title: The landscape of small nucleolar RNA expression in multiple myeloma is determined by cytogenetic alterations (RibomethSeq)

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

summary: We combined mRNA, small RNA and ribosome 2'O-methylation sequencing to investigate snoRNA expression patterns in multiple myeloma and their association with different chromosomal aberrations. We identified snoRNAs dysregulated in molecular subgroups, with SNORD78 being highly expressed in gain1q patients and associated with poor prognosis. Our study shows that the expression of particular snoRNAs and methylation of specific snoRNA-guided rRNA sites are associated with specific chromosome gains, which are common elements in multiple myeloma.

overall_design: We performed RiboMethSeq to measure 2'O-methylation of ribosomal RNA in 26 newly diagnosed multiple myeloma patient samples.

first: Duoduo

last: Zhao

first: Carsten

last: Müller-Tidow


title: Genome-wide characterization of TAZ binding sites in mammary epithelial cells in temporary and special manner (ATAC-seq)

status: Public on Oct 16 2023

city: Buffalo

first: Tao

last: Liu

state: NY

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

country: USA

institute: Roswell Park Comprehensive Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: TAZ, one of the key components of Hippo signaling pathway, is a transcription coactivator and plays an important role in cell proliferation, anti-apoptosis, therapeutic resistance, cancer stemness and tumorigenesis. TAZ mediated transcription program through transcription factors, such as TEAD family members. Genome-wide TAZ occupancy is poorly defined. Here, using a tet-inducible TAZ activation in mammary epithelial MCF10A cells, we characterized genome-wide binding sites in different TAZ activation time points. We found vast majority of TAZ binds to distal enhancer and intergenic regions of genes in the early TAZ activation time point and shift to promoter regions in the later TAZ activation time point. We identified three distinctive TAZ binding patterns to its targets. Furthermore, we found TAZ activation results in chromatin architecture alterations. Our studies provide insight of TAZ regulated transcription program in mammary epithelial cells and indicate potential therapeutic targets for breast cancer.

overall_design: Briefly, inducible TAZ-4SA transduced MCF10A cells treat without or with Dox for 72 h.  50,000 cells were harvested, and transposition reaction were performed. Following transposition, DNA was purified using a Qiagen MinElute PCR Puriﬁ-cation Kit and PCR amplified for 10 cycles. Quality of ATAC-seq libraries were qualified with Bioanalyzer and next generation sequencing were performed by Roswell genomic core facility.

first: Jiaojiao

last: Zhou

first: Yanmin

last: Chen

first: Jia

last: Fang

first: Song

first: Costa

last: Frangou

first: Jianmin

last: Zhang


title: Epigenomic mapping in B-cell acute lymphoblastic leukemia identifies transcriptional regulators and noncoding variants promoting distinct chromatin architectures [ChIP-seq]

status: Public on Oct 17 2023

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: B-cell lineage acute lymphoblastic leukemia (B-ALL) is comprised of diverse molecular subtypes and while transcriptional and DNA methylation profiling of B-ALL subtypes has been extensively examined, the accompanying chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq for 10 B-ALL molecular subtypes in primary ALL cells from 154 patients. Comparisons with B-cell progenitors identified candidate B-ALL cell-of-origin and AP-1-associated cis-regulatory rewiring in B-ALL. Cis-regulatory rewiring promoted B-ALL-specific gene regulatory networks impacting oncogenic signaling pathways that perturb normal B-cell development. We also identified that over 20% of B-ALL accessible chromatin sites exhibit strong subtype enrichment, with transcription factor (TF) footprint profiling identifying candidate TFs that maintain subtype-specific chromatin architectures. Over 9000 inherited genetic variants were further uncovered that contribute to variability in chromatin accessibility among individual patient samples. Overall, our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants which promote unique gene regulatory networks that contribute to transcriptional differences among B-ALL subtypes.

overall_design: ChIP-seq for H3K27Ac on primary cells isolated from acute lymphoblastic leukemia patients


title: The landscape of small nucleolar RNA expression in multiple myeloma is determined by cytogenetic alterations

country: Germany

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The landscape of small nucleolar RNA expression in multiple myeloma is determined by cytogenetic alterations (snoRNA)

summary: We combined mRNA, small RNA and ribosome methylation sequencing to investigate snoRNA expression patterns in multiple myeloma and their association with different chromosomal aberrations. We identified snoRNAs dysregulated in molecular subgroups, with SNORD78 being highly expressed in gain1q patients and associated with poor prognosis. Our study shows that the expression of particular snoRNAs and methylation of specific snoRNA-guided rRNA sites are associated with specific chromosome gains, which are common elements in multiple myeloma.

overall_design: We profiled the expression of snoRNAs in CD138-enriched multiple myeloma cells from 71 newly diagnosed and four relapsed/refractory multiple myeloma patients as well as CD19+ B cells from three healthy donors.


title: Transcriptome profile of cua-1 (H828Q) strain

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

type: Expression profiling by high throughput sequencing

summary: To analyse gene expression differences between cua-1(H828Q) vs control, under growing conditions with or without CuCl2

overall_design: Total RNA was extracted after a growth of three days on a NGM  agar plate for each condition

first: Federico

last: Catalano


title: Pioneer factor Foxa2 mediates chromatin conformation changes in ligand-dependent activation of nuclear receptor FXR

city: Charlottesville

first: Irina

last: Bochkis

state: VA

address: 1340 Jefferson Park Ave Jordon Hall 5030

department: Pharmacology

institute: University of Virginia

summary: Activation of nuclear receptors, a family of ligand-dependent transcription factors, is used extensively in development of drug targets. We have previously shown that pioneer factor Foxa2 opens chromatin for binding of nuclear receptors FXR and LXRα during acute ligand activation. FXR is activated by bile acids and deletion of Foxa2 in the liver results in intrahepatic cholestasis. We hypothesized that Foxa2 also enables chromatin conformational changes during ligand activation.  We performed Foxa2 HiChIP to assess Foxa2-dependent long-range interactions in mouse livers treated with either vehicle control or FXR agonist GW4064. HiChIP contact analysis shows that global chromatin interactions are dramatically increased during FXR activation. Ligand-treated livers exhibit extensive redistribution of topological associated domains (TAD) and substantial increase in  Foxa2-anchored loops, suggesting Foxa2 is involved in dynamic chromatin conformational changes. We demonstrate that chromatin conformation, including genome-wide interactions, TADs, intra-chromosomal and inter-chromosomal Foxa2-anchored loops, drastically changes upon addition of  FXR agonist. Hence, we determine a novel role for Foxa2 in enabling these conformational changes, extending its function in bile acid metabolism.

overall_design: Foxa2 HiChIP-Seq (Hi-C & Foxa2 ChiP)  in mouse livers treated with vehicle or FXR agonist GW4064

middle: M

first: Yi

last: Hao

first: Lu

last: Han

first: Anqi

last: Wu


title: Tsc2 coordinates differentiation [scRNA-seq]

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

summary: Multipotent neural stem cells (NSCs) that reside within the ventricular-subventricular zone (V-SVZ) of the brain generate a variety of cell types. Here we provide transcriptomes of cells that have lost Tsc2 as occurs in the neurodevelopmental disorder Tuberous Sclerosis Complex (TSC).

overall_design: Single nuclei sequencing of wild-type and Tsc2 mutant mouse

first: D

first: Vijay

last: Shankar

first: Trudy

middle: F

last: Mackay


title: Tsc2 coordinates differentiation

summary: Multipotent neural stem cells (NSCs) that reside within the ventricular-subventricular zone (V-SVZ) of the brain generate a variety of cell types. Here we provide transcriptomes of NSCs that have lost Tsc2 as occurs in the neurodevelopmental disorder Tuberous Sclerosis Complex (TSC).

overall_design: Whole transcriptome and translatome sequencing of wild-type and Tsc2 mutant mouse primary neural stem cells grown in monolayer culture.


title: Cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome mice

city: Birmingham

first: Jordan

last: Whitlock

email: jwhitlock@uab.edu, bnp0001@uab.edu

state: AL

address: 1900 University Boulevard

department: Cell, Developmental and Integrative Biology

institute: The University of Alabama at Birmingham

summary:
Schinzel Giedion Syndrome (SGS) is an ultra rare progressive neurodegenerative disease affecting less than 100 inividuals worldwide. SGS is cuased by variants in SETBP1 gene. We used snRNA-seq of cerebral cortex and kidney tissues from mice carrying a heterozygous S858R variant in Setbp1 and constructed cell-type-specific gene regulatory networks to profile the impact of the point mutation on cell-type-specific expression and regulation of Setbp1 and its known targets in atypical SGS.

Grant Number: 1U54oD030167
UAB Pilot Center for Precision Animal Modeling (C-PAM)
Grantee: Brittany Lasseigne

Grant Number: 5T32GM008111-35
UAB CMDB T32
Grantee: Jordan Whitlock

overall_design: We obtained decapsulated whole right kidneys and right cerebral cortex hemispheres from three 6-week-old male C57BL/6JSetbp1em2Lutzy/J  mice heterozygous for Setbp1 S858R, an SGS-associated point mutation (JAX Stock #033235) and three wild-type (WT) age, and sex-matched C57BL6/J mice (JAX Stock #000664)

middle: H

first: Tabea

last: Soelter

first: Timothy

middle: C

last: Howton

first: Brittany

middle: N

last: Lasseigne


title: BCR repertoire analysis of extra- and intravascular WT BL6 mouse kidney B cells at homeostasis and following UPEC challenge.

city: Cambridge

first: Ondrej

last: Suchanek

address: Francis Crick Avenue

department: Department of Medicine, Molecular Immunity Unit

country: United Kingdom

institute: University of Cambridge

summary: B cells play a central role in humoral immunity but also have antibody-independent functions. Studies to date have focused on B cells in blood and secondary lymphoid organs but whether B cells reside in non-lymphoid organs (NLO) in homeostasis is unknown. Here we identify, using intravenous labeling and parabiosis, a bona-fide tissue-resident B cell population in lung, liver, kidney and urinary bladder, a substantial proportion of which are B-1a cells. Tissue-resident B cells are present in neonatal tissues and also in germ-free mice NLOs, albeit in lower numbers than in specific pathogen-free mice and following co-housing with ‘pet-store’ mice. They spatially co-localise with macrophages and regulate their polarization and function, promoting an anti-inflammatory phenotype, in-part via interleukin-10 production, with effects on bacterial clearance during urinary tract infection. Thus, our data reveal a critical role for tissue-resident B cells in determining the homeostatic ‘inflammatory set-point’ of myeloid cells, with important consequences for tissue immunity.

overall_design: To assess whether bacterial challenge might influence kidney BCR repertoire, WT C57BL/6 female mice (8-10 week old) had urinary bladders inoculated twice with UPEC (n=5), or PBS (n=6) to induce pyelonephritis on day 0. After 56 days, their intra- and extravascular kidney B cells were FACS sorted and BCR-sequenced (isotype resolved).

first: Sol

last: Lim

first: Menna

last: Clatworthy


title: Transcriptome profile of WT and GLUT2-KD Human Proximal tubule cells (HK-2)

first: Rossella

summary: To analyze gene expression differences between WT proximal tubule cells and cells in which, by siRNA transfection, we blunted the expression of GLUT2 gene to mimic Fanconi Bickel Syndrome

overall_design: Total RNA was extracted from n=4 WT  and n=3 siRNA-GLUT2 transfected cells

first: R

first: L

last: Staiano


title: Tsc2 coordinates differentiation [bulkRNA-seq]

overall_design: Whole transcriptome sequencing of wild-type and Tsc2 mutant mouse primary neural stem cells grown in monolayer culture.


