title: Functional and transcriptomic dose-response analysis of follicle-stimulating hormone in ex vivo mouse folliculogenesis and oogenesis

city: Piscataway

first: Tingjie

last: Zhan

state: NJ

address: 499 Vernon Ct

institute: Rutgers university

summary: The gonadotropin-dependent phase of ovarian folliculogenesis primarily requires follicle-stimulating hormone (FSH) to support one or multiple early antral follicles, dependent on the species, to mature fully and support steroidogenesis, oogenesis, and ovulation, which critically sustain female reproductive cycles and fertility. At molecular levels, FSH binds to its membrane receptor, FSHR, in granulosa cells to activate a suite of genes and signal transduction pathways. Both insufficient FSH caused by genetic or non-genetic reasons and excessive FSH used for ovarian stimulation in assisted reproductive technology (ART) can cause poor female reproductive outcomes, but the underlying mechanisms remain elusive. Here, we used an ex vivo folliculogenesis and oogenesis system along with single-follicle and -oocyte RNA sequencing analysis and other approaches to investigate the effects of different concentrations of FSH on key follicular events. The results revealed that a minimum FSH threshold is required for follicle maturation, and such threshold is moderately variable among individual follicles. FSH at the subthreshold, threshold, and suprathreshold levels induced distinct expression patterns of follicle maturation-related genes and the entire follicular transcriptomics. The RNA-seq analysis identified several new genes and signaling pathways that may critically regulate follicle maturation. The treatment of excessive FSH resulted in multiple ovarian disorders including premature luteinization, high production of androgen and proinflammatory factors, and reduced expression of energy metabolism-related genes in oocytes.  Together, our study enables a better understanding of the gonadotropin-dependent folliculogenesis, and the novel findings shed crucial insights into how ovarian stimulation with high doses of FSH used in ART impact follicular health, oocyte quality, pregnancy success, and systemic health.

overall_design: Follicles in  eIVFG on day 4 and 6 treated with follicle-stimulating hormone (FSH) of 5, 10, 20 and 30 mIU/mL were collected for single-follicle RNA sequencing; At 16-hours post human chorionic gonadotropin (hCG) treatment, oocytes from follicles treated with FSH of 10 and 30 mIU/mL were collected for single-oocyte SMART-seq RNA sequencing.

first: Jiyang

last: Zhang

first: Ying

first: Qingshi

last: Zhao

first: Nataki

last: Douglas

first: Qiang

first: Shuo

last: Xiao


title: Transcriptome data of hematopoietic stem cells of mice under ionizing radiation

status: Public on Jun 05 2024

city: Chongqing

first: Xinliang

last: Chen

address: Gaotanyan street 30

country: China

institute: Army Medical University

type: Expression profiling by high throughput sequencing

summary: Analysis of hematopoietic stem cells  (HSC, Lineage-Sca-1+c-Kit+Flt3–CD34–). In order to better experiment, we treated mice with total body irradiation and local irradiation respectively. Next, the HSC were purified from the bone marrow of 8 weeks  WT mice (Ctrl), total body radiation mice (IR), irradiated legs of locally irradiated mice (L_IR) and the other leg which unirradiated of locally irradiated mice (Ab_IR).  Results provide the injury effect of IR on HSC under different conditions.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of HSCs of mice at 3 days after IR.

first: Weinian

last: Liao

first: Junping

last: Wang


title: Functional connection between fetal brain development and longevity in mice

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

country: USA

institute: University of Missouri

summary: The objective of the present study is to investigate gene regulation in developing fetal brain in congenic or inbred mice strains that differ in longevity. Gene expression and alternative splice variants were analyzed in a genome-wide manner in the fetal brain of C57BL/6J mice (long-lived), and compared to that of a congenic strain (short-lived) or an inbred strain AKR/J (short-lived) on days 12, 15 and 17 of gestation. The analysis showed a contrasting gene expression pattern during fetal brain development in these mice. Genes related to brain development, aging and spliceosome were significantly differentially regulated in the fetal brain of the short-lived mice when brain developed from d15 to d17. A significantly reduced number of splice variants were observed on d15 compared to d12 or d17 but in a strain-dependent manner.

overall_design: RNA sequencing was performed with the fetal brain of C57BL/6J mice (long-lived), and compared to that of a congenic strain (short-lived) or an inbred strain AKR/J (short-lived) on days 12, 15 and 17 of gestation (three replicates per time point).

first: Maliha

last: Islam

first: Susanta

middle: K

last: Behura


title: Effect of SWI/SNF pertubations on H3K27ac levels during macrophage inflammatory activation [ChIP-seq_Histone]

city: La Jolla

first: Jingwen

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
To understand how macrophage histone modifications respond to LipidA stimulation, we profiled H3K27ac binding for WT BMDMs with 0hr or 4hr LipidA stimulation.
In addition, we also profiled H3k27ac levels for WT BMDMs treated with ACBI1, BRM014, BRDK98, or dBrd9 and for Arid1A-/- and Pbrm1-/- BMDMs after 4hr LipidA stimulation.

overall_design: ChIP-Seq for SWI/SNF factors for WT, drug treated, or SWI/SNF KO BMDMs with 0hr or 4hr LipidA stimulation.


title: Single-cell analyses offer insights into the different remodeling programs of arteries and veins (bulk RNA-Seq)

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: We compared 7 pairs of  arteries (brachial) and veins (6 basilic, 1 cephalic) obtained from the same individuals by bulk RNA sequencing and histology. Independent samples were compared by scRNA-seq.

overall_design: Paired differential gene expression analysis of peripheral arteries and veins from the same anatomical location. Veins are deposited in GSE233264.

first: Laisel

last: Martinez

first: Roberto

middle: I

last: Vazquez-Padron

middle: J


title: Hofbauer cells and fetal brain microglia share transcriptional profiles and responses to maternal diet-induced obesity

city: Medford

first: rebecca

last: batorsky

state: MA

address: 177 College Ave

department: Tufts Institute of Artificial Intelligence

institute: Tufts University

summary: Maternal immune activation is associated with adverse offspring neurodevelopmental outcomes, many mediated by in utero microglial programming. As microglia remain inaccessible throughout development, identification of noninvasive biomarkers reflecting fetal brain microglial programming could permit screening and intervention. We used lineage tracing to demonstrate the shared ontogeny between fetal brain macrophages (microglia) and fetal placental macrophages (Hofbauer cells) in a mouse model of maternal diet-induced obesity, and single-cell RNA-seq to demonstrate shared transcriptional programs. Comparison with human datasets demonstrated conservation of placental resident macrophage signatures between mice and humans.  Single-cell RNA-seq identified common alterations in fetal microglial and Hofbauer cell gene expression induced by maternal obesity, as well as sex differences in these alterations. We propose that Hofbauer cells, which are easily accessible at birth, provide novel insights into fetal brain microglial programs, and may facilitate the early identification of offspring vulnerable to neurodevelopmental disorders in the setting of maternal exposures.

overall_design: Examining the effect of maternal diet-induced obesity on the transcriptomes of fetal brain and placental macrophages

first: Andrea

middle: G

last: Edlow

first: Rebecca

last: Batorsky


title: TCF7L1 regulates colorectal cancer cell migration and invasion by repressing GAS1 expression

city: Hershey

first: Gregory

middle: S

last: Yochum

state: PA

address: 700 HMC Cres Rd

institute: The Pennsylvania State University, College of Medicine

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

overall_design: Refer to individual Series


title: Effect of SWI/SNF pertubations on macrophage inflammatory activation [RNA-seq]

summary:
To characterize macrophage inflammtory activation and the role of the SWI/SNF complex, we first profiled gene expression for WT BMDMs with 0hr, 1hr, or 4hr LipidA stimulation.
In addition, we also profiled gene expression for WT BMDMs treated with ACBI1, BRM014, or BRDK98 treatment and for Arid1A-/- or Pbrm1-/- BMDMs after 1hr or 4hr LipidA or LPS stimulation.

overall_design: RNA-seq for WT, drug treated, or SWI/SNF KO BMDMs with 0hr, 1hr, or 4hr LipidA or LPS stimulation.

first: Josephine

last: Ho


title: Integrated analysis based on RNA immunoprecipitation sequencing (RIP-seq) and m5C methylated RNA immunoprecipitation and sequencing (MeRIP-seq) assays to identify the target genes of NSUN2/YBX1-m5C axis in ESCC progression

city: Zhengzhou

first: Liu

last: liwen

address: NO.101 Kexue Road High-Tech Development Zone Of States Zhengzhou

institute: Zhengzhou University

type: Methylation profiling by high throughput sequencing

summary: The modification and recognition of 5-methylcytosine (m5C) are involved in the initiation and progression of various tumor types. However, the precise role and potential mechanism of Y-box-binding protein 1 (YBX1) in esophageal squamous cell carcinoma (ESCC) remains unclear. Here, we found that YBX1 was frequently upregulated in ESCC compared with matched nontumor tissues. Gain- and loss-of-function assays showed that YBX1 promoted the proliferation and metastasis of ESCC cells both in vitro and in vivo. Functional studies revealed that NOP2/Sun RNA methyltransferase family member 2 (NSUN2) is a critical RNA methyltransferase that facilitates YBX1-mediated ESCC progression. Mechanistically, integrated analysis based on RNA immunoprecipitation sequencing (RIP-seq) and m5C methylated RNA immunoprecipitation and sequencing (MeRIP-seq) assays identified spermine oxidase (SMOX) as a target gene containing an m5C site in its coding sequence (CDS) region, which coincided well with the binding site of YBX1. Overexpression of SMOX-WT but not SMOX-Mut partially restored the proliferation and invasion ability of ESCC cells curbed by YBX1 knockdown. Moreover, YBX1 activated the mTORC1 signaling pathway by stabilizing SMOX mRNA. Our study revealed that YBX1 promotes ESCC development by stabilizing SMOX mRNA in an m5C-dependent manner, thus providing a valuable therapeutic target for ESCC.

overall_design:
We performed an m5C meRIP-seq assay to investigate the effect of silencing NSUN2 on the m5C profiles of ESCC cells
RNA immunoprecipitation sequencing (RIP-seq) was performed to identify the downstream transcripts of YBX1 with m5C sites in ESCC
Overlaying YBX1-binding targets (Fold enrichment >10) with transcripts displaying reduced m5C sites (Foldchange >200) and expression level (logFC <-2) following NSUN2 knockdown in KYSE150 cells.

first: Liwen

last: Liu

first: Yu

first: Tao

last: Zhang

first: Guangying

last: Cui

first: Weiwei

first: Guizhen

first: Jianhao

last: Li

first: Yize

first: Yun

first: Yawen

last: Zou

first: Zhigang

last: Ren

first: Wenhua

last: Xue

first: Ranran

last: Sun


title: SWI/SNF localization during macrophage inflammatory response [ChIP-seq_SWISNF]

first: Jingwen

last: Liao

summary:
To understand how the SWI/SNF complex help establish appropriate epiegentic landscape during macrophage inflammatory response, we profiled the binding sites of BRG1 (all BAF), ARID1A (cBAF), BRD9 (ncBAF), and PHF10 (PBAF) for WT BMDMs with 0hr, 1hr, or 4hr LipidA stimulation.
To assess the modes of action for cBAF inhibitor BRDK98, we also performed ARID1A ChIP for BRDK98-treated BDMDs after 0hr and 4hr of LipidA stimulation.

