title: The impact of hyperglycemia upon BeWo trophoblast cell metabolic function: A multi-OMICS and functional metabolic analysis

city: London

first: Timothy

middle: RH

last: Regnault

state: Ontario

address: Medical Sciences Building, Room 216

department: Physiology and Pharmacology

country: Canada

institute: Western University

summary: Pre-existing and gestationally-developed diabetes mellitus during pregnancy have been linked to impaired metabolic function in the villous trophoblast layer of the placenta. These metabolic impairments have been thought to mediate an increased risk of early life metabolic disease development in the exposed offspring. Previous research using the BeWo trophoblast cell line has suggested that independently, hyperglycemia is an important modulator of placental metabolic function in diabetic pregnancies. However, the direct impacts of hyperglycemia on specific aspects of placental metabolic function known to be impaired in diabetic pregnancies including nutrient storage and mitochondrial respiration, are largely unknown. The current study, therefore, utilized functional readouts of metabolic enzyme activity and endpoint readouts of nutrient storage in conjunction with multi-omics analysis (transcriptomics and metabolomics) in BeWo trophoblasts cultured under hyperglycemia conditions (25 mM glucose) for 72 hours to further characterize the impacts of elevated glucose levels on placental metabolic function. While metabolic enzyme activities and mitochondrial oxidative respiratory function were not altered following 72 hours of hyperglycemia, increased triglyceride and glycogen nutrient stores were observed in the high-glucose exposed BeWo trophoblasts. We speculated that the increased nutrient stores serve to modulate intracellular glucose levels and may reduce the amount of glucose available for oxidation and subsequently protect trophoblast cells from mitochondrial damage during acute high glucose exposures. Additionally, hyperglycemic-culture conditions in BeWo trophoblasts were associated with an altered transcriptomic profile highlighted by altered mRNA expression of metabolic enzymes as well as with an altered metabolome profile highlighted by an intracellular accumulation of lactate, malonate, and riboflavin. Overall, the results demonstrate that exposure to excess glucose modulates placental metabolism and nutrient storage and highlights that increased glucose abundance is an important independent regulator of placental function in diabetic pregnancies.

overall_design: 10 total BeWo cytotrophoblast control, 5 treated with basal F12K media (7 mM glucose, Low glucose (LG) control, and 5 treated with F12K media supplemented to 25 mM glucose (high glucose (HG) treatment)

last: Easton

first: Xian

last: Luo

first: Liang

last: Li

middle: R


title: Ornithine aminotransferase supports polyamine synthesis in pancreatic cancer

status: Public on Jan 01 2023

city: Boston

first: Nada

middle: Y

last: Kalaany

state: MA

address: 3 Blackfan Circle CLS 16067

country: USA

institute: Boston Children's Hospital

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pancreatic ductal adenocarcinoma (PDA) cells have a distinct dependence on de novo ornithine synthesis from glutamine via ornithine aminotransferase (OAT), which supports polyamine synthesis and is required for tumor growth. This directional OAT activity is normally largely restricted to infancy and contrasts with the reliance of most adult normal tissues and other cancer types on arginase (ARG) to generate arginine-derived ornithine, the substrate for polyamine synthesis. This dependence associates with arginine depletion in PDA tumor microenvironment, and is driven by mutant KRAS, which induces the expression of OAT and polyamine synthesis enzymes, including the rate-limiting enzyme ornithine decarboxylase-1 (ODC1). Loss of OAT, but not ARG2, largely mimics loss of ODC1, altering the transcriptional profiles in PDA cells, which in turn correlate with alterations in open chromatin states.

overall_design: RNA-seq and ATAC-seq analyses of pancreatic ductal adenocarcinoma cells with single knockdown of either ornithine decarboxylase1 (ODC1), ornithine aminotransferase (OAT) or arginase2 (ARG2), using 2 distinct hairpins, as compared to Scrambled (Scr) control. Either three (RNA-seq) or two (ATAC-seq) biological replicates are presented for each hairpin.

first: Min-Sik

last: Lee

first: Courtney

last: Dennis

first: Insia

last: Naqvi

first: Lucas

last: Dailey

first: Alireza

last: Lorzadeh

first: George

last: Ye

first: Tamara

last: Zaytouni

first: Ashley

last: Adler

first: Daniel

middle: S

last: Hitchcock

first: Lin

last: Lin

first: Megan

middle: T

last: Hoffman

first: Aladdin

middle: M

last: Bhuiyan

first: Jaimie

middle: L

last: Barth

first: Miranda

middle: E

last: Machacek

first: Mari

last: Mino-Kenudson

first: Stephanie

middle: K

last: Dougan

first: Unmesh

last: Jadhav

first: Clary

middle: B

last: Clish


title: Post-secretory synthesis of a natural analog of iron-gall ink in the black nectar of Melianthus spp.

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

summary: The black nectar of Melianthus flowers is thought to serve as a visual attractant to pollinators, but the chemical identity and synthesis of the black pigment are unknown. Here we report that the black nectar contains a natural analog of iron-gall ink, which humans have used since medieval times. Specifically, dark black nectar at anthesis contains high levels of ellagic acid and iron; synthetic solutions of ellagic acid and iron(III) recapitulate the black color of the nectar. Conversely, lightly colored nectars before and after anthesis contain significantly lower levels of ellagic acid and iron, but higher levels of gallic acid. We then explored the possibility of post-secretory synthesis of ellagic acid from gallic acid. Indeed, Melianthus nectar contains a peroxidase that oxidizes gallic acid to form ellagic acid. Reactions containing the nectar peroxidase, gallic acid, hydrogen peroxide, and iron can fully recreate the black color of the nectar. Visual modeling indicates that the black color is both visible and conspicuous to birds within the context of the flower. In summary, the black nectar of Melianthus is derived from an ellagic acid-Fe complex analogous to iron-gall ink and is likely involved in the attraction of passerine bird pollinators.

overall_design: Melianthus minor (also known as M. elongatus) plants were grown at the University of California Davis Arboretum and Public Garden at the University of California Davis campus in Davis, California, USA. Plants were grown and maintained outdoors on campus and received yearly maintenance of pruning and the application of fertilizer as needed.   From 26 January 26 2022 to 1 February 2022, leaf, flower, nectary, and nectar samples were collected from the University of California Davis Arboretum and Public Garden. Collections took place each day between 10:00 AM and 5:00 PM. Previous studies have noted the terminal inflorescences of this species are sterile (Linder et al., 2006), but we noted they still produce some nectar. Plant tissue and nectar samples were collected and placed immediately in either a formalin aceto-alcohol (FAA) solution or an RNAlater stabilizing solution (Thermo Fisher Scientific catalog no. AM7020). Collected samples were stored at -80°C no later than February 4, 2022. Fresh leaf samples for fixation were collected and placed in 50 mL conical tubes containing FAA solution. Parafilm tape was used to seal the conical tubes, which were then stored at 4°C. Smaller leaf samples (~4 cm2) were collected in a 1.5 mL microcentrifuge tube containing an RNAlater stabilizing solution and immediately placed on dry ice before being stored at -80°C. Fresh flower samples were taken at various stages of development. Flowers were placed in FAA solution in 50 mL conical tubes. The conical tubes were wrapped in parafilm and stored at 4°C. Fresh inflorescences (Fig. S1) were collected and stored in 250 mL glass bottles with small amounts of sterile water and stored at 4°C until the collection of reflectance data. The collected nectary samples from fresh flowers occurred in the field and were placed in 1.5 mL microcentrifuge tubes with RNAlater stabilizing solution. The nectary samples (Fig. S1) were immediately placed in dry ice until stored at -80°C. The nectary dissections left some surrounding tissue intact, which was removed before further investigations occurred. Pipettes collected nectar in screw-top 1.5 mL microcentrifuge tubes and immediately placed on dry ice before storing at -80°C or were held at 4°C.

first: Clay

middle: J

last: Carter

first: Evin

last: Magner


title: Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice

city: Omaha

first: Holly

last: Feser Stessman

state: NE

address: 2500 California Plaza

department: Pharmacology & Neuroscience

institute: Creighton University

summary: Pathogenic variants in KMT5B, a lysine methyltransferase, are associated with global developmental delay, macrocephaly, autism, and congenital anomalies (OMIM# 617788). Given the novelty of this disorder, it has not been fully characterized. Deep phenotyping of the largest (n=43) patient cohort to date identified that hypotonia and congenital heart defects are novel prominent features. Both missense variants and putative loss-of-function variants resulted in slow growth in patient derived cell lines. KMT5B homozygous knockout mice were smaller in size than their wildtype littermates but did not have significantly smaller brains, suggesting relative macrocephaly, also noted as a prominent clinical feature. RNA-sequencing of patient lymphoblasts and Kmt5b-haploinsufficient mouse brains identified differentially expressed pathways associated with nervous system development and function including axon guidance signaling. Overall, we identified novel pathogenic variants and clinical features in KMT5B-related neurodevelopmental disorder and provide insights into the molecular mechanisms of the disorder using multiple model systems.

overall_design:
Whole brain RNA-seq from E14.5 Kmt5b gene trap mice; 3 brains per genotype (WT, HET, KO) for both males and females.

RNA-seq from patient derived lymphoblast cell lines; 7 KMT5B patients and 7 age- and sex-matched controls.

middle: A

first: Rochelle

middle: N

last: Wickramasekara

first: Sarah

last: Sheppard

first: Laura

last: Bryant

first: Courtney

last: Vaccaro

first: Elizabeth

last: Bhoj


title: Cancer prevention by phenethyl isothiocyanate (PEITC) in transgenic adenocarcinoma of the mouse prostate (TRAMP) mice [methyl-Seq]

city: Piscataway

first: Renyi

last: Wu

state: NJ

address: 160 Frelinghuysen road

department: Pharmacy School

institute: Rutgers University

type: Methylation profiling by high throughput sequencing

summary: The glucosinolate-derived phenethyl isothiocyanate (PEITC) has been widely reported to reduce the risk of prostate cancer by modulating multiple biologically relevant activities. Emerging evidence suggests that PEITC may exert its anti-cancer effects through epigenetic mechanisms including alterations of DNA methylation. The purpose of this study was to examine the effects of PEITC on prostate carcinogenesis in a murine prostate cancer model (TRAMP). 8 weeks old TRAMP males were fed AIN-93M control diet or diet containing 0.05% PEITC for 8 or16 weeks. We observed reduced tumor incidence in PEITC group (0/5) at 24 weeks of age as compared to control diet group (6/7). We also performed Next-generation sequencing (RNA-seq and SureSelect Methyl-seq) with non-tumor and tumor prostate tissue collected from the above-mentioned TRAMP groups and time matching wildtype (not TRAMP) control diet groups at the same time points. Our bioinformatic analyses reveal that several carcinogenesis pathways as well as pathways of inflammation and cell proliferation were activated in TRAMP group as compared to wildtype group. Surprisingly, these pathways were inhibited by PEITC diet administration. We also identified a number of genes with inverse regulation relationship between their RNA expression and their CpG methylation during prostate carcinogenesis and cancer prevention by PEITC in TRAMP mice. Our study demonstrated that PEITC administration can suppress prostate cancer by epigenetic regulation of key genes. [This GEO/dataset is the bisulfite methyl-seq part of the study.]

