title: Characterization of age-associated gene expression changes in mouse sweat glands

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH


title: Characterization of age-associated gene expression changes in mouse sweat glands [FP_YO]

status: Public on May 17 2024

country: USA

type: Expression profiling by high throughput sequencing

summary: Evaporation of sweat on the skin surface is the major mechanism for dissipating heat in humans.  The secretory capacity of sweat glands (SWGs) declines during aging, leading to heat intolerance in the elderly, but the mechanisms responsible for this decline remain incompletely understood.  We investigated the molecular changes accompanying SWG aging in mice, where sweat tests confirmed a significant reduction of active SWGs in old mice relative to young mice.  We first identified SWG-enriched mRNAs by comparing the transcriptome of Eda mutant Tabby mice, which lack SWGs, with that of wild-type control mice by RNA-sequencing analysis.  This comparison revealed 171 mRNAs enriched in SWGs, including 47 mRNAs encoding core secretory proteins such as transcription factors, ion channels, ion transporters, and trans-synaptic signaling proteins.  Among these, 28 SWG-enriched mRNAs showed significantly altered abundance in the aged footpad skin, and 11 of them, including Foxa1, Best2, Chrm3, and Foxc1 mRNAs belonged to the ‘core secretory’ category.  Consistent with the changes in mRNA expression, immunohistology revealed that higher numbers of secretory cells from old SWGs express FOXC1 protein, the product of Foxc1 mRNA.  In sum, our study identified mRNAs enriched in SWGs, including those that encode core secretory proteins, and changes in these mRNAs and proteins with SWG aging in mice.

overall_design: Footpad skin from fore paws of 3 months old and 28 months old C57BL/6JN male mice were isolated under a dissection microscope.  Four biological replicates for each age group.  One mouse = one biological replicate.  Total RNA was isolated using Qiagen RNeasy Fibrous Tissue Mini Kit (Qiagen Cat# 74704).  Sequencing library was prepared using Illumina TruSeq Stranded mRNA Library prep kit (Illumina Cat# 20020594).  Libraries were subsequently sequenced for Paired-End sequencing with Illumina NovaSeq 6000 sequencer.

first: Alexandra

last: Zonnefeld

first: Chang-Yi

last: Cui

first: Dimitrios

last: Tsitsipatis

first: Yulan

last: Piao

first: Jinshui

last: Fan

first: Krystyna

last: Mazan-Mamczarz

first: Yutong

last: Xue

first: Fred

middle: E

last: Indig

first: Myriam

last: Gorospe


title: RNA SEQUENCING DATA OF VANCOMYCIN TREATED HTB172 LUNG CANCER CELL LINE AND CONTROL,

city: Elizabeth City

first: Hirendranath

last: Banerjee

state: North Carolina

address: 1704 Weeksville Rd,

department: Department of Natural, Pharmacy and Health sciences

institute: Elizabeth City State University

summary: RNA sequencing data of 48 hours  Vancomycin treated HTB172 lung cancer cell lines along with control

overall_design: Cell culture, Drug treatment for 48 hours, RNA isolation by Trzol method

first: Narendra

first: Anasua

first: Hirendra

first: Soumya

first: Zahidur

last: Abedin

first: Karrington

last: Perry

first: Brent

last: Lake

first: Colby

last: Hunter

first: Kuldeep

last: Rawat


title: Characterization of age-associated gene expression changes in mouse sweat glands [FP_WT_TA]

first: Supriyo

overall_design: Footpad skin from fore paws of 3 months old Eda mutant Tabby male mice and age and sex matched C57BL/6J control mice was colllected under a dissection microscope.  Three biological replicates for each genotype.  One mouse = one biological replicate.  Total RNA was isolated using Qiagen RNeasy Fibrous Tissue Mini Kit (Qiagen Cat# 74704).  Sequencing library was prepared using Illumina TruSeq Stranded mRNA Library prep kit (Illumina Cat# 20020594).  Libraries were subsequently sequenced for Paired-End sequencing with Illumina NovaSeq 6000 sequencer.

first: Alexandra

first: Chang-Yi

first: Dimitrios


title: Senescent Characteristics of Human Corneal Endothelial Cells upon Ultraviolet-A Exposure

city: Kyoto

first: Kohsaku

last: Numa

state: Kyoto

address: 465 Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Ophthalmology

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: Purpose: The objective of this study was to investigate the senescent phenotypes of human corneal endothelial cells (hCEnCs) upon treatment with ultraviolet (UV)-A. Methods: We assessed cell morphology, senescence-associated β-galactosidase (SA-β-gal) activity, cell proliferation and expression of senescence markers (p16 and p21) in hCEnCs exposed to UV-A radiation, and senescent hCEnCs induced by ionizing radiation (IR) were used as positive controls.  We performed RNA sequencing and proteomics analysis to compare gene and protein expression profiles between UV-A- and IR-induced senescent hCEnCs, and we also compared the results to non-senescent hCEnCs. Results: Cells exposed to 5 J/cm2 of UV-A or to IR exhibited typical senescent phenotypes, including enlargement, increased SA-β-gal activity, decreased cell proliferation and elevated expression of p16 and p21.  RNA-Seq analysis revealed that 83.9% of the genes significantly upregulated and 82.6% of the genes significantly downregulated in UV-A-induced senescent hCEnCs overlapped with the genes regulated in IR-induced senescent hCEnCs.  Proteomics also revealed that 93.8% of the proteins significantly upregulated in UV-A-induced senescent hCEnCs overlapped with those induced by IR.  In proteomics analyses, senescent hCEnCs induced by UV-A exhibited elevated expression levels of several factors part of the senescence-associated secretory phenotype. Conclusion: In this study, where senescence was induced by UV-A, a more physiological stress for hCEnCs compared to IR, we determined that UV-A modulated the expression of many genes and proteins typically altered upon IR treatment, a more conventional method of senescence induction, even though UV-A also modulated specific pathways unrelated to IR.

overall_design: To investigate the gene profiles of senescent corneal endothelial cells by UVA and X-ray exposure. Expression profiling by high throughput sequencing. Four biological replicates were analyzed for each of 3 conditions (untreated, irradiation, UVA exposure)

first: Sandip

middle: K

last: Patel

first: Akifumi

last: Matsumoto

first: Koji

last: Kitazawa


title: BTK drives neutrophil activation for sterilizing antifungal immunity

city: Bethesda

first: Gustaf

last: Wigerblad

state: MD

address: 10 Center Dr

department: NIAMS

institute: National Institutes of Health

summary: We describe a previously unappreciated role for Bruton's tyrosine kinase (BTK) in fungal immune surveillance against aspergillosis, an unforeseen complication of BTK inhibitors (BTKi) used for treating B-cell lymphoid malignancies. We studied BTK-dependent fungal responses in neutrophils from diverse populations, including healthy donors, BTKi-treated patients, and X-linked agammaglobulinemia patients. Upon fungal exposure, BTK was activated in human neutrophils in a TLR2-, Dectin-1-, and FcgR-dependent manner, triggering the oxidative burst. BTK inhibition selectively impeded neutrophil-mediated damage to Aspergillus hyphae, primary granule release, and the fungus-induced oxidative burst by abrogating NADPH oxidase subunit p40phox and GTPase RAC2 activation. Moreover, neutrophil-specific Btk deletion in mice enhanced aspergillosis susceptibility by impairing neutrophil function, not recruitment nor lifespan. Conversely, GM-CSF partially mitigated these deficits by enhancing p47phox activation. Our findings underline the crucial role of BTK signaling in neutrophils for antifungal immunity and provide a rationale for GM-CSF use to offset these deficits in susceptible patients.

overall_design: Peripheral blood was drawn and neutrophils purified using negative selection (StemCell Technologies).

first: Stephen

last: Brooks

first: Jigar

last: Desai

first: Michail

last: Lionakis


title: RNA SEQUENCING DATA OF NOVEL GOLD NANOPARTICLE TREATED PANCREATIC CANCER CELLS.

first: Hirendranath

summary: BxPC3 pancreatic cancer cell lines were treated with Gold Nanoparticles and RNA was isolated from untreated and treated cells, RNA was sequences by NGS method and data reported

first: Anasua

first: Santanu

last: Bhattacharya

first: Hirendra

first: Soumya

first: Narendra

first: Zahidur


title: Gene expression profile at single level of 8 cell lines isolated from IDH1-mutant diffuse  glioma tumors

city: MOntpellier

first: jean-philippe

last: hugnot

state: languedoc

address: IGF INSERM UM 141 rue de la cardonille

country: France

institute: inserm inm u1191

summary: Diffuse low-grade gliomas are incurable brain tumours that often carry a mutation in the IDH1 gene. These tumours are heterogeneous and have different types of tumour cells. They can progress toward high grade gliomas. To understand the diversity of tumour cells and how they arise, we have performed single RNA seq of  8 cell lines derived from IDH1 mutant patients.  Some cell lines maintained the IDH1 mutation while others lost it. We analysed these cultures when growth factors are present or absent for 4 days to promote differentiation.

overall_design: The 8 cell lines (LGG85, LGG275, LGG336, LGG349, BT138, BT237, BT54, BT88) were grown in neurospheres in DMEM/F12 media + N2 + B27 and EGF/FGF2/Heparin (GF= growth factor condition) or on poly-D-lysin/laminin without  EGF/FGF2/Heparin (noGF= no growth factor condition). Ater 4 days, cells were dissociated and processed for scRNA seq analysis using 10X Chromium technology. The libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent kits V3.1 (Dual Index) from 10X Genomics. The clustering and sequencing steps were performed on an Illumina NovaSeq 6000 using the SBS (Sequence By Synthesis) technique with the NovaSeq Reagent Kits.

first: Jean-Philippe

last: Hugnot

first: Leonor

last: Garcia

first: Stefan

last: Nicolescu

first: Donovan

last: Pineau


title: In Vitro Mesenchymal Stem Cell Differentiation Landscape

city: Houston

first: Danh

last: Truong

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: We employed a tissue engineered system designed to recapitulate mesenchymal stem cell differentiation and performed single-cell profiling to identify differentiation states. We constructed the Mesenchymal Tissue Landscape (MTL) using single-cell RNA-sequencing (scRNA-seq) data from multiple mesenchymal lineages (osteogenic and adipogenic) at various differentiation stages.

overall_design: Human primary bone marrow-derived MSCs were differentiated on polyacrylamide-based hydrogels of different stiffnesses (low = 1.5 kPa, high = 25-40 kPa) corresponding to the stiffnesses of the related mesenchymal tissues (adipose ~ 1-2 kPa, osteoid ~ 25-40 kPa). Upon adding differentiation induction medium, cells were collected at specified time points until terminal differentiation.