overall_design: ChIP-Seq for SWI/SNF factors for WT or BRDK98-treated BMDMs after 0hr, 1hr, or 4hr LipidA stimulation.


title: TCF7L1 regulates colorectal cancer cell migration and invasion by repressing GAS1 expression (ChIP-Seq)

first: Gregory

summary: Dysregulation of the canonical Wnt/β-catenin signaling pathway is a hallmark of colorectal cancer (CRC). The T-cell factor/lymphoid enhancer factor (TCF/LEF; hereafter, TCF) family of transcription factors are critical regulators of canonical Wnt/β-catenin target gene expression. Despite similarity across DNA-binding and protein-binding domains, TCF family members differentially regulate target gene expression in CRC. Of the four TCF family members, TCF7L1 predominantly functions as a transcriptional repressor and it has an oncogenic role in CRC. Despite this role, few target genes regulated by TCF7L1 in CRC have been identified. Through RNA-sequencing of transcripts differentially expressed in control and TCF7L1-overexpressing HCT116 cells, we identified 397 genes that were repressed directly, or indirectly, by TCF7L1. Gene set enrichment analysis found genes associated with epithelial-mesenchymal transition amongst those that are differentially expressed. By silencing and overexpressing TCF7L1 in CRC cell lines, we found that TCF7L1 promoted migration, invasion, and adhesion in vitro. Chromatin immunoprecipitation followed by sequencing (ChIP-sequencing) localized 3661 TCF7L1 binding sites within the CRC genome. Comparison of genes whose expression was downregulated by TCF7L1 and genes with TCF7L1 binding sites revealed 41 novel targets directly regulated by TCF7L1. Among these, we localized a TCF7L1 promoter-proximal binding site within the growth arrest specific 1 (GAS1) gene. We found that ectopic GAS1 expression rescued the TCF7L1-mediated increase in migration and invasion in CRC cells. These findings uncover a novel role for TCF7L1 in repressing GAS1 expression to promote migration and invasion of CRC cells in vitro.

overall_design:
Chromatin immunoprecipitation (ChIP) sequencing for DNA fragments immunoprecipitated with an anti-FLAG antibody for FLAG-tagged TCF7L1 in Dox-treated TCF7L1-depleted HCT116 cells expressing exogenous TCF7L1 or TCF7L1-MUT (DNA binding domain mutant)
----------------------------------
***Authors state the following regarding their missing raw data:
The library was constructed and processed by Novogene Co., Ltd in 2021. However, we      currently only have the BED, bigWig, and narrowPeaks file formats.

first: Carli

last: King

first: Melani

last: Eshelman


title: TCF7L1 regulates colorectal cancer cell migration and invasion by repressing GAS1 expression (RNA-Seq)

overall_design:
To investigate the genes regulated directly or indirectly by TCF7L1, we establed stable HCT116 cell lines that expressed Dox-inducible pCW57.1-empty vector, pCW57.1-TCF7L1, pCW57.1-TCF7L1-MUT
We utilized lentiviral delivery of shTCF7L1-2 to knockdown endogenous TCF7L1. We treated stable cell lines with Dox to induce expression of an shRNA-resistant TCF7L1 or TCF7L1-MUT
Comparison of differentially expressed genes, gene set enrichment analysis, and gene ontology using data obstained from RNA-sequencing


title: LYVE-1-expressing macrophages modulate the extracellular matrix in the mammary gland and contribute to mammary tumor growth

city: Minneapolis

first: Kathryn

last: Schwertfeger

state: MN

address: 2231 6th St SE

department: Lab Medicine and Pathology

institute: University of Minnesota Medical School

summary: Macrophages represent a heterogeneous myeloid population with diverse functions in normal tissues and tumors. While LYVE-1 macrophages have been identified in stromal regions of the normal mammary gland and mammary tumor, their functions in these regions remain unknown. Using a genetic LYVE-1+ macrophage deletion model, we demonstrate that loss of LYVE-1+ macrophages leads to accumulation of the extracellular matrix glycosaminoglycan hyaluronan. Consistent with this finding, we demonstrate that LYVE-1 expression correlates with an increased ability of macrophages to bind, internalize, and degrade hyaluronan. Furthermore, we demonstrate that deletion of LYVE-1+ macrophages results in increased hyaluronan accumulation in mammary tumors, which correlates with reduced tumor growth. Finally, using scRNA-seq, we demonstrate that deletion of LYVE-1 macrophages in tumors results in a shift in the remaining macrophages towards a pro-inflammatory phenotype. Together, these findings demonstrate that LYVE-1+ macrophages represent an anti-inflammatory macrophage population that contributes to tissue remodeling in the tumor microenvironment.

overall_design: Two Lyve1CreCsf1rfl/fl female mice and two Csf1rfl/fl female mice were orthotopically injected with EO771 tumor cells. Tumors were grown to 1.5cm3 and CD45+ leukocytes were flow sorted for single cell RNA sequencing

first: Alexis

last: Elfstrum

first: Annisa

last: Rumahorbo

first: Emma

last: Nelson

first: Braedan

last: McCluskey


title: Imprinting but not cytonuclear interactions affects parent-of-origin effect on seed size in Arabidopsis hybrids

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: The parent-of-origin effect on seed size can result from imprinting or a combinational effect between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding effects, we generated cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in theArabidopsis thalianaecotypes Col-0 and C24. These CNS lines differ only in the nuclear genome (imprinting) or in the cytoplasm. The CNS reciprocal hybrids with the same cytoplasm display a ∼20% seed size difference as observed in the conventional hybrids. However, seed size is similar between the reciprocal cybrids with fixed imprinting. Transcriptome analyses in the endosperm of CNS hybrids using laser-capture microdissection have identified 104 maternally expressed genes (MEGs) and 90 paternally-expressed genes (PEGs). These imprinted genes are involved in pectin catabolism and cell wall modification in the endosperm.HDG9, an epiallele and one of 11 cross-specific imprinted genes, controls seed size. In the embryo, a handful of imprinted genes is found in the CNS hybrids but only one is expressed higher in the embryo than endosperm.AT4G13495encodes a long-noncoding RNA (lncRNA), but no obvious seed phenotype is observed in the lncRNA knockout lines.NRPD1, encoding the largest subunit of RNA Pol IV, is involved in the biogenesis of small interfering RNAs. Seed size and embryo is larger in the cross usingnrpd1as the maternal parent than in the reciprocal cross. In spite of limited ecotypes tested, these results suggest potential roles of imprinting andNRPD1-mediated small RNA pathway in seed size variation in hybrids.

overall_design: Embryo and endosperm were collected using laser capture microdissection from controlled reciprocal crosses form standard and CNS lines

first: Viviana

last: June

first: Xiaoya

last: Song

first: Jeffrey

middle: Z

first: Ryan

last: Kirkbride


title: Hyperglycemia potentiates brain susceptibility to lipopolysaccharide-induced neuroinflammation by astrocytes reprogramming

city: Seoul

first: Kyung-Seo

last: Lee

address: ABMRC,50-1, Yonsei-ro, Seodaemun-gu

department: College of Medicine

country: South Korea

institute: Yonsei University

summary: Hyperglycemia has been shown to modulate the immune response of peripheral immune cells and organs, but the impact of hyperglycemia on neuroinflammation within the brain remains elusive. In the present study, we provide evidences that streptozotocin (STZ)-induced hyperglycemic condition in mice drives a phenotypic switch of brain astrocytes to a proinflammatory and neurotoxic state, and increases brain vulnerability to mild peripheral inflammation. In particular, we found that hyperglycemia led to a significant increase in the astrocyte proliferation as determined by flow cytometric and immunohistochemical analyses of mouse brain. Transcriptomic analysis of isolated astrocytes from Aldh1l1CreER;tdTomato mice revealed that peripheral STZ injection induced astrocyte reprogramming into proliferative, proinflammatory and neurotoxic phenotype. Additionally, STZ-induced hyperglycemic condition significantly enhanced the infiltration of circulating myeloid cells into the brain and the disruption of blood-brain barrier in response to mild lipopolysaccharide (LPS) administration. Systemic hyperglycemia did not alter the intensity and sensitivity of peripheral inflammation in mice to LPS challenge, but increased the inflammatory potential of brain microglia. Furthermore, hyperglycemic mice exhibited a significant impairment in cognitive function after mild LPS administration compared to normoglycemic mice as determined by novel object recognition and Y-maze tasks. Taken together, these results demonstrate that hyperglycemia directly induces astrocyte reprogramming towards a proliferative and proinflammatory phenotype, which potentiates mild LPS-triggered inflammation within brain parenchymal regions.

overall_design:
To investigate the phenotypic changes in immune regulatory functions of astrocytes in hyperglycemic conditions. We sorted astrocytes from mice treated either with streptozotocin (STZ) or vehicle (Veh). Vehicle group being the control group, and  three samples (replicates) are assigned to each group for comparison.
We then performed gene expression profiling analysis using data obtained from RNA-seq of astrocytes from two different groups (Veh and STZ group). Comparative gene expression profiling is done for the two group.

first: Je-Wook

last: Yu


title: Repeated Exposure to Wood Smoke Alters Pulmonary Gene and Metabolic Profiles

city: Research Triangle Park

first: Colette

last: Miller

state: NC

address: 109 TW Alexander

institute: U.S. Environmental Protection Agency

summary: Wildfires have increased in frequency, size, and intensity in recent decades, due to increasing global temperatures and dryer climates attributable to anthropogenic climate change. Adverse respiratory effects from wildfire smoke are of specific concern for wildland firefighters who have prolonged or repeated exposure to woodsmoke. Following repeated exposure of low and high woodsmoke in rats, we performed bulk RNA sequencing on lung tissue.

overall_design: Lungs were collected from rats exposed to air or low or high smoke (n=8/group) for RNA isolation. Samples were sequenced using the Illumina NextSeq 500 platform.

middle: N

first: Kymberly

middle: M

last: Gowdy


title: Effect of SWI/SNF pertubations on chromatin accessibility during macrophage inflammatory activation [ATAC-seq]

first: Jingwen

summary:
To understand how macrophage chromatin respond to LipidA stimulation, we profiled accessibility for WT BMDMs with 0hr, 1hr, or 4hr LipidA stimulation.
In addition, we also profiled accessibility for WT BMDMs treated with ACBI1, BRM014, BRDK98, or dBrd9 and for Arid1A-/- Pbrm1-/- BMDMs after 0hr, 1hr, or 4hr LipidA stimulation.

overall_design: ATAC-seq for WT, drug treated, or SWI/SNF KO BMDMs with 0hr, 1hr, or 4hr LipidA stimulation.