overall_design: DNA CpG methylation profiles of prostate samples (dorsolateral and ventral) lobes from Wildtype C57BL/6 and TRAMP transgenic mice treated with control AIN93M or PEITC (0.05% w/w) diet.

first: Davit

last: Sargsyan

first: Ran

last: Yin

first: Hsiao-chen

last: Kuo

first: Lujing

last: Wang

first: Shanyi

last: Li

first: Rasika

last: Hudlikar

first: Xia

last: Liu

first: Ah-Ng

last: Kong


title: Monitoring the differential expression of miRNAs, tRNAs and tRFs in lung cancer biopsies.

city: Patras

first: Constantinos

last: Stathopoulos

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

type: Non-coding RNA profiling by high throughput sequencing

summary: Translational rate has been deregulated in many cancers through small non-coding RNAs aberrations. Herein we focus on miRNAs, tRNAs and tRFs paterns in lung cancer biopsies.

overall_design: We performed semiconductor sequencing with modification of the standard protocol to enrich the tRNAs and tRFs and analyze the data measuring their abundance.

first: Ilias

last: Skeparnias

first: Dimitrios

last: Anastasakis

first: Katerina

last: Grafanaki

first: Panagiotis

last: Alexopoulos

last: Dougenis

first: Andreas

last: Scorilas

first: Christos

last: Kontos


title: TRAP-seq of spinal cord motor neurons from ALS diseased mice versus healthy mice

city: Hamburg

first: Kent

middle: Edward

last: Duncan

address: Falkenried 94

department: Center for Molecular Neurobiology

country: Germany

institute: University Medical Center, Hamburg-Eppendorf

summary: Amyotrophic lateral sclerosis (ALS) is an incurable neurological disease featuring progressive loss of motor neuron (MN) function in the brain and spinal cord. Mutations in TARDBP, encoding the RNA-binding protein TDP-43, are one cause of ALS and TDP-43 mislocalization in MNs is a key pathological feature of >95% of ALS cases. While numerous studies support altered RNA regulation by TDP-43 as a major cause of disease, specific changes within MNs that trigger disease onset remain unclear. Here, we combined Translating Ribosome Affinity Purification (TRAP) with RNA sequencing to identify molecular changes in spinal MNs of TDP-43–driven ALS at motor symptom onset. By comparing the MN translatome of hTDP-43A315T mice to littermate controls and to mice expressing wildtype hTDP-43, we identify hundreds of mRNAs that were selectively up- or downregulated in MNs. We validated effects on Tex26, Syngr4, and Plekhb1 mRNAs in an independent TRAP experiment. Moreover, by quantitative immunostaining of spinal cord MNs we found corresponding protein level changes for SYNGR4 and PLEKHB1. We also observed these changes in spinal MNs of an independent ALS mouse model caused by a different patient mutant allele of TDP-43, suggesting that they may be a general feature of TDP-43-driven ALS. Thus, we have identified two new proteins deregulated in MNs at motor symptom onset in TDP-43-driven ALS models. This spatial and temporal pattern suggests that deregulation of these proteins could be functionally important for driving the transition to the symptomatic phase of disease.

overall_design: mRNA of Chat+ spinal cord motor neurons derived from mice with TDP43^A315T mutation and control mice (wildtype and TDP43^WT) was enriched by translating ribosome affinity purification (TRAP) and sequenced by RNA-seq.

first: Jan

last: Engler

first: Rita

last: Marques


title: Cancer prevention by phenethyl isothiocyanate (PEITC) in transgenic adenocarcinoma of the mouse prostate (TRAMP) mice [RNA-Seq]

first: Renyi

last: Wu

summary: The glucosinolate-derived phenethyl isothiocyanate (PEITC) has been widely reported to reduce the risk of prostate cancer by modulating multiple biologically relevant activities. Emerging evidence suggests that PEITC may exert its anti-cancer effects through epigenetic mechanisms including alterations of DNA methylation. The purpose of this study was to examine the effects of PEITC on prostate carcinogenesis in a murine prostate cancer model (TRAMP). 8 weeks old TRAMP males were fed AIN-93M control diet or diet containing 0.05% PEITC for 8 or16 weeks. We observed reduced tumor incidence in PEITC group (0/5) at 24 weeks of age as compared to control diet group (6/7). We also performed Next-generation sequencing (RNA-seq and SureSelect Methyl-seq) with non-tumor and tumor prostate tissue collected from the above-mentioned TRAMP groups and time matching wildtype (not TRAMP) control diet groups at the same time points. Our bioinformatic analyses reveal that several carcinogenesis pathways as well as pathways of inflammation and cell proliferation were activated in TRAMP group as compared to wildtype group. Surprisingly, these pathways were inhibited by PEITC diet administration. We also identified a number of genes with inverse regulation relationship between their RNA expression and their CpG methylation during prostate carcinogenesis and cancer prevention by PEITC in TRAMP mice. Our study demonstrated that PEITC administration can suppress prostate cancer by epigenetic regulation of key genes. [This GEO/dataset is the RNA-seq part of the study.]

overall_design: mRNA profiles of prostate samples (dorsolateral and ventral) lobes from Wildtype C57BL/6 and TRAMP transgenic mice treated with control AIN93M or PEITC (0.05% w/w) diet.

first: Davit

last: Sargsyan

first: Ran

last: Yin

last: Kuo


title: Cancer prevention by phenethyl isothiocyanate (PEITC) in transgenic adenocarcinoma of the mouse prostate (TRAMP) mice

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

overall_design: Refer to individual Series


title: CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation [RNA-seq]

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

summary: Hematopoietic stem and progenitor cell (HSPC) formation and lineage differentiation involve gene expression programs orchestrated by transcription factors and epigenetic regulators. Knockdown of the chromatin remodeler chromodomain-helicase-DNA-binding protein 7 (CHD7) expanded phenotypic HSPCs, erythroid, and myeloid lineages in zebrafish and mouse embryos. CHD7 acts to suppress hematopoietic differentiation in a cell autonomous manner in the embryo and adult. CHD7 chromatin immunoprecipitation in human CD34+ and mouse HSPCs revealed enrichment of binding motifs for hematopoietic transcription factors including Runx1 and GATA factors, and decreased Runx1 occupancy correlated with loss of CHD7 occupancy. CHD7 physically interacts with Runx1 and suppresses Runx1-induced expansion of HSPCs during development, providing both physical and genetic evidence for the Runx1-CHD7 interaction. CHD7 modulates Runx1 activity to provide proper timing and function of HSPCs as they emerge during hematopoietic development or mature in adults, representing a distinct and evolutionarily conserved control mechanism to ensure accurate hematopoietic lineage differentiation.

overall_design: Effects of CHD7 knockout on erythroid differentiation of G1ER cells.

first: Avik

last: Choudhouri

first: Michael

last: Superdock

first: Song

last: Yang


title: Expression analysis of Chd7 in mouse hematopoietic stem and progenitor cells [microarray]

summary:
Hematopoietic stem and progenitor cell (HSPC) formation and lineage differentiation involve gene expression programs orchestrated by transcription factors and epigenetic regulators. Knockdown of the chromatin remodeler chromodomain-helicase-DNA-binding protein 7 (CHD7) expanded phenotypic HSPCs, erythroid, and myeloid lineages in zebrafish and mouse embryos. CHD7 acts to suppress hematopoietic differentiation in a cell autonomous manner in the embryo and adult. We performed gene expression analysis to determine the expression of chd7 in adult sorted HSPC populations. Loss of Chd7 in long term hematopoietic stem cells (LT-HSCs) results in upregulation of genes that function in hematopoietic system development and function. Genes representative of each blood lineage including erythroid, myeloid, and lymphoid were upregulated, suggesting that Chd7 deficiency results in LT-HSCs that are more primed for multilineage differentiation. Together with the physical and genetic interaction, the data support a model in which CHD7 interacts with and modulates Runx1 activity to provide proper timing and function of HSPCs as they emerge during hematopoietic development or mature in adults. This represents a distinct and evolutionarily conserved control mechanism to ensure accurate hematopoietic lineage differentiation.
We used microarrays to detail the expression of Chd7 in adult sorted HSPC populations.

overall_design: To determine the expression of Chd7 in adult mouse HSPCs, long-term and short-term hematopoietic stem cells and multi-potent progenitor populations were sorted for microarray analysis.

first: Yi

last: Zhou


title: CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation [ATAC-seq]

overall_design: Effects of CHD7 knockout on chromatin accessibility in G1ER cells.


title: Signature analyses for circulating extracellular vesicle in chronic kidney disease

status: Public on Dec 31 2022

city: Bunkyo

first: Shintaro

last: Mandai

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University, Graduate School of Medical and Dental Sciences

summary: Chronic kidney disease (CKD) accelerates vascular calcification (VC) via phenotypic switching of vascular smooth muscle cells (VSMCs). We investigated the roles of circulating small extracellular vesicles (sEVs) between the kidneys and VSMCs and uncovered relevant sEV-propagated microRNAs (miRNAs) and their biological signaling pathways. We established CKD models in rats and mice by adenine-induced tubulointerstitial fibrosis. The miRNA transcriptome of sEVs revealed a depletion of several miRNAs in CKD. Their expression levels in sEVs from CKD patients were correlated to kidney function. This study revealed the transcriptomic landscape of miRNAs propagated in sEVs in CKD. We investigated the therapeutic potential of miRNAs in VC.

overall_design: Eight samples derived from small extracellular vesicles of control (n = 4) and CKD model rats (n = 4).


title: TRIM21 aggravates cardiac injury after myocardial infarction via promoting M1 macrophage polarization

city: Shanghai

first: Zhiqiang

last: Li

state: Shanghai

address: 301 Middle Yanchang Road

department: Department of Cardiology

country: China

institute: Shanghai Tenth People's Hospital

summary: Macrophage polarization followed by acute myocardial infarction (MI) is essential for the regulation of inflammation and scar formation. Tripartite motif-containing protein 21 (TRIM21), a member of E3 ubiquitin ligases, is a crucial mediator in the process of inflammation and heart failure. However, the potential roles of TRIM21 in modulating post-MI inflammation and macrophage polarization remain elusive. We detected that the levels of TRIM21 were significantly reduced in macrophages of WT mice after MI. In contrast, MI was ameliorated in TRIM21 knockout (TRIM21-/-) mice with improved cardiac remodeling, characterized by a marked decrease in mortality, increased wall thickness, and improved cardiac function in comparison with wild-type (WT) MI mice. Importantly, TRIM21 deficiency decreased the post-MI apoptosis and DNA damage in the hearts of mice, and the accumulation of M1 phenotype macrophages in infarcted hearts significantly decreased in TRIM21-/- mice compared with WT controls. Mechanistically, depletion of TRIM21 orchestrated the process of M1 macrophage polarization via a PI3K/Akt signaling pathway. Overall, these data reveal that TRIM21 drives the inflammatory response and cardiac remodeling after MI via stimulating M1 macrophage polarization through a PI3K/Akt signaling pathway.