first: Joe

last: Ludwig


title: Trametinib sensitizes KRAS-mutant lung adenocarcinoma tumors to PD-1/PD-L1 axis blockade via Id1 downregulation

city: Pamplona

first: Elizabeth

last: Guruceaga

address: Pio XII 55

country: Spain

institute: CIMA

summary:
The identification of novel therapeutic strategies to overcome the intrinsic or acquired resistance to trametinib in mutant KRAS lung adenocarcinoma (LUAD) is a major challenge. This study analyzes the effects of trametinib in Id1, a key factor involved in the oncogenic KRAS pathway, and investigates the Id1 role in acquire resistance and synergy with immunotherapy in KRAS-driven LUAD. Restoring the antitumor immune response by blocking programmed-cell death protein 1 (PD-1) and programmed-cell death-ligand 1 (PD-L1) pathway represents a major breakthrough in non-small-cell lung cancer (NSCLC) treatment. Nevertheless, a high proportion of LUAD patients with KRAS alterations remain refractory to this therapy.
Material and Methods: To explore whether MEK1/2 inhibition reduces Id1 expression, in vitro and in vivo experiments were conducted in KRAS-mutant NSCLC cells and murine models. RNAseq analysis was performed to elucidate the pathways involved in Id1 inhibition. Apoptosis and PD-L1 expression was measured by flow cytometry. Synergy of trametinib combined with anti-PD1 was investigated in KRAS-mutant LUAD mouse models.
Results: Using preclinical syngeneic KRAS-mutant lung cancer mouse models, we demonstrate that trametinib synergizes with PD-1 blockade to reduce lung cancer progression and increase mice overall survival. This antitumor activity was linked to the degradation of Id1 via proteasome, and an enhanced INF-Y-mediated PD-L1 tumor cell expression in KRAS-mutant tumor cells. This effect required CD8+ T cells, boosted the intratumoral CD8+/Treg ratio, reducing the intratumoral Treg/CD4+ ratio.
Conclusions: Our data may support the role of Id1 in the trametinib antitumoral effect, sustaining the mitogen-activated protein kinases (MAPK) signaling pathway involved in the trametinib acquired resistance cells and sensitizing KRAS-mutant lung tumors to PD-1 inhibitors, through PD-L1 overexpression.

overall_design: In order to investigate the molecular mechanisms involved in the trametinib-mediated Id1 downregulation, a global transcriptomic profiling using RNA sequencing analysis was performed on murine CMT167 and KLA lung cancer cells treated or not with trametinib.

first: Ignacio

last: Gil-Bazo

first: Daniel

last: Ajona


title: PTEN-L induce PTEN-null tumor cells dormancy but lung outgrowth.

city: Zhengzhou

first: Pan

middle: Zhen

last: Zhen

state: Henan

address: No. 1, Jianshe East Road, Erqi District

country: China

institute: First Affiliated Hospital of Zhengzhou University

summary: PTEN is one of the most frequently mutated tumor suppressor genes, its loss has been reported in multiple tumor types and is associated with a poor outcome. PTEN-L, as a secreted isoform of PTEN, with the ability to enter cells and inhibit tumor cell growth via inhibiting AKT mediated cell proliferation. However, the distinct effect of PTEN-L on PTEN-expression or PTEN-loss tumor cells is not known yet. Here, we identified PTEN-L treatment facilitate E0771-PTEN-null tumor cells, but not PTEN-wide-type tumor cells lung outgrowth. RNA-seq and Western blot analysis suggest PTEN-L stimulation induced PTEN-null tumor cells dormancy, namely, upregulation of dormancy markers p16 and p27, cell cycle arrest, reduced cell proliferation and chemotherapy drugs resistance. Further study suggested PTEN-L mediated p38 signaling activation play the major role for PTEN-null tumor cell dormancy. The p38 inhibitor, SB202190 significantly reversed the PTEN-L induced PTEN-null tumor cells dormancy and outgrowth in lungs. Further investigation indicated the dormant PTEN-null tumor cells could escape from immunosurveillance and thus outgrowth in lungs, as PTEN-L did not promote PTEN-null tumor cells outgrowth in lung of SCID mice. Therefore, we propose that PTEN-L protects PTEN-null tumor cells from immune attack during lung metastasis via activating dormancy related pathways. This study identified PTEN-L as an activator of PTEN-loss tumor cells dormancy, which enables the efficient seeding and outgrowth of tumor cells in metastatic niches. Overall, we highlight PTEN expression status decides the outcome of PTEN-L mediated anti-tumor therapy.

overall_design: The differential gene expression between the PTEN-L treated group and the untreated group.


title: SH-SY5Y human neuronal cells with mutation of the CDKN2B-AS1 gene are vulnerable under cultured conditions

city: Sendai

first: Kota

last: Sato

state: Miyagi

address: 1-1, Seiryo-machi, Aoba-ku

department: Ophthalmology

institute: Tohoku University

summary: We show that gene expression change of CDKN2B-AS1 overexpressed SH-SY5Y neuroblastoma cells.

overall_design: Examination of CDKN2B-AS1 overexpression (tripricate)

first: Michiko

last: Ohno-Oishi

first: Zou

last: Meiai

first: Seiya

last: Kanno

first: Chihiro

last: Kawano

first: Makoto

last: Ishikawa

first: Toru

last: Nakazawa


title: Role of reducing Hmbox1 in cardiac ischemia/reperfusion injury

city: shanghai

first: Yujiao

last: Zhu

address: Nanchen Road 381

institute: Shanghai University

summary: This RNA-sequencing was performed to determine the differentially expressed mRNA after inhibition of Hmbox1 in cardiac ischemia/reperfusion injury

overall_design: To investigate the function of Hmbox1 in cardiac ischemia/reperfusion (I/R) injury, we established  cardiac I/R injury mouse model in which Hmbox1 was knocked down via adeno-associated virus 9 (AAV9). Total RNAs were extracted from heart tissues from mice at 3 weeks post I/R injury. Four groups were set in this animal experiment (n=3 per group): (1) control AAV9+Sham (Con_Sham); (2) sh-Hmbox1 AAV9+Sham (shHmbox1_Sham); (3) control AAV9+IRI (Con_IRI); (4) sh-Hmbox1 AAV9+IRI (shHmbox1_IRI). The mRNA expression profiling analyses were performed using data obtained from RNA-seq of 4 different groups.

first: Junjie

last: Xiao

first: Yihua

last: Bei


title: Biomarkers to Measure Treatment Response for Alcohol Dependence

first: Chamindi

last: Seneviratne

address: 670 W. Baltimore street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: The goal of this study was to identify molecular mechanisms regulated by pharmacological and placebo effects of binge-drinking at a transcriptome-wide level. We performed RNA-seq on PBMC samples collected from healthy heavy social drinkers (N=18) enrolled in an upto 12-day in-patient, randomized, double-blind, cross-over human laboratory trial testing three alcohol doses: Placebo, medium (0.05g/kg (men), 0.04g/kg (women)), and binge (1g/kg (men), 0.9g/kg (women)), administered in three 4-day experiments, separated by minimum of 7-day washout periods. Effects of beverage doses on differential expression of genes (DEGs) within each experiment compared to its own baseline, across experimental sequences in which each beverage dose was administered, and responsiveness to regular alcohol compared to placebo assessing pharmacological effects of alcohol were analyzed.

overall_design: Randomized, double-blind, cross-over human laboratory trial. Samples from baseline (D0) and final experimental day (D3) within each sequentially performed experiment were sequenced.

first: Suvarna

last: Nadendla

first: Jain

last: Aluvathingal

first: Nastaran

last: Badrzadeh

first: Amol

middle: C

last: Shetty

first: Xin-Qun

last: Wang

first: Jessica

last: Cornell

first: John

last: Sivinski

first: Maureen

last: Kane

first: Nageshwara

last: Pilli

first: Lisa

last: Sadzewicz


title: Ambient RNA analysis of cortex-specific single-nuclei RNA-Seq (snRNA-seq) data in the sham and bilateral carotid artery stenosis (BCAS) groups

city: Shanghai

first: Yuan

last: Zhang

state: Shanghai

address: 130 Dong an Road, Shanghai 200032, China

institute: Fudan University

summary:
When compared with the sham group, ambient RNAs were more predominant in the BCAS group, which originated from damaged neuronal nuclei. After CellBender and subcluster cleaning treatments, detectable ambient RNA contamination could be largely reduced, and cortex-specific transcriptomic maps in the sham and BCAS groups were generated successfully.
The underlying cellular and molecular mechanisms related to cortex damage and glial activation after severe cerebral hypoperfusion were further investigated at single nuclei resolution.

overall_design: Cortex-specific gene expression profiling analysis at single-nuclei resolution was performed using data obtained from RNA-seq in sham and BCAS mice


title: Dual AAV gene therapy in combination with rapamycin rescues muscle and liver impairment in a mouse model of GSDIII.

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

summary: Glycogen storage disease type III (GSDIII) is a rare metabolic disorder due to glycogen debranching enzyme (GDE) deficiency. Reduced GDE activity leads to pathological glycogen accumulation in liver, and in cardiac and skeletal muscles, responsible for impaired hepatic metabolism, heart function impairment, and muscle weakness. To date, there is no curative treatment for GSDIII. The large 4.6 kb coding sequence of GDE represents a major limitation toward the development of clinically relevant AAV gene transfer strategy for GSDIII. We previously reported that liver and heart/muscle correction of the GSDIII phenotype can be achieved in a mouse model of GSDIII by using two distinct overlapping AAV vectors encoding GDE. Here, results of a long-term stability of an approach based on a dual AAV vector encoding for GDE under the control of a recently developed tandem liver-muscle promoter suggests that stable but partial correction of the muscle phenotype can be achieved at very long-term (12 months). In liver, the dual AAV had an only transient efficacy supporting the need for an optimization of the approach. We then assessed the efficacy of rapamycin, an autophagy inducer used in the clinic as an immunosuppressive drug that has shown efficacy in GSDIII. Combination of rapamycin with the dual vector expressing GDE resulted in better correction of glycogen accumulation and muscle strength impairment than AAV vector alone thus supporting a synergic effect of the two treatments. The combined treatment synergic effect was also demonstrated at the molecular level by transcriptomic analysis that indicated a better rescue of the lysosomal pathway in muscle, possibly due to the induction of autophagy by rapamycin and the clearance of glycogen achieved with the combination therapy. In GSDIII mice liver, rapamycin was also able to counteract an unexpected immune reaction to the AAV vector that seems specific of this model. In conclusion, these results indicate that correction of both liver and muscle can be achieved in symptomatic GSDIII mice by an overlapping vector expressing GDE with a tandem promoter when combined with rapamycin treatment. These data also indicate that the effect of rapamycin on AAV gene transfer although disease- and tissue-specific has a net positive impact on dual AAV gene therapy for GSDIII thus opening the way to the clinical translation of this combination approach.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of triceps or liver biopsies from Agl+/+ and Agl-/- mice, treated with the AAV9-LiMP-GDEov in combination or not with rapamycin.

first: Louisa

last: Jauze

first: Mallaury

last: Vie

first: Quentin

last: Miagoux

first: Margot

last: Jarrige

last: Polveche

first: Patrice

last: Vidal

first: Valle

last: Montalvo-Romeral

first: Lucille

last: Rossiaud

first: Justine

last: Nozi

first: Pierre-Romain

last: Le Brun

first: Jérémy

last: Rouillon

first: Fanny

last: Collaud

last: Bordier

first: Emilie

last: Bertil-Froidevaux

first: Christophe

last: Georger

first: Laetitia

last: van Wittenberghe

first: Adeline

last: Miranda

first: Nathalie

last: Daniele

first: Lucile

last: Hoch

first: Xavier

last: Nissan

first: Giuseppe

last: Ronzitti


title: Glutamine antagonist JHU083 reprograms immunosuppressive tumor-associated macrophages to drive tumor immunity in urologic cancer

first: Alex

middle: Jea-Eun

last: Lee

address: 1650 Orleans Street

institute: Johns Hopkins University

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

overall_design: Refer to individual Series


title: Generation of immune-enhancing neutrophils by subclinical super-low dose LPS