first: Josephine

last: Ho


title: BiAux modulates auxin co-receptors activity to form lateral roots

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

summary: The root system plays an essential role in plant growth and adaptation to the surrounding environment. Lateral roots (LR) originate postembryonically from a group of pericycle founder cells (FC) that are specified by a root clock in an auxin dependent manner and extend the root´s surface. Auxin perception entails the physical interaction of TIR1 or AFBs proteins with Aux/IAA repressors to form a co-receptor system. Despite the apparent simplicity, how a specific TIR1/AFBs - Aux/IAA module is assembled is not completely understood. Here, we have identified and characterized a novel natural compound, called BiAux, that is a N-glucoside bisindole conjugate. This compound or rBiAux, an improved reduced form, precisely promote FC specification and lateral root emergence without affecting other auxin-related responses, including root growth. Genetic analyses demonstrated that rBiAux signaling requires the function of TIR1 and AFB2 receptors. Remarkable, rBiAux enhances TIR1 or AFB2 interaction with Aux/IAA28 and Aux/IAA18, two regulators of FCs and lateral root formation. Furthermore, rBiAux signaling seems to be dependent on ARF7, a transcription factor involved in FC specification and LR formation. Taken together, our data indicate that BiAux enhances the activity of auxin co-receptors involved in FC specification and lateral root formation.

overall_design:
To understand teh role of BiAux, we  have analyzed the effect of BiAux or IAA or BiAux+IAA in roots of Arabidopsis seedlings.
RNAseq analyses of polyA mRNAs isolated from roots of wild type seedlings grown at 22ºC in half strength MS medium for 4 days and then treated with 5 µM BiAux or 10 nM IAA or 5 µM BiAux plus 10 nM IAA for 3 extra days.

middle: C

first: Mary

middle: P

last: González-García

first: Angela

last: Saez


title: Elucidating and Pharmacologically Targeting Master Regulators of Stem-like Breast Cancer Cell State (CROP-Seq)

city: New York

first: Andrea

last: Califano

state: NY

address: 1130 St. Nicholas Avenue

department: Systems Biology

institute: Columbia University

summary: In many tumors, small subpopulations of stem-like cells can exist in drug-resistant states that are transient and epigenetically governed. Single-cell RNA sequencing (scRNA-seq) provides transcriptional profiles for individual cells which, although sparse and noisy, may provide insight into how they are regulated and how they may be targeted. We took a systems-biology approach to analyzing cancer stem-like cells (CSLCs) in breast tumors and predicting Master Regulator (MR) proteins responsible for governing the transcriptional state of these cells, thus revealing drug sensitivities that may be leveraged via combination therapy. The MRs were validated by pooled, CRISPR-KO mediated CROP-seq profiling of single cells representing either the CLSC or the differentiated breast cancer (BRCA) cells.

overall_design:
For control samples, the four breast cancer cell lines (MCF7, HCC2157, HCC38, and HCC1143) were incubated, dissociated, and subjected to scRNA-seq (10X Genomics).
For the CROPSeq screening, total 50 genes, identified as top 25 activated proteins in breast CSLCs and top 25 activated proteins in well-differentiated BRCA cells, were targeted with 3 sgRNAs/gene for HCC1143 and HCC38 cells. In addition, 15 intergenic sgRNAs experiments were included a negative controls. Cells were grown for 14 days of post sgRNA transduction before the scRNAseq (10X Genomics).

first: Mikko

last: Turunen

first: Heeju

last: Noh

first: Jeremy

last: Worley


title: Single-cell analysis of bronchoalveolar cells in inflammatory and fibrotic post-COVID lung disease

city: London

first: Gillian

last: Tomlinson

address: Gower Street

department: Infection and Immunity

country: United Kingdom

institute: University College London

summary: Rationale: Persistent pulmonary sequelae are evident in many survivors of acute coronavirus disease 2019 (COVID-19) but the molecular mechanisms responsible are incompletely understood. Post-COVID radiological lung abnormalities comprise two broad categories, organising pneumonia and reticulation, interpreted as indicative of subacute inflammation and fibrosis, respectively. Whether these two patterns represent distinct pathologies, likely to require different treatment strategies is not known. Objectives: We sought to identify differences at molecular and cellular level, in the local immunopathology of post-COVID inflammation and fibrosis. Methods: We compared single-cell transcriptomic profiles and T cell receptor (TCR) repertoires of bronchoalveolar cells obtained from convalescent individuals with each radiological pattern of post-COVID lung disease (PCLD). Measurements and Main Results: Inflammatory and fibrotic PCLD single-cell transcriptomes closely resembled each other across all cell types. However, CD4 central memory T cells (TCM) and CD8 effector memory T cells (TEM) were significantly more abundant in inflammatory PCLD. A greater proportion of CD4 TCM also exhibited clonal expansion in inflammatory PCLD. High levels of clustering of similar TCRs from multiple donors was a striking feature of both PCLD phenotypes, consistent with tissue localised antigen-specific immune responses, but there was no enrichment for known SARS-CoV-2 reactive TCRs. Conclusions: There is no evidence that radiographic organising pneumonia and reticulation in post-COVID lung disease are associated with differential immmunopathological pathways. Inflammatory radiology is characterised by greater bronchoalveolar T cell accumulation. Both groups show evidence of shared antigen-specific T cell responses, but the antigenic target for these T cells remains to be identified.

overall_design: Comparison of bronchoalveolar cells from individuals with either inflammatory or fibrotic post-COVID lung disease.

first: Puja

last: Mehta

first: Blanca

last: Sanz-Magallon Duque de Estrada

first: Emma

last: Denneny

first: Kane

last: Foster

first: Kaylee

middle: B

last: Worlock

first: Masahiro

last: Yoshida


title: Murine mesenchymal stem cells undergo molecular changes after a single passage in culture

city: NEDLANDS

first: Vincent

last: Kuek

state: WA

address: Telethon Kids Institute, Northern Entrance, Perth Children's Hospital,  15 Hospital Ave

department: Telethon Kids Cancer Centre

country: Australia

institute: Telethon Kids Institute

summary:
The properties of MSCs can be affected by long term culture, therefore casting doubt over the ability of late passage MSCs to accurately recapitulate their biology. Additionally, assumption within the scientific community is often made that early passage MSCs are still representative of the primary MSC population, however, little research has been done to support this.
We compared the transcriptomic profiles of murine MSCs freshly isolated from the long bones to MSCs that had been expanded in culture for 10 days. Interestingly, we identified that a single passage in culture induced extensive alterations to MSC molecular signatures associated with cell cycling, differentiation and immune response.

overall_design: Comparative differential gene expression profiling analysis of RNA-seq data for  1) murine long bone MSCs freshly isolated from 10-week old female C57BL/6J mice (primary MSCs or pMSCs), versus 2) murine long bone MSCs from 10-week old female C57BL/6J mice that had been cultured for a single passage (cultured MSCs or cMSCs).

first: Anastasia

last: Hughes


title: ATAC-seq analyses of AR-V7.

city: Boston

first: Maryam

last: Labaf

address: 100 William T Morrissey Blvd

department: Biology

institute: University of Massachusetts Boston

summary: Although AR-V7 has been intensively studied, it remains unclear whether AR-V7 and other AR splicing variants can specifically activate a distinctive transcriptional program from the full-length AR (AR-FL), and whether AR-V7 may play a role in accelerating the metastatic progression of castration-resistant PCa (CRPC). In this study, we hypothesize that AR-V7 can drive a distinct transcription program from AR-FL in CRPC condition. To test this, we performed ATAC-seq using LNCaP model with inducible overexpression of AR-V7 to examine the function of AR-V7. We demonstrated that AR-V7 has “pioneer factor-like” activities to access the androgen-responsive elements (AREs) located at compact chromatin regions. More importantly, we found that SOX9, a critical metastasis driver gene, was a direct target and downstream effector of AR-V7, and its protein expression was dramatically upregulated at AR-V7-induced bone lesions.

overall_design: ATAC-seq analyses in LNCaP table cells with or without overexpression of AR-V7 and stimulated with or without DHT under 5% charcoal-stripped FBS condition. The stable cells were generated by stably infecting LNCaP cells with tetracycline inducible overexpression of wild-type AR-V7 virus. These stable cells were grown in the medium containing 10% tetracycline-free FBS.

first: Dong

last: Han

first: Mayram

first: Kourosh

last: Zarringhalam

first: Changmeng

last: Cai


title: Topoisomerase I poisoning induces R-loop changes and DNA damage in human cancer cells [END-seq]

city: Bologna

first: Giovanni

last: Capranico

state: BO

address: Via Selmi 3

department: FABIT

country: Italy

institute: University of Bologna

summary: DNA topoisomerase I is an essential enzyme in higher eukaryotes that regulates DNA torsional tension during fundamental processes, such as replication and transcription. During its catalytic activity, a transient Topoisomerase I-DNA cleavage complex, called Top1cc, forms to allow strand rotation and duplex relaxation. However, the stabilization of Top1cc can lead to increased DNA:RNA hybrid duplexes, DNA double-strand cuts (DSBs) and genome instability as shown by formation of micronuclei, extranuclear chromatin enveloped by a nuclear membrane. To better comprehend the underlying mechanisms, we have established genomic maps of Top1cc-mediated R-loop changes and DSBs at short times upon Top1cc induction. Our findings show that Top1ccs dynamically changed the genomic distribution of R-loops, with regions of stable hybrid gains. DSBs were at specific gene loci, strongly associated with stable anterior R-loops at highly-transcribed genes and close to backtracked RNA polymerase II. Moreover, DSBs and stable anterior R-loops were highly enriched at early replication origins, thus revealing the location of replication conflicts with backtracked RNA polymerases.

overall_design: END-seq experiments were performed on HCT116 cells treated with Camptothecin (CPT) for 10 and 20 minutes and in untreated cells.  We produced 2 biological replicates per condition.

first: Marco

last: Russo

first: Sara

last: Morelli

first: Renée

last: Duardo

first: Jessica

last: Marinello

first: Simona

last: Pepe

first: Federico

last: Guerra

first: Belen

last: Gomez

first: Andrés

last: Aguilera


title: Topoisomerase I poisoning induces R-loop changes and DNA damage in human cancer cells [DRIP-seq]

overall_design: DRIP-seq experiments were performed on HCT116 cells treated with Camptothecin (CPT) for 5 and 60 minutes and in untreated cells. For each DRIP library a library on RnaseH-treated sample was produced to filter false positive DRIP regions. We produced 2 biological replicates per condition.


title: Membrane phospholipid remodeling modulates nonalcoholic steatohepatitis progression by regulating mitochondrial homeostasis [LKO_NASH]

city: Urbana

first: Ye

last: Tian

state: IL

address: 2001 South Lincoln Avenue, room 3612

department: Comparative Biosciences

institute: University of Illinois ar Urbana-Champaign

summary: Nonalcoholic steatohepatitis (NASH), characterized by inflammation and fibrosis, is emerging as a leading etiology of hepatocellular carcinoma (HCC). However, the mechanisms underlying the pathogenesis of NASH are not well understood. Here, we show that membrane phospholipid (PL) composition determined by a remodeling process modulates the progression of NASH. The expression of lysophosphatidylcholine acyltransferase 3 (LPCAT3), a PL remodeling enzyme that produces polyunsaturated PLs, is dramatically suppressed in human NASH livers compared to controls. LPCAT3 expression is inversely correlated with NAFLD activity score and fibrosis stage. Loss of Lpcat3 in mouse liver promotes the development of both spontaneous and diet-induced NASH/HCC. Mechanistically, Lpcat3 deficiency increases reactive oxygen species production, likely due to impaired mitochondrial homeostasis as demonstrated by reduced mitochondrial DNA content and fragmented mitochondrial morphology. Overexpressing Lpcat3 in the liver ameliorates inflammation and fibrosis of NASH. These results suggest that manipulating LPCAT3 expression may be an effective therapeutic strategy for NASH.

overall_design: Lpcat3f/f (con) and Lpcat3f/f Albumin-Cre (LKO) mice were fed with NASH diet for 12 weeks. 5 male mice from each group were used to extract liver total RNA and proceed to RNA sequancing.

first: Bo

last: Wang


title: Topoisomerase I poisoning induces R-loop changes and DNA damage in human cancer cells.