overall_design: Six BMDM samples were analyzed comprises of LPS stimulated control (n = 3), and LPS stimulated TRIM21 knockout (n = 3)

first: Xiangdong

last: Liu

first: Xingxu

last: Zhang

first: Wenming

first: Mengmeng

last: Gong

first: Xiaoming

last: Qin

first: Jiachen

last: Luo

first: Yuan

last: Fang

first: Baoxin

first: Yidong

last: Wei


title: Volatile organic compounds from the mycoparasite Pythium oligandrum contribute to microbial antagonism and have wide-ranging adverse effects on host survival

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

summary: The oomycete P. oligandrum is a soil-inhabiting parasite and predator of both fungi and oomycetes and uses hydrolytic enzymes extensively to penetrate and hydrolyze its host or prey. Other mechanisms have been overlooked, and we investigated whether P. oligandrum-produced volatile organic compounds (VOCs) could also be contributing to antagonism. VOCs have diverse functions, including contributing to antagonism in ecological interactions and potential applications in biocontrol. The growth-inhibiting activity of P. oligandrum VOCs was tested on P. myriotylum – a host or prey of P. oligandrum – coupled with electron microscopy, biochemical assays and transcriptomic analysis. The total VOCs produced by P. oligandrum reduced P. myriotylum growth by 80% and zoospore levels by 60%. GC-MS identified twenty-three VOCs, and methyl heptenone, D-limonene, 2-undecanone and 1-octanal were potent inhibitors of P. myriotylum growth and led to increased production of reactive oxygen species at a concentration that did not inhibit P. oligandrum growth. Exposure to the total VOCs of P. oligandrum led to shrinkage of P. myriotylum hyphae, and lysis of the cellular membranes and organelles. Transcriptomic analysis of P. myriotylum exposed to the P. oligandrum VOCs at increasing levels of growth inhibition showed initially a strong upregulation of putative detoxification related genes that was not maintained later during exposure to the VOCs. The inhibition of P. myriotylum growth continued after the exposure to the VOCs was discontinued and led to reduced leaf lesion size during P. myriotylum infection of its plant host. The VOCs produced by P. oligandrum could be another factor alongside hydrolytic enzymes contributing to its ecological role as a microbial antagonist where the concentration of the VOCs may be inhibitory in particular ecological niches such as in soil. The VOCs analyzed here may also be contributing to the biocontrol of diseases using P. oligandrum commercial preparations.

overall_design: Compare gene expression profiles of Pythium myriotylum with and without exposure to volatile compounds produced by Pythium oligandrum at three time-points with triplicate biological replicate samples.

first: Taha

last: Sheikh

first: Dongmei

last: Wang

first: Siqiao

last: Chen

first: Sheng

last: Deng

first: Lihui


title: Brain injury accelerates the onset of a reversible age-related microglial phenotype associated with hyperphagocytosis and inflammatory neurodegeneration

city: Baltimore

first: Rodney

middle: Matthew

last: Ritzel

state: MD

address: 655 W. Baltimore Street

department: Anesthesiology

institute: University of Maryland School of Medicine

summary: Lipofuscin is an autofluorescent (AF) pigment formed by lipids and misfolded proteins that accumulates in post-mitotic cells with advanced age.  Here we immunophenotyped microglia in the brain of old C57BL/6 mice (>18 months-old) and demonstrate that in comparison to young mice, one third of old microglia are AF, characterized by profound changes in lipid and iron content, phagocytic activity, and oxidative stress.  Pharmacological depletion of microglia in old mice eliminated the AF microglia following repopulation and reversed microglial dysfunction.  Age-related neurological deficits and neurodegeneration after traumatic brain injury (TBI) were attenuated in old mice lacking AF microglia.  Furthermore, hyperphagocytic activity and lipid accumulation in microglia persisted for up to one year after TBI, was modified by Apoe4 genotype, and chronically driven by phagocyte-mediated oxidative stress.  Thus, AF may reflect a pathological state in aging microglia associated with hyperphagocytosis and inflammatory neurodegeneration that can be further accelerated by TBI.

overall_design: RNA-seq data of FACS-sorted microglia in young, old, and PLX-treated mice.

first: Yun

last: Jiao

first: Zhuofan

last: Lei

first: Sarah

last: Doran

first: Junyun

last: He

first: Rami

last: Shahror

first: Rebecca

last: Henry

first: Shaolin

first: Bogdan

last: Stoica

first: Alan

middle: I

last: Faden

first: Gregory

last: Szeto

first: David

last: Loane

first: Junfang

last: Wu


title: Whole-organism C. elegans L2 GRH-1 ChIP-seq (experiment 2 of 2)

city: Basel

first: Helge

last: Grosshans

state: Basel-Stadt

address: Maulbeerstrasse 66

department: Multicellular Systems

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: We performed ChIP-seq to determine chromatin regions binding Transcription Factor GRH-1, and thereby potential binding motifs and sites, in C. elegans (larval stage 2) whole organisms.

overall_design: One sample was used as "input", ie non-specific pulldown. 1 new GRH-1-specific pulldown sample was generated. Samples were collected at two time points to broadly cover the L2 stage, before pooling. Additionally, two samples (1 input and 1 pulldown, 500mM salt) from experiment 1 were re-extracted, prepared and sequenced.

first: Chiara

last: Azzi

first: Kathrin

last: Braun

first: A

last: Smith

first: Dimosthenis

last: Gaidatzis

first: Milou

middle: W

last: Meeuse


title: Whole-organism C. elegans L2 GRH-1 ChIP-seq

institute: Friedriche Miescher Institute for Biomedical Research (FMI)


title: Whole-organism C. elegans L2 GRH-1 ChIP-seq (experiment 1 of 2)

summary: We performed ChIP-seq to determine chromatin regions binding Transcription Factor GRH-1, and thereby potential binding motifs and sites thereof, in C. elegans (larval stage 2) whole organisms.

overall_design: One sample was used as "input", ie non-specific pulldown. 3 GRH-1-specific samples were generated, using 3 different salt concentrations for protocol optimisation and potential replication. Samples were collected at two time points to broadly cover the L2 stage, before pooling.


title: RNA-seq Analysis of  Mier1 Effects in HFD Aging and Adipose Tissue Lipe  Knockout Mice after 70% Partial Hepatectomy

first: Yanhao

last: Chen

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: To explore how Mier1 affiects high-fat diet-fed, aging and adipose tissue Lipe knockout mice liver regeneration, we specifically knocked out  liver Mier1 in high-fat diet-fed, aging and adipose tissue Lipe knockout mice through adeno-associated virus (AAV). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals. To assess the role of MIER1 in liver regeneration, we performed 70% partial hepatectomy on high-fat diet-fed, aging and adipose tissue Lipe knockout mice. We then performed RNA sequencing analysis on liver tissues collected from control and Mier1 ko groups at 0 h, 48h or 36 h after partial hepatectomy. RNA-seq analysis showed that after partial hepatectomy, MIER1 loss caused significant upregulation of genes enriched in cell proliferation relevant pathways.

overall_design: For liver regeneration analysis in chronic high-fat diet-fed mice, 6-week-old Cas9 knockin mice were fed with normal chow diet or HFD for 8 weeks to induce hepatic steatosis. After 5 weeks on HFD, AAV8 vectors were administered by tail vein injection to deplete MIER1 in hepatocytes. For liver regeneration analysis in aging mice, about one-year-old Cas9 knockin mice were administered with AAV8 vectors expression Cre recombinase and Mier1 sgRNA to deplete MIER1 in liver cells. Lipe loxp/loxp mice were generated by a homologous recombination and classic embryonic stem cell targeting strategy. Loxp sequences were inserted flanking the second exon. Adipose tissue-specific Lipe knockout mice were generated by crossing Lipe loxp/loxp mice with Adiponectin-Cre mice. Lipe loxp/loxp mice were then bred with Lipe loxp/loxp mice: Cre/+ animals to generate Lipe loxp/loxp mice (used as control) and Lipeloxp/loxp: Cre/+ mice (Lipe-AKO) as adipose-specific knockout animals. To further deplete MIER1 in the Lipe-AKO animals, Cas9 knockin mice were bred with the Lipe-AKO mice to generate the Lipe-AKO; Cas9 animals, which were then subjected to MIER1 depletion via treatment with AAV-delivered Mier1 sgRNA. Animals were subjected to PHx surgery for liver regeneration analysis at around 8-11 weeks’ old. Each RNA-seq sample contained pooled RNA from three biological replicas that were mixed with an equal mass of RNA. Two samples from each group were included for sequencing.

first: Qiurong

last: Ding

first: Lanlan

first: Yuchen

last: Wang


title: A complex role of Arabidopsis CDKD;3 in meiotic progression and cytokinesis

city: Brno

first: Neha

last: Shukla

address: Kamenice 753

department: Plant Molecular Biology

country: Czech Republic

institute: CEITEC

summary: Meiosis is a specialized cell division that halves the number of chromosomes in two consecutive rounds of chromosome segregation. In angiosperm plants is meiosis followed by mitotic divisions to form rudimentary haploid gametophytes. In Arabidopsis, termination of meiosis and transition to gametophytic development is governed by TDM1 and SMG7 that mediate inhibition of translation. Mutants deficient in this mechanism do not form tetrads, but instead undergo multiple cycles of aberrant nuclear divisions, that are likely caused by the failure to downregulate cyclin dependent kinases during meiotic exit. A suppressor screen to identify genes that contribute to meiotic exit uncovered a mutation in CDKD;3 that alleviates meiotic defects in smg7 deficient plants. The CDKD;3 deficiency prevents aberrant meiotic divisions observed in smg7 mutants, or delays their onset after initiation of cytokinesis, which permits formation of functional microspores. Although CDKD;3 acts as an activator of CDKA;1, the main cyclin dependent kinase that regulates meiosis, cdkd;3 mutation appears to promote meiotic exit independently of CDKA;1. Furthermore, analysis of CDKD;3 interactome revealed enrichment for proteins implicated in cytokinesis suggesting a more complex function of CDKD;3 in cell cycle regulation.

overall_design: RNASeq profiles from leaves of 3-week old plants: wild type (WT; Col-0) and mutants (smg7-6, cdkd3-1 and cdkd3-1/smg7-6)

first: Sorin

last: Tanasa

first: Albert

last: Cairo

first: Ranjani

last: Ganji

first: Pavlina

last: Mikulkova

first: Sona

last: Valuchova

first: Vivek

last: Raxwal

first: Claudio

last: Capitao

first: Arp

last: Schnittger

first: Zbyněk

last: Zdráhal

first: Karel

last: Riha


title: MIF promotes cell invasion by LRP1-uPAR interaction in pancreatic cancer cells

city: Tianjin

first: Jing

last: Mo

state: Tianjin

address: 22 Qixiangtai Road, Heping District

department: Pathology

institute: Tianjin medical university

summary:
To investigate the role of MIF in the regulation of malignant phenotype of pancreatic cancer , MIF gene has been knocked down by shRNA in PANC-1 cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of shMIF (MIF knockdown) and shNTC (non-targeting control) cells at normoxia and hypoxia.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for shMIF-PANC-1 cells and its control shNTC-PANC-1 cells.

