title: Identification of LncRNAs and mRNAs involved in adipogenesis

city: Dongguan

first: Changqing

last: Zuo

address: 1 Xincheng Avenue, Songshan Lake Industrial and Technology Park

department: Department of Pharmacology

institute: Guangdong Medical University

summary: Genome wide lncRNA and mRNA expression profiling at day 0 and day 4 after induction of adipocyte differentiation in C3H10T1/2 and 3T3-L1 cells were analyzed by Arraystar Mouse LncRNA Microarray V3.0

overall_design: C3H10T1/2 and 3T3-L1 cells were induced for adipocyte differentiation. Total RNA was extracted at day 0 and day 4 post-induction using Trizol reagent according to the manufacture's protocol. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Arraystar Mouse LncRNA Microarray V3.0 was used to identify differentially expressed lncRNAs and mRNAs


title: A diverse fibroblastic stromal cell landscape in the spleen directs tissue homeostasis and immunity

status: Public on Dec 17 2021

city: Melbourne

first: Hyun Jae

last: Lee

address: 792 Elizabeth Street

country: Australia

institute: University of Melbourne

type: Expression profiling by high throughput sequencing

summary: We reveal the transcription factor SpiB as a critical regulator required to support white pulp TRC numbers development in the spleen

overall_design: RNA sequencing on spleen WT and SpiB -/- TRC

first: Scott

middle: N

last: Mueller

first: Yannick

middle: O

last: Alexandre


title: A glioma immune cell atlas identifies prognostic macrophage signatures and a novel immunotherapy target, S100A4

status: Public on Dec 15 2021

city: Farmington

first: Parveen

last: Kumar

state: Connecticut

address: 10 Farmington Drive

country: USA

institute: Application Computational Scientist

summary: Here, we report defining molecular signatures of immune-suppressive and inflammatory immune cells in human gliomas. We identified nine robust macrophage subtypes with distinct molecular signatures, each of which predicted good or poor survival for glioma patients. Our analysis of signature genes associated with immune suppressive macrophages, underscored S100A4 as a strong candidate for in vivo validation.

overall_design: We performed multiregional sampling coupled with multidimensional analyses of 18 GBM patients.  Each patient tumor was sampled from one or multiple regions, and each region was analyzed separately using droplet-based single-cell capture and sequencing. We analyzed a total of 201,986 cells that passed all QC from the 44 samples

first: Nourhan

last: Abdelfattah

first: Kyuson

last: Yun


title: Small RNA pathways in the nematode Ascaris in the absence of piRNAs

city: Knoxville

first: Maxim

middle: Vladimirovich

last: Zagoskin

state: TN

address: 1311 Cumberland Avenue

department: Biochemistry & Cellular and Molecular Biology

institute: The University of Tennessee, Knoxville

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA pathways play diverse regulatory roles in the nematode C. elegans. However, our  understanding of small RNA pathways, their conservation, and their roles in other nematodes is limited.  Here, we analyzed small RNA pathways in the parasitic nematode Ascaris. Ascaris has ten Argonautes  with five worm-specific Argonautes (WAGOs) that are associated with secondary 5’-triphosphate small  RNAs (22-24G-RNAs). These Ascaris WAGOs and their small RNAs target repetitive sequences (WAGO-1, WAGO-2, WAGO-3, and NRDE-3) or mature mRNAs (CSR-1, NRDE-3, and WAGO-3) and are similar  to the C. elegans mutator, nuclear, and CSR-1 small RNA pathways. Ascaris CSR-1 likely functions to  “license” gene expression in the absence of an Ascaris piRNA pathway. Ascaris ALG-4 and its associated  26G-RNAs target and appear to repress specific mRNAs during meiosis in the testes. Notably, Ascaris  WAGOs (WAGO-3 and NRDE-3) small RNAs change their targets between repetitive sequences and  mRNAs during spermatogenesis or in early embryos illustrating target plasticity of these WAGOs. We  provide a unique and comprehensive view of mRNA and small RNA expression throughout nematode  spermatogenesis that illustrates the dynamics and flexibility of small RNA pathways. Overall, our study  provides key insights into the conservation and divergence of nematode small RNA pathways.

overall_design: Examination of small RNAs associated with 7 Argonaut proteins in early embryo, female/male germline and different male germline regions of parasitic worm Ascaris.

middle: V

first: Jianbin

last: Wang

first: Richard

middle: E

last: Davis


title: Next-generation sequencing of tumors with oral squamous cell carcinoma

first: Yamin

last: Zhang

address: Kaixuan Road

country: China

institute: Zhejiang University

summary: Comparing the differentially expressed genes between OSCC tumors with lymph-node metastasis (LNM) and those without LNM, which were obtained though NGS, we found that immune response plays an important role in the process of OSCC LNM and the candidate genes involved in the anti-tumor immunity were validated with qRT-PCR.

overall_design: mRNA profiles of OSCC patients with LNM (n=5) and those without LNM (n=4).


title: RNA sequencing of rhabdomyosarcoma RD cells transfected with NRAS siRNAs for 48 h or treated with 300nM ERKi SCH772984 for 24 h

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: To compare gene transcription changes induced by NRAS knockdown or ERK inhibition, we performed RNA-seq analyses in the NRAS Q61H RD cells after 48 h NRAS suppression by 2 independent NRAS siRNAs, or 24 hours after ERK inhibitor treatment (ERKi).

overall_design: RD cells were transfected with nonspecific (NS) or two independent NRAS siRNAs (NRAS1 and NRAS2) for 48 h or treated with DMSO or 300nM ERK inhibitor SCH772984 for 24 h. Each condition was done in duplicates.

first: Angelina

last: Vaseva

first: Natalia

last: Garcia


title: Integrative molecular and clinical profiling of acral melanoma links focal amplification of chr22q11.21 to metastasis

status: Public on Dec 14 2021

city: New Haven

first: Ruth

last: Halaban

state: CT

address: 15 York St.

department: Dermatology

institute: Yale University

summary: Acral melanoma, the most common melanoma subtype among non-Caucasian individuals, is associated with poor prognosis. However, its key molecular drivers remain obscure. Here, we perform integrative genomic and clinical profiling of acral melanomas from a cohort of 104 patients treated in North America or China. We find that recurrent, late-arising amplifications of cytoband chr22q11.21 are a leading determinant of inferior survival, strongly associated with metastasis, and linked to downregulation of immunomodulatory genes associated with response to immune checkpoint blockade. Unexpectedly, LZTR1 – a known tumor suppressor in other cancers – is a key candidate oncogene in this cytoband. Silencing of LZTR1 in melanoma cell lines caused apoptotic cell death independent of major hotspot mutations or melanoma subtypes. Conversely, overexpression of LZTR1 in normal human melanocytes initiated processes associated with metastasis, including anchorage-independent growth, formation of spheroids, and increased levels of MAPK and SRC activities. Our results provide insights into the etiology of acral melanoma and implicate LZTR1 as a key tumor promoter and therapeutic target.

overall_design:
We applied single-cell RNA-seq to characterize acral melanomas from 4 patients treated in the United States comparing expression differences of patients with 22q11.21 amplification (n = 1) and without 22q11.21 amplificaiton (n = 3).
>>> Due to patient privacy concerns, raw data have been submitted to dbGaP (phs000933.v3.p1). <<<

first: Farshad

last: Farshidfar

first: Kahn

last: Rhrissorrakrai

first: Chaya

last: Levovitz

first: Cong

last: Peng

first: James

last: Knight

first: Antonella

last: Bacchiocchi

first: Juan

last: Su

first: Mingzhu

last: Yin

first: Mario

last: Sznol

first: Stephan

last: Ariyan

last: Clune

first: Kelly

last: Olino

first: Laxmi

last: Parida

first: Joerg

last: Nikolaus

first: Meiling

first: Shuang

last: Zhao

first: Yan

first: Gang

last: Huang

first: Miaojian

last: Wan

first: Xianan

last: Li

first: Jian

last: Cao

first: Qin

last: Yan

first: Xiang

first: Aaron

middle: M

last: Newman


title: Integrative Molecular and Clinical Profiling of Acral Melanoma Identifies LZTR1 as a Key Tumor Promoter and Therapeutic Target

first: Ruth

last: Halaban

summary:
Acral melanoma, the most common melanoma subtype among non-Caucasian individuals, is associated with poor prognosis. However, its key molecular drivers remain obscure. Here, we performed integrative genomic and clinical profiling of acral melanomas from a cohort of 104 patients treated in North America or China. We found that recurrent, late-arising amplifications of cytoband chr22q11.21 are a leading determinant of inferior survival, strongly associated with metastasis, and linked to downregulation of immunomodulatory genes associated with response to immune checkpoint blockade. Unexpectedly, LZTR1 – a known tumor suppressor in other cancers – is a key candidate oncogene in this cytoband. Silencing of LZTR1 in melanoma cell lines caused apoptotic cell death independent of major hotspot mutations or melanoma subtypes. Conversely, overexpression of LZTR1 in normal human melanocytes initiated processes associated with metastasis, including anchorage-independent growth, formation of spheroids, and increased levels of MAPK and SRC activities. Our results provide new insights into the etiology of acral melanoma and implicate LZTR1 as a key tumor promoter and therapeutic target.

Keywords: Expression profiling by high throughput sequencing

overall_design:
We applied whole exome (tumor/normal) and RNA sequencing to characterize acral melanomas from 104 patients treated in the United States (n = 37) and China (n = 67), most of whom had long-term follow-up data available. Through comparative genomic analysis with 157 sun-exposed melanomas, we identified novel molecular features of acral melanoma; generated the first prognostic map linking highly recurrent somatic aberrations in acral melanoma to risk of death; and found that late-arising focal amplifications in chr22q11.21 are associated with lymph node involvement and distant metastasis, leading to poor outcomes. Within chr22q11.21, we identified LZTR1 – a known tumor suppressor in other cancers – as a key candidate driver of metastasis. Our findings reveal novel molecular insights of acral melanoma pathogenesis and designate LZTR1 as a new therapeutic target.
-------------------------------------
Authors state "We will submit the raw data to dbGAP."

first: Farshad

last: Farshidfar

first: Cong

last: Peng

first: Chaya

last: Levovitz

first: James

last: Knight

first: Antonella

first: Juan

first: Kahn

last: Rhrissorrakrai

last: Zhang

last: Wang

last: Chen


title: A global timing mechanism regulates cell-type specific wiring programs

city: Los Angeles

first: Ying

last: Lin

state: California

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The assembly of neural circuits is dependent upon precise spatiotemporal expression of cell recognition molecules1–6. Factors controlling cell-type specificity have been identified7–9, but how timing is determined remains unknown. Here we describe the induction of a cascade of transcription factors by a steroid hormone (Ecdysone) in all fly visual system neurons spanning target recognition and synaptogenesis. We demonstrate through single cell sequencing that the Ecdysone pathway regulates the expression of a common set of targets required for synaptic maturation and cell-type specific targets enriched for cell surface proteins regulating wiring specificity. Transcription factors in the cascade regulate the expression of the same wiring genes in complex ways, including activation in one cell-type and repression in another. We show that disruption of the Ecdysone-pathway generates specific defects in dendritic and axonal processes and synaptic connectivity, with the order of transcription factor expression correlating with sequential steps in wiring. We also identify shared targets of a cell-type specific transcription factor and the Ecdysone pathway which regulate specificity. We propose neurons integrate a global temporal transcriptional module with cell-type specific transcription factors to generate different cell-type specific patterns of cell recognition molecules regulating wiring.

