group); BCG (mice vaccinated with Bacille Calmette Geurin vaccine and infected with Mycobacterium tuberculosis); NTM (Mice exposed to 1X10^5 CFU/mL Myobacterium avium via drinking water and infected with Mycobacterium tuberculosis), and BCG+NTM (Mice vaccinated with BCG, exposed to 1X10^5 CFU/mL Myobacterium avium via drinking water and infected with Mycobacterium tuberculosis).

first: Taru

last: Dutt


title: Effects of arbuscular mycorrhizal symibiosis on gene expression in the foxtail millet roots

status: Public on Oct 20 2022

city: Taipei

first: Wei-Yi

last: Lin

state: Taipei City

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Agronomy

country: Taiwan

institute: National Taiwan University

summary:
To investigate the involvement of arbuscular mycorrhizal symbiosis in the moleular regulation in foxtail millet roots and the effects of genetic variation on AMS-mediated molecular regulation, we isolated total RNA from the roots of 3 different landraces for comprehensive transcriptomic analysis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different landraces (Hanevalval, TT8, ICE36) after 6-week mock or arbuscular mycorrhizal fungi treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mock- and fungal-treated millet roots.


title: Single cell RNA Sequencing (scRNA-Seq) of patient with ARPC5 deficiency and healthy control

status: Public on Oct 16 2022

city: Bethesda

first: Julie

last: Niemela

state: MD

address: 10 Center Dr.

department: Dept. of Lab. Medicine

institute: NIH Clinical center

summary: We performed a targeted scRNA-seq approach using the BD Rhapsody™ Single Cell Analysis Systems (BD Biosciences). Peripheral blood mononuclear cells (PBMCs) were labeled with sample tags (BD Human Single Cell Multiplexing Kit) and AbSeq antibodies (CD1c, CD3, CD4, CD5, CD8, CD11c, CD14, CD16, CD18, CD19, CD20, CD21, CD23, CD24, CD25, CD27, CD28, CD31, CD38, CD40, CD44, CD45RA, CD45RO, CD56, CD62L, CD123, CD127, CD134, CD137, CD161, CD183, CD185, CD186, CD196, CD197, CD272, CD278, CD279, CD303, CD314, CD337, CD357, CD366, HLA-DR, IgD, IgM, TCRαβ, TCRγ8, Vα24-Jα18) and counted. Single-cell capture was performed using the BD Rhapsody Express following manufacturer’s instructions. The libraries were pooled and sequenced on NovaSeq 6000 S2 as a dual index pair-end run. Fastq files were processed using BD's Rhapsody analysis pipeline on the Seven Bridges Platform using default parameters, the GRCh38-PhiX-gencodev29 reference genome and the gencodev29-20181205 transcriptome annotation. Data (molecules per gene per cell based on DBEC error correction) were analyzed using BD SeqGeq v1.8 and the Seurat plug-in to perform dimensionality reduction (UMAP) and differential analysis output for selected cell subsets (CD4+ T cells, CD8+ T cells, NK cells, NKT cells, classical monocytes, intermediate monocytes, non-classical monocytes).

overall_design: Peripheral blood mononuclear cells (PBMCs) were labeled with sample tags (BD Human Single Cell Multiplexing Kit) and AbSeq antibodies (BD Human Single Cell Multiplexing Kit). Single-cell capture was performed using the BD Rhapsody Express following manufacturer’s instructions. Samples were sequenced using the Illumina NovaSeq and analyzed using SeqGeq v1.8 from BD

first: Sergio

middle: D

last: Rosenzweig

first: Cristiane

middle: J

last: Nunes-Santos

first: HyeSun

last: Kuehn

first: Jennifer

last: Stoddard


title: Epididymal adipose tissue gene sequencing of mice on a normal diet, with or without gavage of Oscillibacter valericigenes

status: Public on Oct 13 2022

city: Corvallis

first: Andrey

last: Morgun

state: Oregon

address: Pharmacy Building, 1601 SW Jefferson Way

department: College of Pharmacy

institute: Oregon State University

summary: Paper abstract: Microbiota contribute to the induction of type 2 diabetes by high-fat/high-sugar (HFHS) diet, but which organs/pathways are impacted by microbiota remain unknown. Using multiorgan network and transkingdom analyses, we found that microbiotadependent impairment of OXPHOS/mitochondria in white adipose tissue (WAT) plays a primary role in regulating systemic glucose metabolism. The follow-up analysis established that Mmp12+ macrophages link microbiota-dependent inflammation and OXPHOS damage in WAT. Moreover, the molecular signature of Mmp12+ macrophages in WAT was associated with insulin resistance in obese patients. Next, we tested the functional effects of MMP12 and found that Mmp12 genetic deficiency or MMP12 inhibition improved glucose metabolism in conventional, but not in germ-free mice. MMP12 treatment induced insulin resistance in adipocytes. TLR2-ligands present in Oscillibacter valericigenes bacteria, which are expanded by HFHS, induce Mmp12 in WAT macrophages in a MYD88-ATF3–dependent manner. Thus, HFHS induces Mmp12+ macrophages and MMP12, representing a microbiota-dependent bridge between inflammation and mitochondrial damage in WAT and causing insulin resistance.