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

overall_design: Refer to individual Series


title: Effects of Estradiol and Fulvestrant on gene expression in steroid-deprived MCF-7 cells

city: Jupiter

first: Jerome

last: Nwachukwu

state: Florida

address: 130 Scripps Way

department: Department of Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: We treated steroid-deprived MCF7 cells with DMSO (Vehicle),  1 nM 17b-estradiol (E2), 100 nM fulvestrant (Fulv), or a combination of fulvestrant and estradiol for 24 hours

overall_design: We then performed gene expression profiling analysis using data obtained from mRNA-seq of 3 biological replicates.

first: Jacqline

middle: W

last: Njeri

first: Kendall

last: Nettles


title: The super-healing MRL strain promotes muscle growth in muscular dystrophy through a regenerative extracellular matrix

city: Chicago

first: Joseph

last: O'Brien

address: 445 E Ohio St, Apt 1818

department: Genetics

institute: Northwestern

summary: Genetic background shifts the severity of muscular dystrophy.  In mice, the DBA/2J strain confers a more severe muscular dystrophy phenotype, whereas the Murphy’s Roth Large (MRL) strain has “super-healing” properties that reduce fibrosis.  A comparative analysis of the Sgcg null model of Limb Girdle Muscular Dystrophy in the DBA/2J versus MRL strain showed the MRL background supported greater myofiber regeneration with reduced structural degradation of muscle.  Transcriptomic profiling of dystrophic muscle in the DBA/2J and MRL strains indicated strain-dependent expression of the extracellular matrix (ECM) and TGF-b signaling genes.  To investigate the MRL ECM, cellular components were removed from dystrophic muscle sections to generate decellularized “myoscaffolds”.  Decellularized myoscaffolds from dystrophic mice in the protective MRL strain had significantly less deposition of collagen and matrix-bound TGF-b1 and TGF-b3 throughout the matrix.  Dystrophic myoscaffolds from the MRL background were enriched in myokines. C2C12 myoblasts were seeded onto decellularized matrices from Sgcg-/- MRL and Sgcg-/- DBA/2J matrices. Acellular myoscaffolds from the dystrophic MRL background induced myoblast differentiation and growth compared to dystrophic myoscaffolds from the DBA/2J matrices. These studies establish that the MRL background also generates its effect through a highly regenerative ECM, which is active even in muscular dystrophy.

overall_design:
Build a transcriptomic profile of the quadriceps in the dystrophic Sgcg-D2 and Sgcg-MRL models. These models were compared to eachother and their respective WT controls (WT-D2 and WT-MRL)
I analyzed 4 cohorts (WT-MRL, Sgcg-MRL, WT-D2, Sgcg-D2). Each cohort contained 3 females, 16-weeks of age.


title: Chemical Genetics Screen Identifies COPB2 Tool Compounds That Alters ER Stress Response and Induces RTK Dysregulation in Lung Cancer Cells

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

summary: Activating mutations in the epidermal growth factor receptor (EGFR) are common driver mutations in non-small cell lung cancer (NSCLC). First, second and third generation EGFR tyrosine kinase inhibitors (TKIs) are effective at inhibiting mutant EGFR NSCLC, however, acquired resistance is a major issue, leading to disease relapse. Here, we characterize a small molecule, EMI66, an analog of a small molecule which we previously identified to inhibit mutant EGFR signalling via a novel mechanism of action. We show that EMI66 attenuates receptor tyrosine kinase (RTK) expression and signalling and alters the electrophoretic mobility of Coatomer Protein Complex Beta 2 (COPB2) protein in mutant EGFR NSCLC cells. Moreover, we demonstrate that EMI66 can alter the subcellular localization of EGFR and COPB2 within the early secretory pathway. Furthermore, we find that COPB2 knockdown reduces the growth of mutant EGFR lung cancer cells, alters the post-translational processing of RTKs, and alters the endoplasmic reticulum (ER) stress response pathway. Lastly, we show that EMI66 treatment also alters the ER stress response pathway and inhibits the growth of mutant EGFR lung cancer cells and organoids. Our results demonstrate that targeting of COPB2 with EMI66 presents a viable approach to attenuate mutant EGFR signalling and growth in NSCLC.

overall_design:
We used genome-wide CRISPR/Cas9 screens to test for gene deletions that affect fitness in human cells treated with the EGFR inhibitor EMI1.

The 'sgRNA_read_counts.txt' contains 3 data columns as the read counts of all (7) control samples were summed together into a single control read count column.
The sgRNA_read_counts_9samples.txt has one column for each of the 9 independently sequenced samples.

first: Punit

last: Saraon

first: Jamie

last: Snider

first: Wiebke

last: Schormann

first: Ankit

last: Rai

first: Nikolina

last: Radulovich

first: María

last: Sánchez-Osuna

first: Jasmin

last: Coulombe-Huntington

first: Caroline

last: Huard

first: Evelyne

last: Lima-Fernandes

first: Brigitte

last: Thériault

first: Levon

last: Halabelian

first: Mohammed

last: Mohammed

first: Manuel

last: Chan

first: Dhananjay

last: Joshi

first: Luka

last: Drecun

first: Zhong

last: Yao

first: Shivanthy

last: Pathmanathan

first: Victoria

last: Wong

first: Anna

last: Lyakisheva

first: Farzaneh

last: Aboualizadeh

first: Li

last: Niu

first: Taira

last: Kiyota

first: Ratheesh

last: Subramanian

first: Babu

last: Joseph

first: Ahmed

last: Aman

first: Fengling

last: Li

first: Michael

last: Prakesch

first: Methvin

last: Isaac

last: Mamai

first: Gennady

last: Poda

first: Masoud

last: Vedadi

first: Richard

last: Marcellus

first: David

last: Uehling

first: Miroslav

last: Samaržija

first: Adrian

last: Sacher

first: Natasha

last: Leighl

first: Mike

first: Ming-Sound

last: Tsao

first: Cheryl

last: Arrowsmith

last: Andrews

first: Rima

last: Al-awar

first: Marko

last: Jakopović

first: Igor

last: Stagljar


title: NTHi infection of Normal Human Nasal Epithelia (NHNE) for 14 days

city: St. Lucia

first: Ulrike

last: Kappler

state: Qld

address: Cooper Rd B76

department: School of Chemistry and Molecular Biosciences

institute: The University of Queensland

sample_organism:
Haemophilus influenzae
Homo sapiens

platform_organism:
Haemophilus influenzae
Homo sapiens

overall_design: Normal human nasal epithelia (NHNE) from five healthy human donors were infected with Haemophilus influenzae strain 86-028NP (MOI 1:100, NHNE:bacteria). Samples for RNA isolation were collected prior to infection (day0) for uninfected NHNE and bacterial pre-cultures, and on day1, 3, 7 and 14 post-infection for NTHi-infected NHNE. RNA was isolated using TRIZOL, treated with EZDnase to remove remaining gDNA and concentrated usingRNA Clean and Concentrate Kits (Zymo). 2-3 microg total RNA (RIN >8.0) were ribodepleted using the RiboMinus kit (Termo Fisher) and the ribodepleted RNA used for library preparation. For all NHNE samples ~ 70 million reads were collected per sample and mapped to human and NTHi reference genomes. for NTHi infected NHNE samples, approximately 2 milion reads could be mapped to the bacterial genome.

first: Emmanuelle

last: Fantino


title: Apolipoprotein E2 expression drives increased brain exosome levels during aging to mitigate neuronal endosomal dysfunction

city: Orangeburg

first: Paul

last: Mathews

address: 140 Old Orangeburg Rd.

department: Psychiatry

institute: New York University Grossman School of Medicine

summary: The polymorphic APOE gene is the greatest genetic determinant of sporadic Alzheimer’s disease risk: the APOE4 allele increases risk while the APOE2 allele is neuroprotective compared with the risk-neutral APOE3 allele. The neuronal endosomal system is inherently vulnerable during aging, and APOE4 exacerbates this vulnerability by driving an enlargement of early endosomes and reducing exosome release in humans and mice. We hypothesized that the protective effects of APOE2 are mediated through the endosomal pathway during aging. In contrast to Alzheimer’s disease and APOE4 models, we detected normal morphology and abundance of early endosomes within cortical neurons of APOE2 targeted-replacement mice during aging despite decreased rab5b recruitment to early endosomes. Similarly, the morphology and abundance of retromer-associated vesicles was normal in APOE2 mice, despite reduced recruitment of vesicle-associated VPS35. Significantly, we observed increased brain extracellular levels of endosome-derived exosomes in APOE2 compared with APOE3 mice during aging, indicative of an enhanced endosomal cargo clearance to the extracellular space that contributes to a homeostatic balance of endosomal functions. Our findings thus demonstrate that APOE2 effectively offsets endosomal pathway changes during aging to preserve its integrity by enhancing exosome biogenesis, mitigating age-driven endosomal dysfunction that contributes to Alzheimer’s disease risk.

overall_design: Hemibrain genetic profiles of targeted-replacement APOE2, APOE3, and APOE4 mice at 18 months of age

first: Katherine

middle: Y

last: Peng

first: Braison

last: Liemisa

first: Jonathan

last: Pasato

first: Pasquale

last: D'Acunzo

first: Monika

last: Pawlik

first: Adriana

last: Heguy

first: Sai

last: Penikalapati

first: Amanda

last: Labuza

first: Harshitha

last: Pidikiti

first: Melissa

last: Alldred

first: Stephen

last: Ginsberg

first: Efrat

last: Levy


title: Analysis of genes regulated by miRNAs upon Toll pathway activation in shmCherry and shAgo1 flies

city: STRASBOURG

first: Nicolas

last: MATT

address: 15 rue René Descarte

department: IBMC

country: France

institute: CNRS

summary: This micro-array helps establish Toll activated-genes dampened by miRNAs in Drosophila melanogaster.

overall_design: Flies depleted of Ago1 by short hairpin in adult fat body (yolk>shmAgo1) or of control mCherry (yolk>shmCherry) were obtained and infected by Micrococcus luteus. RNA was extracted, purified and analysed by a micro-array.

first: Alexandre

last: Cammarata-Mouchtouris

first: Aleksandra

last: Krupa

first: Vincent

last: Leclerc

last: Matt

first: Jean-Marc

last: Reichhart

first: Laurent

last: Troxler


title: Transcriptome analyses of AR-V7 and ARv567es

first: Maryam

last: Labaf

summary: Although AR-V7 has been intensively studied, it remains unclear whether AR-V7 and other AR splicing variants can specifically activate a distinctive transcriptional program from the full-length AR (AR-FL), and whether AR-V7 may play a role in accelerating the metastatic progression of castration-resistant PCa (CRPC). In this study, we hypothesize that AR-V7 can drive a distinct transcription program from AR-FL in CRPC condition. To test this, we used LNCaP model with inducible overexpression of AR-V7 or AR-V7-S81A to examine the transcriptional function of AR-V7 and the role of S81 phosphorylation on AR-V7 transcriptome. We also studied the endogenous AR-V7 transcriptome in CWR-22Rv1 cells using siRNA against AR-V7. Lastly, we used LNCaP model with inducible overexpression of AR-V567es to examine the AR-V567es transcriptome.