overall_design: Single cell RNA-seq for 5 developing lamina neurons (L1-L5) in Drosophila visual system with different genetic perturbations (EcRDN, EcR RNAi, and Hr3 RNAi) at multiple time points (24hAPF, 48hAPF, 72hAPF and adult). Bulk RNA-seq and bulk ATAC seq for wild type developing L1 neurons.

first: Saumya

last: Jain

first: Yerbol

middle: Z

last: Kurmangaliyev

first: S

middle: L

last: Zipursky


title: Hepatocytic p62 suppresses ductular reaction and tumorigenesis in mouse livers with mTORC1 activation and defective autophagy

city: Kansas City

first: Hong-Min

last: Ni

state: KS

address: 3901 Rainbow Blvd, MS-1018

department: Pharmacology, Toxicology and Therapeutics

institute: University of Kansas Medical Center

summary: The purpose of this study is to identify the differential transcriptome profiles in WT, hepatic Atg5 KO, TSC1 KO, Atg5/TSC1 DKO, Atg5/TSC1/p62 TKO and Atg5/TSC1/Nrf2 TKO mouse livers. Hepatic mRNA from 2-month-old mice from 5 different mouse strains were extracted and performed for Nextseq analysis in quadruplicates.

overall_design: Hepatic mRNA profiles of 2-month-old WT, Atg5 KO, TSC1 KO, Atg5/TSC1 DKO, Atg5/TSC1/p62 TKO and Atg5/TSC1/Nrf2 TKO.

first: Wen-Xing

last: Ding

first: Wanqing

last: Liu

first: Xiaojuan

last: Chao


title: Examining Pathogenesis in Genome Instability Associated Neurodegenerative Mouse Model [TotalStranded-RNA-seq]

city: Memphis

first: Peter

middle: J

last: McKinnon

state: Tennessee

address: 262 Danny Thomas Place

department: Center for Pediatric Neurological Disease Research

institute: St. Jude Children's Research Hospital

summary: To investigate the molecular basis for ataxia in the DNA repair deficient mice we utilized RNA-seq to evaluate the transcriptome of AtmNes-cre;Aptx-/- (and AtmNes-cre;Parp1-/-) cerebellar and cortical tissue. Using total RNA from symptomatic 10-month-old double-mutant mice and littermate controls, we performed the transcriptome analysis.   top 1,000 expressed genes in each genotype

overall_design: Total Stranded RNA sequencing of the cerebellum and cortex examining gene expression  in ATM APTX null and associated control  brains.

first: Timothy

last: Shaw

first: Hongjian

last: Jin

first: Youngdon

last: Kwak


title: Examining Pathogenesis in Genome Instability Associated Neurodegenerative Mouse Model [Total_PolII_Chip-seq]

summary: Alterations in RNA Polymerase II kinetics can affect key co-transcriptional processes such as normal splicing and transcript elongation and can influence nonsense mediated decay (Fong et al., 2014; Jonkers and Lis, 2015). Specific types of DNA damage can variably influence RNA Pol II activity. We performed Total RNA Pol ll ChIP-seq to investigate how the chronic DNA damage can affect RNA Pol ll activity in the cerebellum tissues.

overall_design: Chip- sequencing of the cerebellum looking at RNA polymerase II in ATM APTX null and associated control  brains.


title: Examining Pathogenesis in Genome Instability Associated Neurodegenerative Mouse Model [ATAC-seq]

summary: Purkinje cells are large (>40um) and highly euchromatic, although detailed structural aspects of chromatin in these cells is lacking. To understand if the susceptibility of Purkinje neurons to DNA damage involves chromatin structure, we used ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) to examine chromatin accessibility.

overall_design: ATAC- sequencing of the cerebellum and sorted cells for Purkinje and Granule examining open chromatin  in ATM APTX null and associated control  brains.


title: Neural Epidermal Growth Factor-Like Like Protein 2 (NELL2) is Expressed in Human Oligodendroglial Cell types

status: Public on Dec 13 2021

city: St Lucia

first: Mohammed

middle: R

last: Shaker

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd,, Brisbane

department: AIBN

institute: The University of Queensland

summary: NELL2 is a cytoplasmic and secreted glycosylated protein with six epidermal growth factor-like domains. In animal models, Nell2 is predominantly expressed in neural tissues where it regulates neuronal differentiation, polarization, and axon guidance, but little is known about the role of NELL2 in human brain development. In this study, we show that rostral neural stem cells (rNSC) derived from human iPSC exhibit particularly strong NELL2 expression, and that NELL2 protein is enriched at the apical side of neural rosettes in hiPSC derived brain organoids. Following differentiation of human rostral NSC into neurons, NELL2 remains robustly expressed but changes its subcellular localization from >20 small cytoplasmic foci in NSC to 1-5 large peri-nuclear puncta per neuron. Unexpectedly, we discovered that in human brain organoids NELL2 is readily detectable in oligodendroglia and that the number of NELL2 puncta increases as oligodendrocytes mature. Artificial intelligence-based machine learning further predicts a strong association of NELL2 with multiple human white matter diseases, suggesting that NELL2 may possess yet unexplored roles in regulating oligodendrogenesis and/or myelination during human cortical development and maturation.

overall_design: Examination of human spinal cord organoids at 3 months old of in vitro culture

first: Ju-Hyun

last: Lee

first: Ernst

last: Wolvetang

first: Woong

last: Sun


title: Examining Pathogenesis in Genome Instability Associated Neurodegenerative Mouse Model [PolII_Ser5_Chip-seq]

summary: Alterations in RNA Polymerase II kinetics can affect key co-transcriptional processes such as normal splicing and transcript elongation and can influence nonsense mediated decay (Fong et al., 2014; Jonkers and Lis, 2015). Specific types of DNA damage can variably influence RNA Pol II activity. Thus, we performed RNA Pol ll pSer5 ChIP-seq to investigate how the chronic DNA damage can affect to RNA Pol ll activity in the cerebellum tissues.

overall_design: Chip- sequencing of the cerebellum looking at RNA polymerase II Serine 5 in ATM APTX null and associated control  brains.


title: Proteomic profiling reveals CDK6 upregulation as a targetable resistance mechanism for lenalidomide in multiple myeloma

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

country: Germany

institute: Charité Universitätsmedizin Berlin

summary: Multiple myeloma is a genetically heterogeneous disease of plasma cells. The thalidomide analog lenalidomide is a mainstay in the treatment of multiple myeloma and is used in combination with other drugs such as corticosteroids, chemotherapy and proteasome inhibitors, achieving high remission rates. However, most patients relapse due to acquired resistance of the malignant cells. Genetic analyses have revealed mutations in CRBN, the target of all IMiDs, as a resistance mechanism in 10% of patients, while for the majority of cases, the mechanism of resistance is unknown. Here, we performed integrated global quantitative tandem mass tag (TMT)-based proteomic and phosphoproteomic analyses and RNA sequencing in five paired pre-treatment and relapse samples from multiple myeloma patients. These analyses revealed proteins highly upregulated at relapse, including TRIP13, RRM1 and CDK6, which was not reflected on the RNA expression level. Overexpression of CDK6 in multiple myeloma cell lines reduced sensitivity to lenalidomide and pomalidomide in a kinase-dependent fashion. CDK6 inactivation by palbociclib or a CDK6-specific proteolysis targeting chimera (PROTAC) plus lenalidomide or pomalidomide was highly synergistic. Proteomic analyses in cell lines revealed that CDK6 inhibition reverses a complex protein resistance signature including RRM1 and TRIP13 and in combination with IMiDs promotes metabolic remodeling and c-MYC downregulation .  In conclusion, our global proteomic analyses identified CDK6 upregulation as a drug target to overcome lenalidomide resistance in multiple myeloma.

overall_design: mRNA profiles of CD138+ (Multiple Myelom) were generated using TruSeq RNA Exome (TruSeq RNA Access Kit) (Illumina) followed by sequencing with 50 bp single-end reads on HiSeq 2000.

first: Yuen

last: Ng

first: Evelyn

last: Ramberger

first: Jan

last: Krönke


title: A Point Mutation R122C in RUNX3 Promotes the Expansion of Isthmus Stem Cells and Inhibits Their Differentiation in the Stomach

city: Singapore

first: Daisuke

last: Douchi

address: 14 Medical Drive

department: Centre for Translational Medicine

country: Singapore

institute: Cancer Science Institute of Singapore

summary:
Background & Aims: RUNX transcription factors play pivotal roles in embryonic development and neoplasia. We previously identified the single missense mutation R122C in RUNX3 from human gastric cancer. However, how RUNX3R122C mutation disrupts stem cell homeostasis and promotes gastric carcinogenesis remained unclear.
Methods: To understand the oncogenic nature of this mutation in vivo, we generated the RUNX3R122C knock-in mice. Stomach tissues were harvested, followed by histological and immunofluorescence staining, organoid culture, flow cytometry to isolate gastric corpus isthmal and non-isthmal epithelial cells, and RNA extraction for transcriptomic analysis.
Results: The corpus tissue of RUNX3R122C/R122C homozygous mice exhibited a precancerous phenotype such as spasmolytic polypeptide-expressing metaplasia (SPEM). We observed mucous neck cell hyperplasia, massive reduction of pit, parietal, and chief cell populations, as well as a dramatic increase in the number of rapidly proliferating isthmal stem/progenitor cells in the corpus of RUNX3R122C/R122C mice. Transcriptomic analyses of the isolated epithelial cells showed that the cell cycle-related MYC target gene signature was enriched in the corpus epithelial cells of RUNX3R122C/R122C mice compared with the wild-type corpus. Mechanistically, RUNX3R122C mutant protein disrupted the regulation of the restriction point where cells decide to enter either proliferative or quiescent state, thereby driving stem cell expansion and limiting the ability of cells to terminally differentiate.
Conclusions: RUNX3R122C missense mutation is associated with the continuous cycling of isthmal stem/progenitor cells, maturation arrest and development of a precancerous state. This work highlights the importance of RUNX3 in prevention of metaplasia and gastric cancer.

overall_design: Examinination of RNA expression profiles in tdTomato+/EpCAM+ (IQ3pos) and tdTomato-/EpCAM+ (IQ3neg) corpus stomach cell fractions from Runx3 WT;Iqgap3-2A-tdTomato and Runx3 R122C;Iqgap3-2A-tdTomato reporter mice.

first: Yoshiaki

last: Ito

first: Akihiro

last: Yamamura

first: Junichi

last: Matsuo

first: Jung-Won

first: Napat

last: Nuttonmanit

first: Yi

middle: H

last: Lim

first: Kazuto

last: Suda

first: Mitsuhiro

last: Shimura

first: Sabirah

last: Chen

first: ShuChin

last: Pang

first: Kazuyoshi

last: Kohu

first: Mari

last: Kaneko

first: Hiroshi

last: Kiyonari

first: Atsushi

last: Kaneda

first: Hideyuki

last: Yoshida

first: Ichiro

last: Taniuchi

first: Henry

last: Yang

first: Michiaki

last: Unno

first: Jimmy

middle: B

last: So

first: Khay

middle: G

last: Yeoh

first: Linda

middle: S

last: Chuang

first: Suk-Chul

last: Bae

first: Motomi

last: Osato


title: hsa_circ_0098181-mRNA-seq

city: Shanghai

first: Yuan-Yuan

last: Luo

address: Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China

institute: Tongji University

summary: To explore the potential downstream mRNA of hsa_circ_0098181, we performed a mRNA sequencing.