first: Huizhi

last: Sun


title: Reduced sphingolipid biosynthesis modulates proteostasis networks to enhance longevity

city: Lexington

first: Robert

middle: C

last: Dickson

state: KY

address: 741 South Limestone St.

department: Molecular & Cellular Biochemistry

institute: University of Kentucky College of Medicine

summary: Treating Saccharomyces cerevisiae cells with myriocin reduces the intracellular free pool of most amino acids.  We find that transcriptional changes within the first 6 hours of drug treatment seem to have little impact on free pool changes. Rather the changes are driven early by post-translational events including impaired amino acid transporter activity, due to a reduced rate of sphingolipid biosynthesis, and an increased rate of endocytosis of at least some amino acid transporters, particularly the major methionine transporter Mup1.

overall_design: Budding yeast mRNA-enriched profiles from 42 individual samples of prototrophic BY4741 cells, including 3 replicates of 7 time points and 2 treatments (control and drug-treated). Additionally 2 different mixes of ERRC spike-in RNA controls were added to the samples; one mix for the control samples, and one mix for the drug-treated samples.

first: Dickson

last: Robert

first: Blalock

last: Eric

first: Hepowit

last: Nathaniel

first: MacGurn

last: Jason

first: Sangderk

last: Lee


title: TIGIT blockade elicits potent anti-tumor immunity in naturally occurring hepatitis B virus-related hepatocellular carcinoma in mice

city: Hefei

first: Yuwei

last: Wu

address: Huangshan Road #443

institute: the university of science and technology of China

summary:
Background and Aims: Chronic hepatitis B virus (HBV) infection is the leading cause of hepatocellular carcinoma (HCC) and is a serious health problem in China, East Asia, and North African countries. Effective treatment of HBV-related HCC is currently unavailable. This study evaluated the therapeutic potential of TIGIT blockade in HBV-related HCC.
Approach and Results: A mouse model of spontaneous HBV-related HCC was generated by replacing wild-type hepatocytes with HBsAg+ hepatocytes (namely HBs-HepR mice). The tumors in HBs-HepR mice were inflammation-associated HCC, similar to HBV-related HCC in patients, which was distinguished from other HCC mouse models, such as diethylnitrosamine (DEN)-induced HCC, Tak1-knockout-induced HCC, HCC in stelic animal model (STAM), or nonalcoholic steatohepatitis (NASH)-induced HCC. HCC in HBs-HepR mice was characterized by an increased number of CD8+T cells whereas the production of IL-2, TNF-α, and IFN-γ by intrahepatic CD8+T cells was decreased. Increased expression of TIGIT on CD8+T cells was responsible for functional exhaustion. The therapeutic effect of TIGIT blockade was investigated at the early and middle stages of HCC progression in HBs-HepR mice. TIGIT blockade reinvigorated intrahepatic CD8+T cells with increased TNF-α and IFN-γ production and an increased number of CD8+T cells in tumors, thereby slowing the development of HCC in HBs-HepR mice. Blocking PD-L1 did not show direct therapeutic effects or synergize with TIGIT blockade.
Conclusions: Blockade of TIGIT alone enhanced the anti-tumor activity of CD8+T cells during the progression of HBV-related HCC in a spontaneous HCC mouse model.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different mouse model at 3 time points.
Comparative gene expression profiling analysis of RNA-seq data for hepatology or liver tissue in B6-HepR mice and HBs-HepR mice.

first: Xiaolei

last: Hao

first: Yongyan

last: Chen

first: Zhigang

last: Tian


title: GAD antibody-associated epilepsy: T cells kill neurons, plasma cells and antibodies are bystanders

city: Linz

first: Anna

middle: Regina

last: Tröscher

address: Krankenhausstraße 5

department: Center for Medical Research

country: Austria

institute: Johannes Kepler University Linz

summary: We compared temporal lobe tissue from patients with GAD65 antibody associated temporal lobe epilepsy to control tissue transcriptomically and histopathologically and evaluated clincal data

overall_design: 9 GAD antibody-associated epilepsy (5 early = short disease duration, 4 late = long disease duration), 7 control epilepsy control cases (epilepsy resective surgery without immune-mediated causes)

middle: R

first: Katharina

last: Mair

first: Laia

middle: V

last: De Juan

first: Ulrike

last: Köck

first: Anja

last: Steinmaurer

first: Hartmut

last: Baier

first: Albert

last: Becker

first: Ingmar

last: Blümcke

first: Martin

last: Finzel

first: Christian

last: Geis

first: Romana

last: Höftberger

last: Mawrin

first: Tim

last: von Oertzen

first: Julika

last: Pitsch

first: Rainer

last: Surges

first: Berthold

last: Voges

first: Serge

last: Weis

first: Michael

last: Winklehner

first: Friedrich

last: Woermann

first: Jan

last: Bauer

middle: G

last: Bien


title: Next Generation Sequencing Facilitates Quantitative Analysis of Zebrafish Osteoporosis Model Transcriptomes

city: SHANGHAI

first: Peng

last: Jin

state: SHANGHAI

address: No.197 RUIJIN ER RD

institute: SHANGH RUIJIN HOSPITAL

summary: The development of predictive markers to determine the tipping point prior to the onset of osteoporosis is essential to mitigate further irrevocable deterioration. In order to determine the early warning signs before osteoporosis, we used the dynamic network biomarker (DNB) approach to analyze the time series gene expression data in the zebrafish osteoporosis model and revealed that cyclin-dependent kinase inhibitor 1A (cdkn1a) is one core member of DNB. We demonstrated that cdkn1a negatively regulates osteogenesis, evidenced by the loss-of-function and gain-of-function studies. On one hand, CRISPR/Cas9-mediated cdkn1a knockout in the zebrafish significantly altered skeletal development and increased bone mineralization. On the other hand, inducible cdkn1a expression significantly contributed to the osteoclast differentiation. We also provide mechanistic clues that cdkn1a participates in osteoclast differentiation by regulating its upstream signaling cascades. Our data provided new insights into the dynamic nature of osteoporosis, and identified cdkn1a as the early-warning signals of osteoporosis onset.

overall_design: Zebrafish samples treated with DEX for 3, 4, 5, 6 and 7 dpf (N=3) as well as those from the WT and cdkn1a Cas9/sgRNA crispants (N=5) were collected to perform RNA-seq.

first: Guo

last: Weiming

first: Jin

last: Peng


title: RAINBOW-seq to capture the spatial transcriptome of bacterial biofilm

first: Tianmin

last: Wang

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: We developed a spatially resolved method to profile the spatial transcriptome of biofilm. In detail, we used fluorescent dyes to label the different regions of biofilm cultured in a microfluidic chip. After staining, the bacterial cells in biofilm were sorted into relevant bins according to their spatial information marked by the fluorescent pattern. Finally, miniBac-seq (RNA-seq) method was applied to capture the transcriptome of each bin.

overall_design: We profiled the spatial transcriptome of five E. coli k12 BW25113 biofilms (b1~b5) as biological replicates. We sorted each sample into 3-7 bins, giving rise to totally 24 spatial transcriptome. Then we used the same strain   to profile the temporal transcriptomes of the planktonic culture as a reference for comparison (two replicates, planktonic_r1/2).

first: Ping

last: Shen


title: Transcriptome profiling reveals potential key genes involved in metabolic resistance to malathion in Southern house mosquito, Culex quinquefasciatus

city: College Station

first: Xinyue

last: Huang

state: TX

address: 300 Spruce street, Apt 303

department: Entomology

institute: Texas A&M University

summary: To compare different differential expression profile between malathion resistant and susceptible Cx. quinquefasciatus in Harris County and to identify candidate genes involved in matabolic detoxification of malathion

overall_design: We compared different gene expression patterns in both comparisons between malathion resistant (MR) versus malathion susceptible (MS) group, and between field collected Cx. quinquefasciatus that were not exposed to malathion (WI) versus a laboratory-maintained susceptible Sebring strain (CO)


title: Comparative transcriptome and metabolme analysis reveals the molecular insights of multiple stress tolerance in Citrus aurantifolia overexpressing a novel trypsin inhibitor from  Putranjiva roxburghii

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

summary: Being a sessile organism, plants are constantly confronted by various biotic (pest and pathogen) and abiotic (drought, salinity, flood, extreme temperatures, etc.) stresses. In response to these environmental stresses, plants have developed numerous defense mechanisms. One of the basal defense responses in plants are mediated by trypsin inhibitors (TIs). Putranjiva roxburghii trypsin inhibitor (PRTI), a potent trypsin inhibitor from P. roxburghii showing sequence similarity with a group of genes known to have defense and storage function such as wound inducible (WIN) proteins, vegetative storage proteins (VSPs), and Bark storage protein (BSPs) was overexpressed in Citrus aurantifolia. PRTI overexpressing lines were tolerant to various abiotic stresses (salinity, drought, and alkalinity) and two pests namely, Scirtothrips citri and Papilio demoleus. The molecular insights underlying the heterologous overexpression of PRTI at the transcriptomic level reveals the upregulation of stress responsive genes and involvement of hormonal signal transduction and transporters. Further, genes related to DNA repair, amino acid synthesis, and development were also found to be upregulated. Our study also reveals the nuclear-cytoplasmic localization and alteration phytohormone profile by PRTI overexpression in transgenic lines as compared to wild-type which clearly indicates the role of abscisic acid ABA in stress tolerance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Citrus aurantifolia wild type and transgenic overexpressing a novel trypsin inhibitor from  Putranjiva roxburghii.

first: Sweta

last: Singh

first: Chanderkant

last: Chaudhary


title: Comparison of the effects upon gene expression of i.v. injection of plasma exosomes isolated from mice fed with differemt diets

city: Barcelona

first: Carlos

last: Castaño

address: Rossello 153

country: Spain

institute: CIBER

summary:
We isolated plasma exosomes from mice fed for 6 weeks with either standard chow,  a high-fat diet or standard chow with sucrose supplemented drinking water. We injected these exosomes into control mice fed standard chow and sacrificed them 72 h after the injection for tissue analysis
We used microarrays to detail the global changes of gene expression induced by the injected exosomes in liver, adipose and muscle tissues

overall_design: C57BL6/J male mice were injected with exosomes isolated from plasma of mice maintained for 6 weeks with standard chow and tap drinking water (iCT), fed with 45% high-fat diet and tap drinking water (iHFD), or fed with standard chow and drinking water supplemented with 50% sucrose (iSAC)

first: Marcelina

last: Parrizas


title: CellMap: Characterizing the types and composition of iPSC-derived cells from RNA-seq data

city: Cambridge

first: Baohong

last: Zhang

address: 225 Binney St

institute: Biogen Inc.

summary: Induced pluripotent stem cell (iPSC) derived cell types are increasingly employed as in vitro model systems for drug discovery. For these studies to be meaningful, it is important to understand the reproducibility of the iPSC-derived cultures and their similarity to equivalent endogenous cell types. Single-cell and single-nucleus RNA sequencing (RNA-seq) are useful to gain such understanding, but they are expensive and time consuming, while bulk RNA-seq data can be generated quicker and at lower cost. In silico cell type decomposition is an efficient, inexpensive, and convenient alternative that can leverage bulk RNA-seq to derive more fine-grained information about these cultures. We developed CellMap, a computational tool that derives cell type profiles from publicly available single-cell and single-nucleus datasets to infer cell types in bulk RNA-seq data from iPSC-derived cell lines.