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

summary: We have generated immune-enhancing neutrophils by culturing murine primary bone marrow derived neutrophils with either super-low dose of LPS.  Immune-enhancing neutrophils preferentially express co-stimulatory molecules such as CD74, CD44 and CD86, and exhibit reduced expression of CD11b. Purified bone marrow neutrophils were treated with PBS or 100 pg/ml LPS overnight in the presence of GM-CSF, and harvested for scRNAseq analysis to examine their profiles of gene expression.

overall_design: WT murine neutrophils were stimulated by GM-CSF, and then treated with either PBS or LPS overnight

first: Yao

last: Zhang

first: Ziyue

last: YI

first: Shuo

last: Geng


title: Effect of neonatal right ventricular pressure overload on gene expression and regions of open chromatin during postnatal heart development

first: Yuqing

last: Hu

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the effect of pressure overload (PO) during postnatal right ventricular (RV) development, we established the RV PO model by conducting pulmonary artery banding (PAB) surgery on neonatal Sprague-Dawley (SD) rats. We then performed gene expression and chromatin openness profiling analysis using data obtained from RNA-seq and ATAC-seq of RV free walls from PO and sham-operated rats at postnatal day 21 (P21).

overall_design: Comparative gene expression and chromatin openness profiling analysis of RNA-seq and ATAC-seq data for right ventricular free wall myocardium in pressure overload and sham-operated Sprague-Dawley (SD) rats on postnatal day21.

first: Debao

first: Lincai

last: Ye

first: Fen


title: Transcriptome profiling of multi-chambered stomachs in developing lambs

city: Hangzhou

first: Bin

last: Yang

email: rayyangbin@163.com, binyang@zju.edu.cn

state: Zhejiang

address: No. 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

summary: We perform transcriptomic sequencing of rumen, reticulum, omasum, and abomasum epithelial tissues from developing lambs.

overall_design: Transcriptomic data from rumen, reticulum, omasum, and abomasum of developing lambs at d15 and d25 were generated.

first: Kailang

last: Huang

first: Hongwei

last: Chen

first: Jiakun

last: Wang


title: Transcriptome profiling of multi-chambered stomachs in developing lambs [Day 5 and 10]

summary:
We perform transcriptomic sequencing of rumen, reticulum, omasum, and abomasum epithelial tissues from developing lambs.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points (day5 and day10).

overall_design: Transcriptomic data from rumen, reticulum, omasum, and abomasum of developing lambs at d5 and d10 were generated.

first: B

first: K

first: H

first: J


title: Loss of RUNX1 favors mesenchymal stem cells development at the expense of hematopoiesis in hPSC-derived hematopoiesis

city: Guangzhou

first: Cuihua

state: Guangdong

address: 601 Huangpu Ave, Guangzhou

institute: Guangzhou Lab

summary: Our data demonstrated an unprecedented role of RUNX1 in regulating hematopoietic and mesenchymal fate decisions in human pluripotent stem cells (hPSC)-derived hematopoiesis

overall_design: We designed an alternative fluorescent gene tdTomato (tdT) and venus reporter and targeted into the non-coding region of exon 3 of RUNX1 gene, which is adjacent to the proximal promoter of RUNX1 gene, using TALEN-mediated homologous recombination

first: Igor

middle: M

last: Samokhvalov


title: Transcriptome analysis of JMML patients compare to healthy prenatal and postnatal samples.

status: Public on May 16 2024

city: Paris

first: Chloé

last: Arfeuille

address: 48, boulevard Sérurier

institute: APHP

summary: JMML (Juvenile myelomonocytic leukaemia) is a leukaemia that only develops in young children and is thought to have a prenatal initiation. To study the relationship between JMML and normal ontogeny we studied the transcriptome of HPC (hematopoietic progenitor cells) sorted from sporadic JMML patients, healthy prenatal samples and from healthy age matched donors. Bulk transcriptome of sorted HPC reveals that some JMML samples cluster with prenatal samples whereas other from a distinct cluster apart from any healthy samples.

overall_design: Bulk RNAseq data on sorted HPC.

first: Hélène

last: Cavé

first: Marion

last: Strullu

first: Aurélie

last: Caye


title: LPS preconditioning enhances the therapeutic efficacy of MSC-derived exosomes in sepsis by altering miRNA expression profile

city: Tianjin

first: Ting

last: Zheng

state: Tianjin

address: No.154 Anshan Road, Heping District, Tianjin, China

institute: Tianjin Medical University General Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Studies have shown that stimulation of Mesenchymal stem cells (MSCs) with biophysical or biochemical cues could influence the contents and biological activities of subsequent MSC-derived exosomes. However, the underlying mechanisms have not been fully clarified. Here, we pretreated MSCs with lipopolysaccharide (LPS) and evaluated exosomes (LPS-Exo) therapeutic effects in sepsis. Analysis of exosomes activity revealed that LPS-Exo treatment improved sepsis to a greater extent than normal MSCs-derived exosomes (Exo). Further analysis revealed that LPS-Exo exert their protective effects mainly through RNA contents. Thus, we hypothesized that LPS preconditioning enhances the therapeutic efficacy of LPS-Exo in sepsis by altering miRNA expression profile.

overall_design: In order to explore the effect of LPS pretreatment on the miRNA expression profile of MSC-derived exosomes, the miRNAs in the normal exosomes and LPS-stimulated exosomes were sequenced and compared.

first: Sipeng

first: Tao

last: Ma


title: Multimodal single cell analyses reveal mechanisms of perianal fistula in diverse Crohn’s disease [scRNA-seq]

city: New York

first: Judy

last: Cho

state: NY

address: 1470 Madison Avenue, 8th Fl., Box 1498;

department: Pathology, Molecular and Cell-Based Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Crohn’s disease (CD) is a chronic inflammatory condition that can affect any part of the gastrointestinal tract. African ancestry (AA) populations have been substantially under-represented in genome-wide association studies (GWAS) of CD and inflammatory bowel disease (IBD), reflecting in part the lower prevalence of CD in AA compared to European ancestry (EA) populations. Importantly, CD complicated by perianal fistulae has been found to be more prevalent and severe in African-ancestry patients. Perianal fistulae arise from the distal rectal mucosa and can course to a cutaneous surface, resulting in highly morbid complications. Monoclonal antibodies against anti-TNF are the mainstay of treatment, but recurrence and secondary loss-of-response is common. In severe, uncontrolled cases, complete proctectomy is required. The intestine is unique among adult tissues in that under homeostasis, residential macrophages are continually replenished from recruited blood monocytes. In EA cohorts, we established that chronic monocyte cultures stimulated with NOD2 agonists result in aberrant myeloid-stromal differentiation stratified by risk allele carrier status. NOD2 risk alleles are not associated with perianal fistulae; African-American patients with CD do not carry them (except via recent European ancestry admixture). There is no direct association between known CD GWAS risk loci and the risk of developing perianal fistula. Here, we present direct ex-vivo, single cell multiomic analyses of colorectal tissues and perianal fistulous tracts in AA and EA cases to define mechanisms of perianal fistula development. We implicate myeloid-stromal crosstalk and define cell subtypes using single cell RNA (scRNASeq), ATAC sequencing, and chronic, unstimulated monocyte cultures. Transcription factor motifs and ATAC signals co-localized with fine-mapped GWAS loci provide insight to cell-specific and transcriptional network regulation.

overall_design: Single cell RNA seq, ATAC seq and chronic, unstimulated monocyte cultures were preformed to analyze rectum, sigmoid colon and fistula samples from inflamed and uninflamed area collected from diverse patients.

first: Rachel

last: Levantovsky

first: Christopher

last: Tastad

first: Jiayu


title: Profiling and Rewiring Dysfunctional NK cells to Restore Anti-Tumor Activity

city: Ramat Gan

first: Tirza

middle: T

last: Doniger

state: Not US or Canada

address: Bar Ilan University

department: The Mina and Everard Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

summary: Unraveling the molecular mechanisms of NK cell dysfunction and implications for anti-tumor immunotherapy.

overall_design: CD56+CD3neg cells were isolated from the PBMCs of 4 control healthy donors and sorted for Anergic (NKG2A-panKIR-) and Responsive (NKG2A+ panKIR+)

first: Batel

last: Sabag

first: Abhishek

last: Puthenveetil

first: Mira

last: Barda-Saad


title: Region-specific pathogenesis and dissipation of intraregional heterogeneity in cerebellar neurodegeneration

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Heterogeneity and selective vulnerability are among the key features of the healthy and diseased brain. Cerebellum contains majority of brain cells, and is thought to be relatively uniform in structure. We explore heterogeneity in the context of healthy cerebellum and during selective vulnerability in cerebellar disease.

overall_design: RNA-seq of cerebellar tissues in WT and SCA1 mice.

first: Katherine

last: Hamel

first: Emmanuel

last: Labrada Moncada

first: Carrie

last: Sheeler

first: Juao

middle: G

last: Rosa

first: Stephen

last: Gilliat

first: Marija

last: Cvetanovic


title: Transcription profiles of  the control and Med23KO primary muscle stem cells cultured for 3 days in vitro

first: Lu

last: CHENGJIANG

state: China, Mainland

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: To understand the impacts of Med23 deletion on muscle stem cells, we performed RNA-seq analysis using the ctrl and Med23KO muscle stem cells  cultured for 3 days in vitro.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the control and Med23KO muscle stem cells

first: Yi

last: Fang

first: Chonghui

last: Li

first: Chengjiang

last: Lu


title: Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish

city: Suita

first: Hiroyuki

last: Nakajima

state: Osaka

address: 6-1 Kishibeshinmachi

department: Department of Cell Biology

institute: National Cerebral and Cardiovascular Center Research Institute

summary: To investigate what kind of gene expression is regulated downstream of Tie1 signaling, we performed RNA-seq analyses on venous and lymphatic endothelial cells (ECs) between homozygous tie1 mutant embryos and their wild-type and heterozygous siblings during secondary sprouting, respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration, proliferation, and differentiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for endothelial cells from homozygous tie1 mutant embryos and their wild-type and heterozygous siblings in zebrafish.