overall_design: 3 overexpressing hsa_circ_0098181 Huh7 cells and 3 control cells were used to extract total RNA for RNA sequencing.

first: Xin

last: Zeng

first: Ke-Gong

last: Tao

first: Yi-Ting

last: Lu

first: Bin-Bin

last: Li


title: Acral Melanoma

first: Ruth

last: Halaban

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

overall_design: Refer to individual Series

first: Farshad

last: Farshidfar

first: Cong

last: Peng

first: Chaya

last: Levovitz

first: James

last: Knight

first: Antonella

last: Bacchiocchi

first: Juan

last: Su

first: Kahn

last: Rhrissorrakrai

first: Mingzhu

last: Yin

first: Mario

last: Sznol

first: Stephan

last: Ariyan

last: Clune

first: Kelly

last: Olino

first: Laxmi

last: Parida

first: Joerg

last: Nikolaus

first: Meiling

last: Zhang

first: Shuang

last: Zhao

first: Yan

last: Wang

first: Gang

last: Huang

first: Miaojian

last: Wan

first: Xianan

first: Jian

last: Cao

first: Qin

last: Yan

first: Xiang

last: Chen

first: Aaron

last: Newman


title: Ang II enhances group 2 innate lymphoid cell responses via AT1a during airway inflammation

city: Tianjin

first: Jie

last: Zhou

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

summary: Group 2 innate lymphoid cells (ILC2s) have emerged as critical mediators in driving allergic airway inflammation. Here, we identified angiotensin (Ang) II as a positive regulator of ILC2s. ILC2s expressed higher levels of the Ang II receptor AT1a, and colocalized with lung epithelial cells expressing angiotensinogen. Administration of Ang II significantly enhanced ILC2 responses both in vivo and in vitro, which were almost completely abrogated in AT1a-deficient mice. Deletion of AT1a or pharmacological inhibition of the Ang II - AT1 axis resulted in a remarkable remission of airway inflammation. The regulation of ILC2s by Ang II was cell-intrinsic and dependent on interleukin (IL)-33, and was associated with marked changes in transcriptional profiling and upregulation of ERK1/2 phosphorylation. Furthermore, higher levels of plasma Ang II correlated positively with the abundance of circulating ILC2s as well as disease severity in asthmatic patients. These observations reveal a critical role for Ang II in regulating ILC2 responses and airway inflammation.

overall_design: lung ILC2s were stimulated with IL-33, or IL-33 plus Ang II 6 hours for RNA-sequencing.

first: Gaoyu

last: Liu


title: Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis [RNA-seq]

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

summary: TP53 and ARID1A are frequently mutated across cancer but rarely in the same primary tumor. Endometrial cancer has the highest TP53-ARID1A mutual exclusivity rate. However, the functional relationship between TP53 and ARID1A mutations in the endometrium has not been elucidated. We used genetically engineered mice and in vivo genomic approaches to discern both unique and overlapping roles of TP53 and ARID1A in the endometrium. TP53 loss with oncogenic PIK3CA*H1047R in the endometrial epithelium results in features of endometrial hyperplasia, adenocarcinoma, and intraepithelial carcinoma. Mutant endometrial epithelial cells were transcriptome profiled and compared to control cells and ARID1A/PIK3CA mutant endometrium. In the context of either TP53 or ARID1A loss, PIK3CA mutant endometrium exhibited inflammatory pathway activation, but other gene expression programs differed based on TP53 or ARID1A status, such as epithelial-to-mesenchymal transition. Gene expression patterns observed in the genetic mouse models are reflective of human tumors with each respective genetic alteration. Consistent with TP53-ARID1A mutual exclusivity, the p53 pathway is activated following ARID1A loss in the endometrial epithelium, where ARID1A normally directly represses p53 pathway genes in vivo, including the stress-inducible transcription factor, ATF3. However, co-existing TP53-ARID1A mutations led to invasive adenocarcinoma associated with mutant ARID1A-driven ATF3 induction, reduced apoptosis, TP63+ squamous differentiation and invasion. These data suggest TP53 and ARID1A mutations drive shared and distinct tumorigenic programs in the endometrium and promote invasive endometrial cancer when existing simultaneously. Hence, TP53 and ARID1A mutations may co-occur in a subset of aggressive or metastatic endometrial cancers, with ARID1A loss promoting squamous differentiation and the acquisition of invasive properties.

overall_design: EPCAM+ endometrial epithelial cells from LtfCre^0/+; (Gt)R26^Pik3ca*H1047R; Trp53^fl/fl CD-1 mice were purified and assayed via RNA-seq.

first: Jake

last: Reske

first: Mike

last: Wilson


title: Definition of a mouse microglial subset that regulates neuronal development and pro-inflammatory responses in the brain

city: Chongqing

first: Yiguo

last: Qiu

state: Chongqing

address: 13 Tianchi Road, Banan Distri

institute: Chongqing International Institute for Immunology

summary: Expression of Itgax (encoding the CD11c surface protein) and Spp1 (encoding OPN) have been associated with activated microglia that can develop in healthy brains and some neuroinflammatory disorders. Here, we show that OPN production in the brain is confined to a small CD11c+ microglial subset that differentiates from CD11c- precursors in perinatal life after uptake of apoptotic neurons. Our analysis suggests that co-expression of OPN and CD11c genes marks a microglial subset that is expressed at birth and persists into late adult life, independent of environmental activation stimuli. Definition of OPN-producing CD11c+ microglia as a functional microglial subset provides new insight into microglial differentiation in health and disease.

overall_design: Microglial mRNA profiles of CD11c+ subset versus CD11c- subset in postnatal day 5 (P5), 9-month old wild type (WT) mice.

first: Xianli

last: Shen

first: Andrew

last: Wight

first: Hye-Jung

last: Kim

first: Harvey

last: Cantor


title: Response of efflux system deletion mutants of Cupriavidus metallidurans to Zn and EDTA

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

summary: Response of Cupriavidus metallidurans AE104 and 2 deletion mutants to Zn and EDTA

overall_design: In this study Zn and EDTA treatment was performed to acquire expression profiles of the total transcriptome of Cupriavidus metallidurans and 2 mutants

last: Grosse

first: Dietrich

last: Nies


title: Lung tumor MHCII immunity depends on in situ antigen presentation by fibroblasts.  [CD4 T cells]

city: Vari

first: Maria

last: Tsoumakidou

state: Attica

address: 34 Fleming Street

country: Greece

institute: B.S.R.C. "Alexander Fleming"

summary: A key unknown of the functional space in tumor immunity is whether physiologically relevant cancer antigen presentation occurs solely in draining lymph nodes versus tumors. Professional antigen presenting cells, i.e. the dendritic cells, are scarce and immature within tumors, greatly outnumbered by MHCII expressing non-hematopoietic cells, such as antigen-presenting cancer-associated fibroblasts (apCAFs). We hypothesized that after their exit from tumor-draining lymph nodes T cells depend on a second wave of antigen presentation provided in situ by structural cells.  We show that dense apCAF regions in human lung tumors define hot immunological spots with increased numbers of CD4 T cells. The transcriptomic profile of human lung apCAFs aligned to that of pancreatic apCAFs across mice and humans and were both enriched for alveolar type II genes, suggesting an epithelial origin. Mechanistically, human apCAFs directly activated the TCRs of adjacent effector CD4 T cells and at the same time produced high levels of c1q, which acted on surface c1qbp on T cells to rescue them from apoptosis. Fibroblast-specific deletion of MHCII in mice impaired local MHCII immunity and accelerated tumor growth, while inducing c1qbp overexpression in adoptively transferred T cells expanded their numbers within tumors and reduced tumour burden. Collectively, our work shows that tumor T cell immunity post lymph node exit requires peripheral antigen presentation by a subset of CAFs and proposes a new conceptual framework upon which effective cancer immunotherapies can be built.

overall_design: mRNA profiles of CD4 T cells from orthopotic lung tumors of I-AbF/FCol1a2-cre vs I-AbF/F mice (gender and age-matched, over 8-week-old mice) were analysed. Intratumoral CD4 T cells were isolated from 5 biological replicates of I-AbF/F mice (control) and 2 from I-AbF/FCol1a2-cre mice (experimental).

first: Dimitra

last: Kerdidani

first: Emmanouil

last: Aerakis

first: Kleio-Maria

last: Verrou

first: Petros

last: Stamoulis

first: Katerina

last: Goudevenou

first: Alejandro

last: Prados

first: Christos

last: Tzaferis

first: Ioannis

last: Vamvakaris

first: Evangelos

last: Kaniaris

first: Konstantinos

last: Vachlas

last: Sepsas

last: Potaris

first: Anastasios

last: Koutsopoulos


title: Lung tumor MHCII immunity depends on in situ antigen presentation by fibroblasts.  [CAF]

overall_design: mRNA profiles of MHCII+ and MHCII- cancer assosiated fibroblasts (apCAFs and nonapCAFs respectively) from orthopotic lung tumors of wt mice (over 8-week-old mice) were analysed. ApCAFs and nonapCAFs were isolated simultaneously from pulled tumors in 3 independent experiments.


title: Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis [CUT&RUN]

first: Ronald

last: Chandler

overall_design: EPCAM+ endometrial epithelial cells from adult, wild-type CD-1 mice were purified and assayed for ARID1A genome-wide binding by CUT&RUN.

first: Jake

last: Reske

first: Mike

last: Wilson


title: ChIP-seq from WT vs. Letmd1 KO brown adipose tissue (BAT) for BRG1

city: Davis

first: John

last: Yoon

state: CA

address: One Shields Avenue

institute: University of California Davis

summary: The chromatin remodeler BRG1 is altered in the Letmd1 KO mice.  We performed chromatin IP for BRG1 from BAT of wild-type (WT) versus Letmd1 KO mice.

first: Jung

last: Kim

first: Kyung-Mi

last: Choi

first: Hee-Woong

last: Lim


title: Examining Pathogenesis in Genome Instability Associated Neurodegenerative Mouse Model [polyA-RNA-seq]

first: Peter

last: McKinnon

summary: DNA damage can promote altered RNA splicing and decreased gene expression (Gregersen and Svejstrup, 2018; Milek et al., 2017; Munoz et al., 2009; Shkreta and Chabot, 2015), and aberrant splicing is implicated in neurodegenerative diseases including amyotrophic lateral sclerosis (ALS), Fragile X syndrome and spinal muscular atrophy (SMA) (Conlon et al., 2016; Jia et al., 2012; Loomis et al., 2014; Qiu et al., 2014; Scotti and Swanson, 2016). Therefore, we used RNA-seq data to assess RNA-splicing in double-mutant brain tissue using multivariate analysis of transcriptional splicing (rMATS) (Shen et al., 2014) and a splicing deficiency score algorithm (Bai et al., 2013) to assess intron retention.