overall_design: Different iPSC derived cell types were generated to access the accuracy of proposed deconvolution method

first: Zhengyu

last: Ouyang

first: Nathanael

last: Bourgeois

first: Eugenia

last: Lyashenko

first: Paige

last: Cundiff

first: Patrick

middle: F

last: Cullen

first: Ravi

last: Challa

first: Kejie

last: Li

first: Xinmin

first: Fergal

last: Casey

first: Sandi

last: Engle

first: Maria

last: Zavodszky


title: ORE-seq: genome-wide absolute occupancy measurement by restriction enzyme accessibilities

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: Digestion with restriction enzymes is a classical approach for probing DNA accessibility in chromatin. It allows to monitor both the cut and the uncut fraction and thereby the determination of accessibility or occupancy (= 1- accessibility) in absolute terms as the percentage of cut or uncut out of the total molecules. The here presented protocol takes this classical approach to the genome-wide level. After exhaustive restriction enzyme digestion of chromatin, DNA is purified, sheared and converted into libraries for high throughput sequencing. Bioinformatic analysis counts DNA fragments cut by the restriction enzyme as well as DNA ends generated by restriction enzyme digest and derives thereof the fraction of accessible DNA. This straight forward principle is technically challenged as preparation and sequencing of the libraries leads to biased scoring of DNA fragments with ends generated by restriction enzymes versus by shearing. Our protocol includes two orthogonal approaches to correct for this bias, the “corrected cut-uncut” and the “cut-all cut” method, so that accurate measurements of absolute accessibility/occupancy at restriction sites throughout a genome are possible. The protocol is presented for the example of S. cerevisiae chromatin but may be adapted for any other species.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: calibration samples for ORE-seq: generated by mixing defined ratios of S. cerevisiae genomic DNA completely cut or uncut with a respective restriction enzyme (either AluI, BamHI or HindIII); for normalization, S. pombe genomic DNA completely digested with EcoRI was spiked into (about 10% of S. cerevisiae DNA mass) the completely cut or uncut S. cerevisiae genomic DNA prior to mixing the defined ratios.

first: Elisa

last: Oberbeckmannn

first: Michael

last: Wolff

first: Nils

last: Krietenstein

first: Andrea

last: Schmid

first: Ulrich

last: Gerland

first: Philipp

last: Korber


title: Genome-wide distribution of chromatin accessibility and transcriptome of Set2-deficient Drosophila photoreceptor neurons

city: West Lafayette

first: Vikki

middle: M

last: Weake

state: Indiana

address: 175 S University St

department: Biochemistry

institute: Purdue University

summary: We report the chromatin accessibility landscape and transcriptome of Drosophila photoreceptor neurons that are Set2-deficient (via siRNA) obtained using a tissue-specific approach from 10-day old flies

overall_design: Photoreceptor neuron-specific chromatin accessibility and transcriptome profiling at day 10 after eclosion. Three biological replicates. Negative control corresponds to flies expressing an siRNA against non-Drosophila gene mCherry

first: Juan

middle: P

last: Jauregui-Lozano


title: CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation [G1ER ChIP-seq]

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: Hematopoietic stem and progenitor cell (HSPC) formation and lineage differentiation involve gene expression programs orchestrated by transcription factors and epigenetic regulators. Knockdown of the chromatin remodeler chromodomain-helicase-DNA-binding protein 7 (CHD7) expanded phenotypic HSPCs, erythroid, and myeloid lineages in zebrafish and mouse embryos. CHD7 acts to suppress hematopoietic differentiation in a cell autonomous manner in the embryo and adult. CHD7 chromatin immunoprecipitation in human CD34+ and mouse HSPCs revealed enrichment of binding motifs for hematopoietic transcription factors including Runx1 and GATA factors, and decreased Runx1 occupancy correlated with loss of CHD7 occupancy. CHD7 physically interacts with Runx1 and suppresses Runx1-induced expansion of HSPCs during development, providing both physical and genetic evidence for the Runx1-CHD7 interaction. CHD7 modulates Runx1 activity to provide proper timing and function of HSPCs as they emerge during hematopoietic development or mature in adults, representing a distinct and evolutionarily conserved control mechanism to ensure accurate hematopoietic lineage differentiation.

overall_design: ChIP sequencing of GATA2, RUNX1 and PolII-phospho-serineII in G1ER cells.

first: Avik

last: Choudhouri

last: Superdock

first: Song

last: Yang


title: Activation of MAP2K signaling by genetic engineering or HF-rTMS promotes corticospinal axon sprouting and functional regeneration

city: White Plains

first: Jian

last: Zhong

state: New York

address: 785 Mamaroneck Ave

institute: Burke Neurological Institute

summary: B-RAF activation in mature corticospinal neurons upregulated a discrete set of transcription factors overlapping with a set induced early in axotomized zebrafish retina ganglion cells which can fully regenerate their axons. Conditional genetic activation of B-RAF promoted robust regeneration and sprouting of corticospinal tract axons after experimental spinal cord injury. Newly sprouting axon collaterals formed synaptic connections, correlating with recovery of skilled motor function. We also found that non-invasive suprathreshold high-frequency repetitive transcranial magnetic stimulation activates the RAF effector MEK and promotes regeneration and sprouting of corticospinal tract axons, dependent on MEK signaling. Our findings demonstrate a central role of neuron-intrinsic RAF–MEK signaling in enhancing the growth capacity of mature corticospinal neurons and propose transcranial magnetic stimulation as a potential therapy for spinal cord injury.

overall_design: Comparison of expression profiles induced in mature fezf2-positive corticospinal neurons by conditional expression of constitutively-active B-RAF (V600E point mutation) or by conditional deletion of PTEN, with littermate controls.

first: Yanjie

last: Zhu

first: Xiaofei

last: Guan

first: Youngjae

last: Ryu

first: Paul

last: Zumbo


title: Comprehensive microRNA-sequencing of small extracellular vesicles derived from HPV-positive head and neck carcinoma cells

city: Cincinnati

first: Scott

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

summary: Exosomes are nano-sized (30-150 nm), membrane encapsulated vesicles that are released by cells into the extracellular space and function as intercellular signaling vectors through the horizontal transfer of biologic molecules, including microRNA (miRNA). Although secreted by both normal and malignant cells, there is evidence that cancer-derived exosomes enable the tumor to manipulate its microenvironment, contributing to the capacity of the tumor for immune evasion, growth, invasion, and metastatic spread. The purpose of this study was to apply miRNA-sequencing to exosomes isolated from conditioned culture media to comprehensively characterize miRNA secreted in exosomes from 4 distinct head and neck squamous cell carcinoma (HNSCC) cell lines and normal oral epithelial cells.

overall_design: Cell culture.

first: Mario

last: Medvedovic


title: An XBP1s-PIM-2 positive feedback loop controls IL-15-mediated survival of natural killer cells

city: duarte

first: Shoubao

last: Ma

state: California

address: 1500 East Duarte Road

institute: City of Hope

summary: We previously reported that XBP1s, an essential transcription factor downstream of IL-15 and AKT signaling, controls cell survival and effector functions of human natural killer (NK) cells. However, the precise mechanisms remain unknown. In this study, by using XBP1 conditional knock-out mice, we found that XBP1s is critical for IL-15-mediated NK cell survival but not proliferation in vitro and in vivo. Mechanistically, XBP1s regulates homeostatic NK cell survival through targeting PIM-2, a critical anti-apoptotic gene, which in turn stabilizes XBP1s protein by phosphorylating it at Thr58. In addition, XBP1s enhances the effector functions and anti-tumor immunity of NK cells by recruiting T-bet to the promoter region of Ifng. Collectively, our findings identify a previously unknown mechanism by which IL-15–XBP1s signaling regulates the survival and effector functions of NK cells.

overall_design: 5 × 10E6 purified mouse primary NK cells from Il15TgXbp1f/f  mice were pretreated with IL-15 (50 ng/ml) for 1 h. chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-Seq) was performed.

first: Jianhua

last: Yu


title: Landscapes of collateral fitness effects of mutations in antibiotic resistance genes

city: Baltimore

first: Marc

last: Ostermeier

address: 3400 N. Charles St.

department: Chemical & Department of Chemical & Biomolecular Engineering

institute: Johns Hopkins University

summary: We performed RNA-seq experiments to compare the gene expression profiles of cells expressing single-codon substitutions in the antibiotic resistance genes NDM-1, CAT-I, or aadB in the absence of antibiotics. Mutations with deleterious fitness effects in the absense of antibiotics also caused significant changes in gene expression in a number of genes related to stress-response pathways including the regulator of colanic acid capsule synthesis (Rcs) response, the phage shock protein response (Psp), and the oxidative stress response. Fold differences in gene expression were mutation- and gene-dependent.

overall_design: E. coli cells containing single-codon substitutions in either the NDM-1, CAT-I, or aadB antibiotic resistance genes were grown in monoculture growth assays. Controls consisted of cells with the wildtype allele that were not induced with IPTG as well as cells harboring a Δ antibiotic resistance gene deletion that were induced with IPTG. Growth was halted at about 330 minutes to ensure the cells were still in exponential growth phase based on OD measurements. Total RNA was extracted from pelleted cell cultures. mRNA was enriched and used to synthesize double-stranded cDNA. The double-stranded cDNA was end prepped and purified. Illumina adaptor sequences were ligated to the double stranded cDNA and PCR enriched before being purified and pooled for Illumina Tru-Seq (2 x 75 bp reads).

first: Jacob

last: Mehlhoff


title: Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy [mouse]

city: San Francisco

first: Amy

last: Fan

state: CA

address: 769 25th Ave

institute: UCSF

summary: Therapeutic cancer vaccination seeks to elicit activation of tumor-reactive T cells capable of recognizing tumor-associated antigens (TAAs) and eradicating malignant cells. Here, we present a cancer vaccination approach utilizing myeloid lineage reprogramming to directly convert cancer cells into tumor reprogrammed-APCs (TR-APCs). Using syngeneic murine leukemia models, we demonstrate that TR-APCs acquire both myeloid phenotype and function, process and present endogenous TAAs, and potently stimulate TAA-specific CD4+ and CD8+ T cells. In vivo TR-APC induction elicits clonal expansion of cancer-specific T cells, establishes cancer-specific immune memory, and ultimately promotes leukemia eradication. We further show that both hematologic cancers and solid tumors, including sarcomas and carcinomas, are amenable to myeloid-lineage reprogramming into TR-APCs. Finally, we demonstrate the clinical applicability of this approach by generating TR-APCs from primary clinical specimens and stimulating autologous patient-derived T cells. Thus, TR-APCs represent a cancer vaccination therapeutic strategy with broad implications for clinical immuno-oncology.

overall_design: CD45.1+ endogenous immune cells and CD45.2+ RAW-112 tumor cells were FACS sorted from digested tumors following 5 and 10 days of tumor reprogramming or mock treatment.