first: Nanami

last: Morooka

first: Naoki

last: Mochizuki


title: TET2 Promotes Tumor Antigen Presentation and T Cell-Directed Tumor Cell Cytotoxicity Which is Enhanced by Vitamin C Treatment

city: Chapel Hill

first: Meng

last: Cheng

state: NC

address: 107 Pinegate Cir, Apt 9

department: Lineberger Cancer Center

institute: UNC-CH

summary: Immune evasion by tumors is promoted by low T cell infiltration, an immunosuppressive tumor microenvironment, poor T cell activity directed against the tumor, and reduced tumor antigen presentation.  We showed previously that tumor expression of the DNA dioxygenase TET2 enhances recruitment of T cells through activating the expression of CXCL9, 10 and 11.  Vitamin C treatment was shown to increase these effects in a TET2 dependent manner.  Using scSeq analysis, we show that an additional function for TET2 in tumors is to enhance the expression of genes involved in antigen presentation, including those encoding H-2 MHC proteins, B2M, TAP1, TAPBP, and components of immunoproteasome.  Using the B16-OVA melanoma model, we show that antigen expression  in tumors is blocked if TET2 expression is eliminated and that vitamin C further promotes tumor antigen presentation in a TET2-dependent manner.  Consistently, T cell killing assays demonstrate that effective killing of tumor by antigen-specific T cells requires TET2 expression in the tumor cells.  Analysis of patient tumor samples indicates that TET2 activity, as measured through 5hmC levels, correlates directly with expression of antigen-presentation gene expression and with patient outcomes.

overall_design: WT or TET2-KO B16-OVA melanoma cells were transplanted to C57BL/6 syngeneic mice and then treated with PBS or 1g/kg Vitamin C (I.V.) for 2 weeks starting from Day 6. Tumor tissues were then collected and single cell population were isolated for single-cell RNA Seq using 10X Genomics NGS.

first: Angel

last: Chu

first: Josh

last: Welch

first: Albert

last: Baldwin


title: Multimodal single cell analyses reveal mechanisms of perianal fistula in diverse Crohn’s disease [Multiome]

first: Judy

last: Cho

overall_design: multiome ATAC seq and chronic, unstimulated monocyte cultures were preformed to analyze rectum, sigmoid colon and fistula samples from inflamed and uninflamed area collected from diverse patients.

first: Rachel

last: Levantovsky

first: Christopher

last: Tastad

first: Jiayu

last: Zhang


title: Altered Chromatin State Drives Hypersocial Behaviors in Canids

city: Princeton

first: Dhriti

last: Tandon

state: New Jersey

address: 106A Guyot Hall

department: Ecology and Evolutionary Biology

institute: Princeton University

summary: Polymorphic transposable elements found in regulatory sequences can impact the associated transactional modules. We investigated such molecular alterations for these elements in the dog genome that evolved from directional selection during domestication. We find that the polymorphic element in canine GTF2I intron 17 is associated with altered looping, and hence distinct cis-regulatory landscapes. We report supporting evidence of an E2F1-DNA binding peak concordant with the altered loop and higher expression of GTF2I exon 18. Additionally, we find altered looping with the canine LIMK1 gene and an increase in LAT2 expression within the loop. At a more global level, we discover differences in pathways regulating the extra-cellular matrix between samples of differential TE number. Our study emphasizes the role of chromatin architecture in social evolution.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27ac and E2F1 in dog brainstem tissue of old males (12-16 years).

first: Enikő

last: Kubinyi

first: Sára

last: Sándor

first: Hannah

last: Faughnan

first: Ádám

last: Miklósi

first: Bridgett

last: vonHoldt


title: ISRH-seq: a sensitive and robust methodology for R-loop profiling

city: Nanjing

first: Wu

last: Jing

address: No.1 Weigang, Nanjing, Jiangsu

institute: Nanjing Agricultural University

summary: R-loops serve as key modulators in various biological processes in humans and plants.Current high-throughput methodologies for R-loop profiling have their own intrinsic pros and cons. Therefore, any robust, sensitive, and amenable methods, complementary and/or advantageous to existing methodologies, are much needed for advancing R-loop biology. We here present an RNase H based cleavage combined with DNA polymerase-mediated in situ biotin-dATP/dCTP labeling of newly synthesized DNA for sequencing, termed ISRH-seq, an antibody-independent approach for strand-specific mapping of R-loops. After conducting a parallel comparison with DRIP-seq, we found that ISRH-seq can identify more R-loop peaks with the same sequencing depth. Moreover, ISRH- and DRIP-specific R-loops had distinct genomic and epigenetic features, exhibited distinct relationships with expression of overlapping genes, and functional divergence. Importantly, we found that ISRH-seq can be scalable down to 250-100ng DNA input, indicative of a robust and sensitive high-throughput methodology. In addition, it can be applied for R-loop profiling under stress conditions. Thus, our study provides a valuable orthogonal methodology for comprehensive profiling of R-loops in plants. It could be easily adapted to other non-plant systems, especially for these biologically important tissues or cell types with limited cell numbers, thereby advancing understanding of R-loop biology.

overall_design: ISRH-seq

first: Wenli

first: Ying

last: Yang

first: Jing

last: Wu

first: Mengqi

last: Li


title: Underlying mechanisms for selected disease resistance and enhanced non-specific resistance in rainbow trout

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: A critical problem facing all U. S. aquaculture is loss due to disease. In the past year alone, diseases accounted for 90% of all losses of trout intended for sale, greatly impacting the livelihood of our farmers. Previously, we focused on sustainable aquaculture efforts by evaluating the effects of dietary replacement (marine-based to plant-based protein sources) on rainbow trout. Through this effort, we developed a rainbow trout strain that thrives on an all plant-protein formulated diet (PSel/UI strain). In selecting for diet tolerance, we discovered this strain has also undergone positive selection for nonspecific disease resistance to Infectious Hematopoietic Necrosis Virus (IHNV). Therefore, the goal of this project was to determine the mechanisms behind this nonspecific immunity by performing a pathogen challenge and measuring several disease performance characteristics among PSel/UI and two other trout strains commonly used in the commercial aquaculture industry, one selected for disease resistance to these pathogens for several generations and the other completely unselected. We examined lysozyme activity changes in serum and innate gene expression using RNA-sequencing by sampling kidney, spleen, intestine, and liver at time zero and at 4, 12, 24, and 48 hours post-infection with IHNV. We then integrated innate gene expression with disease performance characteristics and made comparisons among strains to identify significant differentially expressed genes and compared with the genetic background of the fish. Through these objectives, we narrowed a set of candidate genes useful in the co-selection of two aquaculturally-important traits: enhanced nonspecific disease resistance with diet utilization. This project was supported by Agriculture and Food Research Initiative Competitive Grant no. USDA-NIFA-SRGP-006544 from the USDA National Institute of Food and Agriculture.

overall_design: 270 samples of kidney, spleen, intestine, and liver tissue were taken from three trout strains at time zero and at 4, 12, 24, and 48 hours post-infection with IHNV.

first: Jacob

middle: W

last: Bledsoe

first: Jia

last: Ma

first: Ken

last: Cain

first: Tim

last: Bruce

first: Anna

last: Rawles

first: Tom

last: Welker

last: Overturf


title: Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation

city: Chengdu

first: Mao

last: Chen

address: Section 4-13, Renmin Rd. South

institute: Biogas Institute of Ministry of Agriculture and Rural Affairs

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

overall_design: Refer to individual Series


title: Natural killer cell regulation of breast cancer stem cells mediates metastatic dormancy

status: Public on May 15 2024

city: Ann Arbor

first: Grace

last: Bushnell

state: MI

address: 2800 Plymouth Rd NCRC B26

department: Internal Medicine

institute: University of Michigan

summary: Breast cancer patients with estrogen receptor positive tumors face a constant risk of disease recurrence for the remainder of their lives. Dormant tumor cells residing in tissues such as the bone marrow may generate clinically significant metastases many years after initial diagnosis. Previous studies suggest that dormant cells display “stem like” properties (CSCs), which may be regulated by the immune system. Although many studies have examined tumor cell intrinsic characteristics of dormancy, the role of the immune system in controlling dormancy and its escape is not well understood. This scientific gap is due, in part, to a lack of immunocompetent mouse models of breast cancer dormancy with many studies involving human xenografts in immunodeficient mice. To overcome this limitation, we studied dormancy in immunocompetent, syngeneic mouse breast cancer models. We find that PyMT, Met-1 and D2.0R cell lines contain CSCs that display both short- and long-term metastatic dormancy in vivo, which is dependent on the host immune system. Natural killer cells were key for the metastatic dormancy phenotype observed for D2.0R and the role of NK cells in regulating CSCs was further investigated. Quiescent D2.0R CSC are resistant to NK cytotoxicity, while proliferative D2.0R CSC were sensitive to NK cytotoxicity both in vitro and in vivo. This resistance was mediated, in part, by the expression of Bach1 and Sox2 transcription factors. NK killing was enhanced by the STING agonist MSA-2. Collectively, our findings demonstrate the important role of immune regulation of breast tumor dormancy and highlight the importance of utilizing immunocompetent models to study this phenomenon.

overall_design: D2.0R tumor cells were labeled with celltrace far red and cultured for one week in 2% FBS DMEM media. After a week of culture CTFR+ label retaining cells (quiescent) and CTFR- non-label retaining cells (proliferative) were FACS sorted.

first: Max

last: Wicha


title: GDF15 links beta-adrenergic induced lipolysis with anxiety

city: Hamilton

first: Russta

last: Fayyazi

state: ON

address: 1280 Main St W

department: Medicine

country: Canada

institute: McMaster University

summary: Psychological stress activates the autonomic nervous system to protect organisms through an integrated response involving changes to both behavior and metabolism. Epinephrine is an important driver of this response, activating adipose tissue lipolysis3and inducing anxiety-like behavior. Interestingly, anxiety correlates with circulating free fatty acid levels and can be alleviated by a b-blocker that does not cross the blood brain barrier suggesting a peripheral signal linking metabolism with behavior, however, to date this has not been defined. Herein, we identify that the most upregulated secreted gene product induced by epinephrine within white adipose tissue of mice is growth differentiating factor 15 (GDF15). This increase in GDF15 occurs within one hour and is not observed in liver, brown adipose, kidney, or skeletal muscle, and is also observed with the more specific b2/3-agonist, CL316,243. Genetic inhibition of adipose triglyceride lipase (ATGL), the rate limiting enzyme for the release of free fatty acids in white adipose tissue, or genetic deletion of b-adrenergic receptors, blocks b-adrenergic induced increases in GDF15. Increases in circulating GDF15 are not derived from adipocytes but instead require free fatty acid-induced stimulation of macrophages within white adipose tissue. Remarkably, anxiety-like behavior elicited by epinephrine or restraint stress are eliminated in mice lacking the GDF15 receptor, GFRAL. Importantly in patients with severe burns, increases in catecholamines are associated with GDF15 and this relationship is eliminated with the b-blocker propranolol. These data provide important insight into the mechanisms linking metabolism and behavior and suggest that inhibition of GDF15-GFRAL signaling may be important for reducing acute anxiety.

overall_design: To investigate transcriptomic effects of anxiety, RNA-seq data was obtained from mice in two conditions, each with 6 biological replicates. First condition was 'Vehicle': mice injected with saline (control condition). Second condition was 'Epinephrine': mice injected with sodium epinephrine.