overall_design: PolyA-enriched RNA sequencing of the cerebellum and cortex examining splicing deficiencies in ATM APTX null and ATM PARP null brains.

first: Timothy

last: Shaw

first: Hongjian

last: Jin

first: Youngdon

last: Kwak


title: Examining Pathogenesis in Genome Instability Associated Neurodegenerative Mouse Model


title: Single cell analysis of murine Dendritic Epidermal T Cells (DETC)

status: Public on Dec 12 2021

city: London

first: Duncan

last: McKenzie

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

summary:
Purpose: To establish the steady state heterogeneity of murine Dendritic Epidermal T Cells (DETC) and to investigate the function of their constitutive interaction with neighbouring keratinocytes via Skint1
Methods: CD3+ cells were FACS purified from ear epidermal suspensions prepared from FVB mice administered isotype control or anti-Skint1 antibody 7d prior, then loaded into the 10x Genomics Chromium Platform and sequenced using Illumina HiSeq 4000.
Conclusions: This analysis identifies four states of DETC in unperturbed epidermis, and reveals that DETC TCR sensing of keratinocytes via Skint1 potentially enables natural immune surveillance and maintains their thymic maturation signature in the periphery

overall_design: Epidermal T cells sorted from iostype- or anti-Skint1-treated mouse skin were used for single-cell RNA-sequencing (10xGenomics Chromium Platform), and sequenced using Illumina HiSeq 4000.

first: Nourdine

last: Bah

first: Adrian

last: Hayday


title: Transcriptome analysis of Trunking and Non-trunking Metroxylon sagu leaf tissue

city: Kota Samarahan

first: Wei Jie

last: Yan

state: Sarawak

address: Jln Datuk Mohammad Musa

department: Molecular Biology

country: Malaysia

institute: Universiti Malaysia Sarawak

summary: Sago palm is an important agricultural starch producing plant which contributes to the economics of Malaysia where the trunk is the main plant part which the starch is stored. However, there are sago palms that planted on peat soil failed to develop its trunk even after 17 years been planted. This phenomenon is known as 'non-trunking', which eliminates the economic value of the plants. Numeral researches have been done to address the phenomenon but the molecular mechanisms of sago palm respond toward the responsible stresses are still lacking. Therefore, in this study we collected samples from Trunking (Normal) and Non-Trunking sago palm leaf samples which planted on peat soil for total RNA extraction followed by next generation sequencing using BGISEQ-500 platform. The raw reads were cleaned and de novo assembled using TRINITY software package. Total of 40.11 Gb bases were sequenced from the sago palm leaf samples and after assembled producing 102,447 unigenes, with N50 score 1,809 bp and GC ratio of 44.34%. Unigenes by aligning with 7 (NR, NT, GO, KOG, KEGG, SwissProt & InterPro) functional databases and 65,523 (63.96%) unigenes were annotated. Functional annotation results in the detection of 46,335 Coding DNA sequences by Transdecoder. 30,039 Simple-sequence repeats distributed on 21,676 Unigenes were detected using Primer3 software, and 2,355 Transcription Factor coding Unigenes were predicted using getorf and hmmseach software. A total of 492 up-regulated and 444 down-regulated at least two-fold differential expressed gene were detected using DESeq2 algorithm with 95% confidence.

overall_design:
Comparison between trunking and non-trunking sago palm leaf tissue

grant ID: RDCRG/CAT/2019/23
grant title: Sarawak Research Development Council Grant
name of the funding source: Sarawak Research Development Council (SRDC)

Grant information:
grant ID: F07/TOC/1743/2018
grant title: Tun Openg Sago Chair Grant UNIMAS
name of the funding source: Sarawak Government

first: W

first: Hasnain

last: Hussain


title: Camellia oleifera seed transcriptomics

city: Hangzhou

first: Hengfu

last: Yin

state: Zhejiang

address: Daqiao 73

institute: Research Institute of Subtropical Forestry, Chinese Academy of Forestry

summary: We report the expression analysis of seed kernel in Camellia oleifera cultivars. In total 221 cultivars are sequenced by the Illumina sequencing experiments to obtain the gene expression profiles.

overall_design: Transcriptomics association analysis in BioProject accession PRJNA732216: EXPERIMENT from SRX11246770 to SRX11246990, RUN from SRR14934120 to SRR14934340 .

first: Yin

last: Hengfu

first: Lin

last: Ping

first: Yao

last: Xiaohua


title: Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis

first: Ronald

last: Chandler


title: B cell intrinsic TBK1 is essential for germinal center formation during infection and vaccination

city: Tokyo

first: Michelle Sue Jann

last: Lee

state: Tokyo

address: Minato-ku, Shirokanedai 4-6-1, Building 1, 3F, Room 333

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

summary: Germinal center (GC) is a site where somatic hypermutation and clonal selection are coupled for antibody affinity maturation against infections. However, how GCs are formed and regulated is incompletely understood. Here, we identified an unexpected role of Tank-binding kinase-1 (TBK1) as a crucial B-cell-intrinsic factor for GC formation. Using immunization and malaria infection models, we show that TBK1-deficient B cells failed to form GC despite normal Tfh differentiation, although some malaria-infected B-cell-specific TBK1-deficient mice could survive by GC-independent mechanisms. Mechanistically, TBK1 phosphorylation elevates in B cells during GC differentiation and regulates the balance of IRF4/BCL6 expression by limiting CD40 and BCR activation through non-canonical NF-κB and AKTT308 signaling. In the absence of TBK1, CD40 and BCR signaling synergistically enhanced IRF4 expression in Pre-GC leading to BCL6 suppression, therefore failed to form GC. As a result, memory B cells generated from TBK1-deficient B cells fail to confer sterile immunity upon re-infection, suggesting that TBK1 determines B cell fate to promote long-lasting humoral immunity.

overall_design: mRNA profiles of wild-type Pre-GC B cells and Tbk1-deficient Pre-GC B cells were generated by RNA sequencing using Illumina Novaseq 6000

first: Michelle

first: Julia

last: Matsuo-Dapaah

first: Cevayir

last: Coban


title: 10X Visium Spatial transcriptomics of murine colon at d14 (mucosa healing) in B cell sufficient/deficient mice

status: Public on Dec 10 2021

city: Solna

first: Ludvig

middle: Ale

last: Larsson

state: Stockholm

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: SciLifeLab

summary: The limitation of single-cell or bulk transcriptomic profiling is the lack of spatial topographical context. Spatial transcriptomics (ST) allows sequencing of polyadenylated transcripts from a tissue section which can be spatially mapped onto the histological brightfield image using an array of barcoded oligo-dT capturing probes. Using the 10X Visium platform, here, we unbiasedly characterized the spatial transcriptomic landscape of murine colon during mucosal healing upon dextran sodium sulfate (DSS) induced injury in mice in which B cell has been depleted and control.

overall_design: Female C57BL/6J mice were irradiated and received BM transplants with either CD19cre (ctrl) or CD19cre x iDTR cells. 8 weeks after BM transfer mice were treated with 2%DSS via the drinking water followed by 7 days of recovery. On days 9, 10, 12 and 13 mice received i.p. injections of diphteria toxin (25ng/g BW) in PBS. On day 14 colonic epithelial cells and stromal cells were sorted by flow cytometry and processed according to 10x Genomics protocol for visium and submitted for sequencing.

first: Srustidhar

last: Das

first: Eduardo

last: Villablanca


title: Reuterin in the healthy gut microbiome suppresses colorectal cancer growth through altering redox balance

city: Ann Arbor

first: Yatrik

last: Shah

state: Michigan

address: 500 S State Street

institute: University of Michigan

summary: Microbial dysbiosis is a colorectal cancer (CRC) hallmark and contributes to inflammation, tumor growth, and therapy response. Gut microbes signal via metabolites, but how the metabolites impact CRC is largely unknown. We interrogated fecal metabolites associated with mouse models of colon tumorigenesis with varying mutational load. We found that microbial metabolites from healthy mice or humans were growth-repressive, and this response was attenuated in mice and patients with CRC. Microbial profiling revealed that Lactobacillus reuteri and its metabolite, reuterin were downregulated in mouse and human CRC. Reuterin altered redox balance, and reduced survival, and proliferation in colon cancer cells. Reuterin induced selective protein oxidation, and inhibited ribosomal biogenesis and protein translation. Exogenous Lactobacillus reuteri restricted mouse colon tumor growth, increased tumor reactive oxygen species, and decreased protein translation in vivo. Our findings indicate that a healthy microbiome and specifically, Lactobacillus reuteri, is protective against CRC through microbial metabolite exchange.

sample_organism:
Bacteria
synthetic construct
mouse gut metagenome
feces metagenome

overall_design: 16s rRNA-sequencing of FECES from 16 CRE negative (control), 11 APC/p53 KO (Double mutant), and 14 APC/p53 KO + KrasG12D knock-in (Triple mutant). They are futher subdivided into early/late fecal samples (CRE: 8/8, Double: 5/6, Triple: 7/7). 16s rRNA sequencing of COLONIC TISSUE from 8 CRE negative (control), 7 APC/p53 KO (DoubleMut) and 10 APC/p53 KO w/ Kras G12D knock in (Triple mut) where early is pre-tamoxifen injection and late is 10 days following tamoxifen injection. COLONIC TISSUE collected 10 days following tamoxifen injection.

first: Hannah

last: Bell

first: Ryan

last: Rebernick

first: Joshua

last: Goyert


title: Bispecific antibodies increase the therapeutic window of CD40 agonists through selective dendritic cell targeting

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Therapeutic use of agonistic anti-CD40 antibodies is a potentially powerful approach for activating the immune response to eradicate tumors. However, the translation of this approach to clinical practice has been significantly restricted due to the severe dose-limiting toxicities observed in multiple clinical trials. Here, we demonstrate that conventional type-1 dendritic cells are essential for triggering antitumor immunity but not toxicity by CD40 agonists, while macrophages, platelets, and monocytes lead to the toxic events. Therefore, we designed bispecific antibodies that target CD40 activation preferentially to dendritic cells. These bispecific reagents demonstrate a superior safety profile compared to their parental CD40 monospecific antibody, while triggering potent anti-tumor activity. We suggest such cell-selective bispecific agonistic antibodies as a drug platform to bypass the dose-limiting toxicities of anti-CD40, and of additional types of agonistic antibodies used for cancer immunotherapy.

overall_design: 2 MARS seq experiments were done: 1) MC38 tumor bearing mice were treated with either mono specific CD40 (5 mice), bi specific CD40/CD11c (7 mice) and PBS (6 mice), and harvested 7 days post treatment for single-cell RNA seq analysis. 2) Mice were treated with mono specific CD40 (2 mice) and bi specific CD40/CD11c 92 mice). 3 hours post treatment LN and spleen were harvested and pooled together from each 2 mice for single-cell RNA seq analysis.

first: Ran

last: Salomon

first: Hagar

last: Rotem

first: Yonatan

last: Katzenelenbogen

first: Assaf

last: Weiner

first: Noy

middle: C

last: Saban

first: Tali

last: Feferman

first: Rony

last: Dahan


title: Translocated Legionella pneumophila small RNAs mimic eukaryotic miRNAs to dampen the host immune response [THP-1]