first: Miles

middle: H

last: Linde

first: Ravindra

last: Majeti


title: Reprogramming Cancer into Antigen Presenting Cells as a Novel Immunotherapy [human]

overall_design: 3 samples


title: Comprehensive microRNA-sequencing of small extracellular vesicles from early-stage HNSCC cases and cancer-free controls with benign neoplastic conditions

overall_design: Case-control pilot study


title: Towards resolution of the intron retention paradox in breast cancer

city: Sydney

first: Charles

last: Bailey

state: NSW

address: Missenden Rd, Building 93

country: Australia

institute: Centenary Institute

summary: We explored intron retention patterns in normal breast epithelial cells (MCF10A) and estrogen receptor positive (ER+) breast cancer cells (MCF7).

overall_design: Total RNA was isolated from MCF7 and MCF10A cells using Trizol (Invitrogen). The RNA quality was assessed using RNA 6000 Nano Chips on an Agilent Bioanalyzer (Agilent Technologies) to confirm an RNA integrity score of >7.0. mRNA-seq was performed by Macrogen (Korea) using the Illumina Hi-Seq 2000 platform. RNA-seq libraries were prepared from > 1 μg of total RNA using TruSeq RNA sample prep kit (Illumina) according to the manufacturers’ instructions.

first: Ulf

last: Schmitz

first: Jaynish

middle: S

last: Shah

first: Michael

last: Milevskiy

middle: Y

last: Au

first: Veronika

last: Petrova

first: Justin

last: Wong

first: Jane

middle: E

last: Visvader

first: John

last: Rasko


title: Knockdown of miR-192 and miR-432 in progenitor cell-derived small extracellular vesicles enhances tissue repair in myocardial infarction

city: Atlanta

middle: E.

last: Davis

address: 2015 Uppergate Dr NE

institute: Emory University

summary: Small extracellular vesicles (sEVs) play a critical role in cardiac cell therapy by delivering molecular cargo and mediating cellular signaling. Among sEV cargo molecule types, microRNA (miRNA) is particularly potent and highly heterogenous. However, not all miRNAs in sEV are beneficial. Two previous studies utilizing computational modeling identified miR-192-5p and miR-432-5p as potentially deleterious in cardiac function and repair. Here, we show that knocking down miR-192-5p and miR-432-5p in cardiac c-kit+ cell-derived sEVs enhances the therapeutic capabilities of sEVs in vitro and in a rat in vivo model of cardiac ischemia reperfusion. miR-192-5p and miR-432-5p depleted CPC-sEVs enhance cardiac function by reducing fibrosis, enhancing mesenchymal stromal cell-like cell mobilization, and inducing macrophage polarization to the M2 phenotype. Knocking down deleterious miRNAs from sEV could be a promising therapeutic strategy for treatment of chronic myocardial infarction.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: This project aims to investigate the anti-fibrotic and anti-inflammatory effects of miR-192-5p-depleted sEVs (?miR-192 sEV) or miR-432-5p-depleted sEVs (?miR-432 sEV) produced from human cardiac c-kit+ cells. The RNA-seq will help us to understand the downstream effects and potential mechanisms of action of ?miR-192 and ?miR-432 sEVs in activated cardiac fibroblasts (RCFs) and stimulated macrophages (THP-1 cells).

first: Hyun-Ji

last: Park

first: Jessica

last: Hoffman


title: Genome-wide expression profiling of NSCLC cancer cell lines upon miR-455-5p overexpression

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary: Non–small-cell lung cancer (NSCLC) is the leading cause of cancer deaths worldwide due to late diagnosis and lack of effective therapies to treat metastatic disease. About one third of NSCLC patients present at diagnosis with locally advanced cancer (stage IIIA) which metastasizes ipsilateral mediastinal or subcarinal lymph nodes (N2). Neoadjuvant chemotherapy (NACT) followed by surgery is the treatment of choice for resectable N2 disease. However, the majority of patients do not respond to NACT and show persistent lymph nodal metastases and an adverse outcome. Our scant knowledge of the molecular biology of lymph node metastases (LNmets) represents a major obstacle to develop more effective therapies. Here, we investigated gene expression profile (coding and non-coding) of LNmets collected by endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA) and mediastinoscopy, in two cohorts of stage IIIA patients before NACT (N=70). We discovered a microRNA expression signature in LNmets predictive of NACT response of N2 patients. Importantly, we unveiled a miR-455-5p/PD-L1 regulatory axis which drives chemotherapy resistance and impact T cell viability in NSCLC. Our data suggests the relevance of LNmets molecular profiling to predict response to NACT likewise presents strong evidences of a miRNA-based mechanism which functionally links chemotherapy response with PD-L1 regulation.

overall_design: A total of 5 different experimental conditions were analyzed in this study. We performed 2 biological replicates for a total of 10 samples profiled.

first: Roberto

last: Cuttano


title: A combination of organic acids and glucose prime a late stage of fungal biotrophy

city: Vancouver

first: James

last: Kronstad

state: BC

address: 2185 E Mall

department: Mircobiology and Immunology

institute: University of British Columbia

summary: We show that combinations of organic acids and glucose trigger phenotypes associated with the late stage of biotrophy for the maize pathogen Ustilago maydis. These phenotypes include the expression of a set of effectors normally observed only during biotrophic development as well as the formation of melanin associated with sporulation in plant tumors.

overall_design: Ustilago Maydis 521 grown in a combination of carbon sources (glucose or glocose + malate) with and without aeration sampled at 24 and 72 hours. 3 replicates are sequenced for each group.

first: Matthias

last: Kretschmer

first: Christopher

last: Lee


title: ATAC-seq Analysis in Control and Mier1 KO Mice Liver at 0 h and 24 h after 70% Partial Hepatectomy

city: Shanghai

first: Yanhao

last: Chen

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: To explore how Mier1 affects liver regeneration, we specifically knocked out Mier1 in mouse liver through adeno-associated virus (AAV). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals. To assess the role of MIER1 in liver regeneration, we performed 70% partial hepatectomy, 3 weeks after AAV injection. We then performed ATAC-seq in Control and Mier1 liver-sepcific knockout mice liver tissues at 0 h and 24 h after PHx to explore the influence of Mier1 on the chromation opening during liver regeneration.

overall_design: For the ATAC-seq analysis, nuclei were extracted from frozen liver tissues. 30mg frozen liver tissue from 3 different samples was added into a pre-chilled 1mL Dounce with 1mL cold homogenization buffer, then dounce with loose pestle for 10 strokes and dounce with tight pestle for 25 strokes. After centrifugation to remove larger cellular debris from the homogenized liver fluid, the supernatant containing the nuclei was further purified by gradient density centrifugation. 50,000 purified nuclei were used to generated ATAC-seq libraries by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501). Final libraries were purified and size selected using VAHTS DNA Clean Beads (Vazyme, N411). ATAC libraries were sequenced using 2×150bp Illumina HiSeq. Liver tissues were collected for analysis at 0 h and 24 h after 70% partial hepatectomy in WT and Mier1 KO mice.

first: Qiurong

last: Ding

first: Lanlan

first: Yuchen

last: Wang


title: Genome-wide profile of BAF45D-DNA binding in human embryonic stem cells(ESCs) and human ESC-derived spinal cord neural stem cells(NSCs).

city: Hefei

first: Chao

last: Liu

state: Anhui

address: 81 Meishan Road

department: Histology and Embryology

institute: Anhui Medical University

summary: We report the application of cleavage under targets and tagmentation (CUT&Tag) assay for profiling DNA-binding sites of BAF45D in human ESCs and human ESC-derived spinal cord NSCs.

overall_design: After human ESCs were induced into spinal cord NSCs, examination of BAF45D-DNA binding profile using CUT&Tag assay in human ESCs and the human ESC-derived NSCs was performed.

first: Chen

last: Xueying

first: Liu

last: Chao


title: Single-Cell RNA sequencing reveals prophylactic Prednisone blunts cellular immunity in hemophilia B gene therapy

city: Tianjin

first: Huiyuan

last: Li

address: 288 Nanjing Road

institute: Institute of Hematology & Blood Diseases Hospital

summary: Seven hemophilia B gene therapy participants were taken blood for single cell sequencing at four timepoints, and then compared the immune status of T and antigen presentation cells of theses patients according to therapy efficacy and different time points. The results showed that cellular immunity was elevated in patients with FIX:C less then 40IU/dl at week 26, glucocorticoids (GCs) effectively suppressed T cell immunity and GCs inhibited T cell immunity indirectly by effecting on APCs.

overall_design: Examination of single cell mRNA profile in peripheral blood mononuclear cell from seven hemophilia B gene therapy participants at following time points：Day-7(before glucocorticoids treatment), Day 0（before AAV infusion）, Day 7(after AAV infusion) and 2 weeks after glucocorticoids withdrawal(stop GCs) .

first: Xue

last: Feng

first: Li

last: Huiyuan

first: Zhang

last: Lei


title: Notch1 and Notch2 signaling from distinct cellular sources exclusively but cooperatively regulate fetal myogenesis

city: Seoul

first: Young-Woo

last: Jo

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: During developmental myogenesis, some continuously proliferating myogenic progenitors (MPs) sustain stem/progenitor states while the rest differentiate into myocytes to form myofibers by fusion. To generate sufficient muscle, fine regulations of cell fate decision of MPs are crucial. Notch signaling has been known to regulate embryonic MPs (eMPs) that play a role in primary myogenesis by promoting cell cycle exit and suppressing premature differentiation. However, the role of Notch signaling in fetal MPs (fMPs) during secondary myogenesis is elusive because the development of fMPs already has been abrogated in Notch manipulation models. In this study, we investigated the role of Notch signaling in fMPs at an individual Notch receptor level. Surprisingly we found that Notch1 and Notch2, most similar among four Notch receptors, distinctly regulate fMPs: Notch1 induces cell cycle exit and Notch2 suppresses premature differentiation, presumably by canonical Notch signaling pathway. Additionally, we suggest that Notch1 and Notch2 signals are regulated by the ligands on myofibers and MP-lineage cells, respectively. This study will lay the groundwork for the in-depth understanding of Notch signaling in muscle formation from embryonic myogenesis to adult muscle regeneration.

overall_design: Total RNA-sequencing analysis was performed using FACS-sorted tdTomato+ myogenic progenitor-lineage cells from limb muscle of Notch1 (Pax7-CreER; Notch1f/f; Rosa-tdTomato), Notch2 (Pax7-CreER; Notch2f/f; Rosa-tdTomato) conditional knock-out and wild-type control (Pax7-CreER; Rosa-tdTomato) E16.5 fetus.