overall_design: RNA-seq analyses were performed to examine genes reglated by AR-V7, AR-V7-S81A mutant, or ARv567es in LNCaP stable cell lines. The stable cells were generated by stably infecting LNCaP cells with tetracycline inducible overexpression of wild-type AR-V7 or S81A AR-V7 lentivirus and cumate inducible overexpression of AR-V567es lentivirus, and were grown in the medium containing 10% tetracycline-free FBS. Endogenous AR-V7 activity was examined by transient transfection of siNTC or siARV7 in CWR-22RV1. The experiments were performed under 5% homemone-depleted medium (CSS) and done in replicates.

first: Dong

last: Han

first: Kourosh

last: Zarringhalam

first: Changmeng

last: Cai


title: Elucidating and Pharmacologically Targeting Master Regulators of Stem-like Breast Cancer Cell State

first: Andrea

last: Califano

summary: In many tumors, small subpopulations of stem-like cells can exist in drug-resistant states that are transient and epigenetically governed. Single-cell RNA sequencing provides transcriptional profiles for individual cells which, although sparse and noisy, may provide insight into how they are regulated and how they may be targeted. We took a systems-biology approach to analyzing stem-like cells in breast tumors and predicting how this drug-resistant subpopulation might be sensitized to treatment. Our analysis predicted that the anthelmintic albendazole would reprogram the stem-like population, and a subsequent sensitizing-then-kill experiment in triple negative breast cancer PDX mice revealed a synergistic relationship between albendazole and the first-line treatment, paclitaxel. These results are a proof of concept that it is possible to use, a systems biology approach to identify drugs that can reprogram cell-state, and that tumor subpopulations which have long been considered intractable may be forced into a sensitive state.

overall_design: Patient-derived xenograft (PDX) models were generated using dissociated tumor cells obtained from a patient with triple-negative breast carcinoma. The mice (n=2/arm) were treated with paclitaxel, ivermectin, albendazole, and DMSO (control) for 15 days, and tumors were harvested 2 hours after administration of the last dose of vehicle or drug. Then, the prepared libraries using Human Tumor Dissociation Kit (Miltenyi) were sequenced on an Illumina Novaseq 6000.

first: Jeremy

last: Worley

first: Heeju

last: Noh

first: Daoqi

last: You

first: Filemon

last: Dela Cruz

first: Andrew

last: Kung


title: The Role of Interleukin-23 in the Early Development of Emphysema in HIV1+ Smokers [Affymetrix]

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Matrix metalloproteinase-9 (MMP-9) expression is up-regulated in alveolar macrophages (AM) of HIV1+ smokers who develop emphysema. Based on the knowledge that lung epithelial lining fluid (ELF) of HIV1+ smokers has increased levels of inflammatory cytokines compared to HIV1- smokers, we hypothesized up-regulation of lung cytokines in HIV1+ smokers may be functionally related to increased MMP-9 expression. Cytokine arrays evaluated cytokine protein levels in ELF obtained from 5 groups of individuals: HIV1‾ healthy nonsmokers, HIV1‾ healthy smokers, HIV1‾ smokers with low diffusing capacity (DLCO) , HIV1 + nonsmokers, and HIV1 + smokers with low DLCO. Among several pro-inflammatory cytokines elevated in ELF associated with smoking and HIV1+, increased levels of the Th17-related cytokine IL-23 were found in HIV1- smokers with low DLCO and HIV1+ smokers and nonsmokers. Relative IL-23 gene expression was significantly increased in AM of HIV1+ individuals, with greater expression in AM of HIV1+ smokers with low DLCO. Infection with HIV1 in vitro induced IL-23 expression in normal AM. Since AM purified by adherence contain a small number of lymphocytes, we hy-pothesized that in an AM/lymphocyte co-culture system, IL-23 would up-regulate MMP-9. IL-23 stimulation of AM/lymphocyte co-cultures in vitro induced increased MMP-9 mRNA levels and protein. AM of healthy individuals did not express IL-23 receptors (IL-23R), lung T lymphocytes express IL-23R and interact with AM in order to up-regulate MMP-9. This mechanism may contribute to the increased tissue destruction in the lungs of HIV1+ smokers and suggests that Th-17 related inflammation may play a role.
IL-23 upregulates MMP-9 expression in human alveolar macrophages via a T lymphocyte/alveolar macrophage interaction, suggesting a possible role for Th-17 related inflammation in accelerated emphysema in HIV1+ smokers.

overall_design: Array-based expression profiling of alveolar macrophages from HIV1+ smokers and HIV1- smokers.

first: Igor

last: Barjaktarevic

first: Ronald

last: Crystal

first: Robert

last: Kaner


title: Assessment of different enrichment methods revealed the optimal approach to identify bovine circRNAs

city: chengdu

first: Yixin

last: Wang

state: sichuan

address: 211 huimin street

department: Institute of Animal Genetics and Breeding, College of Animal Science and Technology

institute: Sichuan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary:
To better study the bovine circRNA, we assessed the outcomes of circRNA identification using six enrichment approaches.
RNA-sequencing analysis revealed that different approaches led to varied the ratio of uniquely mapped reads, false positive rate of identifying circRNAs, and the number of circRNAs per million clean reads. Besides, 507 of 4,051 identified bovine high confident circRNAs had shared splicing sites with human circRNAs.

overall_design: After extracting the total RNA of the liver and rumen from three (Kinsella Composite) beef steers, six enrichment approaches with the combination of ribosomal RNAs removal (Ribo); linear RNAs degradation (R); linear RNAs and RNAs with structured 3′ ends degradation (RTP); ribosomal RNAs coupled with linear RNAs (Ribo-R) elimination; ribosomal RNA, linear RNAs and RNAs with poly (A) tailing elimination (Ribo-RP); and ribosomal RNA, linear RNAs and RNAs with structured 3′ ends elimination (Ribo-RTP) were performed before RNA-seq libraries construction, respectively. Besides, five raw RNA-seq data with the same libraries construction strategies as ribosomal RNAs removal were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) with the accession number GSE116775. These five reanalysis data were aggregated into the Ribo group. Subsequently, we compared circRNAs identified by different enrichment methods based on all RNA sequencing results.

first: Le

middle: L

last: Guan


title: Transcriptome data of bone marrow hematopoietic stem cells (HSCs) with IGF-1 treatment

city: Chongqing

first: Weinian

last: Liao

address: Gaotanyan street 30

institute: Army Medical University

summary: Insulin-like growth factor-1 (IGF-1) is known as a hematopoietic factor which impacts hematopoietic reconstitution and facilitates thrombopoiesis, although its direct effect on hematopoietic stem cells (HSCs) remains unclear. Here, we show that IGF-1 rapidly prompts megakaryocyte (Mk)-lineage differentiation of HSCs by enhancing mitochondrial activity in HSCs. To identify the phenotype switching and function variation in HSCs with IGF-1 treatment, we performed RNA-seq of HSCs from the bone marrow of mice with single-dose IGF-1 treatment (IGF-1) and their age-matched control mice (Ctrl).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of BM HSCs (CD34-Flk2-Lineage-Sca1+c-Kit+) of control or IGF-1 mice.

first: Changhong

last: Du

first: Junping


title: Gene expression profiling study to identify distinct subtypes in Peritoneal metastasis of colorectal cancer

city: Daejeon

first: sungghwan

last: park

address: Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology

summary: The objective of this study is to assess gene expression changes and identify gene sets associated with metastasis into peritoneum in colorectal cancer (CRC) patients. We performed RNA-seq based transcriptome profiling using primary tumor samples obtained from 19 CRC patients with peritoneum metastasis. By a number of statistical tests, a total of 1,422 genes were statistically significant, indicating a gene set significantly associated with metastasis into peritoneum in CRC. To select the genes showing strong gene expression intensities and critically validate the differences between CRCs with metastasis and without metasis, we applied more rigorous cut-off for gene selection, revealing candidates less than 20 genes. These genes were applied to the downstream experimental assays.

first: Jeong-Hwan

last: Kim

first: Seon-Kyu

first: Seong-Hwan

last: Park

first: Seon-Young

first: Ye

last: Ha

first: Yong

last: Yoon


title: The Role of Interleukin-23 in the Early Development of Emphysema in HIV1+ Smokers


title: Membrane phospholipid remodeling modulates nonalcoholic steatohepatitis progression by regulating mitochondrial homeostasis.

last: Tian

summary:
Background and aims: NASH, characterized by inflammation and fibrosis, is emerging as a leading etiology of HCC. Lipidomics analyses in the liver have shown that the levels of polyunsaturated phosphatidylcholine (PC) are decreased in patients with NASH, but the roles of membrane PC composition in the pathogenesis of NASH have not been investigated. Lysophosphatidylcholine acyltransferase 3 (LPCAT3), a phospholipid (PL) remodeling enzyme that produces polyunsaturated PLs, is a major determinant of membrane PC content in the liver.

Approach and results: The expression of LPCAT3 and the correlation between its expression and NASH severity were analyzed in human patient samples. We examined the effect of Lpcat3 deficiency on NASH progression using Lpcat3 liver-specific knockout (LKO) mice. RNA sequencing, lipidomics, and metabolomics were performed in liver samples. Primary hepatocytes and hepatic cell lines were used for in vitro analyses. We showed that LPCAT3 was dramatically suppressed in human NASH livers, and its expression was inversely correlated with NAFLD activity score and fibrosis stage. Loss of Lpcat3 in mouse liver promotes both spontaneous and diet-induced NASH/HCC. Mechanistically, Lpcat3 deficiency enhances reactive oxygen species production due to impaired mitochondrial homeostasis. Loss of Lpcat3 increases inner mitochondrial membrane PL saturation and elevates stress-induced autophagy, resulting in reduced mitochondrial content and increased fragmentation. Furthermore, overexpression of Lpcat3 in the liver ameliorates inflammation and fibrosis of NASH.