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

country: France

institute: Institut Pasteur

summary: Extracellular vesicles (EVs) produced by bacteria, archaea and eukaryotic cells, are increasingly recognized as important mediators of intercellular communication via transfer of a wide variety of molecular cargoes. To characterize the effect of Lp-EVs on THP-1 cells, in particular the immune response, three independent RNAseq libraries were constructed from from THP-1 cells non-infected, incubated with purified wt-EVs or with purified EV from delta-rsmY Legionella bacteria. The RNA deep was purified after 3h of incubation and sequenced using an Illumina platform.

sample_organism:
Legionella pneumophila
Homo sapiens

platform_organism:
Legionella pneumophila
Homo sapiens

overall_design: For each RNAseq experiment, the transcription of THP-1 cells incubated with  extracellular vesicles deriving from wt and delta-rsmY Legionella bacteria or form the non-infected control experiment was compared. In total n=3 independent experiments were performed

first: Tobias

last: Sahr

first: Pedro

last: Escoll Guerrero

first: Carmen

last: Buchrieser


title: Optimized delivery of dual co-stimulation and anti-tumor activity using parallel chimeric antigen receptors (pCARs)

first: John

last: Maher

address: Great Maze Pond

institute: King's College London

summary: Second generation (2G) chimeric antigen receptors (CARs) contain a CD28 or 41BB co-stimulatory endodomain and elicit remarkable efficacy in hematological malignancies. Third generation (3G) CARs extend this linear blueprint by fusing both co-stimulatory units in series. However, clinical impact has been muted despite compelling evidence that co-signaling by CD28 and 41BB can powerfully amplify natural immune responses. We postulate that effective dual co-stimulation requires juxta-membrane positioning of endodomain components within separate synthetic receptors. Consequently, we designed parallel (p)CARs in which a 2G (CD28+CD3) CAR is co-expressed with a 41BB-containing chimeric co-stimulatory receptor. We demonstrate that the pCAR platform optimally harnesses synergistic and tumor-dependent co-stimulation to resist T-cell exhaustion and senescence, sustaining proliferation, cytokine release, cytokine signaling and metabolic fitness upon repeated stimulation. When engineered using targeting moieties of diverse composition, affinity and specificity, pCAR T-cells consistently elicit superior anti-tumor activity both in vitro and in vivo, warranting clinical development.

overall_design: In order to understand the mechanisms underlying the enhanced anti-tumor function of pCAR T-cells, we performed gene expression analysis using the NanoString CAR-T Characterization Panel of M-CSF receptor-targeting pCAR T-cells and compared it to second and third generation CAR-T cells with either 41BB, CD28 or both co-stimulatory domains, as well as to a first generation CAR  paired with a tandem dual chimeric cytokine receptor which provided both 41BB and CD28 co-stimulation. A pCAR in which the endodomain of the CAR was truncated was used as signalling-defective control. 4 samples from 4 individual donors were used for each construct. All T-cells were analyzed 24h after stimulation on either target cells either expressing M-CSF receptor  or lacking M-CSF receptor expression (negative control).

first: Tamara

middle: T

last: Muliaditan

first: Leena

last: Halim

first: Lynsey

last: Whilding

first: Benjamin

last: Draper

first: Daniela

middle: D

last: Achkova

first: Fahima

middle: F

last: Kausar

first: Maya

last: Glover

first: Natasha

middle: N

last: Bechman

first: Appitha

middle: A

last: Arulappu

first: Jenifer

last: Sanchez

first: Katie

middle: K

last: Flaherty

first: Jana

last: Obajdin

first: Kristiana

last: Grigoriadis

first: Pierre

middle: P

last: Antoine

first: Daniel

last: Larcombe-Young

first: Caroline

last: Hull

first: Richard

last: Buus

first: Peter

last: Gordon

first: Anita

first: David

last: Davies

first: Anna

last: Schurich


title: DNA Methylation Profiles of Ovarian Clear Cell Carcinoma

city: Rochester

first: Julie

last: Cunningham

state: MN

address: 200 First Street SW

department: Department of Laboratory Medicine and Pathology

institute: Mayo Clinic

type: Methylation profiling by genome tiling array

summary:
Background. Ovarian clear cell carcinoma (OCCC) is a rare ovarian cancer histotype that tends to be resistant to standard platinum-based chemotherapeutics. We sought to better understand the role of DNA methylation in clinical and biological subclassification of OCCC.
Methods. We interrogated genome-wide methylation using DNA from fresh frozen tumors from 271 cases, applied non-smooth non-negative matrix factorization (nsNMF) clustering, and evaluated clinical associations and biological pathways.
Results. Two approximately equally sized clusters that associated with several clinical features were identified. Compared to Cluster 2 (N=137), Cluster 1 cases (N=134) presented at a more advanced stage, were less likely to be of Asian ancestry, and tended to have poorer outcomes including macroscopic residual disease following primary debulking surgery (p-values <0.10). Subset analyses of targeted tumor sequencing and immunohistochemical data revealed that Cluster 1 tumors showed TP53 mutation and abnormal p53 expression, and Cluster 2 tumors showed aneuploidy and ARID1A/PIK3CA mutation (p-values <0.05). Cluster-defining CpGs included 1,388 CpGs residing within 200 bp of the transcription start sites of 977 genes; 38% of these genes (N=369 genes) were differentially expressed across cluster in transcriptomic subset analysis (p-values <10-4). Differentially expressed genes were enriched for six immune-related pathways, including interferon alpha and gamma responses (p-values < 10-6).
Conclusions. DNA methylation clusters in OCCC correlate with disease features and gene expression patterns among immune pathways.
Impact. This work serves as a foundation for integrative analyses that better understand the complex biology of OCCC in an effort to improve potential for development of targeted therapeutics.

overall_design: Bisulphite converted DNA from 230 samples were hybridised to the Illumina Infinium Methylation EPIC and 41 samples were hybridised to the Illumina InfiniumHumanMethylation 450 BeadChip. Data for one sample is not included in GEO submission due to consent.

first: Ellen

middle: L

last: Goode


title: Lung tumor MHCII immunity depends on in situ antigen presentation by fibroblasts.

first: Maria

last: Tsoumakidou

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

overall_design: Refer to individual Series


title: Single-cell transcriptomics reveals peripheral immune responses in anti-synthetase syndrome-associated interstitial lung disease

city: Beijing

first: Zhong

last: Cao

state: CHINA

address: Tsinghua University

department: Automation

institute: Tsinghua University

summary:
Objective: Interstitial lung diseases (ILDs) secondary to anti-synthetase syndrome (ASS) greatly influence the prognoses of patients with ASS. Here we aimed to investigate the peripheral immune responses to understand the pathogenesis of this condition.
Methods: We performed single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) from 5 patients with ASS-ILD and 3 healthy donors (HDs). Flow cytometry of PBMCs was performed to replenish the results of scRNA-seq.
Results: We used scRNA-seq to depict a high-resolution visualization of cellular landscape in PBMCs from patients with ASS-ILD. Patients showed upregulated interferon responses among all cell types. And the ratio of effector memory CD8 T cells to naïve CD8 T cells was significantly higher than that in HDs. Additionally, Th1, Th2, and Th17 cell differentiation signaling pathways were enriched in T cells, and antigen processing and presentation was enhanced in NK cells. Flow cytometry analyses showed increased proportions of Th17 cells and Th2 cells, and decreased proportion of Th1 cells in patients with ASS-ILD when compared with HDs.
Conclusions: Our study reveals that ASS-ILD is characterized by upregulated interferon responses, altered CD8 T cell homeostasis, involvement of differentiation signaling pathways of CD4 T cells, and enhanced antigen processing and presentation ability in NK cells by scRNA-seq data. And the proportions of Th17 cells and Th2 cells are higher in patients with ASS-ILD than those in HDs using flow cytometry, while the proportion of Th1 cells is lower. These findings may provide foundations of novel therapeutic targets for patients with this condition.

overall_design: Fiive patients with anti-synthetase syndrome-associated interstitial lung disease (ASS-ILD) and three health donors (HDs) were recruited.

first: Lili

last: Zhu

first: Changshui

last: Zhang

first: Huaping

last: Dai

first: Chen

last: Wang


title: RNA sequencing of resident epidermal populations at steady state and following UV challenge

first: Duncan

last: McKenzie

summary:
Purpose: to characterise the steady state gene expression and transcriptomic response of resident murine epidermal immune cells (dendritic epidermal T cells, DETC; Langerhans cells, LCs) and epithelial cells (interfollicualr keratinocytes) to non-microbial stress in the form of ultraviolet B (UVB) radiation
Methods: 6 C57Bl/6 mice were administered 300mJ/cm^2 UVB radiation to the dorsal side of both ears 24hr prior to tissue harvest, and another 6 administered the same dose 4 hr prior. Ears were harvested and dorsal and ventral ear sheets were separated. Samples were pooled from 2 mice to generate 3 biological replicates per timepoint. Dorsal sheets were used for UV samples, while ventral sheets from 24hr UV mice were used as unchallenged skin. Epidermis was separated and digested, and epidermal populations were FACS sorted. Libraries were prepared and sequenced on an Illumina HiSeq 2500.
Conclusions: these data reveal the transcriptomic response of LC, DETC and interfollicular keratinocytes to acute epithelial stress in the form of DNA damage

overall_design: Dendritic epidermal T cells (DETC), Langerhans cells (LC) and interfollicular keratinocytes (KC) sorted from mouse ear skin (unchallenged, or UVB irradiated 4 or 24hr prior) and subjected to RNA sequencing using Illumina HiSeq 2500.

first: Nourdine

last: Bah

first: Adrian

last: Hayday


title: Cut&Run in Drosophila melanogaster control, mutant and knockdown ovaries

city: Lyon

first: Guillermo

last: Orsi

address: 46 allée d'Italie

institute: ENS Lyon/ LBMC-UMR 5239

summary: H3K27me3 profiles using Cleavage under targets and Release using nuclease (Cut&Run) in control and KD Drosophila melanogaster ovaries. We examined the impact on chromatin profiles in Drosophila melanogaster ovaries in which the lid, the Sin3a, the Snr1 or the mod(mdg4) gene have been selectively knocked down by tissue-specific shRNA expression. We additionally explored H3K27me3 and H3K9me3 in control and dhd mutant ovaries either carrying or not a transgene.

overall_design: Cut&Run was used to characterize either H3K27me3 or H3K9me3 profile in control, knockdown or mutant Drosophila melanogaster ovaries in duplicates or triplicates.

first: Daniela

last: Torres-Campana

first: Benjamin

last: Loppin


title: Transcriptome analysis of cultured human lung microvascular endothelial cells (HLMVECs) to explore functional roles for CD26/DPP4 in mediating inflammatory responses by LPS

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

institute: Chiba University

summary:
Purpose: The purpose of this study is to evaluate the role of CD26/DPP4 in HLMVECs in response to the pro-inflammatory stimulus LPS.
Methods: Four primary cell lines of HLMVECs were used. HLMVECs were cultured in endothelial growth medium-2 supplemented with 10% fetal bovine serum. The cells were incubated at 37°C in a 5% CO2 incubator and used at passages 6–8 for all experiments. 2 kinds of CD26/DPP4 siRNA were used. HLMVECS were treated with CD26/DPP4 siRNA or non-specific control siRNA or vehicle for 72 hours, then stimulated with LPS or PBS for 18 hours.
Results: Varieties of DEGs were determined between groups leading to the enrichment analysis.
Conclusions: The results suggest that CD26/DPP4 expression is related to multiple important functions in HLMVECs, including inflammation, barrier function, and regenerative processes.