first: Inkuk

last: Park

first: Young-yun

last: Kong


title: Xbp1s controls IL-15-mediated natural killer cell survival and function by regulating Pim2 and Tbet

first: Shoubao

last: Ma

summary: We previously reported that X-Box Binding Protein 1 (Xbp1s), an essential transcriptional factor downstream of IL-15 and Akt signaling, controls cell survival and effector function in human natural killer (NK) cells. However, the mechanisms by which Xbp1s regulates NK cell survival and function remains unknown. In this study, by using Xbp1s conditional knock-out (KO) mice, we found that Xbp1s is critical for IL-15-mediated NK cell survival but not proliferation in vitro and in vivo. Mechanically, Xbp1s regulates homeostatic NK cell survival through targeting Pim2, a critical anti-apoptotic gene. Pim2 in turn stabilizes Xbp1s protein through phosphorylation at Thr58. Xbp1s enhances NK cell effector function and anti-tumor immunity via recruitment of Tbet to the promoter region of Ifng. Collectively, our findings reveal an important role of IL-15–Xbp1s signaling in NK cell survival and effector function.

overall_design: Total RNA was isolated from  purified splenic NK cells from IL-15Tg-WT and IL-15Tg-Xbp1s cKO mice using a RNeasy Mini Kit (QIAGEN). The RNA libraries were generated using the KAPA Hyper Prep Kit (KAPA Biosystems). Sequencing was performed on the HiSeq2500.

first: Jianhua

last: Yu


title: Downregulation of STAT3 in EBV-positive Hodgkin lymphoma

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

institute: Leibniz Institute DSMZ

summary: STAT3 encodes an oncogenic transcription factor which is activated via various signalling pathways or Epstein Barr virus (EBV)-infection. The tumor cells of Hodgkin lymphoma (HL) are derived from germinal center B-cells and transformed by chromosomal rearrangements, aberrant signal transduction, downregulation of transcription factors mediating B-cell differentiation, and EBV-infection. HL cell lines represent useful models to investigate the molecular pathology and deduced treatment options in this malignancy. Using cell line L-540, we have recently shown that constitutively activated STAT3 drives aberrant expression of hematopoietic NKL homeobox gene HLX. Here, we analyzed HL cell line AM-HLH which is EBV-positive but nevertheless HLX negative. Consistently, AM-HLH expressed decreased levels of STAT3 proteins which were additionally inactivated and located in the cytoplasm. Combined genomic and gene expression profiling data revealed amplified and overexpressed candidates involved in opposed regulation of STAT3 and EBV. Subsequent analyses demonstrated that IRF4 and NFATC inhibited STAT3 expression. However, treatment with IL6 or IL27 activated STAT3, elevated expression of HLX and MIR155, and inhibited IRF4. MIR155 (STAT3 target gene) and BCL11A and SPIB (target genes of HLX) are described as suppressors and activators of EBV and showed reduced and elevated expression levels in AM-HLH, respectively. Taken together, this cell line deals with two conflicting oncogenic drivers, namely JAK2-STAT3-signalling and EBV-infection but is sensitive to cytokine signalling, mediating a switch between these aberrant pathways. Thus, AM-HLH represents an interesting cell line model to study the pathogenic roles of STAT3 and EBV and their therapeutic implications in HL.

overall_design:
EBV-positive Hodgkin lymphoma cell line AM-HLH
Data from DEV cell line (GSM986544) is included in RMA-processed_data.txt file.

first: Stefan

last: Nagel


title: Single nucleus analysis of brain tissues from DAP12 loss-of-function (KΔ75) mice

city: Saint Louis

first: Yingyue

last: Zhou

state: Missouri

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,, Pathology and Immunology

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: The TREM2-DAP12 receptor complex sustains microglia functions. Heterozygous TREM2 variants subtly impair microglia, facilitating manifestation of Alzheimer’s Disease in the elderly. Homozygous inactivating mutations of TREM2 or DAP12 cause Nasu-Hakola disease (NHD), an early-onset dementia with leukoencephalopathy, myelin loss and gliosis. Here we investigated the impact of DAP12 deficiency in microglia and collateral damage to other brain cells by single-nucleus RNA-seq in NHD patients and DAP12 loss-of-function (KΔ75) mice. KΔ75 mice showed signatures of impaired microglia activation that reverberated in mild dysfunction of other brain cells. Paradoxically, NHD microglia were activated and associated with astrocytosis, hypoxia, and neuronal loss signatures. We envision that KΔ75 signatures recapitulate an early NHD stage in which DAP12-deficient microglia fail to clear toxic products generated during brain development and homeostasis. Conversely, NHD signatures reflect a late disease stage in which accumulated toxic products cause a widespread tissue damage that elicits TREM2-DAP12-independent microgliosis, astrogliosis, hypoxia, and neuronal death. This TREM2-DAP12-independent microglia activation in NHD has bearing on potential microglia-based therapies.

overall_design: Compare the transcriptomics of KΔ75 with WT controls

first: Prabhakar

last: Andhey

first: Amanda

last: Swain


title: Single nucleus analysis of post-mortem brain tissues from Nasu-Hakola disease (NHD) patients

overall_design: Compare the transcriptomics of occipital cortex of NHD patients with ancestry-matched controls


title: Understanding biochemical properties and functions of SyYVCV βC1

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

institute: National Centre for Biological Sciences, TIFR

summary: To undersatnd the developmental defects in βC1 O.E. N. Tabacum plants, transcriptome analysis was performed from leaves of verified stable transgenic lines

overall_design: p35S: GFP-βC1 N. tabacum transgenic plants

first: Padubidri

last: Shivaprasad

first: Ashwin

last: Nair

first: Anushree

last: Narjala


title: Phenological transcriptomic profile of double-crested cormorants during embryonic development

city: Quebec

first: Valerie

last: Langlois

state: QC

address: 490 rue de la Courrone

department: Centre Eau Terre Environnement

institute: Intitut national de la recherche scientifique (INRS)

summary: In this study, we tracked the phenology of the transcriptome during double-crested cormorant (Nannopterum auritum) embryogenesis. Fresh eggs were collected from a reference site and artificially incubated from collection until four days prior to hatching. Embryos were periodically sampled throughout incubation for a total of seven time points. A custom microarray was designed for cormorants (over 14,000 probes) and used for transcriptome analysis in whole body (days 5, 8) and liver tissue (days 12, 14, 16, 20, 24). Three main development periods (early, mid, and late incubation) were identified with differentially expressed genes, gene sets, and pathways within and between each developmental transition.

overall_design: During artificial incubation without any exposure, whole body embryos were sampled on days 5 and 8, and the liver was samples from embryos on days 12,14,16,20,24 with n= 3-5 per sampling day. The genetic signature for each sampling day was compared to the previous and next sampling day to create a profile over time.

first: Sarah

middle: J

last: Wallace

first: Shane

last: deSolla


title: Histone methyltransferase SETDB1 selectively regulates cortical HTR3A interneuron development and anxiety-like behavior in mice

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

summary: Histone methyltransferase SETDB1 is critically involved in brain development, but its role in regulating GABAergic interneurons remains unknown. Here, we used RNA-seq and ATAC-seq to study the gene expression and chromatin accessibility in ganglionic eminences (GE) at E15.5 from brain-specific Setdb1 conditional knockout mice (Setdb1-Nestin-cKO) and controls both in vitro and in vivo.

overall_design: ATAC-seq from GE_NPC, 3 animals per genotype; RNA-seq from GE_NPC, 3 animals per genotype; RNA-seq from GE tissue, 2 animals for the control and 3 animals for the Setdb1-Nestin-cKO group.

first: Shenghui

last: Zheng

first: Jiaqi

last: Li


title: ChIP-seq profile of iPSC-derived human developmental cortical interneurons

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

summary: ChIP-seq was carried out by high throughput sequencing in human developmental cortical interneurons derived from healthy control vs schizophrenia iPSCs

overall_design: ChIP-seq assay in human developmental cortical interneuronsderived from healthy control vs schizophrenia iPSCs

first: Dongxin

last: Liu

first: Sangmi

last: Chung


title: Drosophila photoreceptor neuron-specific H3, H3K4me3 and H3K36me3 ChIP-seq from 40-day old flies

city: West Lafayette

first: Vikki

last: Weake

address: 175 S University St

institute: Purdue University

summary: We report the genome-wide distribution of H3, H3K4me3 and H3K36me3 from 40-day old flies

overall_design: Photoreceptor neuron-specific chromatin profiling using 40-day old flies. Four biological replicates. Input control included

first: Juan

last: Jauregui-Lozano


title: Genome-wide transcriptome analysis of human iPSC-derived healthy control vs schizophrenia developmental glutamatergic neurons.

summary: We report changes in gene expression in schizophrenia developmental glutamatergic neurons by genome-wide transcriptome analysis.

overall_design: RNA sequencing analysis (bulk) of healthy control vs schizophrenia glutamatergic neurons, differentiated from 4 healthy control iPSCs vs 5 schizophrenia iPSCs.


title: Time-resolved RNA sequencing reveals distinct post-transcriptional regimes during zebrafish embryogenesis

city: Vienna

first: Stefan

middle: Ludwig

last: Ameres

address: Dr.-Bohr-Gasse 3

institute: Institute of Molecular Biotechnology

summary: We report the characterization of transcript dynamics during maternal to zygotic transition in Zebrafish (MZT) using thiol-linked alkylation for the metabolic sequencing of RNA (SLAMseq).

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: Quantification of de novo transcription during MZT

first: Pooja

last: Bhat


title: Epigenome analysis of DNA samples from children's peripheral blood leukocyte

city: Beijing

first: Pei

last: Cao

address: No 2 Building Guangqu Road Chaoyang District

institute: China National Center for Food Safety Rsik Assessment

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of white blood cells was conducted using the Illumina Infinium Human Methylation 850K Genechip. According to the internal exposure level of deoxynivalenol, 32 participants were divided into two groups (high exposure DON group and low exposure DON group). Samples included 16 peripheral blood samples from children with high DON exposure and 16 peripheral blood samples from children with low DON exposure.

overall_design: About 3 ml of peripheral blood was taken for DNA extraction. White blood cells (WBCs) were isolated from blood specimens. Then total DNA was extracted from WBCs. Bisulphite converted DNA from the 32 samples were hybridised to the Illumina Infinium Human Methylation 850K Genechip

first: Hui

last: Yang


title: scRNAseq of the PDAC tumors from autochtonous KPC mice treated with vehicle or IRAK4 inhibitor CA-4948

city: St. Louis

first: Kian-Huat

last: Lim

state: MO

address: 4566 Scott Avenue, Room 502

department: Internal Medicine/Oncology

institute: Washington University School of Medicine

summary: We treated 6 week-old KPC mice with vehicle or CA-4948 and perform scRNASeq to assess transcriptomic changes in CAFs and immune cells

overall_design: scRNAseq analysis of CAFs and immune cells isolated from KPC tumors treated with vehicle or IRAK4 inhibitor

first: David

last: DeNardo


title: Comparison of the effects of 6 weeks high-fat diet or sucrose-supplemented drinking water upon gene expression in mice

city: Barcelona

first: Carlos

last: Castaño

address: Rossello 153

institute: CIBER

summary:
We fed mice fot 6 weeks with either a high-fat diet or standard chow with sucrose supplemented drinking water
We used microarrays to detail the global changes of gene expression induced by the two dietary regimes in liver, adipose and muscle tissues.

overall_design: C57BL6/J male mice were maintained for 6 weeks with standard chow and tap drinking water (CT), in paralel a second group was fed with 45% high-fat diet and tap drinking water (HFD), and a third group was fed with standard chow and drinking water supplemented with 50% sucrose (SAC).