first: Townsend

last: Logan

first: Fayyazi

last: Russta


title: RNAP stalling-derived genome instability underlies ribosomal antibiotics efficacy and resistance evolution (ChIP-seq data)

city: Beijing

first: Ruochen

last: Chai

address: Haidian District

institute: Tsinghua University

summary: Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here we found that a broad range of ribosome-targeting antibiotics caused mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we found that the translation inhibitor caused genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. Further analysis showed that the stalling was caused by disruption of transcription-translation coupling. Anti-intuitively, the stalled RNAPs subsequently induced lesions to the DNA via transcription-coupled repair. While most of the bacteria were killed by genotoxicity, a small subpopulation acquired mutations via SOS-induced mutagenesis. Given that these processes were triggered shortly after antibiotic addition, resistance rapidly emerged in the population. Our work revealed a new mechanism of action of ribosomal antibiotics, illustrates the importance of dissecting the complex interplay between multiple molecular processes in understanding antibiotic efficacy, and suggests new strategies for countering the development of resistance.

overall_design: To dissect the temporal relationship bewteen RNAP stalling and DNA damage, we profiled RNAP stalling and DNA damage using ChIP-seq on RpoB and Gam respectively. RpoB is the β subunit of RNAP; Gam is a phage protein that can capture the presence of DNA damage in vivo by binding to double-strand DNA ends. Briefly, we engineered a strain with IPTG-inducible 3xFLAG-tagged gam, supplemented 6 μg/ml of gentamicin to exponential phase bacteria (induced Gam expression ~3 h before gentamicin), and harvested the bacteria before and 20, 40, 60 min after gentamicin treatment respectively. We then split the samples in two halves, and performed ChIP-seq on RpoB and Gam-3xFLAG respectively

first: Yayun

last: Zheng


title: The interplay between oxidative stress and inflammation supports autistic-related behaviors in Cntnap2 mutant mice

city: Povo (TN)

first: ENRICO

last: DOMENICI

address: via Sommarive n. 9

department: CELLULAR, COMPUTATIONAL AND INTEGRATIVE BIOLOGY

country: Italy

institute: University of Trento

summary: Autism Spectrum Disorder (ASD) is a highly prevalent neurodevelopmental condition characterized by social communication deficits and repetitive/restricted behaviors. Several studies showed that inflammation may contribute to ASD. Here we used RT-qPCR, RNA sequencing, immunohistochemistry, and flow cytometry to show that pro-inflammatory molecules were increased in the cerebellum and periphery of mice lackingCntnap2(Cntnap2-/-), a robust model of ASD. In parallel, oxidative stress was present in the cerebellum of mutant animals. Systemic treatment with N-acetyl-cysteine (NAC) rescued cerebellar oxidative stress and inflammation as well as motor and social impairments inCntnap2-/-mice. This was accompanied by improved function of microglia cells in NAC-treated mutant animals. Intriguingly, social deficits, cerebellar inflammation and microglia dysfunction were induced by NAC inCntnap2+/+animals. Our findings therefore suggest that the interplay between oxidative stress and inflammation may support ASD-related behaviors in mice.

overall_design:
The experiment is based on cerebellar tissue extracted from CNTNAP2 ko mice sacrificed at different ages;
Samples (S) go from 1 to 39 that constituted height groups composed of 5 paired-end samples or biological replicates (except one group with four (4) samples), each sample have been sequenced on two lanes (L001 and L002):
1. S1-S5 WT-AD-F samples
2. S6-S10 WT-AD-M samples
3. S11-S15 KO-AD-F samples
4. S16-S19 KO-AD-M samples (this is the only group with 4 samples)
5. S20-S24 WT-P30-M samples
6. S25-S29 WT-P30-F samples
7. S30-S34 KO-P30-M samples
8. S35-S39 KO-P30-F samples

first: Luca

last: Pangrazzi

first: Enrica

last: Cerilli

first: Luigi

last: Balasco

first: Chrow

last: Khurshid

first: Caterina

last: Tobia

first: Ginevra

last: Dall’O’

first: Gabriele

last: Chelini

first: Samuel

last: Perini

first: Michele

last: Filosi

last: Barbieri

first: Teresa

last: Ravizza

first: Annamaria

last: Vezzani

first: Giovanni

last: Provenzano

last: Pastore

first: Birgit

last: Weinberger

first: Josep

last: Rubert

first: Enrico

last: Domenici

first: Yuri

last: Bozzi


title: Spatiotemporal hepatocyte heterogeneity impacts in vivo gene engineering [snRNA-Seq]

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

summary: The liver is a central organ for metabolism and hepatocytes are the main cell type responsible for most of its functions. Several previous studies investigated the cell types involved in tissue homeostasis and regeneration, however, the mechanisms underlying post-natal liver growth and establishment of the mature hepatocyte phenotypes remain to be fully understood. Here we investigate liver tissue dynamics in mice during growth and adulthood, by spatial transcriptomics, clonal analysis, and lineage tracing. We observe the progressive establishment of metabolic zonation of hepatocytes following weaning, with the specification of the centrilobular identity only in adults. We report that only a fraction of hepatocytes proliferate in the newborn liver, generating most of the adult tissue, and that preferential gene editing of the more proliferating hepatocytes allows expansion of the genetically engineered liver area. We also describe age-dependent differences in the efficiency and distribution of lentiviral in vivo gene delivery, with higher efficiency of gene transfer in young compared to adult animals and a skewed localization within the liver lobule. We identify high proteasome activity in the peri-central lobular area as the major determinant of the observed outcome and successfully revert it by proteasomal inhibition before vector administration. Overall, our findings provide new insights into the spatiotemporal dynamics of hepatocytes during post-natal growth, which extend our understanding of liver biology and have important implications for therapeutic applications.

overall_design: Single-nuclei RNA sequencing (snRNA-Seq) on 3 livers of WT newborn mice equally pooled into a single samples to be processed.

first: Francesco

last: Starinieri

first: Michela

last: Milani

first: Ivan

last: Merelli

first: Alessio

last: Cantore


title: MATRIN3 deficiency leads to cGAS-STING activation

city: Bethesda

first: Markus

last: Hafner

state: Maryland

address: 50 South Drive

institute: NIAMS/NIH

summary: To determine the direct targets of MATR3 in human HAP1 cells, we performed PAR-CLIP.

overall_design: PAR-CLIP was performed with MATR3 antibody. Upon getting the binding sites we intersected with RNAseq data.


title: Machine learning unveils an immune-related DNA methylation profile in germline DNA from breast cancer patients

city: Singapore

first: Ann

last: Lee

address: 30 Hospital Boulevard

department: Division of Cellular and Molecular Research

country: Singapore

institute: National Cancer Centre Singapore

type: Methylation profiling by genome tiling array

summary: To identify a set of methylation biomarkers capable of reliably distinguishing breast cancer patients from healthy controls, we performed DNA methylation profiling on germline DNA from peripheral blood samples for a predominantly Asian population comprising 256 ethnic Chinese breast cancer patients recruited from genetic testing clinics and 268 age- and ethnicity-matched non-cancer controls.

overall_design: We performed DNA methylation profiling for 256 ethnic Chinese cancer patients recruited from genetic testing clinics and 268 age- and ethnicity-matched non-cancer controls, using the Illumina Infinium MethylationEPIC array.

first: Ning

middle: Y

first: Melissa

last: Hum

first: Guek

middle: P

last: Tan

first: Ai

last: Seah

first: Pei-Yi

last: Ong

first: Patricia

last: Kin

first: Chia

last: Lim

first: Jens

last: Samol

first: Ngiap

first: Hai-Yang

last: Law

first: Min-Han

first: Soo-Chin

first: Peter

last: Ang

middle: S


title: Therapeutic targeting ERRγ suppresses metastasis via extracellular matrix remodeling in small cell lung cancer (ChIP-Seq)

city: Guangzhou

first: Hong

last: Wang

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-sen University

summary: Small-cell lung cancer (SCLC) is the most aggressive and lethal type of lung cancer, characterized by limited treatment options, early and frequent metastasis. However, the determinants of metastasis in SCLC are poorly defined. Here, we show that estrogen-related receptor gamma (ERRγ) is overexpressed in metastatic SCLC tumors, and it is positively associated with SCLC progression. ERRγ functions as an essential activator of ECM remodeling and cell adhesion, two critical steps in metastasis, by directly regulating the expression of major genes involved in these processes. Genetic and pharmacological inhibition of ERRγ markedly reduces collagen production, cell-matrix adhesion, microfilaments production, and eventually blocks SCLC cell invasion and tumor metastasis. Notably, ERRγ antagonists significantly suppress tumor growth and metastasis and restore resistant SCLC vulnerability to chemotherapy in multiple cell-derived and patient-derived xenograft models. Taken together, these findings establish ERRγ as an attractive target for metastatic SCLC and provide a potential pharmacological strategy for treating this lethal disease.

overall_design: ChIP-Seq

first: Huizi

last: Sun

first: Jie

last: Huang

first: Zhenhua

last: Zhang


title: Concurrent loss of LKB1 and KEAP1 enhances SHMT-mediated antioxidant defense in KRAS-mutant lung cancer

city: CHICAGO

first: Constantinos

last: chronis

state: IL

address: 900 S Ashland Ave, Mbrb 2370

department: Biochemistry and Molecular Genetics

institute: UIC

summary: Investigate how loss of Lkb1 in the context of KRAS mutation alters metablism in cancer and contributes in cancer aggressiveness

overall_design: Parental and reconstituted H460 cells lines were grown and propagated in RPMI-10%FBS media, followed by ATAC-seq profiling.

last: Chronis

first: Hyunmin

first: Ken

last: Joves

first: Ji

last: Kim


title: The effect of TRAF6 loss on the gene expression profiles in leukemia cells

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Modeling the Blood-Brain Barrier Formation and Cerebral Cavernous Malformations in human PSCs- and primary tissue-derived organoids

city: San Diego

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Dr, La Jolla

department: Shu Chien-Gene Lay Department of Bioengineering

institute: UC San Diego

summary: The human blood-brain barrier (hBBB) is a highly specialized structure that regulates passage across blood and CNS compartments. Despite its critical physiological role, there are no reliable in vitro models that can mimic hBBB development and function. Here, we constructed hBBB assembloids from brain and blood vessel organoids derived from human pluripotent stem cells. We validated the acquisition of BBB-specific molecular, cellular, transcriptomic, and functional characteristics and uncovered an extensive neuro-vascular crosstalk with a spatial pattern within hBBB assembloids. When we used patient-derived hBBB assembloids to model cerebral cavernous malformations (CCMs), we found that these assembloids recapitulated the cavernoma anatomy and BBB breakdown observed in patients. Upon comparison of phenotypes and transcriptome between patient-derived hBBB assembloids and primary human cavernomas tissues, we uncovered CCM-related molecular and cellular alterations. Taken together, we report hBBB assembloids that mimic core properties of the human BBB and identify a potentially underlying cause of CCMs.

overall_design: BBB assembloids was prepared by combining a H9 ESCs derived cerebral organoids, where the astrocytic differentiation is promotated by adding LIF with 15%FBS, with a blood vessel organoid from H9 ESCs indurced mesoderm. Both organoids were developed separately and embedded in a matrigel droplet.  We then repurposed the used Illumina Nextseq 2000 sequencing flow cells to a spatial barcoded matrix for RNA hybirdizations. By appling the HIFI-Slide protocol on the assembloid fresh frozen sections for RNA capture and library preparations, we sequencing the extracted library to confirm the cell type and gene expression co-localizations of the BBB assembloids.