Conclusions: These results demonstrate that membrane PL composition modulates the progression of NASH and that manipulating LPCAT3 expression could be an effective therapeutic for NASH.

overall_design: Both Lpcat3 liver knockout (LKO) and control mice fed with NASH diet for 12 weeks were used for liver RNA sequencing. LKO and Con groups contain 5 mice each (GSM6734249-GSM6734258). Lpcat3 vs eGFP are mice injected with AAV expressing either eGFP control or Lpcat3 for overexpression. Mice were fed with NASH diet before RNA sequencing. Detailed study design was discussed in the paper (PMID: 36999536).


title: Distinct activity of androgen receptor splice variants in promoting prostate cancer metastasis

first: Maryam

last: Labaf


title: Cistrome analyses of AR-V7.

summary: Although AR-V7 has been intensively studied, it remains unclear whether AR-V7 can specifically activate a distinctive transcriptional program from the full-length AR (AR-FL), and whether AR-V7 may play a role in accelerating the metastatic progression of castration-resistant PCa (CRPC). In this study, we hypothesize that AR-V7 can drive a distinct transcription program from AR-FL in CRPC condition. To test this, we used LNCaP model with inducible overexpression of AR-V7 or AR-FL to examine the effects of AR-V7 overexpression or AR-FL overexpression stimulated with DHT for 4 hours on AR-V7 or AR-FL cistromes. We also studied the effects of AR-V7 on cistromes of pioneer factor FOXA1 and active histone marker H3K27ac, and the function of phosphorylation at Ser81 on AR-V7 function in CRPC.

overall_design: ChIP-seq analyses of V5 tagged AR-V7, AR-C, FOXA1 and H3K27ac were performed to examine AR-V7, AR-C, FOXA1 and H3K27ac binding with or without overexpression of AR-V7 or AR-V7-S81A in LNCaP stable cell line under 5% charcoal-stripped FBS condition. The stable cells were generated by stably infecting LNCaP cells with tetracycline inducible overexpression of wild-type AR-V7 or S81A-AR-V7 virus. These stable cells were grown in the medium containing 10% tetracycline-free FBS.

first: Dong

last: Han

first: Mayram

first: Kourosh

last: Zarringhalam

first: Changmeng

last: Cai


title: Membrane phospholipid remodeling modulates nonalcoholic steatohepatitis progression by regulating mitochondrial homeostasis [Lpcat3_OE]

overall_design: C57BL/6 mice were fed with NASH diet for 7 weeks and were injected AAV-TBG-eGFP as control (eGFP) or AAV-TBG-Lpcat3 (Lpcat3) for overexpression of Lpcat3 specifically in the liver. Both groups of mice were further fed with NASH diet for 9 weeks. Then, total liver RNA were isolated for RNA sequencing.

first: Bo


title: Vitamin-D Responsive SGPP2 Variants Associated with Lung Cell Expression and Lung Function

first: Yael

last: Strulovici-Barel

type:
Expression profiling by array
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
Background: Vitamin D is associated with lung health in epidemiologi studies, but mechanisms mediating observed associations are poorly understood. This study explores mechanisms for an effect of vitamin D in lung through an in vivo gene expression study, an expression quantitative trait loci (eQTL) analysis in lung tissue, and a population-based cohort study of sequence variants.
Methods: Microarray analysis investigated the association of gene expression in small airway epithelial cell with serum 25[OH]D in adult nonsmokers. Sequence variants in candidate genes identified by the microarray were investigated in a lung tissue eQTL database, and also in relation to cross-sectional pulmonary function in Health, Aging, and Body Composition [Health ABC] study, stratified by race, with replication in the Framingham Heart Study [FHS].
Results: 13 candidate genes had significant differences in expression by serum 25[OH]D (nominal p<0.05), and a genome-wide significant eQTL association was detected for SGPP2. In Health ABC, SGPP2 SNPs were associated with FEV1 in both European and African-Americans, and the gene-level association was replicated in European-American FHS participants. SNPs in 5 additional candidate genes (DAPK1, FSTL1, KAL1, KCNS3 and RSAD2) were associated with FEV1 in Health ABC participants.
Conclusions: SGPP2, a sphingosine-1-phosphate, is a novel vitamin D-responsive gene associated with lunh function. The identified associations will need to be followed up in further studies.

overall_design: Bronchial brushing used to collect airway epithelial cells from 26 healthy nonsmokers.  Microarray analysis investigated the association of gene expression in small-airway epithelial cells and genotypes from blood DNA from 116 individuals with serum 25(OH)D for 156 genes regulated by vitamin D

first: Brian

last: Reardon

first: Joyanna

last: Hansen

first: Ronald

first: Denise

middle: K

last: Houston

first: Stephen

last: Kritchevsky

first: Tamara

last: Harris

first: Kurt

last: Lohman

first: Yongmei

last: Liu

first: George

middle: T

last: O’Connor

first: Jemma

last: Wilk

first: Jason

last: Mezey

first: Chuan

last: Gao

first: Patricia

middle: A

last: Cassano


title: Transcription factor EHF interacting with transcription coactivator AJUBA (JUB) aggravates malignancy of gastroesophageal adenocarcinoma [ATAC-seq]

city: Guangzhou

first: Li

last: Peng

address: No. 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

summary: Transcriptional dysregulation of genes is a hallmark of tumors and can be pharmacologically developed in cancer. However, little is known about the interaction or transcriptional cooperativity between TF and transcription cofactor in gastroesophageal adenocarcinoma (GEA).

overall_design: The molecular mechanism was mainly through RNA-seq, ChIP-seq, ATAC-seq, co-IP and MS.

first: Xiao-Qing

last: Yuan


title: Transcription factor EHF interacting with transcription coactivator AJUBA (JUB) aggravates malignancy of gastroesophageal adenocarcinoma [ChIP-seq]


title: Transcription factor EHF interacting with transcription coactivator AJUBA (JUB) aggravates malignancy of gastroesophageal adenocarcinoma.

overall_design: Refer to individual Series


title: Transcription factor EHF interacting with transcription coactivator AJUBA (JUB) aggravates malignancy of gastroesophageal adenocarcinoma [RNA-seq]


title: Biology and Ontogeny of Human Small Airway Epithelium Club Cells Identified with Single Cell Transcriptome and Principle Component Gradient Analysis

summary: Club (“Clara”) cells, dome shaped cells with disease cytoplasmic granules and microvilli, are the major secretory cell of the human small (>6 generation) airways. Little is known regarding the biology of club cells in the human airway, nor of the ontogeny of this cell type. Taking advantage of the SCGB1A1 as the marker for club cells and our ability to sample the normal small airway epithelium by bronchoscopy and brushing healthy volunteers, we defined the transcriptome of the normal human airway club cell using single cell transcriptome sequencing.  Analysis of the human small airway epithelial single cell transcriptome together with in vitro validation provides novel insights into the molecular phenotype and biological functions of the human club cell population and identifies the basal cell as the human progenitor cells for club cells.

overall_design: Three healthy nonsmokers, with no history of exposure to any tobacco products, were assessed using approved clinical protocols by Weill Cornell Medical College Institutional Review Board and the small airway epithelium (10th-12th generations of bronchi) were collected by bronchoscopic brushing.  Single cell capture and RNA-sequencing was performed for 157 single-cell samples.  To assess the ontogeny of human club cells using a computational strategy, semi-supervised, multivariate analysis was carried out using Principal Component Gradient Analysis (PCGA) performed with several pairs of cell-type marker genes including KRT5/SCGB1A1, DNAI1/SCGB1A1, and MUC5AC/SCGB1A1.  To assess whether the pure population of human small airway epithelium KRT5+ BC could differentiate into SCGB1A1+ KRT5‾ club cells, the BC were cultured on air-liquid interface.

first: Wu-Lin

last: Zuo

first: Sushila

last: Shenoy

first: Sheng

last: Li

first: Guoqing

last: Wang

first: Michelle

middle: R

last: Staudt

first: Christopher

last: Mason

first: Sarah

last: O’Beirne

first: Robert

middle: J

last: Kaner

first: Philip

last: Leopold

middle: G

last: Crystal


title: Genotype-Smoking Environment Interactions affecting eQTL in the Human Lung

first: Yael

last: Strulovici-Barel

type:
Expression profiling by array
SNP genotyping by SNP array

summary:
Background: Cases where genotype-phenotype relationships depend on environmental factors have been quantified for many complex diseases.  Such genotype-environment interactions (GEI or GxE) may also affect expression Quantitative Trait Loci (eQTL) present in tissues critical for the manifestation of disease.  To assess this hypothesis, we performed an analysis of eQTL-GEI resulting from an individual's smoking environment in the lung small airway epithelium (SAE).  While the SAE is challenging to sample, this is the cell population that shows the first signs of smoking related stress and gene expression in the SAE appears to play a role in mediating smoking effects on lung disease.
Results: We used expression microarrays to assay the SAE transcriptome for a small sample of African-American individuals and we analyzed SNPs genotyped genome-wide to identify GEI affecting eQTL. While a genome-wide trans- analysis identified few instances of GEI after a multiple test correction, an analysis of cis-genotypes identified a small but significant number of GEI affecting lung SAE gene expression.  We determined that significant cases of eQTL-GEI were not driven by outliers and we were also able to find corroborative evidence for a few of these eQTL-GEI in a small, independent sample of individuals of European ancestry.
Conclusion: Given that the power of GEI tests is low compared to tests of genotype association and that the total sample size of our study was small, including only 61 African American individuals in our focal population, the identification of significant GEI in our study implies that there may be considerable genotype-specific effects on eQTL due to smoking environment.  We discuss individual cases of GEI of interest for lung disease, such as SDC1 and ZAK, as well as the broader implications of our results for the analysis of eQTL and for genome-wide association analysis of complex diseases.

overall_design: Interactions between genetics and environment (genetic-environment interactions or GEI) may affect expression of genes in tissues where diseases manifest.  In this study, we performed an analysis of GEI affecting gene expression in the lung small airway epithelium (SAE), a critical cell population for smoking derived lung disease. SNP samples were acquired from the blood of the subjects.

first: Marcus

last: Butler

first: Timothy

last: O'Connor

first: Neil

last: Hackett

first: Jackie

last: Salit

first: Andy

last: Clark

first: Ronald


title: Positional Identity of Branching-associated HOXB2 and B3 Gene Expression is Maintained by Adult Human Airway Epithelial Progenitor Cells

summary: In the context that HOX mutant mice have profound deficits in airway branching morphogenesis, we asked whether the positional identity of HOX genes is maintained in the epithelium of the adult human tracheobronchial tree and if so, whether these positional differences are embedded in the stem/progenitor population derived from nonbranching vs branching airways. We found that 10 of 39 HOX genes are expressed in varying degrees in the nonbranching (trachea) or branching (large and small airways) human airway epithelium. Strikingly, HOXB2 and B3 were highly expressed in the trachea epithelium, but barely detectable in the branching airway epithelium. This difference in HOXB2 and B3 gene expression was embedded in the airway basal cell stem/progenitor population isolated from the trachea vs branching airways, and maintained during differentiation in vitro. Finally, HOXB2 and B3 expressions in the trachea vs branching airways correlated with the expression of a variety of other transcription and growth factors related to branching morphogenesis. The finding that the adult human airway epithelium expresses some HOX genes in a positional manner, with differences embedded in the transcriptomes of airway epithelial stem/progenitor cells, has implications for the use of stem/progenitor cells for applications relevant to lung regeneration.

overall_design:
Homeobox (HOX) genes are transcription regulators that mediate embryonic morphogenesis and determine positional identity. Microarrays showed that 9 of 39 HOX genes are expressed in varying degrees in the nonbranching (trachea) or branching (large and small airways) human airway epithelium. Most strikingly, HOXB2 and B3 were highly expressed in the trachea epithelium, but barely detectable in the epithelium from branching airways. This difference was not affected by cigarette smoking, but was embedded in the airway stem/progenitor population and maintained during differentiation. The finding has significant implications for the applications of stem/progenitor cells relevant to  lung regeneration and repair.
Examination of nonbranching (trachea) or branching (large and small airways) human airway epithelium+/- cigarette smoke.