overall_design: 10 samples, 2 experimental groups: mice on a control diet with/without Oscillibacter valericigenes gavage

first: Natalia

last: Shulzhenko


title: Gene expression in young and old pituitary

status: Public on Oct 14 2022

city: Beijing

first: Yehua

last: Li

address: shengmingkexueyuanlu7hao, changping

country: China

institute: NIBS

summary: To identify the gene expression change during pituitary aging, we did the RNA-seq of pituitary from 2-3 months young mice and 18-24 months old mice. The mRNA level of different genes were analyzed.

overall_design: Differential gene expression analysis of young and old pituitary.

first: Jiawen

last: Wang

first: Rui

first: Xioadong


title: MYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer

status: Public on Oct 17 2022

city: Portland

first: Zinab

last: Doha

state: OR

address: 2730 S MOODY AVE

country: USA

institute: Oregon Health & Science University

summary: Triple-negative breast cancer (TNBC) patients have a poor prognosis and few treatment options. Mouse models of TNBC are important for development of new therapies, however, few mouse models represent the complexity of TNBC. Here, we develop a female TNBC murine model by mimicking two common TNBC mutations with high co-occurrence: amplification of the oncogene MYC and deletion of the tumor suppressor PTEN. This Myc;Ptenfl model develops heterogeneous triple-negative mammary tumors that display histological and molecular features commonly found in human TNBC. Our research involves deep molecular and spatial analyses on Myc;Ptenfl tumors including bulk and single-cell RNA-sequencing, and multiplex tissue-imaging. Through comparison with human TNBC, we demonstrate that this genetic mouse model develops mammary tumors with differential survival and therapeutic responses that closely resemble the inter- and intra-tumoral and microenvironmental heterogeneity of human TNBC, providing a pre-clinical tool for assessing the spectrum of patient TNBC biology and drug response.

overall_design:
- RNA was extracted from Myc;Ptenfl tumor tissue (n = 13) or normal mammary gland as control (n=3) using Trizol (Invitrogen). Normalized count data was generated using the standard DESeq2 (v1.36.0) workflow with Variance Stabilizing Transformation.
- Single-cell suspensions of 11 Myc;Ptenfl tumors were obtained by enzymatic digestion. Library prepared with the Chromium Single Cell 3’ V3 (10X Genomics) following the manufacturer’s protocol with a targeted recovery of 20,000 cells per library. Libraries were sequenced on an Illumina NovaSeq. BCL files were converted to fastq format with bcl2fastq2 (Illumina), and then aligned to mouse genome build mm10-2020-A (10X Genomics) using Cellranger (10X Genomics, version 6.0.2).

first: Doha

last: Zinab

first: Wang

last: Xiaoyan

first: Sears

last: Rosalie


title: Gene expression analysis of hESCs undergoing neuronal differentiation [scRNA-seq]

city: Oslo

first: Ragnhild

last: Eskeland

address: Sognsvannsveien 9

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Genome-wide gene expression profiling of hESCs undergoing neuronal differentiation at four distinct time-points. hESCs are differentiated using a novel protocol, and day 0, 7, 13 and 20 were charachterized.

overall_design:
Genome wide gene expression profiling of (n= 19) samples from human embryonic stem cells (hESCs) at day 0 (n=5), and day 7(n = 6), 13 (n= 4) and 20 (n=4) of neuronal differentiation
**Raw data are not provided as they can not be shared due to the material transfer agreement**

first: Mari

last: Spildrejorde

first: Athina

last: Samara

first: Ankush

last: Sharma

first: Martin

last: Falck

first: Magnus

last: Leithaug

first: Stefania

last: Modafferi

first: Pål

middle: M

last: Bjørnstad

first: Kristina

last: Gervin

first: Robert

last: Lyle


title: Discovery biomarker to optimize obeticholic acid treatment for non-alcoholic fatty liver disease

city: seoul

first: Seung Min

last: Lee

state: 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Rep. of KOREA

address: 222, Wangsimni-ro, Seongdong-gu, Seoul, Republic of Korea

institute: hanyang university

summary: To compare the gene expression of these groups before OCA treatment in responders with therapeutic effect on OCA and non-responders without therapeutic effect, mRNA-seq was performed on liver biopsy samples before OCA administration.

overall_design:
Comparison of RNA-seq data from liver biopsy of OCA responder, non-responder, and vehicle
*** Raw data has been lost and thus is not provided ***

first: SeungMin

first: DaeWon

last: Jun

first: Eileen

last: Yoon

first: JuHee

last: Oh

first: YoonJin

last: Roh

first: EunJeoung

first: Ji-Hee

last: Shin

first: Young-Do

last: Nam

first: HyunSung

last: Kim