first: Lan

last: Dao

first: Zhen

last: You

first: Lu

last: Lu

first: Tianyang

last: Xu

first: Avijite

last: Sarkar

first: Hui

last: Zhu

first: Miao

last: Liu

first: Riccardo

last: Calandrelli

first: George

last: Yoshida

first: Pei

last: Lin

first: Yifei

last: Miao

first: Sarah

last: Mierke

first: Srijan

last: Kalva

first: Mingxia

last: Gu

first: Sudhakar

last: Vadivelu

first: L

middle: F

first: Ziyuan

last: Guo


title: Therapeutic targeting ERRγ suppresses metastasis via extracellular matrix remodeling in small cell lung cancer (RNA-Seq)

first: Hong

last: Wang

overall_design: RNA-Seq

first: Huizi

last: Sun

first: Jie

last: Huang

first: Zhenhua

last: Zhang


title: Atosiban harness hepatocellular carcinoma progression in human organoid model

city: xinxing

first: huijie

last: yang

address: Hongqi District, Xinxiang City

institute: Xinxiang Medical University

summary: To investigate the  function of  Oxytocin Receptor in human organoid modle.

overall_design: First, three different of human organoid samples were constructed, and then each group of samples was treated with Vehicle and 10 μM Atosiban.


title: A transcriptomic approach for the evaluation of  risk biomarkers in adolescents with a history of a traumatic childhood

city: Rome

first: Luisa

last: Lo Iacono

address: via del fosso di Fiorano 64

department: behavioral neuroscience

institute: Fondazione Santa Lucia IRCCS

summary: The experience of childhood maltreatment (CM) is highly associated with the occurrence of psychiatric disorders. The impact of CM on neurodevelopmental trajectories is not fully elucidated. Here, we aim to investigate, the impact of different types of CM on the transcriptome expressed by peripheral blood mononuclear cells in adolescence. Adolescents who experienced different types of CM or normal environment were exposed to a comprehensive screening aimed to evaluate psychological and behavioural parameters. Among them, we selected four subpopulations, that experienced respectively Abuse (A), Neglect (N), Abuse and neglect (AN), normal childhood (C). To identify biological markers of their respective experience, mRNA-Seq analysis was performed in PBMC extracted from their blood sampling.

overall_design: We recruited 37 young adults individuals that experienced different type of adversities during childhood and distributed them in 4 groups based on the quality of their infancy::1.  Abuse (physical or emotional, n=9 rep), 2. Neglect (Physical or emotional, n=8 rep), 3. Abuse and Neglect (n=10 rep), 4. Control (n=10 rep). Peripheral blood mononuclear cells (PBMC) were isolated from their blood samples and comparative gene expression profiling analysis was performed using data obtained  from mRNA Seq analysis.

first: Valeria

last: Carola

first: Silvia

last: Bussone

first: Chiara

last: Pesca


title: IL-18-secreting multi-antigen targeting CAR T-cells eliminate antigen-low myeloma in an immunocompetent mouse model [in vitro]

city: New York

first: Brandon

last: Ng

state: New York

address: 417 E 68th Street, Z1419

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: Multiple myeloma is a plasma cell malignancy that is currently incurable with conventional therapies. Following the success of CD19-targeted chimeric antigen receptor (CAR) T-cells in leukemia and lymphoma, CAR T-cells targeting B-cell maturation antigen (BCMA) more recently demonstrated impressive activity in relapsed and refractory myeloma patients. However, BCMA-directed therapy can fail due to low expression of BCMA on myeloma cells, suggesting that novel approaches to better address antigen-low disease may improve patient outcomes. We hypothesized that engineered secretion of the pro-inflammatory cytokine interleukin-18 (IL-18) and multi-antigen targeting could improve CAR T-cell activity against BCMA-low myeloma. In a syngeneic murine model of myeloma, CAR T-cells targeting the myeloma-associated antigens BCMA and B-cell activating factor (BAFF-R) failed to eliminate myeloma when these antigens were weakly expressed. In contrast, IL-18-secreting CAR T-cells targeting these antigens promoted myeloma clearance. IL-18-secreting CAR T-cells developed an effector-like T-cell phenotype, promoted interferon-gamma production, reprogrammed the myeloma bone marrow microenvironment through type I and II interferon signaling, and utilized macrophages to mediate anti-myeloma activity. Simultaneous targeting of weakly expressed BCMA and BAFF-R with dual-CAR T-cells enhanced T-cell:target cell avidity, increased overall CAR signal strength, and stimulated anti-myeloma activity. Dual-antigen targeting augmented CAR T-cell secretion of engineered IL-18 and facilitated elimination of larger myeloma burdens in vivo. Our results demonstrate that combination of engineered IL-18 secretion and multi-antigen targeting can eliminate myeloma with weak antigen expression through distinct mechanisms.

overall_design: scRNA of APRIL CAR T cells +/- engineered IL-18 secretion following stimulation with MOPC315.BM.

middle: D

first: Adhithi

last: Rajagopalan

first: Anastasia

middle: I

last: Kousa

first: Jacob

last: Fischman

first: Sophia

last: Chen

first: Alyssa

last: Massa

first: Dylan

last: Manuele

first: Harold

last: Elias

first: Michael

last: Galiano

first: Andri

middle: L

last: Lemarquis

first: Alexander

last: Boardman

first: Susan

last: DeWolf

first: Jonah

last: Pierce

first: Bjarne

last: Bogen

first: Scott

last: James

first: Marcel

last: van den Brink


title: Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia [Cut&Run]

city: Memphis

last: Walsh

address: 262 Danny Thomas

institute: St Jude Children's Research Hospital

summary: MGA (Max-gene associated) is a dual-specificity transcription factor that negatively regulates MYC-target genes to inhibit proliferation and promote differentiation. Loss-of-function mutations in MGA have been commonly identified in several hematological neoplasms, including acute myeloid leukemia (AML) with RUNX1::RUNX1T1, however, very little is known about the impact of these MGA alterations on normal hematopoiesis or disease progression. We show that representative MGA mutations identified in patient samples abolish protein-protein interactions and transcriptional activity. Using a series of human and mouse model systems, including a newly developed conditional knock-out mouse strain, we demonstrate that loss of MGA results in upregulation of MYC and E2F targets, cell cycle genes, mTOR signaling, and oxidative phosphorylation in normal hematopoietic cells, leading to enhanced proliferation. The loss of MGA induces an open chromatin state at promotors of genes involved in cell cycle and proliferation. RUNX1::RUNX1T1 expression in Mga-deficient murine hematopoietic cells leads to a more aggressive AML with a significantly shortened latency. These data show that MGA regulates multiple pro-proliferative pathways in hematopoietic cells and cooperates with the RUNX1::RUNX1T1 fusion oncoprotein to enhance leukemogenesis.

overall_design: Cut&Run genomic occupancy analysis of human (Molm13) or mouse (HSCs) with deletions of MGA

first: Melvin

last: Thomas III

first: Jeffery

last: Klco


title: The effect of TRAF6 loss on the gene expression profiles in leukemia cells I

first: Kwangmin

last: Choi

summary: Although altered TRAF6 expression is observed in human acute myeloid leukemia (AML), its role in the AML pathogenesis remains elusive. In this study, we showed that the loss of TRAF6 in AML cells significantly impairs leukemic function in vitro and in vivo, indicating its functional importance in AML subsets. Loss of TRAF6 induces metabolic alterations, such as changes in glycolysis as well as impaired mitochondrial membrane potential and respiratory capacity. The restoration of growth capacity and metabolic activity in leukemic cells with TRAF6 loss, achieved through either forced expression of OGT or pharmacological inhibition of O-GlcNAcase (OGA) that removes O-GlcNAc, indicates the significant role of O-GlcNAc modification in the TRAF6-related cellular and metabolic dynamics. Our findings highlight the oncogenic function of TRAF6 in leukemia and illuminate the novel TRAF6/OGT/O-GlcNAc axis as a potential regulator of metabolic reprogramming in leukemogenesis.

overall_design: To examine the role of TRAF6 in AML cells, we established HEL and MV4;11 cells transduced with the inducible shTRAF6.

first: Shinichiro

last: Matsui

first: Daniel

last: Starczynowski

first: Emiko

last: Sakaida

first: Tomoya

last: Muto


title: The effect of TRAF6 loss on the gene expression profiles in leukemia cells II

overall_design: To examine the role of TRAF6 in AML cells, we established TF-1, MOLM14 and THP-1 cells transduced with the inducible shTRAF6. In addition, Traf6fl/fl mice were crossed with R26-CreERT2 mice for inducible deletion. Traf6+/+;R26-CreERT2 and Traf6fl/fl;R26-CreERT2 lineage negative bone marrow cells from C57Bl/6 mice were transduced with retrovirus encoding MLL-AF9.


title: Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia [RNA-seq]

overall_design: RNA-seq analysis of human (Molm13) or mouse (HSCs) with deletions of MGA


title: The pluripotency factor NANOG contributes to mesenchymal plasticity and is predictive for outcome in esophageal adenocarcinoma

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: Despite the advent of neoadjuvant chemoradiotherapy (CRT), overall survival rates of esophagealadenocarcinoma(EAC) remain low. A readily induced mesenchymal transition of EAC cells contributes to resistance to CRT. In this study, we aimed to chart the heterogeneity in cell state transition after CRT and to identify its underpinnings. RNA-sequencing was performed on 100 pre-treatment biopsies. After RNA-sequencing, Ridge regression analysis was applied to correlate gene expression to ranked plasticity, and models were developed to predict mesenchymal transitions in patients. Plasticity score predictions of the three highest significant predictive models were projected on the pre-treatment biopsies and related to clinical outcome data. A motif enrichment analysis of the genes associated with all three models revealed NANOG as the key associated transcription factor. In accordance, expression of NANOG in pre-treatment biopsies was highly associated with poor response to neoadjuvant chemoradiation, the occurrence of recurrences, and median overall survival difference in EAC patients (>48 months).

overall_design:
A panel of 12 esophageal cultures were treated with chemoradiotherapy and ranked by their relative epithelial-mesenchymal plasticity. RNA-sequencing was performed on 100 pre-treatment biopsies. After RNA-sequencing, Ridge regression analysis was applied to correlate gene expression to ranked plasticity, and models were developed to predict mesenchymal transitions in patients. Plasticity score predictions of the three highest significant predictive models were projected on the pre-treatment biopsies and related to clinical outcome data. Motif enrichment analysis of the genes associated with all three models was performed. Eligible patients for this study were ≥ 18 years with pathologically confirmed esophageal cancer, both EAC and ESCC, or gastroesophageal junction, cardia and lower gastric adenocarcinomas (GAC). Treatment naïve esophageal tumor biopsy samples were collected in the Amsterdam University Medical Centers (AUMC) and used here.

***************************************************************
Submitter states that missing raw files are due to patient privacy concerns.
***************************************************************
Patient samples are named amc-*.