title: Spatial-temporal tracking of Brca1-driven breast tumorigenesis from sporadic mutant cells with a genetic mosaic mouse model

first: Kevin

middle: A.

last: Janes

address: Box 800759 Health System

department: Department of Biomedical Engineering

summary: We utilized a genetic tool termed Mosaic Analysis with Double Markers (MADM) to achieve a sporadic loss of heterozygosity of Brca1 & Trp53 in mouse mammary epithelial cells and concomitantly label them with GFP. This MADM-based mouse model initiated cancer with sparse GFP+ mutant cells and developed mammary tumors that resemble human disease at pathological, transcriptomic, and genomic levels.  This dataset provides bulk RNA sequencing of twelve mammary tumors from MADM Brca1-Trp53 animals.

overall_design: Twelve MADM tumors from nine animals were homogenized and poly(A) RNA was sequenced.

middle: A

first: Jianhao

last: Zeng

first: Shambhavi

last: Singh

first: Hui

last: Zong


title: Spatial transcriptomics of human plastic and non-plastic breast cancer subtypes

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

summary: Cellular plasticity is a hallmark of rare Claudin-low (CL) and metaplastic (MBC) breast cancer subtypes, with a documented overlap whose exact extent is yet unknown, and which are associated to resistance and poor survival. We used spatial transcriptomics to further characterise these plastic subtypes, respectively defined molecularly and histopathologically. We identified 3 putative CL tumours (CL-like) and 4 genomically unstable TNBC samples via molecular analyses, combined with 4 MBCs identified by a breast pathologist.

overall_design: Fresh frozen tissue slides analysed using the 10X Genomics Visium spatial transcriptomics technology

first: Maria

last: Ouzounova

first: Cyril

last: Degletagne

first: Lauriane

last: Muller

first: Angele

last: Coutant


title: Effects of ash-2, hsf-1, or ash-2 + hsf-1 RNAi on gene expression in Day 1 adult Q40::YFP C. elegans

city: Ann Arbor

first: Bryndon

last: Oleson

state: MI

address: 1100 N. University Ave

institute: University of Michigan

summary: To determine how gene expression changes in long-lived ash-2-deficient worms expressing the amyloidogenic Q40::YFP, and to assess how simultaneous depletion of hsf-1 effects these transcriptomic changes.

overall_design: Q40::YFP C. elegans were synchronized by timed egg lay on plates containing L4440 (control), ash-2, hsf-1, or ash-2 + hsf-1 RNAi E. coli HT115 (DE3) bacteria. Animals were then aged at 20°C for 96 h, then were washed from plates with M9, pelleted, and flash frozen in liquid nitrogen. Parents of animals destined for ash-2 or ash-2 + hsf-1 RNAi plates were also maintained on ash-2 RNAi since egg.

first: Ursula

last: Jakob


title: Consequences of Nkiras deficiency for the EGF response

city: Jersey City

first: Thomas

middle: S

last: Postler

state: New Jersey

address: 95 Greene Street 5-018

department: Discovery Science

institute: International AIDS Vaccine Initiative

summary: Cancer is a disease of aberrant intracellular signaling. The NF-κB family of transcription factors and the Ras family of small GTPases have emerged as particularly important mediators of the pro-proliferative signaling that drives tumorigenesis and carcinogenesis. The κB-Ras proteins, encoded by the genes Nkiras1 and Nkiras2, were previously shown to inhibit both NF-κB and Ras pathway activation through independent molecular mechanisms, implicating them as tumor suppressors with potentially broad relevance to human cancers. In mice, each κB-Ras protein can compensate fully for loss of the other, making the functionally redundant in the context of Ras signaling. To understand the global effects of full κB-Ras deficiency in the context of Ras activation, we use microarray analysis to compare the transcriptome of MEFs lacking only κB-Ras 1 (Nkiras1-/- Nkiras2+/+, 1SKO) and MEFs lacking both isoforms of κB-Ras (Nkiras1-/- Nkiras2-/-, DKO) with and without EGF stimulation.

overall_design: Mouse embyronic fibroblasts (MEFs) of the genotype Nkiras1-/- Nkiras2+/+ and Nkiras1-/- Nkiras2-/- were either left untreated or stimulated with 100 ng/ml EGF for 5 h. Total RNA was isolated and submitted to Arraystar for hybridization to a Nimblegen microarray.

first: Andrea

last: Oeckinghaus

first: Sankar

last: Ghosh


title: A SOX9-B7x axis safeguards dedifferentiated tumor cells from immune surveillance to drive breast cancer progression [RNA-seq and ChIP-seq]

city: New York

first: Wenjun

last: Guo

address: 1301 Morris Park

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: The transcription factor SOX9 can act as a pioneering factor in driving lineage dedifferentiation and tumor progression for breast cancer. To investigate downstream pathways mediating SOX9 function and identify the direct gene targets of SOX9, we performed RNA-seq and SOX9 ChIP-seq on human breast cancer cell line MCF7ras ctrl and SOX9-overexpressing (SOX9OE) cells.

overall_design: RNA-seq and SOX9 ChIP-seq in breast cancer cell lines MCF7ras ctrl and MCF7ras tetO-SOX9 treated with 2 μg/ml doxycycline for three days.

first: Yu

last: Liu

first: Phillip

last: Galbo

first: Boris

last: Bartholdy

first: Deyou

last: Zheng


title: Ligand-dependent hedgehog signaling maintains an undifferentiated, malignant osteosarcoma phenotype

city: Clayton

first: Vijesh

last: Vaghjiani

state: Victoria

address: 27-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Reaserch

summary:
To determine the differentially expreesed genes in osteosarcoma cell lines MG63 and U2OS stimulated with hedgehog ligand (SHH) for 24 hours
MG63 and U2OS cells were treated with PBS or 1ug/ml of recombinat human sonic hedgehog for 24 hours. RNA was isolated from the cells and RNAseq performed
The results present differentially expressed genes when osteosarcoma cell lines are stimulated with SHH

overall_design: mRNA profile of MG63 and U2OS cell lines treated with PBS or SHH

middle: G

first: Jason

middle: E

last: Cain


title: Integrative analysis of transcriptomic and epigenomic dynamics of liver organoids using single cell RNA-seq and ATAC-seq.

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: In this study, to identify the heterogeneity and dynamics of transcriptome and epigenome of liver organoid in single cell level, we applied single cell RNA-seq (scRNA-seq) and single cell ATAC-seq (scATAC-seq) using Chromium’s 10x platform. We analyzed liver organoids treated with two medium conditions (hepatic medium - HM and differentiation medium - DM).

overall_design: For DM and HM liver organoids, single cell RNA-seq and single cell ATAC-seq was performed with repliacte using 10X Genomics Single Cell Solution.

first: Seon

middle: J

last: Mun

first: Myung

last: Son

first: Jong-Hwan

first: Seon-Young


title: Genome-wide analysis of replication timing in preimplantation mouse embryos

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: Replication timing is cell type specific, is tightly linked to the 3D nuclear organisation of the genome and is considered an epigenetic fingerprint. In spite of its importance in maintaining the epigenome the developmental regulation of replication timing in mammals in vivo has not been explored. Here, using single cell Repli-seq, we generated the genome-wide replication timing maps of mouse embryos from the zygote until the blastocyst stage.

overall_design: Examination of replication timing in preimplantation embryos

first: Tsunetoshi

last: Nakatani

first: Luis

last: Altamirano-Pacheco

first: Kyle

last: Klein

first: David

last: Gilbert

first: Maria-Elena

last: Torres-Padilla


title: Activity-induced MeCP2 phosphorylation regulates retinogeniculate synapse refinement [snRNA-Seq]

status: Public on Oct 15 2023

city: Roslindale

first: Tess

last: Whitwam

address: 41 Brookdale Street

institute: Harvard University

summary: Mutations in MECP2 give rise to Rett syndrome (RTT), an X-linked neurodevelop- mental disorder that results in broad cognitive impairments in females. While the exact etiology of RTT symptoms remains unknown, one possible explanation for its clinical presentation is that loss of MeCP2 causes miswiring of neural circuits due to defects in the brain’s capacity to respond to changes in neuronal activity and sensory experience. Here, we show that MeCP2 is phosphorylated at four residues in the brain (S86, S274, T308, and S421) in response to neuronal activity, and we generate a quadruple knock-in (QKI) mouse line in which all four activity-dependent sites are mutated to alanines to prevent phosphorylation. QKI mice do not display overt RTT phenotypes or detectable gene expression changes in two brain regions. However, electrophysiological recordings from the retinogeniculate synapse of QKI mice reveal that while synapse elimination is initially normal at P14, it is significantly compromised at P20. Notably, this phenotype is distinct from the synapse refinement defect previously reported for Mecp2 null mice, where synapses initially refine but then regress after the third postnatal week. We thus propose a model in which activity-induced phosphorylation of MeCP2 is critical for the proper timing of retinogeniculate synapse maturation specifically during the early postnatal period.

overall_design: Single nucleus RNA-sequencing was performed from WT and MeCP2 QKI littermates at P20. Six mice per genotype were sacrificed, followed by isolation of the dLGN. 3 dLGN per genotype were pooled, for total of two replicates.

first: Christopher

middle: P

last: Tzeng

first: Lisa

middle: D

last: Boxer

first: Michael

last: Greenberg


title: A SOX9-B7x axis safeguards dedifferentiated tumor cells from immune surveillance to drive breast cancer progression [10X scRNA-seq]

first: Wenjun

last: Guo

summary: The transcription factor SOX9 can act as a pioneering factor in driving lineage dedifferentiation and tumor progression for breast cancer. To unbiasedly understand how committed luminal stem progenitor cells dedifferentiate into embryonic multipotent progenitor-like cells, we performed scRNA-seq in luminal cells FACS sorted from WT control mice and Sox9-GFP;C3-TAg mice at the age of 3.5 months when C3-TAg mice have developed extensive hyperplastic lesions but not yet malignant tumors.

overall_design: scRNA-seq in luminal cells FACS sorted from 3.5-month-old Sox9-GFP;C3-TAg mice and Sox9-GFP WT control mice.

first: Yu

last: Liu

first: Xusheng

last: Zhang


title: Activity-induced MeCP2 phosphorylation regulates retinogeniculate synapse refinement [ChIP-Seq]

overall_design: MeCP2 ChIP-seq was performed from WT and MeCP2 QKI mouse forebrain with input controls (n=3).