overall_design: Examination of 4 HLMVEC lines, under the following conditions: DPP4 suppression +/-, LPS stimulation +/-.

first: Yukiko

last: Takahashi

first: Hironori

last: Sato

first: Yoshinori

last: Hasegawa

first: Steven

middle: M

last: Dudek

first: Osamu

last: Ohara

first: Koichiro

last: Tatsumi

first: Takuji

last: Suzuki


title: ADAD2 regulates heterochromatin in meiotic and post-meiotic male germ cells via translation of MDC1

status: Public on Dec 11 2021

city: New Brunswick

first: Lauren

last: Chukrallah

state: New Jersey

address: 59 Dudley Road, Foran 328

department: Animal science

institute: Rutgers University

summary: Male germ cells establish a unique heterochromatin domain, the XY-body, early in meiosis. How this domain is maintained through the end of meiosis and into post-meiotic germ cell differentiation is poorly understood. ADAD2 is a late meiotic male germ cell specific RNA binding protein, loss of which leads to post-meiotic germ cell defects. Analysis of ribosome association in Adad2 mutants revealed defective translation of Mdc1, a key regulator of XY-body formation, late in meiosis. As a result, Adad2 mutants show normal establishment but failed maintenance of the XY-body. Observed XY-body defects are concurrent with abnormal autosomal heterochromatin and ultimately lead to severely perturbed post-meiotic germ cell heterochromatin and cell death. These findings highlight the requirement of ADAD2 for Mdc1 translation, the role of MDC1 in maintaining meiotic male germ cell heterochromatin, and the importance of late meiotic heterochromatin for normal post-meiotic germ cell differentiation.

overall_design: Ribotag mRNA profiles of 21-day old Adad2+/+:Stra8iCre+:Rpl22HA  (WT, n = 3) and Adad2M/M:Stra8iCre+:Rpl22HA (MUT, n = 4) mice.  Includes total RNA (Input) as well as Immunoprecipitated RNA (IP)

first: Aditi

last: Badrinath

first: Gabrielle

last: Vittor

first: Elizabeth

last: Snyder


title: Ontogeny and Vulnerability of Lapatinib Drug-Tolerant Persisters in HER2-positive Breast Cancer

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Despite advances in HER2-targeted therapeutics, resistance remains a significant clinical problem in HER2-positive (HER2+) breast cancer, especially in the metastatic setting. Drug-tolerant persisters (DTPs), a sub-population of cancer cells that survive via reversible, non-genetic mechanisms, are implicated in resistance to tyrosine kinase inhibitors (TKIs) in several cancer models, but DTPs for HER2-targeted TKIs have not been characterized extensively. We found that upon treatment with the TKI lapatinib, HER2+ breast cancer lines yielded DTPs with luminal-like or mesenchymal-like transcriptional programs and differential sensitivity to lapatinib/anti-estradiol combinations. Lentiviral barcoding and single cell RNA-sequencing indicate that HER2+/ER+ cells cycle stochastically through a pre-DTP state, characterized by a G0-like signature, which uniquely gives rise to DTPs upon lapatinib exposure.

overall_design: BT474 and HCC1419 cells from untreated,  6h  lapatinib treatment (6h)  and 14-day  lapatinib treatment (DTPs) were submitted for scRNA-seq. SKBR3, EFM192A, SUM225 parental cells were submitted for scRNA-seq. BT474, HCC1419, EFM192A and SKBR3 cells that were either untreated, treated 14 days with lapatinib or treated 14 days with tucatinib were submitted for RNA-seq.

first: Chewei

last: Anderson Chang

last: Neel


title: Comparison of Drosophila melanogaster ovarian transcriptome after germline specific knock down of Snr1 or mod(mdg4) genes

first: Guillermo

last: Orsi

summary: Transcriptomic analysis and identification of differentially expressed genes in control vs KD Drosophila melanogaster ovaries. We compared gene expression profiles in Drosophila melanogaster ovaries in which the Snr1 or the mod(mdg4) gene have been selectively knocked down by tissues specific shRNA expression.

overall_design: Drosophila melanogaster ovaries mRNA profiles of 3-day old wild type (WT), female germline specific Snr1 knock-down (Snr1KD) and female germline specific mod(mdg4) knock-down (mod(mdg4)KD) were generated by deep sequencing, in duplicate, using Illumina Hiseq 4000.

last: Torres-Campana

first: Gérard

last: Benoit


title: Rare germline heterozygous missense variants of the BRCA1-Associated Protein 1 gene, BAP1, heterozygous missense variants cause a syndromic neurodevelopmental disorder

city: Nantes

first: Alice

last: Mollé

address: 30 bd Jean Monnet

institute: University of Nantes

summary: Nuclear deubiquitinase BAP1 (BRCA1-Associated Protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor gene whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a NDD or a tumor predisposition syndrome. Here, we report a series of 11 de novo germline heterozygous missense BAP1 variants associated with a rare syndromic neurodevelopmental disorder (NDD). Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired in matching peripheral blood mononuclear cells, histone H3 K27 acetylation ChIP-seq indicated that these BAP1 variants induced genome-wide chromatin state alterations, with enrichment for regulatory regions surrounding genes of the ubiquitin-proteasome system (UPS). Altogether, these results define a clinical syndrome caused by rare germline missense BAP1 variants that alter chromatin remodeling through abnormal histone ubiquitination and lead to transcriptional dysregulation of developmental genes.

overall_design: Epigenetic analyzes from individuals carrying a BAP1 variants and healthy family members

first: Sébastien

last: Küry

first: Frédéric

last: Ebstein

first: Thomas

last: Besnard

first: Ming-Kang

last: Lee

first: Virginie

last: Vignard

first: Tiphaine

last: Hery

first: Mathilde

last: Nizon

first: Grazia

last: Mancini

first: Jacques

last: Giltay

first: Benjamin

last: Cogné

first: Kirsty

last: Mc Walter

first: Wallid

last: Deb

first: Hagar

last: Mor-Shaked

first: Hong

last: Li

first: Rhonda

middle: E

last: Schnur

first: Ingrid

last: Wentzensen

first: Anne-Sophie

last: Denommé-Pichon

first: Cynthia

last: Fourgeux

first: Frans

middle: W

last: Verheijen

first: Eva

last: Faurie

first: Rachel

last: Schot

first: Cathy

last: Stevens

first: Daphne

middle: J

last: Smits

first: Eileen

last: Barr

first: Ruth

last: Sheffer

first: Jonathan

last: Bernstein

first: Chandler

last: Stimach

first: Eliana

last: Kovitch

first: Vandana

last: Shashi

first: Kelly

last: Schoch

first: Whitney

last: Smith

first: Richard

last: van Jaarsveld

first: Anna

last: Hurst

first: Kirstin

first: Evan

last: Baugh

first: Suzanne

last: Bohm

first: Emílie

last: Vyhnálková

first: Lukas

last: Ryba

first: Capucine

last: Delnatte


title: Normality sensing of Skint1 and immunosurveillance by dendritic epidermal T cells (DETC)

first: Duncan

last: McKenzie


title: Transcriptional alterations in human keratinocytes induced by a novel synthetic atRA-polyamine conjugate

city: Patras

first: Katerina

last: Grafanaki

state: Western Greece

address: Asklipiou 1

department: Department of Biochemistry

institute: University of Patras

summary: Herein, to assess the beneficial properties of aTRA at the molecular level on human keratinocytes (HaCat),  we measured expression levels of important genes using Microarray analysis.

overall_design: We performed Microarray analysis using the standard protocol to identify differential expression of genes after RASP treatment in HaCaT cells.


title: Transcriptional profiles of B. bronchiseptica survived inside Dictyostelium discoideum or cultured in medium

city: Athens

first: Longhuan

last: Ma

state: Georgia

address: 500 D. W. Brooks Dr.

department: Infectious Diseases

institute: University of Georgia

summary: Purpose: To filter genes that may contribute to introcellualr survival of B. bronchiseptica inside Dictyostelium discoideum, the genes that differently expressed when bacteria inside amoebae or in culture medium are selected as target genes.

overall_design:
Comapring the genes expression of intro-amoeba survived bacteria with medium cultured bacteria to see what genes are regulated when bacteria need to resist amoebal phygocytosis.

The processed data has been updated on Jan 2, 2022.

first: Israel

last: Rivera

first: Bodo

last: Linz


title: The landscape of H3K4me3 associate interactions between chromatin and RNAs in rice [ssDRIP-seq]

first: Xingyu

last: Huang

address: 866 Yuhangtang Road, Hangzhou, Zhejiang Province

institute: Life Sciences Institute (LSI), Zhejiang University (ZJU)

summary: High-order rice chromatin contains numerous interactions among DNA, RNA and protein to regulate critical biological processes in various aspects of rice life. We developed an effective method for mapping histone-mediated chromatin associated RNA-DNA interactions, followed by paired-end-tag sequencing (ChRD-PET) in rice. With H3K4me3 ChRD-PET, H3 ChRD-PET and RNase H treated H3K4me3 ChRD-PET, we present a highly comprehensive map of RNA and chromatin interactions around promoters in rice MH63. Through integrating ChIA-PET (published data), ChRD-PET and ssDRIP-seq data analysis, we demonstrated the function of RNAs-chromatin interactions in different level. We also conducted ATAC-seq and integrative analysis uncovered the relationship of epigenetic modifications and ChRD-PET interactions. Our findings firstly revealed the map and features of RNAs-chromatin interactions in rice.

overall_design: Here, we developed a method for mapping histone-mediated chromatin associated RNA-DNA interactions followed by paired-end-tag sequencing (ChRD-PET) and generate H3K4me3-mediated ChRD-PET data in rice. We also performed R-loop positions by ssDRIP-seq, whole-transcriptome by RNA-seq, and chromatin accessibility by ATAC-seq. Together, we revealed the map and features of RNAs-chromatin interactions in rice. Total RNA was isolated from seedlings at 8:00AM using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 2µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).

first: Qin

last: Xiao


title: Characterization of molecular changes associated with aging in the mouse auditory nerve

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Overall goal of the study is to identify key molecular regulators that change in the auditory nerve as a function of aging

overall_design: Three experimental replicates of auditory nerve (AN) from young (2 months) and old (2.5 years) CBA/CaJ mice were compared by RNAseq analysis

first: Hainan

last: Lang

first: Clarisse

last: Paganiban

first: Kenyaria

last: Noble


title: Age-related changes of gene expression profiles in Drosophila

city: Grand Forks

first: Alexei

last: Tulin

state: North Dakota

address: 501 N Columbia Rd Stop 9061

department: Epigenetics Department

institute: University of North Dakota

summary: An individual’s gene expression profile changes throughout life.  This change in gene expression is shaped by differences in physiological needs and functions between the younger and older organism.  Here we report a transcriptomic analysis of Drosophila melanogaster using microarrays.  We compared the expression profiles of two-day-old female adult flies with those of 45-day-old flies.  We identified 1184 genes with pronounced expression level differences between young and old age groups.  Most genes involved in muscle development/maintenance that display different levels of expression with age were downregulated in older flies.  Many of these genes contributed to sarcomere formation and function.  Several of these genes were functionally related to direct and indirect flight muscles; some of them were exclusively expressed in these muscles.  Conversely, several genes involved in apoptosis processes were upregulated in aging flies.  Close to half of these genes, such as different caspases, promote cell death, whereas the other half is associated with the inhibition of apoptosis.  Several genes that inhibit apoptosis contribute to cell-type maintenance for different cell groups, including neurons, cardiac cells, and salivary gland cells.  In addition, several genes involved in resistance to toxic chemicals were upregulated in aging flies, which is consistent with a global upregulation of the defense response system in aging flies.  Finally, 232 of the differentially expressed genes had no known functions.