Raw files are provided for the cell_line samples.

first: Amber

last: van der Zalm

first: Mark

last: Dings

first: Maarten

last: Bijlsma


title: Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia

first: Michael

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

overall_design: Refer to individual Series


title: Increase in ER-mitochondria contacts and mitochondrial fusion are hallmarks of mitochondrial activation during embryogenesis

city: Vienna

first: Anastasia

last: Chugunova

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Mitochondrial energy production is essential for development, yet the mechanisms underlying the continuous increase in mitochondrial activity during embryogenesis remain elusive. Using zebrafish as a model system for vertebrate development, we identify two sequentially acting mechanisms that could contribute to the rise in mitochondrial activity: an increased association between mitochondria and the endoplasmic reticulum (ER) at early stages, followed by the fusion of mitochondria leading to their elongated morphology at later embryonic stages. By comprehensively profiling mitochondrial activity, abundance, morphology, metabolome, proteome and phospho-proteome as well as respiratory chain enzymatic activity, we find that the increase in mitochondrial activity during embryogenesis does not require mitochondrial biogenesis, is not limited by metabolic substrates at early stages, and occurs under steady levels of respiratory chain complexes and enzymatic activities. Instead, our analyses pinpoint a previously unexplored increase in mitochondrial-ER association during early stages in combination with changes in mitochondrial morphology at later stages as possible contributors to the rise in mitochondrial activity during embryogenesis. Overall, our systematic profiling of the molecular and morphological changes to mitochondria during embryogenesis provides a valuable resource for further studying mitochondrial function during embryogenesis.

overall_design: To investigate whether oligomycin-treated embryos, we performed RNA-seq experiment to detect ZGA genes. As a control we used untreated and  actinomycin-injected embryos to block zygotic transcription.

first: Roksolana

last: Kobylinska


title: Effect of 25(OH)D on the small RNA expression of breast cancer cell MDA-MB-453

city: 南京市

first: xinyu

last: wan

state: 江苏省

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

institute: Nanjing medical university

summary: Vitamin D is a pro-hormone that possesses various anticancer effects through diverse mechanisms. The enzyme vitamin D-25-hydroxylase can convert vitamin D into 25-hydroxyvitamin D (25(OH)D) in the liver. 25(OH)D serves as the precursor of 1,25-dihydroxyvitamin D (1,25(OH)2D or calcitriol), which can be transformed into 1,25(OH)2D by the enzyme CYP27B1. CYP27B1 is primarily distributed in the kidneys but can also be found in other tissues, such as the breast and colon. Although 1,25-dihydroxyvitamin D has been the primary object of in vitro studies, emerging evidence suggests that 25(OH)D can also generate anticancer effects by transforming into 1,25(OH)2D in the manner of autocrine and paracrine. Our study aims to investigate the impact of 25(OH)D on breast cancer and its effect on the expression of small RNA in breast cancer cells cultured with 100nM 25(OH)D.

overall_design: To explore the influence of 25(OH)D on breast cancer, we cultured MDA-MB-453 in the physiological concentration of 25(OH)D or its solvent for five days. The groups that MDA-MB-453 cultured with 100nM 25(OH)D or its solvent are named Con or VD3. Each group was duplicated three times.

first: Xinyu

last: Wan

first: Wenjie

last: Shi

first: Lingjun

last: Ma

first: Lexin

last: Wang

first: Xiaoming

last: Zha

first: Jue

first: Lu

last: Xu


title: Effects of knockdowns in SERF related proteins on gene expression

city: Ann Arbor

first: James

middle: CA

last: Bardwell

state: Michigan

address: The University of Michigan Biological Sciences Building 1105 N University Ave

department: MCDB

institute: Univeristy of Michigan

summary: SERF family proteins were originally discovered by their ability to accelerate amyloid formation. Human Znf706 and SERF2 proteins are poorly characterized and their physiological function are enigmatic. To get some ideas as to the roles these well conserved proteins play, we analyzed the changes in gene expression that occur upon the knockdown of the encoded genes.

overall_design: To understand the effect of human Znf706 and Serf2 on gene expression, we used siRNA to transiently knockdown Znf706 or Serf2 in HeLa and HEK293T cells and performed differential gene expression analysis using data obtained from poly(A) RNA.

first: Xiexiong

last: Deng

first: Harry

middle: J

last: Yang

first: Bikash

middle: R

last: Sahoo


title: Effect of tRF-1-Ser on the gene expression of breast cancer cell MDA-MB-453

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

summary: tRNA-derived small RNAs (tsRNA) are a new type of noncoding RNAs that can be mainly classified into two groups: tRFs (tRNA-derived fragments) and tiRNAs (tRNA halves). The abnormal expression of tsRNAs is known to play an important role in the biological progression of breast cancer. However, it's still unclear about the mechanism of tsRNAs in cancer. tRF-1-Ser is a tRF that is high expression in breast cancer and negatively regulated by 25(OH)D. Our study aims to find out the effect of tRF-1-Ser on breast cancer and explore the change of RNA in tRF-1-Ser knock-down breast cancer cells.

overall_design: To explore the influence of tRF-1-Ser on breast cancer, we transfected MDA-MB-453 with shtRF-1-Ser by lentivirus and verified the efficiency of knock-down by qPCR. The groups that MDA-MB-453 transfected with shtRF-1-Ser or shNC are named lv_shtRF or lv_con. Each group was duplicated three times.


title: Functional Characterization of Cooperating MGA Mutations in RUNX1::RUNX1T1 Acute Myeloid Leukemia [ATAC-seq]

last: Walsh

overall_design: ATAC-seq chromatin accessibility analysis of human (Molm13) or mouse (HSCs) with deletions of MGA

first: Melvin

middle: E

last: Thomas III

first: Jeffery

last: Klco


title: Ribosome profiling of Rbfox1 fl/fl-Cre and control cortical culture

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

summary: The goal of this experiment is to analyze differences in translation of mRNA transcripts in absence vs presence of Rbfox1 using ribosome profiling of Rbfox1-cKO and control mature primary neuronal cultures

overall_design: E15 cortical cultres from a Rbfox1 fl/fl pregnant mouse were plated in 10cm plates, cells were infected with AAV-hSyn-Cre-eGFP or AAV-hSyn-eGFP at DIV3, harvested cells at DIV14. Two technical replicates per sample type

first: Reem

last: Halabi

first: Chia-Ho

first: Julia

last: Nikolic

first: Douglas

last: Black


title: Effect of 25(OH)D on the gene expression of breast cancer cell MDA-MB-453

first: xinyu

last: wan

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

summary: Vitamin D as a pro-hormone is known to generate anticancer effects by various mechanisms. Vitamin D can be converted to 25-hydroxyvitamin D(25(OH)D) by the enzyme vitamin D-25-hydroxylase in the liver.25(OH)D is the precursor of 1,25‑dihydroxyvitamin D(1,25(OH)2D, also called calcitriol) and can be transformed by the enzyme CYP27B1. The distribution of CYP27B1 is mainly in the kidney, but also in other tissues like breast and colon. So far, research about the anticancer effects of Vitamin D mainly chooses 1,25‑dihydroxyvitamin D as the study object in vitro. However, there is increasing evidence showing that 25(OH)D also can generate anticancer effects by transforming into 1,25(OH)2D in the manner of autocrine and paracrine. Our study aims to explore the influence of 25(OH)D on breast cancer and provides the variation on the expression of RNA in the breast cancer cells cultured with 100nM 25(OH)D.

overall_design: To explore the influence of 25(OH)D on breast cancer, we cultured MDA-MB-453 in the physiological concentration of 25(OH)D or its solvent for five days. The groups that MDA-MB-453 cultured in 100nM 25(OH)D or its solvent are named as experiment group(EG) or control group(CG). Each group was duplicated three times.

first: Xinyu

last: Wan

first: Wenjie


title: Transcriptomic characterization of circulating neutrophils isolated from patients with metabolic dysfunction-associated steatohepatitis (MASH), formerly known as nonalcoholic steatohepatitis (NASH).

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

address: 1450 Biggy Street, NRT 3514

institute: USC

summary: Neutrophils, a major innate immune cell population, are the most abundant circulating white blood cell in humans. They play a crucial role in host defense against infection; however, aberrant neutrophil activation may induce tissue damage via sterile inflammation. Neutrophil accumulation has been identified as a feature of the inflammatory response observed MASH and has been associated with liver fibrosis and cirrhosis. In the present study, we used RNA-Seq analysis of purified neutrophils to characterize their dysregulation in MASH.

overall_design: Using negative selection, we isolated peripheral neutrophils from subjects with biopsy proven mild and sever MASH and control individuals. Total RNA was extracted, DNase treated, and differential gene expression was assessed using next generation RNA sequencing (RNA-Seq) techniques.

first: A

first: M

last: Salomon

first: L

last: Golden-Mason


title: Periodic Heat Waves-induced neuronal etiology in the elderly is mediated by Gut-Liver-Brain axis: A Transcriptome Profiling Approach

city: Irvine

first: Saurabh

last: Chatterjee

address: 5270 California Avenue

department: Department of Environmental and Occupational Health

institute: University of California, Irvine

summary: Heat stress exposure in intermittent heat waves and subsequent exposure during war theaters is a clinical challenge that can lead to multi-organ dysfunction and long-term complications in the elderly. Using an aged mouse model and high-throughput sequencing, this study investigated the molecular dynamics of the liver-brain connection during heat stress exposure. Distinctive gene expression patterns induced by periodic heat stress emerged in both brain and liver tissues. An altered transciptome showed heat stress-induced altered acute phase response pathways, causing neural, hepatic, and systemic inflammation, and impaired synaptic plasticity. Results also showed that proinflammatory molecules S100B, IL-17, IL-33 and neurological disease signaling pathways were upregulated, while protective pathways like aryl hydrocarbon receptor signaling were downregulated. In parallel, Rantes, IRF7, NOD1/2, TREM1, and hepatic injury signaling pathways were upregulated.

overall_design: To study the underlying pathological changes in exposure to heat stress, an aging mouse model was used. Aged C57BL6/J (24 months old) mice were exposed to heat stress at 40± 0.5°C with a relative humidity of 60% ± 5% for three hours/day for 15 days mimicking a periodic heat wave exposure. The total number of animals in each group (n=3) was determined based on statistical power calculations to ensure adequate statistical analysis. The mice were randomly allocated to their respective cages following a randomization procedure. At 24 months and 16 days of age, all mice were euthanized, and serum and liver tissues were collected for further analysis.

first: Subhajit

last: Roy

first: Punnag

last: Saha

first: Dipro

last: Bose

first: Ayushi

last: Trivedi

first: Madhura

last: More

first: Christina

first: Jenny

last: Wu

first: Melanie

last: Oakes


title: Impact of Maternal Immune Activation and Sex on Placental and Fetal Brain Cytokine and Gene Expression Profiles in a Preclinical Model of Neurodevelopmental Disorders

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

institute: University of British Columbia

summary: Maternal inflammation during gestation is associated with a later diagnosis of neurodevelopmental disorders including autism spectrum disorder (ASD). However, the specific impact of maternal immune activation (MIA) on placental and fetal brain development remains insufficiently understood. This study aimed to investigate the effects of MIA by analyzing placental and brain tissues obtained from the offspring of pregnant dams exposed to polyinosinic:polycytidylic acid (Poly I:C) on embryonic day 12.5. Cytokine and mRNA content in the placenta and brain tissues were assessed using multiplex cytokine assays and bulk-RNA sequencing on embryonic day 17.5. Bulk-RNA sequencing was performed on placenta and brain tissues on embryonic day 17.5.