title: One bout of endurance exercise does not change gene expression or proliferation in a C26 colon carcinoma in immunocompetent mice

city: Planegg

first: Maximilian

middle: Michael

last: Saller

state: Bavaria

address: Fraunhoferstraße 20

department: Department of Orthopedics and Trauma Surgery

institute: LMU Hospital

summary: Purpose. Exercise typically reduces tumour growth, proliferation, and improves outcomes. Many of these effects require exercise to change gene expression within a tumour, but whether exercise affects gene expression within a tumour has not been investigated yet. The aim of this study was therefore to find out whether one bout of endurance exercise alters gene expression and proliferation in a C26 carcinoma in immunocompetent mice. Methods. BALB/c were injected with C26 colon carcinoma cells. Once the tumours had formed, the mice either ran for 65 min with increasing intensity or rested before the tumour was dissected. The tumours were then analysed by RNA-Seq and stained for the proliferation marker KI67.  Results. One bout of running for 65 minutes did not systematically change gene expression in C26 carcinomas of BALB/c mice that ran for 65 minutes when compared to BALB/c mice that were rested. However, when analysed for sex, the RNA expression of 17, mostly skeletal muscle-related genes was higher in the samples of the female mice taken post exercise. Further histological analysis showed that this signal likely comes from the presence of muscle fibres from the panniculus carnosus muscle inside the tumours. Also, we found no differences in the positivity for the proliferation marker KI67 in the control and exercise C26 carcinomas. Conclusion. A bout of exercise did not systematically affect gene expression or proliferation in C26 carcinomas in immunocompetent BALB/c mice.

first: Nik

last: Mahnic

first: Alessia

last: Geremia

first: Tobias

last: Straub

first: Sabrina

last: Zorzato

first: Martin

last: Schönfelder

first: Irene

last: von Lüttichau

first: Katja

last: Steiger

first: Bert

last: Blaauw

first: Henning

last: Wackerhage


title: The effect of TRPC6 inhibition in Breast cancer stem cell (BCSC) enriched models

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

summary: We found several genes differentially regulated by TRPC6, and in this study focused on ESRP1 (Epithelial Splicing Regulatory Protein 1)

overall_design: To identify downstream signaling pathways regulated by TRPC6 we designed a time-course expereiment treating cells with the TRPC6 inhibitor for 6 and 12 hours and DMSO as control for the respective time-points.

first: Dimpi

last: Mukhopadhyay

first: Arthur

last: Mercurio


title: Activity-induced MeCP2 phosphorylation regulates retinogeniculate synapse refinement [RNA-Seq]

first: Tess

last: Whitwam

overall_design: Bulk nucleus RNA-sequencing was performed from WT and MeCP2 QKI littermates at P15 (n=6), P16 (n=10), and P30 (n=6). Visual cortex and dLGN were dissected in either ACSF (P15, P16) or potassium gluconate electrophyisology solution (P30). Bulk RNA-seq was performed from visual cortex of WT and MeCP2 T308A littermates that were housed in the dark from 6 to 8 weeks of age, then exposed to light for 0 or 6 hours (WT 0hr n=3, T308A 0hr n=3, WT 6hr n=5, T308A 6hr n=10). Bulk RNA-seq was performed from dLGN and visual cortex of WT and MeCP2 QKI littermates that were housed in the dark from P20 to P30, then exposed to light for 0 to 4 hours (n=4).

first: Christopher

last: Tzeng

first: Lisa

last: Boxer

first: Michael

last: Greenberg


title: Divergence of TORC1-mediated Stress Response Leads to Novel Acquired Stress Resistance in a Pathogenic Yeast

city: Iowa City

first: Bin

last: He

email: emptyhb@gmail.com, bin-he@uiowa.edu

state: IA

address: 129 East Jefferson St., Biology Building 450

department: Biology

institute: the University of Iowa

summary: Acquired stress resistance (ASR) enables organisms to prepare for environmental changes that occur after an initial stressor. However, the genetic basis for ASR and how the underlying network evolved remain poorly understood. In this study, we discovered that a short phosphate starvation induces oxidative stress response (OSR) genes in the pathogenic yeast C. glabrata and protects it against a severe H2O2 stress; the same treatment, however, provides little benefit in the low pathogenic-potential relative, S. cerevisiae. This ASR involves the same transcription factors (TFs) as the OSR, but with different combinatorial logics. We show that Target-of- Rapamycin Complex 1 (TORC1) is differentially inhibited by phosphate starvation in the two species and contributes to the ASR via its proximal effector, Sch9. Therefore, evolution of the phosphate starvation-induced ASR involves the rewiring of TORC1’s response to phosphate limitation and the repurposing of TF-target gene networks for the OSR using new regulatory logics.

overall_design: To test the hypothesis that phosphate starvation induces oxidative stress response genes in C. glabrata, conferring protection for H2O2 as a secondary stress, we profiled the transcriptional response at 1 hour of phosphate starvation in C. glabrata and compared it with the response to the same treatment in S. cerevisiae from (Zhou and O’Shea 2011). Two biological replicates before phosphate starvation and 3 biological replicates at 1 hour after the start of the starvation were collected and processed.

middle: Z


title: Human monocyte-derived macrophages polarized by M-CSF in the presence or absence of 5 micromolar Methotrexate

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

summary: Macrophage phenotypic and functional heterogeneity derives from tissue-specific transcriptional signatures shaped by the local microenvironment. M-CSF drives the generation of human monocyte-derived macrophages with a potent anti-inflammatory activity upon stimulation. One-carbon metabolism (OCM) is a complex network of biosynthetic pathways that includes de novo biosynthesis of purines and thymidylate, amino acid metabolism, and methylation reactions. We explored the molecular impact of blocking OCM with high-doses of the anti-folate methotrexate (MTX) on the gene expression profile in M-CSF-primed human monocyte derived macrophages.

overall_design: mRNA profiles of human macrophages differentiated with M-CSF (M-MØ) from peripheral blood monocytes in the absence or in the presence of high doses of the antifolate methotrexate (MTX). MTX (5 uM) was added once on monocytes inmediatly before the initation of the M-CSF differentiation process.

first: Clara

last: Lorente-Sorolla

first: Mónica

last: Torres Torresano


title: Whole-genome transcriptome profiling in PFOS-treated uterine artery endothelial cells isolated from pregnant women

city: Madison

first: Sathish

last: Kumar

state: WI

address: 2015 Linden Dr

department: Comparative Biosciences

institute: University of Wisconsin

summary: During pregnancy, perfluorooctane sulfonate (PFOS) exposure is linked to increased risks of preeclampsia and fetal developmental complications. Although experimental and circumstantial data suggest that PFOS induces endothelial dysfunction, leading to decreased uterine arterial blood flow and gestational hypertension, the precise regulatory mechanisms responsible for this effect remain unknown. To address this issue, we treated human uterine artery endothelial cells (hUAECs) isolated from pregnant women with PFOS and conducted a comparative transcriptomic analyses to understand the underlying mechanism of PFOS-induced endothelial dysfunction.

overall_design: Human uterine artery endothelial cells (HUAECs) isolated from pregnant women were treated with 10 µmol/L PFOS or vehicle for 24 hours and total RNA was extracted (n=4). RNA-seq libraries were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Libraries were sequenced on Illumina NovaSeq 6000 instrument and image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequence quality was examined using the FastQC software. The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software. The transcript abundances for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown. The differentially expressed genes and transcripts were also filtered using R package Ballgown.

first: Jay

last: Mishra


title: Effect of Pak4 deficiency on transcriptomic profile in eWAT of mice

city: Jeonju-si

first: Byung-Hyun

last: Park

address: 567 Baekje-daero, Deokjin-gu

institute: Jeonbuk National University Medical School

summary: The excessive energy is primarily stored as triacylglycerol in lipid droplets in adipocytes, which is hydrolyzed by the actions of lipases upon energy demand. In this study, the potential role of PAK4 in the lipolysis process in adipocytes was investigated. To elucidate functional outcomes, we performed RNA-sequencing analysis using littermate WT and adipose tissue-specific Pak4 KO mice in fasted conditions.

overall_design: Examination of RNA profile in eWAT of WT and adipose tissue-specific Pak4 KO mice in 24 h fasted condition

first: Hwang

last: Yu

first: Chang

middle: Y

last: Han

first: Eun

last: Bae


title: Transcriptome profiling of circadian day and night gene expression in the suprachiasmatic nucleus of hypophysectomized (HPX) and control (non-HPX) mice

city: Suita

first: Yoshiaki

last: Yamaguchi

state: Osaka

address: 3-3-35 Yamate-cho

department: Life Science and Biotechnology

country: Japan

institute: Kansai University

summary:
HPX mice show enhanced re-entrainment after jet lag; it isimportant to investigate whether HPX affects gene expression in the SCN, the center of the circadian clock.
We used microarrays to study the effects of HPX on gene expression in the SCN.

overall_design: SCN tissue samples obtained with laser microdissection technique from 10 animals at ZT2 and 10 animals at ZT14 were pooled together into TRIzol reagent (Thermo Fisher Scientific).

first: Hitoshi

last: Okamura


title: shRNA cassette sequencing from MycER MEF cells, treated with 2mM GLN or no GLN for ~35 days

city: Boston

first: Raul

last: Mostoslavsky

state: MA

address: 185 Cambridge St.

institute: The Massachusetts General Hospital Cancer Center-Harvard University

summary: Genome-wide shRNA-based screen to identify resistance genes during GLN starvation

overall_design: 6x10^6 cells transduced with the mouse TRC2 library were starved of GLN for 4-5 weeks to screen for genes affecting survival and proliferation under GLN deprivation.

first: Samantha

last: Linder

first: Matthew

last: Galbraith

first: Kelly

last: Sullivan

first: Joaquín

middle: M

last: Espinosa


title: Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human

status: Public on Oct 22 2023

city: Beijing

first: Wenze

last: Huang

address: Tsinghua street

country: China

institute: Tsinghua University

summary: Genome-wide CRISPR screens identified lncRNAs that promote cell proliferation in HeLa, Huh7, and MCF7 cells

overall_design: The objectives of this study were to identify lncRNAs that promote cell proliferation in HeLa, Huh7, and MCF7 cells. We performed genome-wide CRISPR knockout screens in HeLa, Huh7, and MCF7 cells using designed pair crRNA library. Initial cell libraries were obtained through lentivirus infection at low MOI (~0.3), followed by collecting GFP-positive cells 72 hours after infection . For each replicate, generally a total of two million GFP-positive cells were collected by FACS . Three replicates of the experimental group were arranged for library screening, and at the same time, another two million GFP-positive cells were collected for genomic DNA extraction as the control group (day 0). During screening, samples containing at least four million cells were collected for genomic DNA extraction at three time points (days 15, 30, and 45) after each cell splitting.

first: qiangfeng

middle: c

last: zhang

first: wenze

last: huang

first: tuanlin

last: xiong


title: Hepatic tissue expression profiles of insulin-sensitive obese mice, insulin-resistant mice and control mice

status: Public on Oct 14 2023

first: Yibo

last: Wang

state: Beijin

address: 167 Beilishi Road, Xicheng District, Beijing

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Male C57BL/6J mice were fed a high-fat diet (HFD, 60 kcal% fat, D12492, Research Diets, Inc) or normal standard chow diet with 10 kal% fat (ND, D09100304, Research Diets, Inc). Specifically, 6-week-old mice were fed a HFD for 12 weeks to induce insulin resistance (HFD-12w group); 14-week-old mice were fed a HFD for 4 weeks to induce obesity (HFD-4w group). Control mice were fed a ND continuously for 12 weeks starting at 6 weeks of age (ND group). All mice reached the experimental endpoint at 18 weeks of age. Insulin sensitivity was measured by glucose tolerance test and insulin tolerance test. Mice that developed insulin resistance in HFD-12w group and obese mice with normal insulin sensitivity in HFD-4w group were used for further experiments. Mice in ND group were used as controls. Upon reaching the experimental endpoint, livers from three insulin-resistant mice, three insulin-sensitive obese mice, and three control mice were removed for RNA sequencing.