first: Rui

first: Guoquing

first: Joumana

last: Ahmed

first: Jacqueline


title: DLBCL

status: Public on Jun 04 2024

city: Jinan

first: Yanfeng

last: Liu

address: 107 west wenhua xi road

institute: shandong university

summary: none provided

overall_design: DLBCL vs. normal


title: The Role of Interleukin-23 in the Early Development of Emphysema in HIV1+ Smokers [RNA-seq]

city: New York

overall_design: RNAseq-based expression profiling of alveolar macrophages from HIV1- nonsmokers, smokers, and smokers with COPD.

first: Igor

middle: Z

last: Barjaktarevic


title: Genetic Variability Modulation of SPOCK3 Gene Expression in the Human Small Airway Epithelium

summary: Testican 3 (coded for by SPOCK3), is an extracellular matrix heparan/chondroitin sulphate proteoglycan that possesses serine and cysteine protease inhibitor-like domains Based on the knowledge that serine proteases contribute to the destruction of the lung in cigarette smokers, but that only a fraction of smokers develop smoking-induced lung disease, we hypothesized that smokers expressed SPOCK3 at lower levels in the small airway epithelium, the initial site of smoking-induced disease, and further, that genetic variability modulates the expression of SPOCK3 in the airway epithelium. Assessment of gene expression in the small airway epithelium (10th -12th order bronchi) of healthy non-smokers (n=38) and healthy smokers (n=42), demonstrated that the expression levels of SPOCK3 were significantly lower in healthy smokers compared to healthy nonsmokers (p<0.04). Affymetrix Human SNP array 5.0 was used to assess genome wide single nucleotide polymorphisms (SNPs) within 100 kbp of the SPOCK3 gene in the same nonsmokers and smokers, and these SNPs were correlated with small airway gene expression of SPOCK3, with correction for variation in genetic ancestry. There was a significant correlation of SPOCK3 small airway epithelial gene expression with 13 adjacent SNPs in the SPOCK3 gene (p<10-3, all comparisons, Wald test). For example, the TT allele of rs13124292, located in intron 3, was associated with a small airway epithelial expression levels of 0.56 ± 0.07, and the AA genotype with expression levels of 2.31 ± 0.26 (p<10-6, pairwise t test). Interestingly, smoking appeared to lessen the degree to which genotype associated with SPOCK3 expression level, i.e., smoking to some extent overrode the influence of genetic variation.  The observation that SPOCK3 gene expression in the small airway epithelium is reduced in smokers, and that smoking interacts with cis-genomic variations to determine the levels of SPOCK3 small airway epithelial gene expression, is consistent with the concept that everyone is at risk for smoking-induced lung disease, but that inherited genetic variations contribute to the pathogenesis of susceptibility to smoking-induced disease.

overall_design:
Assessment of gene expression in the small airway epithelium (10th -12th order bronchi) of healthy non-smokers (n=38) and healthy smokers (n=42).
There are 74 SNPs from the Affymetrix Genome Wide 5.0 Array that are within a 100KB region of the gene SPOCK3.  Two SNPs are shown to have a significant correlation between genotype and expression; rs7677172 (Figure 3, in manuscript) and rs2703840 (Figure 5, in manuscript).


title: RNA-seq of monocyte derived macrophages and dendritic cells in a Peruvian Tuberculosis cohort

first: Maria

last: Gutierrez-Arcelus

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: In this study, we sought to analyze the effects of genetic variants on gene expression levels in relation to the history of infectious disease and cell type. To do this, we focused on a Peruvian human cohort that had been previously genotyped who either progressed to active tuberculosis (TB) disease (cases) or did not progress to TB (controls). We isolated monocytes from PBMC samples of these individuals and differentiated in vitro to dendritic cells (DCs) and macrophages (MPs). We performed RNA-seq for each sample using a modified Smart-seq protocol for low-input RNA-sequencing. We measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified cell-type-specific eQTL genes as well as five genes that showed an interaction between eQTL variants and TB progression status in dendritic cells. We found that the top eQTL interaction with disease history was associated with a gene involved in tyrosine catabolism.

overall_design:
We re-recruited a subset of household contacts of index TB patients who had been infected with Mtb and either progressed to active TB disease (progressors, cases) or remained TB-disease-free until sampling (non-progressors, controls) after initial enrollment. We restricted the analysis to high-quality data from 63 progressors and 63 non-progressors, sampled a median of 6 years after exposure to TB in the household. We generated gene expression profiles using RNA-seq in monocyte-derived dendritic cells (118 samples) and macrophages (109 samples) from these previously genotyped participants to conduct an eQTL mapping study.

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Submitter declares that raw data will be available through dbGaP
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first: Victor

middle: E

last: Nieto-Caballero

first: Josephine

middle: F

last: Reijneveld

first: Angel

last: Ruvalcaba

first: Gabriel

last: Innocenzi

first: Nalin

last: Abeydeera

first: Samira

last: Asgari

first: Kattya

last: Lopez

last: Iwany

first: Yang

last: Luo

first: Aparna

last: Nathan

first: Daniela

last: Fernandez-Salinas

first: Marcos

last: Chiñas

first: Chuan-Chin

last: Huang

first: Zibiao

last: Zhang

first: Segundo

last: León

first: Roger

middle: I

last: Calderon

first: Leonid

last: Lecca

first: Jonathan

last: Budzik

first: Megan

last: Murray

first: Ildiko

last: Van Rhijn

first: Soumya

last: Raychaudhuri

first: Branch

last: Moody

first: Sara

last: Suliman


title: Endothelial MMP14 is required for endothelial dependant growth support of human airway basal cells

first: Yael

last: Strulovici-Barel

summary: Human airway basal cells (BC) are the stem/progenitor population of the airway epithelium, and play a central role in anchoring the epithelium to the basement membrane. The anatomic position of BC allows for potential paracrine signaling between BC and the underlying non-epithelial stromal cells. In support of this, we previously demonstrated endothelial cells (EC) support growth of BC during co-culture via vascular endothelial growth factor A (VEGFA)-mediated signaling. Building on these findings, RNA sequencing analysis demonstrated that BC express multiple fibroblast growth factor (FGF) ligands (FGF2, 5, 11 and 13) with only FGF2 and FGF5 capable of functioning in a paracrine manner to mediate FGFR1 signaling. Antibody mediated blocking of FGFR1 during BC-EC co-culture significantly reduced EC dependent BC growth. Stimulation of EC via BC-derived growth factors resulted in EC expression of matrix metallopeptidase 14 (MMP14) and shRNA mediated knockdown of EC MMP14 significantly reduced EC dependent growth of BC. Overall, these data characterize a novel growth factor mediated reciprocal “cross-talk” between human airway BC and EC that regulates proliferation of BC.

overall_design: This study characterizes a novel growth factor mediated reciprocal “cross-talk” between human airway BC and EC that may play a significant role in maintaining normal airway structure.

first: Matthew

middle: S

last: Walters

first: Bi-Sen

last: Ding

first: Kazunori

last: Gomi

first: Shahin

last: Rafii

first: Ronald

last: Crystal


title: Inhibition of ABI2 Ubiquitination-Dependent Degradation Suppresses Breast Cancer Cell Growth via Down-regulating PI3K/Akt Signaling Pathway [RNAseq-20240420]

city: Dalian

first: Linlin

last: Lv

address: No.2 Linggong Road

institute: Dalian University of Technology

summary: TNBC is a type of cancer that lacks receptor expression and has complex molecular mechanisms. Recent evidence shows that the ubiquitin-protease system is closely related to TNBC. In this study, we obtain a key ubiquitination regulatory substrate-abi2 protein by bioinformatics methods, which is also closely related to the survival and prognosis of TNBC. Further, through a series of experiments, we demonstrated that ABI2 expressed at a low level in TNBC tumors, and it has the ability to control cell cycle and inhibit TNBC cell migration, invasion and proliferation. Molecular mechanism studies proved E3 ligase CBLC could increase the ubiquitination degradation of ABI2 protein. Meanwhile, RNA-seq and IP experiments indicated that ABI2 can significantly inhibit PI3K/Akt signaling pathway via the interaction with Rho GTPase RAC1. Finally, we also found that the antibiotic Colistimethate could inhibit the growth of TNBC cells by inhibiting CBLC-induced ABI2 ubiquitination and down-regulating PI3K/Akt signaling pathway.

overall_design: To identify the gene functions of ABI2, MDA-MB-231 cells were seeded in 6-well plates for 48 h and then transfected for gene overexpression. Briefly, the transfected plasmid containing ABI2 were used for gene overexpression, and MDA-MB-231 cells transfected with empty vector were used as a negative control. Pasmids were purchased from GenePharma (Shanghai, China).

first: Huijian

last: Wu


title: Overexpression of extracellular matrix proteins, increased cell death and reduced cell proliferation contribute to the pathophysiology of microphthalmia across in vitro patient-derived models

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

institute: UCL

summary: Genetic perturbations influencing early eye development can result in microphthalmia, anophthalmia and coloboma (MAC). Over 100 genes are associated with MAC, but little is known about common disease mechanisms. In this study, we generated induced pluripotent stem cell (iPSC) derived optic vesicles (OVs) from two unrelated microphthalmia patients and healthy controls. At day 20, 35 and 50 microphthalmia patient OV diameters were significantly smaller, recapitulating the ‘small eye’ phenotype. RNA-seq analysis revealed upregulation of apoptosis-initiating and extracellular matrix (ECM) genes at day 20 and 35.  Western blot and immunohistochemistry revealed increased expression of lumican, nidogen and collagen type IV, suggesting ECM overproduction. Increased apoptosis was observed in microphthalmia OVs with reduced pH3+ cells confirming decreased cell proliferation at day 35. Pharmacological inhibition of caspase-8 activity with Z-IETD-FMK decreased apoptosis in one patient model, highlighting a potential therapeutic approach. These data reveal shared pathophysiological mechanisms contributing to a microphthalmia phenotype.

overall_design: To identify common developmental pathway aberrations in microphthalmia patients with similar phenotypes but varying genotypes, we generated patient-specific induced pluripotent stem cell-derived optic vesicles carrying pathogenic variants. These were differentiated to day 20 and day 35 and taken for RNA-seq analysis. From each patient line, 4 replicates from 2 clones each were included in the RNA-seq analysis. Pairwise comparisons between each patient and the healthy control optic vesicles were performed as well as groupwise patient v control comparisons. Differentially expressed genes and enriched gene ontology terms were analysed in each comparison.