first: Marcelina

last: Parrizas


title: Genome-wide expression profiling of mediastinal lymph nodal metastasis of stage IIIA NSCLC patients before neoadjuvant chemotherapy

first: Fabrizio

last: Bianchi

address: Viale Padre Pio 7

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary: Non–small-cell lung cancer (NSCLC) is the leading cause of cancer deaths worldwide due to late diagnosis and lack of effective therapies to treat metastatic disease. About one third of NSCLC patients present at diagnosis with locally advanced cancer (stage IIIA) which metastasizes ipsilateral mediastinal or subcarinal lymph nodes (N2). Neoadjuvant chemotherapy (NACT) followed by surgery is the treatment of choice for resectable N2 disease. However, the majority of patients do not respond to NACT and show persistent lymph nodal metastases and an adverse outcome. Our scant knowledge of the molecular biology of lymph node metastases (LNmets) represents a major obstacle to develop more effective therapies. Here, we investigated gene expression profile (coding and non-coding) of LNmets collected by endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA) and mediastinoscopy, in two cohorts of stage IIIA patients before NACT (N=70). We discovered a microRNA expression signature in LNmets predictive of NACT response of N2 patients. Importantly, we unveiled a miR-455-5p/PD-L1 regulatory axis which drives chemotherapy resistance and impact T cell viability in NSCLC. Our data suggests the relevance of LNmets molecular profiling to predict response to NACT likewise presents strong evidences of a miRNA-based mechanism which functionally links chemotherapy response with PD-L1 regulation.

overall_design: A total of 4 samples were profiled, 2 for each experimental condition.

first: Roberto

last: Cuttano


title: Wnt signaling promotes cell caudalization and inner ear differentiation in mouse stem cell-derived organoids

city: Miami

first: Pei-Ciao

last: Tang

state: FL

address: 1501 NW 10th Avenue, Miami, FL 33136, 926 F2

department: Otolayrngology

institute: University of Miami

summary: Multiple time points and doses of Wnt activation were sampled. Data showed that precise Wnt modulation promote the cell caudalization and inner ear differentiation

overall_design: single cell RNA-sequencing data were collected from samples with various levels of Wnt activatioin across the early inner ear organoid induction

first: Rick

last: Nelson

first: Li

last: Chen


title: USP7 substrates identified by proteomics analysis reveal the specificity of USP7

city: Houston

first: Litong

last: Nie

state: Texas

address: 6565 MD Anderson Blvd Unit, Desk Z6.2026

department: ERO

institute: The University of Texas MD Anderson Cancer Center

summary: To check whether mRNA level change for the changed proteins in protein level.

overall_design: Whole mRNA profile for 293A, USP7 KO, MGA KO and USP7/MGA DKO cells

first: Junjie


title: Humanized mice for investigating SARS-CoV-2 lung infection and associated human immune responses

city: Changchun

first: Cong

last: Fu

state: Jilin

address: NO.17  Xinmin Street

institute: The First Hospital of Jilin University

summary: There is an urgent need for animal models of COVID-19 to study immunopathogenesis and test therapeutic intervenes. In this study we showed that NSG mice engrafted with human lung (HL) tissue (NSG-L) could be infected efficiently by SARS-CoV-2, and that live viruses capable of infecting human Vero cells were found in the HL grafts and multiple organs from infected NSG-L mice. RNA-seq examination identified a series of differentially expressed genes, which are enriched in viral defense responses, chemotaxis, interferon stimulation, and pulmonary fibrosis between HL grafts from infected and control NSG-L mice. Furthermore, when infecting humanized mice with human immune system (HIS) and autologous HL grafts (HISL mice), the mice had bodyweight loss and hemorrhage in HL grafts, which were not observed in immunodeficient NSG-L mice, indicating the development of anti-viral immune responses in these mice. In support of this possibility, the infected HISL mice showed bodyweight recovery and lack of detectable live viruses at the later time. These results demonstrate that NSG-L and HISL mice are susceptible to SARS-CoV-2 infection, offering a useful in vivo model for studying SARS-CoV-2 infection and the associated immune response and immunopathology, and testing anti-SARS-CoV-2 therapies.

overall_design: NSG mice were implanted subcutaneously with human lung (HL) tissue, and subjected to infection via intra-HL injection of SARS-CoV-2 or PBS 6-8 weeks later. Human lung samples were harvested from uninfected or 5-day and 21-day infected NSG-L mice and analyzed for whole-transcriptome profiling by RNA-seq.

first: Renren

last: Sun

first: Zongzheng

last: Zhao

first: Yixin

last: Wang

first: Zhendong

last: Guo

first: Chunmao

last: Zhang

first: Lina

last: Liu

first: Cheng

first: Chang

last: Shu

first: Jin

last: He

first: Shucheng

last: Hua

first: Yuwei

last: Gao

first: Zheng

last: Hu


city: Helsinki

first: Piet

last: Finckenberg

address: Haartmaninkatu 8

department: Medicum

country: Finland

institute: University of Helsinki

summary: Myocardial regeneration capacity declines during the first week after birth and is linked to the adaptation to oxidative metabolism. Utilizing this regenerative window, we characterized the transcriptomic changes in myocardial injury in 1-day-old regeneration-competent and 7-day-old regeneration-compromised mice. The mice were either sham-operated or received left anterior descending coronary artery ligation to induce myocardial infarction and acute ischemic heart failure. Myocardial tissue samples were collected after 3- and 21-day follow-up period. Whole transcriptome and miRNA NGS data was analyzed. We identified specific time-dependent transcription factors and networks contributing to both regeneration competence and failure.

overall_design: Whole transcriptome analysis of neonatal mice hearts after myocardial infarction performed at  postnatal days 1 or 7.

first: Esko

last: Kankuri

first: Maciej

last: Lalowski

first: Eero

last: Mervaala


title: Rhythmic transcription drives mRNA level oscillations during C. elegans development

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

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

overall_design: Refer to individual Series


title: Base-resolution DNA methylation maps of little skate (Leucoraja erinacea)

city: Sydney

first: Ksenia

last: Skvortsova

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

institute: Garvan Institute

summary: Using MetylC-seq we investigated single-base resolution methylomes of embryonic and adult pelvic and pectoral fins of little skate.

overall_design: MethylC-seq was perfomred on st31 pelvic and pectoral as well as adult pelvic and pectoral fins of little skate.

first: Ozren

last: Bogdanovic


title: Early-Stage Lung adenocarcinoma MDM2 genomic heterogeneity predicts clinical outcome and response to targeted therapy

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Invasive subtypes of lung adenocarcinoma (LUAD) show MDM2 amplification that is associated with poor survival. Mouse double minute 2 (MDM2) is frequently amplified in lung adenocarcinoma (LUAD) and is a negative regulator of p53, which binds to p53 and regulates its activity and stability. Genomic amplification and overexpression of MDM2 together with genetic alterations in p53 leads to genomic and genetic heterogeneity in LUAD that represents a therapeutic target.  In vitro assays in a panel of LUAD cell lines showed that tumor cell response to MDM2 targeted therapy is associated with MDM2 amplification.

overall_design: Transcriptomic analyses of MDM2 amplified LUAD cell lines with p53 WT(A549) and p53 mutant (H1792) treated with MDM2 inhibitor

first: Ayushi

last: Patel


title: Bulk RNA-seq of human adipose-derived CD73-positive cells and heterogeneous mesenchymal stem/stromal cells

status: Public on Dec 30 2022

city: Tokyo

first: Daisuke

last: Hisamatsu

address: 2-1-1 Hongo, Bunkyo-ku

institute: Juntendo University Graduate School of Medicine

summary: To characterize the transplantation efficacy of CD73+ cells in a mouse model of colitis, we established CD73+ cells isolated from human adipose tissue and the conventional heterogeneous cell populations (from now on referred to as cMSCs) attached to the culture dish. We then performed a comparative transcriptome analysis between CD73+ cells and cMSCs derived from three individuals.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD73+ cells and cMSCs derived from the same samples.

first: Akari

last: Ikeda

first: Chihiro

last: Akazawa


title: A combination of novel NSC small molecule inhibitor along with doxorubicin inhibits proliferation of triple-negative breast cancer through metabolic reprograming

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: Treatment of patients with triple-negative breast cancer (TNBC) has been challenging due to the absence of well-defined molecular targets and high invasive and proliferative capacities of these cells. Current treatments against TNBC have shown minimal activity due to the high recurrence rate in the patients. Therefore, a pressing need for novel and efficacious therapies against TNBC. Here, we found a novel small molecule inhibitor (NSC33353) with potent anti-tumor activity against TNBC cells. Anti-proliferative effects of NSC small molecule inhibitor were determined using 2D and 3D culture cell proliferation assays. Using proteomics, NGS and enrichment analysis, we globally investigated top regulatory pathways affected by this compound in TNBC cells. Subsequently, we validated the proteomics and NGS analysis data using seahorse and enzymatic assays. Finally, we showed the inhibitor anti-tumor effects and confirmed its potential mechanism in vivo. In this report, we showed that a novel NSC33353 small molecule inhibitor reduced the proliferation of TNBC cells. Proteomic analysis confirmed a significant metabolic reprograming including suppression of glycolysis and oxidative phosphorylation after treatment. Furthermore, we found that treatment with NSC33353 small molecule inhibitor impaired glycolysis and oxidative phosphorylation via modulating the activity of metabolic regulator enzymes. Altogether, our data indicate that NSC33353 small molecule inhibitor may exhibit anti-tumor activity in TNBC cells and provide a rationale for further investigation of the potential of NSC small molecule inhibitor as an attractive therapeutic drug for TNBC. Doxorubicin is one of the most effective agents in the treatment of TNBC and resistance to this drug is a major problem. We show that the combination of NSC33353 and doxorubicin synergistically suppressed the growth of TNBC cells suggesting the combination enhances the sensitivity to doxorubicin. Further in-depth investigations are required to evaluate the exact targets and mechanism of this potent small molecule inhibitor, and its anti-neoplasm effects on TNBC in vivo.

overall_design: RNA was isolated from NSC33353 treated (2.5 uM) and DMSO treated MDA-MB-231 cells after 24 h treatment time point and samples were sent for RNA sequencing analysis

first: Hassan

last: Yousefi

first: Lothar

last: Lauterboeck

first: Samuel

last: Okpechi

first: David

last: Worthylake

first: Jessie

last: Guidry

first: Mohammad

middle: A

last: Zarandi

first: Janarthanan

last: Jayawickramarajah

first: Josesh

last: Kissil

first: Qinglin

last: Yang

first: Suresh

middle: K

last: Alahari


title: Orthotopic KI tumors treated with vehicle or IRAK4 inhibitor CA-4948 for two weeks

first: Kian-Huat

last: Lim

summary: We treated FVBN/J mice bearing orthotopic KI tumors with vehicle or CA-4948 for two weeks and performed bulk RNASeq to assess transcriptomic changes in the tumor

overall_design: Bulk RNAseq analysis of vehicle and CA-4948 treated orthotopic KI tumors. 4 animals per condition.