overall_design: To investigate the differences in hepatic expression profiles between insulin-sensitive obese mice and insulin-resistant mice, male C57BL/6J mice were fed a high-fat diet (HFD, 60 kcal% fat, D12492, Research Diets, Inc) or normal standard chow diet with 10 kal% fat (ND, D09100304, Research Diets, Inc). Specifically, 6-week-old mice were fed a HFD for 12 weeks to induce insulin resistance; 14-week-old mice were fed a HFD for 4 weeks to induce obesity. Control mice were fed a ND continuously for 12 weeks starting at 6 weeks of age. All mice reached the experimental endpoint at 18 weeks of age.

first: Liang


title: Activation of the interferon pathway in trophoblast cells infected with SARS-CoV-2

city: La Jolla

first: Robert

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: Infection with SARS-CoV-2 in pregnancy has been associated with poor maternal and neonatal outcomes and placental defects. The placenta, which acts as a physical and immunological barrier at the maternal/fetal interface, is not established until the end of the first trimester. Therefore, localized viral infection of the trophoblast compartment early in gestation could trigger an inflammatory response resulting in altered placental function and consequent suboptimal conditions for fetal growth and development. In this study, we investigated the effect of SARS-CoV-2 infection in early gestation placentae using placenta-derived human trophoblast stem cells (TSC), a novel in vitro model, and their extra-villous trophoblast (EVT) and syncytiotrophoblast (STB) derivatives. Consistent with host viral entry protein expression, SARS-CoV-2 was able to productively replicate in TSC-derived STB and EVT but not undifferentiated TSC. Both early EVT and STB elicited an interferon-mediated innate immune response similar to other cells infected with this virus. Therefore, we have also shown that placenta derived TSCs are a robust in vitro model to investigate the effect of this viral infection in the trophoblast compartment of the early placenta. Overall, these results suggest that SARS-CoV-2 infection in early gestation can adversely affect placental development and that might occur via directly infecting the differentiated trophoblast compartment, thus posing a higher risk for poor pregnancy outcomes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hTSCs (1048 and 1049) and their differentiated derivatives (EVT and STB)

first: Sampada

last: Kallol

first: Francesca

last: Soncin


title: MERSCOPE profiling of non-aneurysmal and aneurysmal human ascending aorta

city: Ann Arbor

first: Dogukan

last: Mizrak

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

summary: Single-molecule level spatial distribution of MERFISH (Multiplexed error-robust fluorescence in situ hybridization) probes targeting 140 genes were analyzed on two control (non-aneurysmal) samples and three TAA samples with Thoracic aortic aneurysm (TAA).

overall_design: We examined the spatial distribution of 140 transcripts by single molecule fluorescence in situ hybridization using the Vizgen MERSCOPE platform. MERSCOPE probe library was constructed through Vizgen. Optimal cutting temperature compound (OCT)-embedded ascending aorta samples were processed using an optimized protocol for human aortic tissue.  We captured thousands of cells per subject allowing us to identify spatially-distinct gene expression patterns in human TAA samples.


title: Identification of genes regulated by VSNL1 in colorectal cancer cells

city: Yufu

first: Naoki

last: Hijiya

state: Oita

address: 1-1, Idaigaoka Hasama-machi

department: Medicine

institute: Oita University

summary: We compared expression profiles between colorectal cancer cell lines CW-2 and HCT116 with and without VSNL1 downregulation.

overall_design: Colorectal cancer cell line CW-2 with VSNL1 knockdown vs that without knockdown. Colorectal cancer cell line HCT116 with VSNL1 knockdown vs that without knockdown.


title: Multiplexed assay of variant effect reveals residues of functional importance in the  BRCA1 coiled-coil and serine cluster domains

status: Public on Oct 13 2023

city: Columbus

first: Jeffrey

last: Parvin

state: OH

address: 460 West 12th Ave

department: Department of Biomedical Informatics

institute: The Ohio State University

summary: Delineating functionally normal variants from functionally abnormal variants in tumor suppressor proteins is critical for cancer surveillance, prognosis, and treatment options. BRCA1 is a protein that has many variants of uncertain significance which are not yet classified as functionally normal or abnormal. In vitro functional assays can be used to identify the functional impact of a variant when the variant has not yet been categorized through clinical observation. Here we employ a homology-directed repair (HDR) reporter assay to evaluate over 300 missense and nonsense BRCA1 variants between amino acid residues 1280 and 1576, which encompasses the coiled-coil and serine cluster domains. Functionally abnormal variants tended to cluster in residues known to interact with PALB2, which is critical for homology-directed repair. Multiplexed results were confirmed by singleton assay and by ClinVar database variant interpretations. Comparison of multiplexed results to designated benign or likely benign or pathogenic or likely pathogenic variants in the ClinVar database yielded 100% specificity and 100% sensitivity of the multiplexed assay. Clinicians can reference the results of this functional assay for help in guiding cancer treatment and surveillance options. These results are the first to evaluate this domain of BRCA1 using a multiplexed approach and indicate the importance of this domain in the DNA repair process.

overall_design: In this study, we have assessed the coiled-coil domain of  BRCA1 for the functional impact of single missense and nonsense substitutions using an updated analysis protocol. The samples provided below are the sequencing data for BRCA1 amino acid residues 1280-1576, as well as the barcode map (.tsv) used to mapped the variants.

first: Gregory

last: Nagy

first: Mariame

last: Diabate

first: Tapahsama

last: Banerjee

first: Aleksandra

middle: I

last: Adamovich

first: Nahum

last: Smith

first: Hyeongseon

last: Jeon

first: Shruti

last: Dhar

first: Wenfang

last: Liu

first: Katherine

last: Burgess

first: Dongjun

last: Chung

first: Lea

last: Starita


title: Activity-induced MeCP2 phosphorylation regulates retinogeniculate synapse refinement

first: Tess

last: Whitwam

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

overall_design: Refer to individual Series


title: Mild dehydration effects on the murine kidney single nucleus transcriptome and chromatin accessibility

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

institute: University of Alabama at Birmingham

summary: The kidney is composed of > 40 cell types that work collectively to maintain fluid-electrolyte balance. If not enough fluid is consumed to remain in balance, then vasopressin is released and acts in the kidney to increase water reabsorption.  Here the authors used kidney single nucleus multiome-sequencing to determine cell-specific transcriptomes and chromatin accessibility profiles of male and female control (ad libitum water and food) or mildly dehydrated mice (ad libitum food, water deprivation). There were hundreds of sex- and dehydration-specific differentially expressed genes throughout the kidney, most of which did not have a significant change in chromatin accessibility. Thus, even mild dehydration causes cell- and sex-specific transcriptomic changes even though the kidney function to conserve water is the same.

overall_design:
All are C57BL/6J mice.  A male ad lib, a male water deprived, a female ad lib and a female mouse water deprived.  Water was removed from the cages of the deprived mice at 3 pm. All sample collection occurred at +/-1 h at midnight (6 hours into the active period of the mice).

630	Female, Ad lib
636	Female, water deprived
638	Male, water deprived
641	Male, Ad lib

first: Nha

middle: V

last: Huynh


title: Small molecule-mediated reprogramming of Xenopus blastula stem cells to a neural crest state

city: Evanston

first: Paul

middle: Benjamin

last: Huber

state: Illinois

address: 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

summary:
Here we describe and validate a protocol for small molecule-mediated induction of the neural crest state
as a new tool for generating this important cell type and facilitating future studies of its development.

overall_design:
We induce a neural crest state using a BMP inhibitor (K02288) and wnt agonist (CHIR99021) and compare
the transcriptome to other neural crest data sets.

first: Carole

last: LaBonne


title: Paired box 6 gene delivery preserves beta cells and improves islet transplantation efficacy

city: Singapore

first: Wing Yan

last: So

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology

country: Singapore

institute: Agency for Science, Technology and Research

summary: Loss of pancreatic beta cells is the central feature of all forms of diabetes. Current therapies fail to halt the declined beta cell mass. Thus, strategies to preserve beta cells are imperatively needed. In this study, we identified paired box 6 (PAX6) as a critical regulator of beta cell survival. Under diabetic conditions, the human beta cell line EndoC-bH1, db/db mouse and human islets displayed dampened insulin and incretin signalings and reduced beta cell survival, which were alleviated by PAX6 overexpression. Adeno-associated virus (AAV)-mediated PAX6 overexpression in beta cells of streptozotocin-induced diabetic mice and db/db mice led to a sustained maintenance of glucose homeostasis. AAV-PAX6 transduction in human islets reduced islet graft loss and improved glycemic control after transplantation into immunodeficient diabetic mice. Our study highlights a previously unappreciated role for PAX6 in beta cell survival and raises the possibility that ex vivo PAX6 gene transfer into islets prior to transplantation might enhance islet graft function and transplantation outcome.

overall_design: To investigate if PAX6 gene delivery in normal human islets would enhance islet potency and preserve islet graft post-transplant, AAV-Ctrl or AAV-PAX6 transduction was performed in normal human islets. Gene expression profiling analysis was performed using RNA-seq data obtained from 5 control and 8 PAX6-overexpressing human islet samples.

first: Wing

first: Yilie

last: Liao

first: Wai

middle: N

first: Guy

middle: A

last: Rutter

first: Weiping

last: Han


title: Bulk tissue RNA-seq of in vitro macaque fetal cortical neural stem cells

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

institute: Yale University

summary: Early telencephalic development involves patterning of the distinct regions and fate specification of the neural stem cells (NSCs). These processes, mainly characterized in rodents, remain elusive in primates and thus our understanding of conserved and species-specific features. Here, we profiled 761,529 single-cell transcriptomes from multiple regions of the prenatal macaque telencephalon. We defined the molecular programs of the early organizing centers and their cross-talk with NSCs, finding primatebiased signaling active in the antero-ventral telencephalon. Regional transcriptomic divergences were evident at early states of neocortical NSC progression and in differentiated neurons and astrocytes, more than in intermediate transitions. Finally, we show that neuropsychiatric disease- and brain cancerrisk genes have putative early roles in the telencephalic organizers’ activity and across cortical NSC progression.

overall_design: Macaque cortical region specific NSCs were expanded in vitro for 5 days (DIV 5). Differentiation was induced after DIV5 and cells were grown until DIV20. Total RNA was extracted at NSC state (DIV1-5), differentiation transition DIV (6-8) and terninal differentiation (DIV11-20).

first: Nicola

last: Micali

first: Shaojie

last: Ma

first: Mingfeng

last: Li

first: Suel-Kee

last: Kim

first: Xoel

last: Mato-Blanco

first: Suvimal

last: Sindhu

first: Jon

last: Arellano

first: Tianliuyun

last: Gao

first: Alvaro

last: Duque

first: Gabriel

last: Santpere

first: Pasko

last: Rakic


title: Decoding transcriptomic signatures of Cysteine String Protein alpha-mediated synapse maintenance

city: New Haven

first: Sreeganga

last: Chandra

address: 295 Congress Avenue, BCMM 154D

department: Depts. of Neuroscience and Neurology

summary: Cysteine string protein α  (CSPα), encoded by the Dnajc5 gene, is a synaptic vesicle chaperone that is linked to synapse maintenance and neurodegeneration. To investigate the transcriptional changes associated with synapse maintenance, we performed single nucleus transcriptomics on the cortex of CSPα knockout (KO) mice and littermate controls.