first: Nicholas

last: Owen

last: Eintracht


title: Topical Application of Nitrate Ameliorates Skin Fibrosis by Regulating ST2+CD4+ T Cells in Systemic Sclerosis Mouse Model

city: Beijing

first: Yunshu

address: No.22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

summary: Systemic sclerosis (SSc) is characterized by intractable multiorgan fibrosis caused by vascular and immune dysfunction. Currently, effective therapeutic options for patients with SSc are limited. Nitrate, an abundant nutrient in the diet, has been demonstrated to be preventative and therapeutic for several diseases. To determine whether nitrate can slow or reverse SSc progression, topical application of nitrate delivered by dissolving microneedles was used to treat a bleomycin (BLM)-induced dermal fibrosis mouse model. In this study, nitrate considerably attenuated dermal thickness, stiffness, and collagen deposition.To examine the nitrate regulation of gene expression at the genome-wide level, bulk RNA sequencing of skin was performed. Bulk RNA sequencing of skin revealed that Cd4 was a key hub gene in SSc nitrate therapy. Additionally, BLM-induced cytokines and chemokines were inhibited by nitrate, and CD4+ T cells infiltration markedly declined. Il4, Il6, Il13, and Tgfb expression in CD4+ T cells isolated from skin biopsies also significantly decreased. Mechanistically, Il1rl1, a type2 immune response inducer, was markedly repressed in isolated CD4+ T cells and dermal tissues after nitrate treatment. Remarkably, compared with wild type mice, mice lacking Il1rl1 showed impaired transcriptional profiles after intradermal BLM injection. Adoptive transfer of ST2+CD4+ T cells promoted bleomycin-induced Rag2-/- mice dermal fibrosis. Collectively, these findings demonstrate that nitrate targeting ST2+CD4+ T cells is an effective therapeutic option for SSc.

overall_design: To examine the nitrate regulation of gene expression at the genome-wide level, total RNA from skin biopsies from mice treated with BLM with or without nitrate therapy as well as healthy wild-type mice as a control was isolated and sequenced using the Illumina NovaSeq 6000

first: Jianyu

last: Gu

first: Zekun

last: Zhou

first: Shihan

last: Xu

first: Wen

last: Pan

first: Jinsong

last: Wang

first: Ousheng

last: Liu

first: Songlin

first: Junji


title: Nono stimulates the DNA damage response by mediating the induction of Gadd45b [RNA-seq]

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

summary: RNA-binding proteins (RBPs) are frequently deregulated in cancer and emerge as effectors of the DNA damage response (DDR). The non-POU domain-containing octamer-binding protein NONO/p54nrb is a multi-functional RBP that modulates the production and processing of mRNA in unperturbed cells, but also promotes the repair of DNA double-strand breaks (DSBs). Here, we investigate the impact of Nono deletion in the murine cell-based lung cancer model KP (KRasG12D, Trp53-/-). We show that the deletion of Nono impairs the response to DSBs induced by the topoisomerase-II inhibitor etoposide. Nono-deficient KP (KPN) cells display prolonged activation of DSB signaling and an increased amount of DSBs. The defects in the DDR are accompanied with reduced RNAPII promoter occupancy, elevated levels of DNA-RNA-hybrids (R-loops), and attenuated induction of the DDR factor growth arrest and DNA damage inducible beta (Gadd45b). Our data suggest a Nono-mediated, genome-protective crosstalk of the DDR with the RNA metabolism. Our data characterise Gadd45b as putative Nono-dependent effector of the DDR and suggest that Nono mediates a genome-protective crosstalk of the DDR with the RNA metabolism via induction of Gadd45b.

overall_design: Transcriptome analysis upon NONO knockout with or without etoposide treatment

first: Barbara

last: Trifault

first: Victoria

last: Mamontova

first: Kaspar

last: Burger


title: Nono stimulates the DNA damage response by mediating the induction of Gadd45b [CUT&Run]

overall_design: Mapping of DNA-protein interaction upon NONO knockout with or without etoposide treatment


title: Nono stimulates the DNA damage response by mediating the induction of Gadd45b

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


title: The effect of ZFP36L1 deficiency on gene expression in the U2OS osteosarcoma cancer cell line

first: John

last: Murphy

state: Greater London

address: School of Life Sciences

institute: University of Westminster, London, UK

summary: Post-transcriptional regulation of gene expression by RNA binding proteins (RBPs), one of the major classes of proteins encoded by the human genome, is well established. ZFP36L1 and its protein family members, ZFP36 and ZFP36L2, function as RBPs that primarily regulate gene expression at the post-transcriptional level by binding to adenine uridine (AU) rich elements (AREs) in the 3′ untranslated region (3′UTR) of certain mRNAs and mediating ARE-dependent mRNA decay. In this study, using CRISPR/Cas9 ZFP36L1 gene-editing, we generated ZFP36L1 deficient U2OS cellular models. The aim of the RNASeq experiment was to compare the gene expression profile in wild-type U2OS cells compared to ZFP36L1 deficient U2OS cells. Loss of functional ZFP36L1 leads to widespread changes in gene expression that are associated with dysregulation of KRAS signalling.

overall_design: To study the effect of ZFP36L1 deficiency on U2OS gene expression, we used CRISPR/Cas9 ZFP36L1 gene-editing to generate ZFP36L1 deficient U2OS cellular models. We then performed gene expression analysis on wild-type and ZFP36L1 deficient U2OS cells on three different occasions. Wild-type and ZFP36L1 deficient cells were grown until log phase 65-75% confluency and then total RNA was harvested from both cell types. Three RNA samples from wild-type U2OS cells and three RNA samples from ZFP36L1 deficient U2OS cells were sent for gene expression profiling by RNASeq analysis.

first: Kalpana

last: Surendranath

last: Norton

first: Nahida

last: Bashir


title: ADAT2/3 complex-deposited tRNA inosines drives oncogenic transformation

city: Hangzhou

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

institute: Zhejiang University

summary: Transfer RNAs (tRNAs) are subject to numerous posttranscriptional modifications that influence their maturation, stability, and function. Adenosine to Inosine (A-to-I) editingin thetRNA anticodon stem loop is an important modification that influences anticodon-codon recognition.However,the implications of tRNA editing in cancer and its potential for diagnostic and therapeutic applicationsare not yet well understood.We showed that the ADAT2/3 enzyme complex, responsible for this modification in humans, is amplified and overexpressed in several tumor types,with a higher amplification rate in sarcoma tumors, particularly liposarcomas. We determine that the ADAT complex works as an oncogene in these tumors and that its inhibition reduces tumor growth, offering a new approach to cancer treatment. In addition, we provided insight into the mechanisms of cancer development and progression, demonstrating that tRNA editing is required for higher mRNA translation of oncogenic proteins enriched with specific ADAT-sensitive codons. Thus, ADAT-mediated tRNA modification drives oncogenic transformation by remodeling the set of mRNAs being actively translated to increase expression of proteins that promote proliferation. Our results explain how cancer cells benefit from increased tRNA A-to-I editing and propose ADATs as potential therapeutic targets for the treatment of cancer.

overall_design: To understand the role of A-to-I editing in tRNA in tumor development, we carried out small RNA-seq in ADAT2 knock-down cells. We identify the editing events deposited by ADAT2 enzyme and monitor their molecular functions on translation as well as physiological roles during tumor growth.

first: Julia

last: Ramírez-Moya

first: Richard

last: Gregory


title: Empirical Bayes Conditional Independence Graphs for Dense Regulatory Network Recovery

first: Yael

last: Strulovici-Barel

summary: Motivation: Computational inference methods that make use of graphical models to extract regulatory networks from gene expression data can have difficulty reconstructing dense regions of a network, a consequence of both computational complexity and unreliable parameter estimation when sample size is small. As a result, identification of hub genes is of special difficulty for these methods.Methods: We present a new algorithm, Empirical Light Mutual Min (ELMM), for large network reconstruction that has properties well suited for dense graph recovery. ELMM reconstructs the undirected graph of a regulatory network using empirical Bayes conditional independence testing with a heuristic relaxation of independence constraints in dense areas of the graph. This relaxation allows only one gene of a pair with a putative relation to be aware of the network connection, an approach that is aimed at easing multiple testing problems associated with recovering densely connected structures.Results: Using in silico data, we show that ELMM has better performance than commonly used network inference algorithms including PC Algorithm, GeneNet, and ARACNE. We also apply ELMM to reconstruct a network among 5,400 genes expressed in human lung airway epithelium of healthy nonsmokers, healthy smokers, and smokers with pulmonary diseases assayed using microarrays. The analysis identifies dense subnetworks that are consistent with known regulatory relationships in the lung airway and also suggests novel hub regulatory relationships among a number of genes that play roles in oxidative stress, wound response, and secretion.

overall_design: We present a new approach to extracting regulatory networks from gene expression data. The algorithm is applied to reconstruct the gene regulatory network in human lung airway epithelium using microarray data extracted from healthy nonsmokers and smokers and smokers with pulmonary diseases.

first: Rami

last: Mahdi

first: Guoquing

first: Jacqueline

last: Salit

first: Neil

last: Hackett

first: Ronald

last: Crystal

first: Jason

last: Mezey


title: Inhibition of ABI2 Ubiquitination-Dependent Degradation Suppresses Breast Cancer Cell Growth via Down-regulating PI3K/Akt Signaling Pathway [RNAseq-20240415]

first: Linlin

last: Lv

overall_design: To investigate the molecular mechanism of CS inhibiting the growth of TNBC cells, we performed RNA-seq analysis on MDA-MB-231 cells treated with Colistimethate at the dose of 20 μM. We performed gene expression profiling analysis using data obtained from RNA-seq of two different cells at three repeated experiments. Comparative gene expression profiling analysis of RNA-seq data for control MDA-MB-231 cells and Colistimethate treated MDA-MB-231 cells.

first: Huijian

last: Wu


title: Whole RNA profiling of Tuberculosis-diabetes comorbidity linked to diabetes with poor glycemic control

city: Zacatecas

first: José

middle: Antonio

last: Enciso-Moreno

state: Zacatecas

address: Interior de la Alameda 45

department: Unidad de Investigación Biomédica de Zacatecas

country: Mexico

institute: Instituto Mexicano del Seguro Social

summary: Type 2 diabetes (DM2) is a disease that hinders tuberculosis (TB) control strategies worldwide. TB infection, progression, morbidity, treatment success, adverse effects, relapse, and mortality are worse in these susceptible populations. Therefore, expanding the partially known molecular mechanisms leading to TB-DM2 comorbidity may be essential to face both epidemics. Consequently, a transcriptomic study was conducted on TB-DM2 comorbidity, associated with patients with DM2 who have poor glycaemic control (PDM2), since they have a higher risk of getting TB. Human blood samples from healthy controls (CTRL, HbA1c < 6.5%), TB ( HbA1c < 6.5%), TB-DM2, DM2 (HbA1c < 8.9%), and PDM2 (HbA1c > 10%) groups (n=4 each) were analyzed using high-density human GE 4X44K v2 differential expression microarrays.

overall_design: Human blood samples from healthy controls (CTRL, HbA1c < 6.5%), TB (HbA1c < 6.5%), TB-DM2 (HbA1c>6.5%), DM2 (HbA1c 6.5-8.9%), and PDM2 (HbA1c > 10%) groups (n=4 each) were analyzed using high-density human GE 4X44K v2 differential expression microarrays.

first: Elena

last: Jaime-Sánchez

first: Edgar

last: Lara-Ramírez

first: Juan

last: López-Ramos

first: Elsy

last: Ramos-González

first: Ana

last: Cisneros-Méndez

last: Oropeza-Valdez

first: Roberto

last: Zenteno-Cuevas

first: Gerardo

last: Martínez-Aguilar

first: Yadira

last: Bastian

first: Julio

last: Castañeda-Delgado

first: Carmen

last: Serrano