overall_design: In total 6 samples: 3 biological replicates of 3 days-old flies and 3 biological replicates of 45 days-old flies

first: Bordet

last: Guillaume

first: Lodhi

last: Niraj

first: Kossenkov

middle: V

last: Andrew

first: Tulin

last: Alexei


title: The landscape of H3K4me3 associate interactions between chromatin and RNAs in rice [RNA-seq]

city: Hangzhou


title: A balanced Oct4 protein interaction network is crucial for maintaining pluripotency

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary:
Oct4 is considered a master transcription factor for pluripotent cell self-renewal and embryo development.
It primarily collaborates with other transcriptional factors or coregulators to maintain pluripotency.
However, it is still unclear how Oct4 interacts with its partners.
Here, we show that the Oct4 linker interface mediates competing and balanced Oct4 protein interactions which are crucial for
maintaining pluripotency. Linker mutant ESCs maintain the key pluripotency genes expression,
but show decreased expression of self-renewal genes and increased expression of differentiation genes which result in impaired
ESCs self-renewal and early embryonic lethality. Linker mutation dose not affect Oct4 genomic binding and transactivation potential,
but breaks the balanced Oct4 interactome. In mutant ESCs, the interaction between Oct4 and Klf5 was decreased,
but Oct4-Cbx1, Ctr9, Cdc73 interactions were increased which disrupt the epigenetic state of ESCs.
Overexpression of Klf5 or knockdown Cbx1, Cdc73 rescue the cellular phenotype of linker mutant ESCs by rebalancing Oct4
interactome indicating that different partners interact with Oct4 competitively.
Thus, by showing how Oct4 interacts with different partners, we provide novel molecular insights to explain how Oct4 contributes
to the maintenance of pluripotency.
RNA samples to be analyzed by qRT-PCR and microarrays were prepared using RNeasy Mini Kit (QIAGEN) with
on-column DNA digestion. Complementary DNA for qRT-PCR was synthesized with the M-MLV Reverse Transcriptase (Affymetrix).
Transcript levels were determined using ABI PRISM Sequence Detection System 7900 and gene expression was normalized to the
housekeeping gene Gapdh.
300 ng of total RNA per sample was used as input using a linear amplification protocol (Ambion) which involved synthesis of
T7-linked double-stranded cDNA and 12 hours of in vitro transcription incorporating biotin-labeled nucleotides.
Purified and labeled cRNA was then hybridized for 18 h onto MouseRef-8 v2 expression BeadChips (Illumina) following the manufacturer’s instructions.
After washing, chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina).
The bead intensities were mapped to the corresponding gene information using BeadStudio 3.2 (Illumina) and background correction was performed
using the Affymetrix Robust Multi-array Analysis (RMA) background correction model (Irizarry et al., 2003).
Variance stabilization was performed using the log2 scaling,
and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples
were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.

overall_design:
10 samples were analyzed
WT-res, Mouse wild type Oct4 rescued ZHBTc4, 2 replicates
L80A-res, Mouse L80A Oct4 rescued ZHBTc4, 2 replicates
ZHBTc4, Mouse normal ZHBTc4, 2 replicates
WT/WT, Mouse embryos derived from wild type homozygous Embryonic Stem cells, 2 replicates
L80A/L80A, Mouse embryos derived from 1M homozygous Embryonic Stem cells, 2 replicates

first: Dong

last: Han

first: Guangming

last: Wu

first: Hannes

last: Drexler

first: Daniela

last: Gerovska

first: Kenjiro

last: Adachi

first: Hans

middle: R

last: Schöler


title: Transcriptomic analysis of lung epithelial cells after LPS inhalation

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: Lung ECs express low levels of MHC-I at their surface. These levels are modestly increase 96h after LPS inhalation. At the transcriptional level, AT1, AT2 and Bronchiolar ECs highly increase the expression of MHC-I coding transcripts that reach level as high as mTECs. The amount of transcripts coding for Tap1, Tap2, Psmb8, Psmb9 and Psmb10 stay low compare to mTECs and seems limiting for an efficient surface expression of MHC-I in these three types of lung ECs.

overall_design: The RNA was extracted from primary AT1, AT2, and bronchiolar epithelial cells isolated from mice lung. Three (C57BL/6 LPS and NaCl), two (Stat1/Stat2 dKO LPS and NaCl (AT2)) or one (Nlrc5 KO LPS and NaCl, and Stat1/Stat2 dKO NaCl (AT1 and Bronchiolar ECs)  biological replicates were included per condition. Each biological replicate contained FACS-sorted primary lung ECs pooled from 3 mice. Lung were harvested 96h post LPS or NaCl inhalation.

first: Justine

last: Mathé

first: Mohamed

last: Benhammadi

first: Koichi

middle: S

last: Kobayashi

first: Sylvie

last: Brochu


title: The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice [ChRD-PET]

first: Xingyu

last: Huang

summary: High-order rice chromatin contains numerous interactions among DNA, RNA and protein to regulate critical biological processes in various aspects of rice life. We developed an effective method for mapping histone-mediated chromatin associated RNA-DNA interactions, followed by paired-end-tag sequencing (ChRD-PET) in rice. With H3K4me3-mediated ChRD-PET, H3  ChRD-PET and RNase H treated H3K4me3-mediated ChRD-PET data, we present a highly comprehensive map of RNA and chromatin interactions in rice MH63.  Through integrating ChIA-PET (published data) , ChRD-PET and ssDRIP-seq data analysis, we demonstrated the function of RNAs-chromatin interactions in different level. We also conducted ATAC-seq and integrative analysis uncovered the relationship of epigenetic modification and ChRD-PET interactions. Our findings  revealed the map and features of RNAs-chromatin interactions in rice.

overall_design: Here, we developed a method for mapping  histone-mediated chromatin associated RNA-DNA interactions followed by paired-end-tag sequencing (ChRD-PET)  and  generate H3K4me3-mediated ChRD-PET data in rice. We also performed R-loop positions by ssDRIP-seq, whole-transcriptome by RNA-seq, and chromatin accessibility by ATAC-seq. Together, we revealed the map and features of RNAs-chromatin interactions in rice.

first: Qin

last: Xiao


title: The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice [ATAC-seq]


title: Acute metaplastic injury of wild-type and Ifnar1-/-mice.

status: Public on Dec 09 2021

city: St. Louis

first: Jose

middle: Bernardo

last: Saenz

state: Missouri

address: 660 S. Euclid Avenue

department: Medicine

institute: Washington University in St. Louis School of Medicine

summary: Metaplastic injury of mice using high-dose tamoxifen (HD-Tam) for 2 daily injections.

overall_design: Age-matched, wild-type C57BL/6J or Ifnar1-/- mice were treated with high-dose tamoxifen (HD-Tam) for 48 hours. Gastric corpus tissue was collected, and RNA was isolated from three littermate/cagemate mice per genotype per treatment.

middle: B


title: Metaplastic injury in mice with Adar1-sufficient and -deficient chief cells

summary: Metaplastic injury of Adar1-sufficient (WT) and -deficient (Adar1fl/fl;Mist1Cre-ERT/+) mice using vehicle or high-dose tamoxifen (HD-Tam) for 2 daily injections.

overall_design: Age-matched wild-type (C57BL/6) mice were treated with either vehicle (24 hours) or HD-Tam for 2 daily injections. In addition, Adar1fl/fl;Mist1Cre-ERT/+ mice were treated with 7 days of low-dose tamoxifen to induce Cre recombination, followed by 2 daily injections of either vehicle or high-dose tamoxifen (HD-Tam) for 48 hours. For all mice, gastric corpus tissue was collected, and RNA was isolated.


title: Acute and chronic gastric injury (corpus)

summary: Metaplastic injury of mice using high-dose tamoxifen (HD-Tam) or chronic Helicobacter pylori (Hp) infection.

overall_design: Wild-type C57BL/6J were treated with either vehicle (24 hours), high-dose tamoxifen (HD-Tam) for 48 hours, or infected with Helicobacter pylori (Hp) for 6.5 months. Gastric corpus tissue was collected, and RNA was isolated from two littermate/cagemate mice per treatment.


city: Münster

address: Röntgenstraße 20

department: Cell and developmental biology

summary: Oct4 is considered a master transcription factor for pluripotent cell self-renewal and embryo development. It primarily collaborates with other transcriptional factors or coregulators to maintain pluripotency. However, it is still unclear how Oct4 interacts with its partners. Here, we show that the Oct4 linker interface mediates competing and balanced Oct4 protein interactions which are crucial for maintaining pluripotency. Linker mutant ESCs maintain the key pluripotency genes expression, but show decreased expression of self-renewal genes and increased expression of differentiation genes which result in impaired ESCs self-renewal and early embryonic lethality. Linker mutation dose not affect Oct4 genomic binding and transactivation potential, but breaks the balanced Oct4 interactome. In mutant ESCs, the interaction between Oct4 and Klf5 was decreased, but interactions between Oct4 and Cbx1, Ctr9, Cdc73 were increased which disrupt the epigenetic state of ESCs. Overexpression of Klf5 or knockdown Cbx1, Cdc73 rescue the cellular phenotype of linker mutant ESCs by rebalancing Oct4 interactome indicating that different partners interact with Oct4 competitively. Thus, by showing how Oct4 interacts with different partners, we provide novel molecular insights to explain how Oct4 contributes to the maintenance of pluripotency.

overall_design: Examination of Oct4, H3K4me3, H3K36me3 , H3K9me3 Chip-seq and ATAC-seq in mouse WT and L80A Oct4 embryonic stem cells


title: Tissue metabolites in diffuse glioma and their modulations by IDH1 mutation, histology and treatment

city: Tuebingen

first: Christoph

last: Trautwein

address: Roentgenweg 13

department: Werner Siemens Imaging Center

institute: University of Tuebingen

summary: The discovery of the oncometabolite 2-hydroxyglutarate in isocitrate dehydrogenase (IDH)1-mutated tumor entities affirmed the role of metabolism in cancer. Yet, large databases with gene expression data and tissue metabolites that are modulated by IDH1 mutation remain an area of development.

overall_design: Here, we present an unprecedented and valuable resource for tissue gene expression in diffuse glioma and their modulations by IDH1 mutation, histology and tumor treatments in 88 tissue samples (32 astrocytoma, 23 oligodendroglioma, 33 glioblastoma) from 71 diffuse glioma patients (17 patients with two resection time points), investigated by RNA sequencing (and NMR-based metabolomics).