overall_design: Nuclei was isolated from CSPα KO and littermate WT mice. DEGs, GO, RNA velocity and CellchatDB analysis were performed for the WT and KO samples.


title: Mild dehydration effects on the murine kidney single nucleus transcriptome and chromatin accessibility [RNA-seq]

first: Kelly

last: Hyndman

overall_design: All are C57BL/6J mice.  A male ad lib, a male water deprived, a female ad lib and a female mouse water deprived.  Water was removed at 3 pm from the deprived mice. All sample collection occurred at +/-1 h at midnight (6 hours into the active period of the mice).

first: Nha

last: Huynh


title: Mutational analysis of IVT mRNAs

city: Cambridge

first: Thomas

last: Mulroney

address: Tennis Court Road

institute: University of Cambridge

summary: RNA-seq analysis of in vitro transcribed mRNAs, containing modified nucleotides, or unmodified/canonical nucleotides, in order to assess the effect on the frequency of INDELS during transcription.

overall_design: Comparison of single nucleotide insertions or deletions for unmodified IVT mRNA and N1-methylpseudouridylated IVT mRNA.


title: Only the loss-of-function but not the gain-of-function properties of mutant TP53 are critical for the sustained proliferation, survival and metastasis of a broad range of cancer cells

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute


title: Only the loss-of-function but not the gain-of-function properties of mutant TP53 are critical for the sustained proliferation, survival and metastasis of a broad range of cancer cells [breast cancer]

summary: The loss of mutant TP53 did not sensitise tumour cells to chemotherapeutic agents.

overall_design: CRISPR/Cas9 was used to delete mutant TP53 a cancer cell line, then responses were detected to the treatment of anticancer drug in the control cells and its mutant TP53 deficient variant.

middle: S

first: Zilu

last: Wang

first: Andreas

last: Strasser

first: Gemma

middle: L

last: Kelly


title: Antagonizing IL-1β to treat GBM

city: New York

first: Dolores

last: Hambardzumyan

state: NY

address: 1425 Madison Ave.

department: Oncological Sciences

institute: Icahn School of Medicine

summary: Monocytes and monocyte-derived macrophages (MDM) from blood circulation infiltrate and promote glioblastoma growth by, at least partially, expressing pro-inflammatory cytokine IL-1β . Using SC-RNA seq, we analyze how IL1a and IL1b differentially contibute to tumor growth.

overall_design: We induced de novo brain tumor in WT, IL1b-KO and IL1ab-KO mice of both genders. We isolated brain tumor cells at the humane endstage of these mice and run sc-RNA seq on these cells to compare their funcitonal differences.

first: Zhihong

last: Chen

first: Alexander

last: Tsankov

first: Bruno

last: Giotti


title: Diurnal cycles drive rhythmic physiology and promote survival in facultative phototrophic bacteria

status: Public on Oct 12 2023

city: Neuchâtel

first: Diego

last: Gonzalez

address: Rue Emile-Argand

country: Switzerland

institute: Laboratory of Microbiology, University of Neuchâtel

summary: Bacteria have evolved many strategies to spare energy when nutrients become scarce. One widespread such strategy is facultative phototrophy, which helps heterotrophs supplement their energy supply using light. Our knowledge on the impact that such behaviors have on bacterial fitness and physiology is, however, still limited. Here, we study how a representative of the genus Porphyrobacter, in which aerobic anoxygenic phototrophy is ancestral, responds to different light regimes under nutrient limitation. We show that bacterial survival in stationary phase relies on functional reaction centers and varies depending on the light regime. Under dark‑light alternance, our bacterial model presents a diphasic life history dependent on phototrophy: during dark phases, the cells inhibit DNA replication and part of the population lyses and releases nutrients, while subsequent light phases allow for the recovery and renewed growth of the surviving cells. We correlate these cyclic variations with a pervasive pattern of rhythmic transcription which reflects global changes in diurnal metabolic activity. Finally, we demonstrate that, compared to either a phototrophy null mutant or a bacteriochlorophyll a overproducer, the wild type strain is better adapted to natural environments, where regular dark‑light cycles are interspersed with additional accidental dark episodes. Overall, our results highlight the importance of light‑induced biological rhythms in a new model of aerobic anoxygenic phototroph representative of an ecologically important group of environmental bacteria.

overall_design:
The wild-type (WT) and a bacteriochlorophyll-a-null mutant (Biz) Porphyrobacter sp. ULC335 strains were cultured under 12:12 dark/light cycles (150µmol/s/m2).
Cells were collected in stationary phase one hour before light were switched on (7), one hour after lights  were switched on (9), one hour before light were switched off (19) and one hour after lights were switched off (21).

first: Camille

last: Tinguely

first: Céline

last: Terrettaz

first: Mélanie

last: Paulméry


title: Only the loss-of-function but not the gain-of-function properties of mutant TP53 are critical for the sustained proliferation, survival and metastasis of a broad range of cancer cells [colon cancer]

summary: The loss of mutant TP53 has no impact on the growth of patient derived colon cancer organoids in vivo

overall_design: CRISPR/Cas9 was used to delete mutant TP53 patient derived colon cancer organoids, then the tumour growth was detected in the control organoids (3 samples) and its mutant TP53 deficient variant (3 samples) both in vivo.


title: Transcriptome of human primary macrophages from X-linked adrenoleukodystrophy patients and healthy controls before and after long-term myelin phagocytosis

city: Vienna

first: Isabelle

last: Weinhofer

address: Spitalgasse 4

country: Austria

institute: Medical University of Vienna


title: High neighborhood deprivation impacts DNA methylation and gene expression in cancer-related genes (MethylationEPIC)

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

summary: Background: Low socioeconomic status (SES) has been linked to chronic stress and poorer health outcomes for marginalized communities in the U.S. The biological processes mediating the impact of SES on health to promote chronic diseases, such as cancer, remain poorly understood. Here, we aim to determine how changes in DNA methylation are linked to neighborhood-level socioeconomic deprivation, thereby promoting cancer initiation and progression through cancer- and immune-related pathways.      Methods: We extracted DNA from 402 fresh frozen tissues from 289 women in the NCI-Maryland Breast Cancer Cohort, including 185 tumor samples, 113 additional paired adjacent normal samples, and 104  normal tissues from reduction mammoplasty. Census-tract level socioeconomic deprivation was measured via a Neighborhood Deprivation Index (NDI) using the geocoded addresses from our study participants. DNA methylation values were acquired using the Illumina Infinium MethylationEPIC 850K Beadchip. We conducted a differentially methylated probe (DMP) analysis between tumor and adjacent normal tissue to characterize methylation profiles by NDI status. We also used methylCIBERSORT to estimate immune cell subpopulation differences by tissue type and NDI status.    Results: NDI was significantly associated with self-reported race in our cohort in both normal (p<0.0001, 95% CI -4.32, -2.58) and tumor (p<0.0001, 95% CI -4.22, -2.79) tissue. Our DMP analysis showed more significant methylation events (hypo- or hyper- methylation of the tumor tissue compared to adjacent normal tissue) in the NDI high group compared to the NDI low group. We also identified five CpG sites that were significantly hypomethylated in the tumors of the NDI high group, including two tumor suppressor genes, LRIG1 (p=1.99 x10-10) and WWOX (p=6.47 x 10-9). These methylation changes translated to an inverse relationship between gene expression for these tumor suppressor genes and NDI. We also identified significantly lower neutrophils in the NDI high tumors compared to NDI low tumors (p=0.001, 95% CI -0.112, -0.028).     Conclusions: Overall, our analysis provides evidence that high neighborhood deprivation can lead to pro-tumorigenic changes in DNA methylation and gene expression that may impact the immune microenvironment, breast cancer progression, and overall survival.

overall_design: Bisulphite converted DNA from the 402 samples were hybridised to the Illumina Infinium MethylationEPIC 850K Beadchip v1.0

first: Brittany

last: Lord

first: Emily

last: Rossi

first: Tiffany

middle: H

last: Dorsey

first: Ajao

last: Anuoluwapo

first: Catherine

last: Pichardo

first: William

last: Wooten

first: Margaret

first: Wei

last: Tang

first: Ruby

last: Hutchison

first: Maeve

last: Bailey-Whyte


title: DL3 formation of Bursaphelenchus xylophilus

first: Peng

last: Wang

address: Qing Long Qiao Street

institute: Chinese Academy of Forestry

type: Methylation profiling by high throughput sequencing


title: A cooperative organelle biogenesis program in mammalian cells

city: Perth

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

institute: The Kids Research Institute Australia

summary: The compartmentalisation of distinct organelles within eukaryotic cells is essential for their diverse functions, however, how their structures and functions depend on each other has not been systematically explored. We combined a fluorescent reporter of mitochondrial stress with genome-wide CRISPR knockout screening and identified networks of genes involved in the biogenesis and metabolism of diverse organelles. Targeted organelle gene knockouts identified that defects in peroxisomes, Golgi, and ER cause mitochondrial fragmentation and dysfunction. Correlative light and electron microscopy analysed using artificial intelligence-directed voxel extraction revealed in unprecedented detail how impaired mitochondrial interactions with diverse organelles caused cell-wide defects in their morphology and biogenesis. Multi-omics analyses identified a unified proteome stress response and global shifts in lipid and glycoprotein homeostasis that are elicited when organelle biogenesis is compromised. Our comprehensive resource has defined metabolic and morphological interactions between organelles that can be mined to understand how changes in organelle components drive diverse cellular pathologies.

overall_design: RNA-Seq performed on PEX26, GOLGA5, SEC61A2, GOLGA8M and SEC61 knockouts and wild type mice, in triplicate.

first: Richard

middle: G

last: Lee

first: Danielle

last: Rudler

first: Samuel

last: Raven

first: Elle

last: Pang

first: Edward

last: Moh

first: Tim

last: McCubbin

first: Nicholas

last: Debono

first: Maike

last: Stentenbach

first: Jasmin

last: Browne

first: Filip

middle: F

last: Rackham

first: Ji

last: Li

first: Kaylene

last: Simpson

first: Esteban

last: Marcellin

first: Nicolle

last: Packer

first: Gavin

last: Reid

first: Benjamin

last: Padman

first: Oliver

first: Aleksandra

last: Filipovska


title: RNA sequencing analysis during the DL3 formation of Bursaphelenchus xylophilus

city: Beijing

first: Peng

last: Wang

summary: DNA methylation is a pivotal process that regulates gene expression and facilitates rapid adaptation to challenging environments. The pine wood nematode (PWN; Bursaphelenchus xylophilus), the causative agent of pine wilt disease, survives and spreads at low temperatures through third-stage dispersal larvae, making it a major pathogen for pine wood in Asia. To comprehend the impact of DNA methylation on the formation and environmental adaptation of third-stage dispersal larvae, we conducted whole-genome bisulfite sequencing and transcriptional sequencing on both the third-stage dispersal larvae and three other stages propagative larvae of PWN.

overall_design: Analysis of environmental adaptability of four different developmental stages of pine wood nematode：L2, second-stage propagative larvae; L3, third-stage propagative larvae; L4, fourth-stage propagative larvae; DL3, third-stage dispersal larvae.Analysis using whole genome bisulfite sequencing and transcriptome sequencing.