overall_design: C57BL/6 mice were purchased from Taconic Biosciences. 8–10 week-old female C576B/L mice were paired with males. Insemination was confirmed by the presence of a vaginal plug the following morning, marking the gestational time as embryonic day (ED) 0.5. On embryonic day 12.5, pregnant dams were intraperitoneally administered 20mg/kg γ-irradiated Poly I:C (Sigma) to stimulate maternal immune activation. Control groups were administered saline. On ED17.5, fetal brains and placenta were collected and flash frozen and stored at -80 until cytokine and RNA analysis. To control for litter effect, 2 pups from each litter (1 male and 1 female) were used.

first: Paul

last: Ashwood


title: SIVA mutation, a candidate metastasis gene identified from clonally related bilateral breast cancers, promotes breast cancer cell aggressiveness in vitro and in vivo

city: Portland

first: Shiuh-Wen

last: Luoh

state: OR

address: 3181 SW Sam Jackson Park Rd

department: MMG

institute: Oregon Health & Science University

summary: Our purpose is to identify candidate genes involved in the early steps of breast cancer metastasis and examine their pro-invasive functions both in vitro and in vivo. A percentage of bilateral breast cancers were clonally related based on copy number variation profiling. Whole exome sequencing and comparative sequence analysis revealed that a limited number of somatic mutations were acquired in this “breast to breast” metastasis. These mutations might promote breast cancer distant spread. The pro-invasive functions of a candidate metastasis gene were assessed in vitro by its abilities to promote proliferation, migration and invasion and in vivo as tumor xenografts in immunocompromised mice or a syngeneic orthotopic mouse breast cancer model. RNAseq analysis was performed to probe the transcription programs modulated by this candidate metastasis gene. SIVA1-D160N was one somatic mutation acquired in the breast to breast metastasis. Over-expression of SIVA1-D160N promoted migration and invasion of human MB-MDA-231 breast cancer cells in vitro, consistent with a dominant negative interfering function. When introduced via tail vein injection, 231 cells over-expressing SIVA1-D160N displayed enhanced distant spread on IVIS imaging. Over-expression of SIVA1-D160N promoted anchorage independent growth of mouse 4T1 breast cancer cells in vitro. When introduced orthotopically via mammary fat pad injection in syngeneic Balb/c mice, over-expression of SIVA1-D160N in 4T1 cells increased mammary gland tumor growth as well as liver metastasis. We conclude clonally related bilateral breast cancers represent a novel system to investigate metastasis and revealed a role of SIVA1-D160N in breast cancer metastasis.

overall_design: Differential gene expression analysis and pathway enrichment analysis of OVCAR8, SKOV3, HCC1954, and MDA-MB-231 parental cell lines as compared to their SIVA1-WT or SIVA1-D160N transformed counterparts.

first: Anke

last: Vermehren-Schmaedick

last: Spellman

first: Rosalie

last: Sears

first: Xiaoyan

last: Wang

first: Elizabeth

last: Ramsey

first: Kami

last: Chiotti

first: Wendy

last: Wagoner

first: Myron

last: Peto


title: Transcriptome of blood leukocytes in response to conceptus proteins in dairy cattle [PBLs]

city: University Park

first: Troy

last: Ott

state: PA

address: 107 AVBS Building

department: Animal Science

institute: Penn State University

summary: This study reproduced in vivo aspects of the temporal  signaling of interferon tau (IFNT) and pregnancy associated glycoproteins (PAG) during bovine early pregnancy. The objective of this study was to analyze the short and long-term effects of IFNT, and the effect of PAG on the transcriptome of blood leukocytes.

overall_design: Holstein heifers (N = 6/treatment) were estrous synchronized and received intrauterine infusions of one of the following treatments: 200 μg/mL bovine serum albumin (BSA; vehicle) from day 14 to 16 of the estrous cycle (BSA), vehicle + 10 μg/mL of IFNT from day 14 to 16 (IFNT3), vehicle + 10 μg/mL of IFNT from day 14 to 19 (IFNT6), and vehicle + 10 μg/mL of IFNT from day 14 to 16 followed by vehicle + 10 μg/mL of IFNT + 5 μg/mL of PAG from day 17 to 19 (IFNT+PAG). RNA was extracted from peripheral blood leukocytes (PBLs, N = 4/treatment) and transcriptomic data were obtained through BGI (Shenzhen, China) services.

first: Maria

last: da Silva

first: Joy

last: Pate


title: Transcriptome of endometrium and blood leukocytes in response to conceptus proteins in dairy cattle


title: Transcriptome of endometrium in response to conceptus proteins in dairy cattle [ENDO]

summary: This study reproduced in vivo aspects of the temporal  signaling of interferon tau (IFNT) and pregnancy associated glycoproteins (PAG) during bovine early pregnancy. The objective of this study was to analyze the short and long-term effects of IFNT, and the effect of PAG on the transcriptome of endometrium.

overall_design: Holstein heifers (N = 6/treatment) were estrous synchronized and received intrauterine infusions of one of the following treatments: 200 μg/mL bovine serum albumin (BSA; vehicle) from day 14 to 16 of the estrous cycle (BSA), vehicle + 10 μg/mL of IFNT from day 14 to 16 (IFNT3), vehicle + 10 μg/mL of IFNT from day 14 to 19 (IFNT6), and vehicle + 10 μg/mL of IFNT from day 14 to 16 followed by vehicle + 10 μg/mL of IFNT + 5 μg/mL of PAG from day 17 to 19 (IFNT+PAG). RNA was extracted from endometrium (N = 4/treatment) and transcriptomic data were obtained through BGI (Shenzhen, China) services.


title: BALF single-cell landscape in CARDS and non-ARDS patients at two time points

city: Beijing

first: Longxiang

last: Su

state: Beijing

address: 1 Shuaifu Yuan

department: Department of Critical Care Medicine

institute: Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science

summary: In this study, single-cell sequencing of the BALF of CARDS patients yielded the following results: (1) IL1B+ neutrophils were significantly increased in the BALF of CARDS patients with exacerbated disease, which was associated with poor prognosis of CARDS patients, and this type of neutrophils underwent fatty acid metabolism reprogramming in comparison with other types of neutrophils, which may be related to their high-inflammatory response. (2) IL1B+ neutrophils promoted TNF secretion from hyperinflammatory type M1 macrophages through a caspase-dependent pathway, suggesting that neutrophil-macrophage interactions play an important role in the mechanism of CARDS development.

overall_design: A total of 8 patients with severe ARDS, including 4 CARDS patients and 4 non-CARDS patients (2 bacterial pneumonia, 2 fungal pneumonia), were included in this study, of which 2 patients were treated with ECMO, and the rest of the patients received hormone therapy except for 1 patient who did not receive hormone therapy. BALF was retained in each patient at the time point of admission to the ICU (t1) and at the time point of development of an MS change value ≥1 point (t2).

first: Yingying

last: Yang

first: Haochen

last: Li

first: Peng

last: Liu

first: Yun

last: Long


title: IL-18-secreting multi-antigen targeting CAR T-cells eliminate antigen-low myeloma in an immunocompetent mouse model [in vivo]

city: Duarte

first: Anastasia

last: Kousa

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

summary: Multiple myeloma is a plasma cell malignancy that is currently incurable with conventional therapies. Following the success of CD19-targeted chimeric antigen receptor (CAR) T-cells in leukemia and lymphoma, CAR T-cells targeting B-cell maturation antigen (BCMA) more recently demonstrated impressive activity in relapsed and refractory myeloma patients. However, BCMA-directed therapy can fail due to low expression of BCMA on myeloma cells, suggesting that novel approaches to better address antigen-low disease may improve patient outcomes. We hypothesized that engineered secretion of the pro-inflammatory cytokine interleukin-18 (IL-18) and multi-antigen targeting could improve CAR T-cell activity against BCMA-low myeloma. In a syngeneic murine model of myeloma, CAR T-cells targeting the myeloma-associated antigens BCMA and B-cell activating factor (BAFF-R) failed to eliminate myeloma when these antigens were weakly expressed. In contrast, IL-18-secreting CAR T-cells targeting these antigens promoted myeloma clearance. IL-18-secreting CAR T-cells developed an effector-like T-cell phenotype, promoted interferon-gamma production, reprogrammed the myeloma bone marrow microenvironment through type I and II interferon signaling, and utilized macrophages to mediate anti-myeloma activity. Simultaneous targeting of weakly expressed BCMA and BAFF-R with dual-CAR T-cells enhanced T-cell:target cell avidity, increased overall CAR signal strength, and stimulated anti-myeloma activity. Dual-antigen targeting augmented CAR T-cell secretion of engineered IL-18 and facilitated elimination of larger myeloma burdens in vivo. Our results demonstrate that combination of engineered IL-18 secretion and multi-antigen targeting can eliminate myeloma with weak antigen expression through distinct mechanisms.

overall_design: scRNA and CITE-seq analysis of CD45+ mouse bone marrow following treatment with CAR T cells engineered to secrete IL-18

first: Brandon

last: Ng

first: Adhithi

last: Rajagopalan

first: Jacob

last: Fischman

first: Sophia

last: Chen

first: Alyssa

last: Massa

first: Dylan

last: Manuele

first: Harold

middle: K

last: Elias

first: Michael

last: Galiano

first: Andri

last: Lemarquis

first: Alexander

last: Boardman

first: Susan

last: DeWolf

first: Jonah

last: Pierce

first: Bjarne

last: Bogen

first: Scott

last: James

first: Marcel

last: van den Brink


title: Exosomal miRNA differences in Plasma in Adolescent idiopathic scoliosis  patients

city: KunMing

first: Ping

last: Yuan

state: YunNan

address: No.295 Xichang Road, Wuhua District

institute: The First Affiliated Hospital of Kunming Medical University

summary: Plasma exosomal miRNA may differ between adolescent idiopathic scoliosis patients and healthy individuals. Sequencing analysis was used to find these differential miRNAs.

overall_design: Peripheral blood was collected from adolescents with idiopathic scoliosis and healthy individuals.  Plasmawere collected and total RNA was extracted. RNA-seq sequencing was used to compare the genetic differences.

first: Wei-Zhou

last: Wang

first: Zhi-Hua

first: Fei

last: He


title: FOXO-regulated Deaf1 controls muscle regeneration through autophagy

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

summary: We performed RNAi screens to identify regulators of muscle regeneration. We identified Deaf1 and hypothesized that this transcription factor may regulate autophagy and in turn control myogenesis. We therefore performed chromatin-immunoprecipitation followed by next-generation sequencing (ChIP-seq) to identify Deaf1 downstream targets. The results suggest that Deaf1 binds to the promoters the multiple ATG genes, suppressing their transcription.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Deaf1 in C2C12 mouse myoblast cells.

first: Hong-Wen

last: Tang

first: Qian

middle: H

last: Tan

first: Nathan

last: Harmston Nathan