first: Laimdota

last: Zizmare

first: Irina

last: Mäurer

first: Benjamin

last: Bender

first: Björn

last: Bayer

first: Ulrike

last: Ernemann

last: Tatagiba

first: Stefan

last: Grau

first: Bernd

last: Pichler

first: Marco

last: Skardelly

first: Ghazaleh

last: Tabatabai

first: Nicolas

last: Casadei

first: Caspar

last: Groß

first: Jakob

last: Amend

first: Antje

last: Schulze Selting


title: HIF-1a tunes T follicular helper cell differentiation during acute viral infection

city: Hamilton

first: Brendan

middle: McNie

last: Jeffrey

state: MT

address: 903 South 4th Street

department: BCBB

institute: NIH

summary: T follicular helper (Tfh) cells provide signals to initiate and maintain the germinal center (GC) reaction and are crucial for the generation of robust antibody responses. We found that hypoxia inducible factor-1 (HIF-1a) is an inhiibitor of Tfh generation in a mouse model of acute viral infection, and that HIF-1a mediates its effects by suppressing mTORC1 activity.

overall_design: Bulk RNA-seq of WT or HIF-1a knockout LCMV-specific CD4 T cells, sorted into Th1, pre-Tfh, and GC Tfh populations.

first: Bonnie

last: Huang

first: Pamela

last: Schwartzberg


title: The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.

city: Chicago

first: WEN-CHING

last: CHAN

state: IL

department: Biological Sciences Division

institute: The University of Chicago

summary: Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However, purifying them from within the bulk tumor has been challenging, so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC-transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells (more precisely referred to as leukemia propagating cells within our transplantation model). In addition, the side population within the leukemia evolves with serial transplantation, increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non-side population cells when transplanted into syngeneic recipients. RNA-sequencing analysis of sorted side population cells compared to non-side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt-signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt-signaling were significantly upregulated in the side population. Overall, these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt-pathway as a likely genetic driver of leukemia stem cell fate.

overall_design: mRNA expression comparison between sorted side population and non-side population in 3 zebrafish ALL tumors

first: Jeremy

middle: T

last: Baeten

first: Michael

last: Waarts

first: Margaret

last: Pruitt

first: W

last: Chan

first: J

last: Andrade

first: Jill

middle: O

last: de Jong


title: Hsa_circ_0098181 suppresses hepatocellular carcinoma through miR-18a-3p/PPARA axis

city: Shanghai

first: Gong

middle: Ke

last: Tao

address: Jimo Road 150#

institute: easthospital

summary: To explore the potential downstream miRNA of hsa_circ_0098181, we performed a miRNA sequencing.

overall_design: Ten human samples have been analyzed, including five HCC samples and five para-carcinoma samples.

first: Yuan-Yuan

last: LUO

first: Ke-Gong

last: TAO

first: Yong

last: LIN

first: Xin

last: ZENG


title: Sequence properties of human acidic transcriptional activation domains

status: Public on Dec 08 2021

first: Barak

middle: A

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University School of Medicine

summary: Acidic activation domains are intrinsically disordered regions of transcription factors that bind coactivators. The intrinsic disorder and low evolutionary conservation of activation domains have made it difficult to identify the sequence features controlling AD activity. To address this problem, we designed thousands of variants in seven acidic activation domains and measured their activities with a new high-throughput assay in human cell culture. We found that strong activation domain activity required a balance between the number of acidic residues and aromatic and leucine residues. These findings motivated a predictor of activation domains that scans the human proteome for clusters of aromatic and leucine residues embedded in regions of high acidity. This predictor identifies known activation domains and accurately predicts new ones. Our results support a flexible model of activation domains in which acidic residues solubilize hydrophobic motifs so that they can interact with coactivators.

overall_design: To measure transcriptional activation domain activity, we used FACS to separate cells with different GFP levels of a reporter construct. We sequenced the barcodes attached to each activation domain in each sorted population.

first: Max

last: Staller


title: Ribosome profiling of H9 PUS7KO

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

institute: Lund University

summary: Transfer RNA (tRNA)-derived fragments (tRF) are emerging small noncoding (nc) RNAs that, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here we show that pseudouridylation (Y) of a stem-cell-enriched tRF subtype, mTOG, selectively modulates malignant protein synthesis programs, thereby promoting differentiation of myelodysplastic syndrome (MDS) hematopoietic stem and progenitor cells (HSPC). Building on evidence that mTOG targets the polyadenylate-binding protein cytoplasmic 1 (PABPC1), we employed isotope exchange proteomics to reveal critical interactions between mTOG and functional RNA-recognition motif (RRM) domains in PABPC1. Mechanistically, this hinders the recruitment of the translational co-activator PABPC1-interacting protein 1 (PAIP1)3 and selectively represses translation of transcripts sharing pyrimidine-enriched sequences (PES) in their 5’UTR including 5’ terminal oligopyrimidine tracts (TOP) that encode protein machinery components, and are frequently altered in cancer4. Significantly, mTOG dysregulation leads to aberrant 5’PES mRNA translation in malignant MDS-HSPC and is clinically associated with leukemic transformation and decreased patient survival. Taken together, these results unveil a critical role for tRF and Y in difficult-to-treat subsets of MDS characterized by high risk of progression to acute myeloid leukemia.

overall_design: Evaluation of hESC WT and PUS7-KO translatome using ribosome profiling

first: Nicola

last: Guzzi

middle: C

last: Ngoc

first: Cristian

last: Bellodi


title: Interferon gamma constrains type 2 lymphocyte niche boundaries during mixed inflammation

city: San Francisco

first: Kelly

last: Cautivo

state: California

address: 513 Parnassus Av

institute: UCSF

summary: We used RNAseq to define how IFNγ signaling restricts the activated T2L transcriptome in vivo, including potentital pathways associated with T2L trafficking or tissue residency

overall_design: RNAseq was performed on lung and adipose tissue ILC2s from naïve or IL33+/- IFNγ treated mice

first: Ari

last: Molofsky


title: Multiomic profiling of checkpoint inhibitor-treated melanoma: Identifying predictors of response and resistance, and markers of biological discordance

city: Herston

first: Felicity

last: Newell

address: 300 Herston Rd

institute: QIMR Berghofer Medical Research Institute

summary: This study concurrently examined the genome, transcriptome, methylome and immune cell infiltrates in baseline tumors from advanced cutaneous melanoma patients treated with anti-PD-1 +/- anti-CTLA-4 immune checkpoint immunotherapy. Illumina MethylationEPIC BeadChip array analysis of 43 melanoma tumors was carried out as part of the study. Higher PSMB8 methylation (and therefore lower PSMB8 expression) was associated with poor response to immunotherapy. There were higher amounts of CD8+ T cells, as estimated by methylCIBERSORT, in the tumor microenvironment of good responders. Although we observed a significant correlation between PD-L1 expression and methylation of the cg197224470 CpG site, there was no significant difference between PD-L1 methylation in good and poor responders.

overall_design: Illumina Infinium MethylationEPIC BeadChip array analysis of 43 melanoma tumours. Samples were collected prior to immune checkpoint immunotherapy

first: Ines

last: Silva

first: Peter

last: Johansson

first: Alexander

last: Menzies

first: James

last: Wilmott

first: Venkateswar

last: Addala

first: Matteo

last: Carlino

first: Helen

last: Rizos

first: Katia

last: Nones

first: Jarem

last: Edwards

first: Vanessa

last: Lakis

first: Stephen

middle: H

last: Kazakoff

first: Pamela

last: Mukhopadhyay

last: Ferguson

first: Conrad

last: Leonard

first: Lambros

last: Koufariotis

first: Scott

last: Wood

first: John

middle: F

last: Thompson

first: Andrew

last: Spillane

first: Robyn

middle: P

last: Saw

first: Kerwin

last: Shannon

last: Pearson

first: Graham

last: Mann

first: Nicholas

middle: K

last: Hayward

first: Richard

last: Scolyer

last: Waddell

first: Georgina

last: Long


title: Deconvolution of breast tumors for optimal chemotherapy selection

city: Amsterdam

first: Lennart

last: Kester

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Extensive work in pre-clinical models has shown that microenvironmental cells influence many aspects of cancer cell behavior including metastatic potential and their sensitivity to therapeutics. In the human setting, this behavior is mainly correlated with the presence of immune cells, whilst the relevance of other cell types have been largely ignored. Here, in addition to T cells, B cells, macrophages and mast cells, we identified the relevance of non-immune cell types for breast cancer survival and therapy benefit, including fibroblast, myoepithelial cells, muscle cells, endothelial cells, and 7 distinct epithelial cell types. Using single-cell sequencing data, we generated reference profiles for all these cell types. We used these reference profiles in deconvolution algorithms to optimally detangle the cellular composition of over 3500 primary breast tumors of patients that were enrolled in the SCAN-B and MATADOR clinical trials, and for which bulk mRNA sequencing data was available. This large data set enables us to identify and subsequently validate the cellular composition of microenvironments that distinguish differential survival and treatment benefit for different treatment regiments in primary breast cancer patients.

overall_design: Single-cell mRNA sequencing of 12 breast tumors for generation of reference profiles to use in bulk mRNA sequencing deconvolution

first: L

first: D

last: Seinstra

last: van der Velden

first: E

last: Voest

first: A

last: van Oudenaarden

first: J

last: van Rheenen


title: Transcriptional alterations in human keratinocytes induced by a novel synthetic atRA-polyamine conjugate (miRNA-Seq)

city: Patras

first: Katerina

last: Grafanaki

address: Asklipiou 1

institute: University of Patras

summary: Herein, to assess the beneficial properties of aTRA at the molecular level on human keratinocytes (HaCat),  we measured expression levels of miRNAs using NGS analysis

overall_design: We performed semiconductor sequencing using the standard protocol to analyze the data measuring the abundance of miRNAs.

first: Dimitrios

last: Anastasakis


title: Genome-scale Screening in a Rat Haploid System Identifies Thop1 as a Modulator of Pluripotency Exit

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

institute: Nankai University

summary: Rat embryonic stem cells (ESCs), which are widely studied, can self-renew and exhibit pluripotency in long-term culture, but the mechanism underlying how they exit pluripotency remains obscure. Rat haploid ESCs (haESCs) enable advances in the discovery of unknown functional genes owing to their homozygous and pluripotent characteristics. Herein, we performed genome-wide mutation using piggyBac transposons in rat haESCs and obtained differentiation-retarded mutants assisted by Rex1-GFP reporter selection. High-throughput sequencing analysis further revealed numerous insertions related to various pathways affecting random differentiation. Thereafter, deletion of Thop1 (one candidate gene in the screened list) arrested the differentiation of rat ESCs by inhibiting the phosphorylation of ERK1/2, whereas overexpression of Thop1 promoted rat ESCs exit from pluripotency. Our findings provide an ideal tool to study functional genomics in rats: a homozygous haploid system carrying a pluripotency reporter that facilitates robust discovery of the mechanisms involved in the self-renewal or pluripotency of rat ESCs.

overall_design: Comparation of the transcriptomes between and rat WT-haESCs and Thop1-KO haESCs by RNA-seq analysis

first: Mei

last: Xu

first: Wenhao

last: Zhang

first: Yiding

last: Zhao