first: Zhenkai

last: Liu

first: Yongxia


title: TIME-Seq Enables Scalable and Inexpensive Epigenetic Age Predictions

city: Boston

first: Patrick

middle: T

last: Griffin

address: 77 Avenue Louis Pasteur

department: Harvard Medical School, Dept. of Genetics

institute: Patrick Griffin

summary: We report a high-throughput and low-cost targeted bisulfite sequencing method called TIME-Seq for discovery and assay of DNA methylation clocks. Data is related to the initial publication of TIME-Seq clocks and shallow sequencing-based predictions using scAge. Demultiplexing information as well as more detailed metadata for each sample in the pools will be posted at: https://github.com/patricktgriffin/TIME-Seq

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of DNA methylation by TIME-Seq in mouse and human blood samples as well as mouse liver samples.

first: Alice

middle: E

last: Kane

first: Alexandre

last: Trapp

first: Jien

first: Matthew

last: Arnold

first: Jesse

middle: R

last: Poganik

first: Maeve

last: McNamara

first: Margarita

last: Meer

first: Noah

last: Hoffman

first: João

last: Amorim

first: Xiao

last: Tian

first: Michael

last: RMacArthur

first: Sarah

last: Mitchell

first: Amber

last: Mueller

first: Colleen

last: Carmody

first: Daniel

last: Vera

first: Csaba

last: Kerepesi

first: Nicole

last: Noren Hooten

first: James

first: Michele

middle: K

last: Evans

first: Vadim

last: Gladyshev

first: David

last: Sinclair


title: Whole genome bisulfite sequencing analysis during the DL3 formation of Bursaphelenchus xylophilus

first: Peng

last: Wang

first: Zhenkai

last: Liu

first: Yongxia

last: Li


title: SERPINB3 induces the aggressive basal-like/squamous subtype and promotes invasion and metastasis in pancreatic cancer III

first: Stefan

last: Ambs

summary: Pancreatic cancer is a heterogenous disease and consists of distinct subtypes. Here, we searched for candidate driver genes of the basal-like/squamous subtype, a more aggressive molecular subtype of pancreatic ductal adenocarcinoma (PDAC). Through an integrated transcriptome analysis, we identified the serine/cysteine protease inhibitor, SERPINB3 (squamous cell carcinoma antigen 1, SCCA1), as being upregulated in the basal-like/squamous PDAC using a discovery and validation approach. SERPINB3 upregulation associated with decreased patient survival and a transcriptome profile indicative of the basal-like/squamous subtype. The goal of this study was aimed to identify SERPINB3 induced molecular signatures in PDAC.

overall_design: RNA was isolated from human PDAC patient tumors using TRIzol method. The mRNA profiles of the above human PDAC tumors were generated by deep sequencing using Illumina Novaseq.

first: Ohara

last: Yuuki

first: Tang

last: Wei

first: Liu

last: Huaitian

first: Yang

last: Shouhui

first: He

last: Peijun

first: Cawley

last: Helen

first: Valenzuela

last: Paloma

first: Zhang

last: Lin

first: Gaedcke

last: Jochen

first: Ghadimi

last: B Michael

first: Gaida

last: Matthias M.

first: Bergmann

last: Frank

first: Alexander

last: H Richard

first: Hanna

last: Nader

first: Guest

last: Mary

first: Chari

last: Raj

first: Wolcott

last: Karen

first: Livak

last: Ferenc

first: Ambs

last: Stefan

first: Hussain

last: S Perwez


title: Single-cell mulitome (paired scRNA-seq + scATAC-seq) analysis of PBMCs from infants and young children during COVID-19 infection

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

summary: Purpose: To understand the single cell transcriptional and epigenetic landscape of immune cells from infants and young children infected with COVID-19

overall_design: PBMCs from infants and young children (aged 1-24 months) collected before (n=9), during (n=18), and after (n=9) COVID-19 infection (omicron and pre-omicron) as well as age- and sex-matched healthy controls (n=7) were analyzed using the 10X genomics single-cell multiome assay. Pre, acute, and convalescent samples from non-omicron infection are longitudinally collected from the same subjects.

first: Florian

last: Wimmers

first: Hong

last: Zheng


title: NR5A2 connects genome activation to the first lineage segregation in totipotent embryos

first: Fangnong

last: Lai

state: Beijing

address: Haidian district

institute: Tsinghua University

summary: Zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which gives rise to inner cell mass (ICM), where pluripotent epiblast arises, and extraembryonic trophectoderm. While much has been learned about pluripotency regulation, how ZGA is connected to the first lineage segregation in early embryos remains elusive. Here, we investigated the role of nuclear receptor transcription factors (NR TFs), whose motifs are highly enriched in accessible chromatin at the 2-cell (2C) to 8-cell (8C) stages after ZGA. We found NR5A2, an NR TF highly induced upon ZGA, is required for early development. Genome-wide chromatin binding in 2C and 8C embryos showed NR5A2 bound cis-regulatory elements which strongly enrich B1 elements where its motif is embedded. RNA-seq showed while the zygotic genome was largely activated at the 2C stage, 4-8C-specific gene activation was substantially impaired in Nr5a2 KD embryos. At the 8C stage, NR5A2 preferentially regulated its targets including a subset of early ICM genes. Consistently, NR5A2 was required for opening 8C-specific binding sites. Interestingly, while NR5A2’s 2C-binding sites are largely closed in blastocyst, 8C-specific binding sites tend to stay open and are bound by master pluripotency TFs (NANOG, SOX2, and OCT4) in blastocyst or ESC. Further analyses showed NR5A2 regulates early ICM genes at the 8C stage, master pluripotency TFs regulate both early and late ICM genes at later stages. Taken together, these data identify NR5A2 as a key regulator in totipotent embryos that connects ZGA to the first lineage segregation in early mouse development.

overall_design: By employing CUT&RUN, ATAC-seq, ChIP-seq and RNA-seq, we systematically examined the genome wide NR5A2 chromatin binding and function in mouse early embryos and  mESC cell lines.

first: Lijia

last: Li

first: Wei

last: Xie

first: Xiaoyu

last: Hu

first: Bofeng

last: Liu


title: SERPINB3 induces the aggressive basal-like/squamous subtype and promotes invasion and metastasis in pancreatic cancer I

first: Stefan

last: Ambs

overall_design: RNA was isolated from PDAC xenografts (n = 6 AsPC-1_SB3 and n = 6 AsPC-1_control) using the RNeasy Plus Mini Kit (QIAGEN, Venlo, Netherlands). The mRNA profiles of the above PDAC xenografts were generated by deep sequencing using Illumina NovaSeq 6000 SP.

first: Yuuki

last: Ohara

last: Tang

first: Huaitian

first: Shouhui

last: Yang

first: Peijun

last: He

first: Helen

last: Cawley

first: Paloma

last: Valenzuela

first: Lin

last: Zhang

first: Jochen

last: Gaedcke

first: B

middle: M

last: Ghadimi

first: Matthias

last: Gaida

first: Frank

last: Bergmann

first: H

last: Alexander

first: Nader

last: Hanna

first: Mary

last: Guest

first: Raj

last: Chari

first: Karen

last: Wolcott

first: Ferenc

last: Livak

first: S

middle: P

last: Hussain


title: Gene expression of cardiac organoids at a single cell resolution in healthy and cardiac injury conditions

city: Toronto

first: Gordon

last: Keller

state: Ontario

address: 101 College St

country: Canada

institute: McEwen Stem Cell Institute

summary: Cardiac fibroblast heterogeneity has been observed increasingly in data sets coming from model organisms during regeneration and cardiac injury. This works provides the first characterization of cardiac fibroblasts derived from hPSC epicardial cells in a healthy and injured state with single cell resolution.

overall_design: hPSC derived cardiac cells were seperated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of RFP or GFP signal and analyzed using multi-seq labeling and subsequent scRNAseq.

first: Ian

last: Fernandes

first: Shunsuke

last: Funakoshi


title: Myelin-Associated Oligodendrocytic Basic Protein-Dependent Myelin Repair Confers the Long-lasting Antidepressant Effect of Ketamine

city: Nanjing

first: Chaoli

last: Huang

state: Jiangsu

address: 300 Guangzhou Road

institute: he First Affiliated Hospital of Nanjing Medical University

summary: To examine ketamine’s long-lasting effects on gene expression in the brains of mice exhibiting depression-like behaviors, we used spatial transcriptomics (ST) to analyze transcriptomics on the cortices of mice exposed to chronic social defeat stress (CSDS) and treated with ketamine.

overall_design: Wild type C57 mice went through CSDS and resilient and susceptible mice were selected by social interaction test. Some susceptible mice were randomly selected and treated with ketamine. the depression-like behaviors were examined by behavioral tests and the brain samples for ST were collected 7 days after ketamine-administration.

first: Qidong

last: Zu

first: Xiaohua

last: Yao

first: Yuanyuan

last: Wang


title: RNA-seq analysis of the transcriptomic program regulated by DeltaNp63 in Human Papillomavirus-positive oropharyngeal cancer cell line models

city: Strasbourg

first: Alain

last: Jung

address: 17 Rue Albert Calmette

institute: Institut de cancérologie Strasbourg Europe

summary: We report the analysis of the transcriptomic program regulated by DeltaNp63. In short, RNA was extracted from SCC90 cells transfected with siRNA against ∆Np63 or non-specific scrambled siRNA, and total RNA was harvested from the cells using a TRIzol-mediated cell lysis approach. To identify the deregulated genes, RNA-Sequencing was performed on extracted total RNAs and the sequences obtained were selectively aligned on a chimeric genome composed of the human genome (hg38) using STAR version 2.5.3a.

overall_design: RNA-sequencind data from the SCC90 HPV-positive oropharyngeal squamous cell carcinoma cell line models transfected with control or anti-DeltaNp63 siRNA

first: Cyril

last: BOUR

first: Tao

last: YE

first: Christelle

last: THIBAULT-CARPENTIER

first: Anaïs

last: NICOL

first: Bohdan

last: WASYLYK

first: Christian

last: GAIDDON

last: JUNG


title: SERPINB3 induces the aggressive basal-like/squamous subtype and promotes invasion and metastasis in pancreatic cancer II

first: Stefan

last: Ambs

overall_design: RNA was isolated from PDAC cell lines (n = 8 Panc 10.05 ± SERPINB3, n = 8 AsPC-1 ± SERPINB3, n = 8 AsPC-1 SERPINB3 ± a MYC inhibitor, n = 8 Panc 10.05 SERPINB3 ± a MYC inhibitor, n = 8 BxPC-3 ± SERPINB3 knockout) using TRIzol method. The mRNA profiles of the above human PDAC cell lines were generated by deep sequencing using Illumina NextSeq.

first: Yuuki

last: Ohara

first: Wei

last: Tang

first: Huaitian

last: Liu

first: Shouhui

last: Yang

first: Tiffany

last: Dorsey

first: Helen

last: Cawley

first: Paloma

last: Moreno

first: Raj

last: Chari

first: Mary

last: Guest

first: Azadeh

last: Azizian

first: Jochen

last: Gaedcke

first: Michael

last: Ghadimi

first: Nader

last: Hanna

last: Perwez Hussain


title: CPT1A induction following epigenetic perturbation promotes MAVS palmitoylation and activation to potentiate antitumor immunity

city: Hangzhou

first: Wanqiang

last: Sheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Immunology

institute: Zhejiang University School of Medicine

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

overall_design: Refer to individual Series


title: Inhibition of METTL3 results in a cell-intrinsic interferon response that enhances anti-tumour immunity

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

institute: Peter MacCallum Cancer Centre


title: Hedgehog activation promotes osteogenic fates of growth plate resting zone chondrocytes through transient clonal competency [NovaA-237]

status: Public on Oct 11 2023

city: Houston

first: Shion

last: Orikasa

state: TX

address: 7500 Cambridge St

institute: University of Texas Health Science Center at Houston School of Dentistry

summary: A single cell transcriptional profile of growth plate cells of the murine femur at postnatal day 36 (P36), lineage-marked by PTHrP-creER at P6, Control

overall_design: tdTomato+ cells were FACS-isolated from PTHrP-creER; Ptch1(fl/+); R26R-tdTomato (Control) growth plate at P36 (tamoxifen at P6). 10,000 cells were loaded onto 10X Genomics Chromium Single Cell Expression Solution version 3 platform. cDNA was sequenced by Illumina NovaSeq 6000

first: Noriaki

last: Ono

first: Yuki

last: Matsushita


title: Off-target effect of CWG-cPIP on gene expression of mouse Striatum

city: Honjo, Chuo-ku, Kumamoto

first: Kazuya

last: Matsuo

department: IMEG

institute: Kumamoto University

summary: CWG-cPIP targets CAG/CTG (CWG) triplet repeat DNA to inhibit the transcription in a repeat length-dependent manner. To investigate off-target effects of CWG-cPIP on gene expression in the brain, CWG-cPIP (664 ug/kg) was intracerebroventricularly injected into mouse. RNA sequencing analysis was performed using vehicle- or CWG-cPIP-injected mouse striatum 3 weeks later, mixing with ERCC RNA spike-in controls.

overall_design: Comparative gene expression profiling analysis of RNA sequencing data for the hippocampus of vehicle- or CWG-cPIP-treated C57BL/6J mice (n = 3 mice each).

first: Norifumi

last: Shioda


title: Off-target effect of CWG-cPIP on gene expression of mouse hippocampus

summary: CWG-cPIP targets CAG/CTG (CWG) triplet repeat DNA to inhibit the transcription in a repeat length-dependent manner. To investigate off-target effects of CWG-cPIP on gene expression in the brain, CWG-cPIP (83 ug/kg) was injected into mouse hippocampus. RNA sequencing analysis was performed using vehicle- or CWG-cPIP-injected mouse hippocampus 3 weeks later, mixing with ERCC RNA spike-in controls.


title: small RNAs sequencing in sweet sorghum under cadmium stress

first: YinXin

last: Li

address: Nanxin Cun 20th, Xiangshan, Haidian district

institute: Institute of Botany, Chinese Academy of Sciences

summary: Four small RNA libraries from two contrasting sweet sorghum genotypes were sequenced. In this study, One hundred and ninety-five conserved miRNAs belonging to 56 families and 25 putative novel miRNAs from 28 precursors were identified, among which 38 conserved and 24 novel miRNAs were differentially expressed under Cd stress and/or between H18 and L69. Two groups of them: miR169p/q-nov_23 and miR408 were further focused through the coexpression analysis and might be involved in Cd transport, cytoskeleton activity and cell wall construction by regulating their targets. This study presents new insights into the regulatory roles of miRNAs in Cd accumulation and tolerance in sweet sorghum and will help to develop high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum through molecular breeding and/or genetic engineering approaches.

overall_design: Four sRNA libraries were constructed from the roots of H18 and L69 (high-Cd accumulation one H18, and low-Cd accumulation one L69) treated with 10 µM CdCl2 for 24 hours, using the plants without CdCl2 treatment as control (named H18-CK, H18-Cd, L69-CK and L69-Cd, respectively). High throughput sequencing of miRNAs was then performed.

first: Yinxin

first: Weitao

last: Jia

first: Juanjuan

last: Feng

first: Kangqi

last: Lin

first: Sulian

last: Lv

first: Ping

last: Jiang

first: Xuan

last: Zhang

first: Ze

last: Yi

first: Duoliya

last: Wang

first: Zijing

last: Guo


title: Hedgehog activation promotes osteogenic fates of growth plate resting zone chondrocytes through transient clonal competency [NovaA-186]

summary: A single cell transcriptional profile of growth plate cells of the murine femur at postnatal day 36 (P36), lineage-marked by PTHrP-creER at P6

overall_design: tdTomato+ cells were FACS-isolated from PTHrP-creER; Ptch1(fl/fl); R26R-tdTomato (Ptch1-cKO) growth plate at P36 (tamoxifen at P6). 26,000 cells were loaded onto 10X Genomics Chromium Single Cell Expression Solution version 3 platform. cDNA was sequenced by Illumina NovaSeq 6000


title: The Cytoskeletal Stress Response Pathway: a homeostatic system driven by Dual Leucine Zipper Kinase (DLK)

city: St Louis

first: Laura

last: DeVault

state: MO

address: 4523 Clayton Avenue

department: developmental biology

institute: Washington University

summary: Injury to peripheral axons initiates a complex cascade of cellular responses, including cytoskeletal disassembly, axon transport disruption, and ultimately axon regeneration. Central to this process is the MAP triple kinase Dual-Leucine Zipper Kinase (DLK), activated by injury and other neuronal stressors. Here, we propose the existence of a homeostatic mechanism termed the Cytoskeletal Perturbation Response (CPR). We investigate this hypothesis by examining the response of cultured dorsal root ganglion (DRG) neurons to low dose nocodazole treatment, a cytoskeletal perturbing agent. To gain insights into DLK-dependent transcriptional changes following cytoskeletal insult, we performed bulk RNA sequencing on cultured neurons treated for 16 hours. Using a fully crossed two-factor design, we determined the interactive effect of DLK on nocodazole- dependent transcriptional changes.  Our study demonstrates that cytoskeletal perturbation triggers DLK-dependent signaling cascades, leading to significant transcriptional changes. These changes involve transcription factors (Jun, Egr1, Atf3) and MAP kinase regulators (DUSPs), pointing to a regulatory network that attenuates DLK signaling. Taken together, our findings suggest that cytoskeletal perturbation activates a DLK-dependent homeostatic mechanism, the CPR, which orchestrates transcriptional changes and morphological adaptations to repair neuronal damage. The CPR bears similarities to established homeostatic responses, offering insights into the intricate processes that underlie axon regeneration and cellular repair.

overall_design: Primary DRGs were cultured from CD1 mouse embryos. At 6 days in vitro (DIV), neurons were pretreated with DMSO or 500nM DLK inhibitor (GNE3511). After 15 minutes, neurons were then treated with DMSO, or 200nM nocodazole. This produced 4 groups: ((1)DMSO, DMSO; (2) DMSO, Noc; (3) DLKi, DMSO and (4) DLKi, Noc). We collected 4 replicates per group. We performed differential gene expression profiliing using data obtained from RNA seq of these 4 group using 4 replicates.

first: DeVault

last: Laura

first: Mateusiak

last: Chase

first: DiAntonio

last: Aaron

first: Brent

last: Micheal

first: Milbrandt

last: Jeff

first: Palucki

last: John


title: Deletion of Vβ3+CD4+ T cells by endogenous mouse mammary tumor virus 3 prevents type 1 diabetes induction by autoreactive CD8+ T cells

city: Columbia

first: John

last: Driver

address: 1201 Rollins Street

institute: University of Missouri

summary: To characterize B6.H2g7 Vb3+(Trbv26+) CD4+ T-cells, which are deleted by NOD-encoded Mtv3 in B6.H2g7.Idd32NOD/NOD mice, paired single-cell RNA sequencing and single-cell TCR sequencing was performed on two separate pools of B6.H2g7 CD4+ T-cells 14 days after they were adoptively transferred into two NOD.Rag1null recipient mice.

overall_design: 5 x 10^6 magnetic column purified CD4+ T-cells harvested from spleens of B6.H2g7 donor mice were transferred to NOD.Rag1null hosts and recovered from host spleens 14 days later by flow cytometric sorting for single cell sequencing analysis

first: Weihong

last: Gu


title: Hedgehog activation promotes osteogenic fates of growth plate resting zone chondrocytes through transient clonal competency

first: Shion

last: Orikasa


first: Wanqiang

last: Sheng

summary: Targeting epigenetic regulators to potentiate anti-PD-1 immunotherapy converges on the activation of type I interferon (IFN-I) response, mimicking cellular response to viral infection, but how its strength and duration are regulated to impact combination therapy efficacy remains largely unknown. Here, we show that mitochondrial CPT1A downregulation following viral infection restrains, while its induction by epigenetic perturbations sustains, a double-stranded RNA-activated IFN-I response. Mechanistically, CPT1A recruits the endoplasmic reticulum-localized ZDHHC4 to catalyze MAVS Cys79-palmitoylation, which promotes MAVS stabilization and activation by inhibiting K48- but facilitating K63-linked ubiquitination. Further elevation of CPT1A incrementally increases MAVS palmitoylation and amplifies the IFN-I response, which enhances control of viral infection and epigenetic perturbation-induced antitumor immunity. Moreover, CPT1A chemical inducers augment the therapeutic effect of combined epigenetic treatment with PD-1 blockade in refractory tumors. Our study identifies CPT1A as a stabilizer of MAVS activation, and its link to epigenetic perturbation can be exploited for cancer immunotherapy.

overall_design: In vitro cultured scramble and LSD1 KO B16 cells as well as scramble B16 cells infected with VSV-GFP for 12 h were used for total RNA extraction, followed by poly(A)+ RNA purification, which were subjected to library construction and high throughput sequencing for gene expression profiling.

first: Guiheng


title: Sclerotic-type chronic graft-versus-host disease exhibits enrichment of Th1 and TSLP-OX40 cytokines

city: New York

first: Madeline

last: Kim

address: 1 Gustave Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: In this study we performed the first global RNA-seq analysis in pediatric to young-adult patients with sclerotic-type graft-versus-host disease/scGvHD (n=7), age- and sex-matched to 8 healthy controls and 10 patients with atopic dermatitis/AD. Differentially expressed genes (DEGs) were defined based on fold changes/FCH>1.5 and false discovery rate/FDR<0.05 criteria. We found robust and significant Th1 (e.g. CXCR9/10/11, IFNG) and OX40-skewing in ScGvHD (e.g. OX40L, TLSP, IL-33) that sometimes exceeded that in AD and was validated on RT-PCR.

overall_design: RNA-seq data was profiled from skin biopsies of 7 pediatric/young-adult patients with sclerotic-type chronic graft-versus-host disease, age- and sex- matched to 10 patients with moderate-to-severe atopic dermatitis (lesional and non-lesional) and 8 healthy controls.

first: Yael

last: Renert-Yuval

first: Polina

last: Stepensky

first: Ehud

last: Even-Or

first: Irina

last: Zaidman

first: Tahel

last: Fachler

first: Michal

last: Neumark

first: Mariana

last: Zamir

first: Monali

last: Nandymazumdar

first: Digpal

last: Gour

first: Paola

last: Facheris

first: Britta

last: Carroll

first: Ying

last: Liu

first: Mitchelle

last: Yu Ekey

first: Elizabeth

last: Andrews

first: Marguerite

last: Meariman

first: Michael

last: Angelov

first: Swaroop

last: Bose

first: Yeriel

last: Estrada

first: Vered

last: Molho-Pessach

first: Emma

last: Guttman-Yassky


first: Wanqiang

last: Sheng

summary: argeting epigenetic regulators to potentiate anti-PD-1 immunotherapy converges on the activation of type I interferon (IFN-I) response, mimicking cellular response to viral infection, but how its strength and duration are regulated to impact combination therapy efficacy remains largely unknown. Here, we show that mitochondrial CPT1A downregulation following viral infection restrains, while its induction by epigenetic perturbations sustains, a double-stranded RNA-activated IFN-I response. Mechanistically, CPT1A recruits the endoplasmic reticulum-localized ZDHHC4 to catalyze MAVS Cys79-palmitoylation, which promotes MAVS stabilization and activation by inhibiting K48- but facilitating K63-linked ubiquitination. Further elevation of CPT1A incrementally increases MAVS palmitoylation and amplifies the IFN-I response, which enhances control of viral infection and epigenetic perturbation-induced antitumor immunity. Moreover, CPT1A chemical inducers augment the therapeutic effect of combined epigenetic treatment with PD-1 blockade in refractory tumors. Our study identifies CPT1A as a stabilizer of MAVS activation, and its link to epigenetic perturbation can be exploited for cancer immunotherapy.

overall_design: GFP-labeled scramble, LSD1 KO and LSD1/CPT1A DKO B16/F10 tumors were implanted in C57BL/6 mice for 14 days. Tumors were harvested, dissociated into single cells, and subjected to GFP+ tumor cell isolation by FACS. Total RNA was extracted and used to poly(A)+ RNA enrichment by magnetic mRNA isolation kit for constructing library. The prepared libraries were sequenced at 150 bp from both ends.

first: Guiheng

last: Zhang


title: Effect of CWG-cPIP on alternative splicing defects in CUG mouse brain

first: Kazuya

last: Matsuo

summary: CWG-cPIP targets CAG/CTG (CWG) triplet repeat DNA to inhibit the transcription in a repeat length-dependent manner. To investigate effects of CWG-cPIP on alternative splicing defects in the brain of CUG300 mice, which we developed as a model of DM1, CWG-cPIP (83 ug/kg) was injected into mouse hippocampus. RNA sequencing analysis was performed using mouse hippocampus 10 days later.

overall_design: Alternative splicing analysis of RNA sequencing data for the mouse hippocampus. The groups consist of 1) CUG10 + vehicle (n = 1 mouse); 2) CUG300 + vehicle (n = 1 mouse); 3) CUG300 + CWG-cPIP (n = 1 mouse).

first: Norifumi

last: Shioda


title: Effect of CWG-cPIP on transcriptome defects in CUG mouse brain

summary: CWG-cPIP targets CAG/CTG (CWG) triplet repeat DNA to inhibit the transcription in a repeat length-dependent manner. To investigate effects of CWG-cPIP on transcriptome defects in the brain of CUG300 mice, which we developed as a model of DM1, CWG-cPIP (83 ug/kg) was injected into mouse hippocampus. RNA sequencing analysis was performed using mouse hippocampus 10 days later.

overall_design: Gene expression of RNA sequencing data for the mouse hippocampus. The groups consist of 1) CUG10 + vehicle (n = 3 mice); 2) CUG300 + vehicle (n = 3 mice); 3) CUG300 + CWG-cPIP (n = 3 mice).


title: Off-target effect of CWG-cPIP on gene expression of human fibroblasts

summary: CWG-cPIP targets CAG/CTG (CWG) triplet repeat DNA to inhibit the transcription in a repeat length-dependent manner. To investigate off-target effects of CWG-cPIP on gene expression in cells, CWG-cPIP (1 μM) was treated to human fibroblasts. RNA sequencing analysis was performed using vehicle- or CWG-cPIP-treated human fibroblasts 7 days later, mixing with ERCC RNA spike-in controls.

overall_design: Comparative gene expression profiling analysis of RNA sequencing data for the human fibroblasts treated with vehicle or CWG-cPIP (n = 3 replicates each).


title: Effect of CWG-cPIP on CAG/CTG triplet repeat mouse brain


title: Subtype-selective prenylated isoflavonoids disrupt regulatory drivers of MYCN-amplified cancers

status: Public on Oct 10 2023

city: New York City

first: Alessandro

last: Vasciaveo

address: 1130 Saint Nicholas Ave., 910

department: Department of Systems Biology

institute: Columbia University

summary: Transcription factors have proven difficult to target with small molecule inhibitors because they often lack deep pockets necessary for potent binding. Alternatively, disruption of protein expression can suppress difficult targets and enable therapeutic intervention. To this end, we have developed a drug discovery workflow that incorporates cell line-selective screening and high-throughput expression profiling followed by regulatory network analysis to identify compounds that suppress regulatory drivers of disease. Applying this approach to neuroblastoma (NBL), we screened bioactive molecules in cell lines representing the MYC-dependent (MYCNA) and mesenchymal (MES) subtypes to identify selective compounds, followed by PLATESeq profiling of treated cells. This revealed compounds that disrupt a network of MYCNA-specific regulatory proteins, resulting in MYCN degradation in vivo. The top hit was isopomiferin, a prenylated isoflavonoid that inhibited Casein Kinase 2 (CK2) in cells. Isopomiferin and its structural analogs inhibited MYC and MYCN in NBL and lung cancer cells, highlighting the general MYC-inhibiting potential of this unique scaffold.

overall_design:
First Experiment (PLATESeq): To identify NBL MYCNA subtype-selective inhibitors, we systematically screened >5,000 compounds from three chemical libraries chosen for their enrichment of bioactive molecules, diversity in chemical structure, and for inclusion of compounds with known mechanisms of action. Compounds were initially tested at a single concentration and time-point (20 µM for 72 h) to eliminate those with no in vitro activity in NBL cell lines. Lethal compounds were rescreened across a five-point dilution series ranging from 20 µM to ~250 nM, to determine IC50 values in each of the four cell lines. By ranking compounds based on average IC50 values for each of the two subtypes, MYCNA or MES-selective compounds were identified. The top 90 compounds with the highest relative MYCNA-specific selectivity were then used to generate PLATESeq expression profiles following 24 hours of treatment in SK-N-Be2 cell lines at their respective IC20 concentration.
Second Experiment (PLATESeq): top 15 compounds were screened with PLATESeq at 6 and 24 hours at multiple concentrations in three replicates
Third Experiment (PLATESeq): In an effort to identify a potent analog of isopomiferin, we assembled a small collection of structurally-related analogs and known CK2 inhibitors, and tested them in SK-N-Be2 cells using PLATESeq
TruSeq Experiment (RNASeq): To uncover kinase targets of isopomiferin and its functional analogs, we developed a novel algorithm, the Virtual-Inference of Kinase INhibiton by Gene regulatory networks (VIKING), to enable data-driven inference of drug targets based on activity dysregulation of protein-protein interactions (PPIs). VIKING was run using RNASeq (TruSeq) data on isopomiferin, pomiferin and its null analog, at multiple concentrations and timepoints.

last: Stokes

first: Andrea

last: Califano

first: Brent

last: Stockwell


title: Effect of condensate perturbing CR3 peptide on HCT116 gene expression

city: Utrecht

first: Jurian

last: Schuijers

address: Universiteitsweg 100

department: Center for Molecular Medicine

country: Netherlands

institute: University Medical Center Utrecht

summary: To measure the effect of CR3 condensate perturbing we generated HCT116 clonal cell lines that inducibly express mCherry, mCherry-CR3, mCherry-scramble-control peptides

overall_design: All HCT116 cell clones were induced with doxycycline to induce expression of CR3 and variants and expression profiling was performed


title: RNA sequencing of Patient-Derived Xenografts

city: Salt Lake City

first: Gennie

last: Parkman

state: UT

address: 2000 Circle of Hope, Rm 5263

institute: University of Utah

summary:
Goal: Comparison of mRNA expression profiles in patient-derived xenograft primary tumors
Methods: RNA sequencing performed at the High-Throughput Genomics and Bioinformatics Analysis Core at the University of Utah. Detailed procedures available in methods and DNA processing pipline sections.
Results: Focus of study compared mRNA expression profiles of samples pre and post passaging in vivo.  Unsupervised heirarchical clustering revealed samples clustered together appropriately.
Conclusions: The PDX maintain the gene expression profiles of the original tumor.

overall_design: Six primary tumor samples are included in the analyses. These same six samples were sequenced again after being passed in mice. Replicates are included.

first: Holmen

last: Sheri L

first: Parkman

last: Gennie L


title: SERPINB3 induces the aggressive basal-like/squamous subtype and promotes invasion and metastasis in pancreatic cancer

city: Bethesda

first: Stefan

last: Ambs

address: Building 37, Room 3050B

institute: NCI

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


title: Azotobacter vinelandii str. DJ transcriptomic time-course under nitrogenase derepressing conditions

city: Madrid

first: Luis

middle: M.

last: Rubio

address: Campus de Montegancedo UPM. Crta. M-40 km 38

institute: Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC)

summary: Comparison of Azotobacter vinelandii str. DJ transcriptomes using either ammonium or dinitrogen as sole nitrogen source. Transcriptomes from cells in early stages of nitrogenase derepression (10 min and 30 min) and at the peak of nitrogenase derepression (4 hours) were compared against the corresponding controls from cells using ammonium as nitrogen source. Kinetics of the nitrogen fixation (nif) genes expression profiles resemble those previously published (Poza-Carrion, 2013; doi: 10.1128/jb.00942-13).

overall_design: Azotobacter vinelandii str. DJ were cultivated in Burk’s modified medium at 30°C with or without nitrogen sources. For nitrogenase derepression experiments (diazotrophic growth conditions), NH4+ grown cells were diluted in fresh NH4+ containing medium at an optical density at 600 nm (OD600) of 0.005 and further cultivated for 17 h. Cells were then collected by centrifugation, washed with NH4+ free or NH4+ containing medium (control cultures), and resuspended in the same medium at a final OD600 of 0.5. Cells were then incubated at 30°C with shaking (200 rpm) in independent Erlenmeyer flasks. At different times, samples were collected and RNA it´s isolated from the cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of different growth condition at three time points.

first: César

last: Poza-Carrión


title: Differential effects of aneuploidy on growth and differentiation in human intestinal stem cells

city: Baltimore

first: Rong

last: Li

address: 855 N. Wolfe St., Suite 440.

department: Cell Biology

institute: Johns Hopkins School of Medicine

summary: Aneuploidy, a near ubiquitous genetic feature of tumors, is a context-dependent driver of cancer evolution, but the mechanistic basis of this role remains unclear. By inducing heterogeneous aneuploidy in non-transformed human colon organoids (colonoids), we investigate how the effects of aneuploidy on cell growth and differentiation may promote malignant transformation. Here, we use single-cell RNA sequencing to identify the karyotype heterogenous aneuploid cells and analyze their gene expression.

overall_design: Human colonoids were treated with 0.05% DMSO or 0.5 µM reversine for 24 hours followed by proliferation media for 24 hours. Colonoids were then dissociated to single cells and sequenced.

first: Blake

last: Johnson

first: Yi

last: Dong

first: Tatianna

middle: C

last: Larman