title: RNA N6-methyladenosine reader YTHDC1 is essential for TGF-beta-mediated metastasis of triple negative breast cancer [RNA-Seq]

city: Monrovia

first: Jianjun

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: RNA N6-methyladenosine (m6A) modification and its regulators fine tune gene expression and contribute to tumorigenesis. Here, we uncover the oncogenic role and mechanism of YTHDC1, an m6A reader positively correlated to poor prognosis in breast cancer patients. In a mammary fat pad mouse model, YTHDC1 significantly promoted lung metastasis of triple negative breast cancer (TNBC) cells. Using transcriptome-wide sequencing techniques, we found dysregulation of metastasis-related pathways following YTHDC1 depletion and demonstrated that YTHDC1 is critical for nuclear export of SMAD3 mRNA. YTHDC1 depletion desensitizes TNBC cells to TGF-β, resulting in impaired TGF-β-induced gene signature and inhibition on epithelial-mesenchymal transition (EMT) and cell migration/invasion, which could be at least partially restored by SMAD3 overexpression. Furthermore, we show that the ability of YTHDC1 to recognize m6A on SMAD3 RNA is important for its oncogenic role. Collectively, our study unravels YTHDC1 as vital for distant TNBC metastasis by promoting TGF-β-mediated EMT via SMAD3.

overall_design: For whole cell RNA-seq, MDA-MB-231 YTHDC1 KO cells (sgA and sgB) and a control (sgNS) was sequenced in biological replicates. For nuclear and cytoplasmic RNA-seq, nuclear and cytoplasmic fractions of sgB and sgNS groups were sequenced in biological duplicates.

first: Brandon

last: Tan

first: Keren

last: Zhou


title: RNA N6-methyladenosine reader YTHDC1 is essential for TGF-beta-mediated metastasis of triple negative breast cancer

status: Public on Mar 25 2023

last: Chen

state: CA

country: USA

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Reading and writing of mRNA m6A modification orchestrate mouse maternal-to-zygotic transition

status: Public on Mar 28 2023

city: Shanghai

first: Juan

last: Meng

address: Yueyang Road Street

country: China

institute: Center for Excellence in Brain Science and Intelligence Technology, Chineses Academy of Sciences

summary: Background: Maternal and zygotic mRNAs play critical roles in maternal-to-zygotic transition (MZT) stage and N6-methyladenosine (m6A) has been proven as an important RNA metabolism regulation system. However, the dynamic profiles of m6A modification during mammalian MZT and its potential functions remain largely unknown.  Results: Here we utilized m6A-seq, low-input RNA-seq, LiRibo-seq and low-input proteomic analysis to examine the mRNA regulation dynamics during mouse MZT. We found that m6A could be inherited from maternal origin or de novo added after fertilization. Interestingly, we observed the de novo m6A modification on mRNA during zygotic genome activation (ZGA), especially at major ZGA. Further analysis showed that m6A modification on maternal mRNAs not only correlates with mRNA degradation after fertilization, but also maintains the stability of a small group of mRNAs thereby promoting their translation after fertilization. Using CRISPR-Cas13d mediated RNA editing, we systemically evaluated the functions of ten m6A regulators and identified Ythdc1 and Ythdf2 as key m6A readers for mouse preimplantation development. By combining low-input RNA-seq, RNA immunoprecipitation (RIP) and qRT-PCR, we uncovered and verified that Ythdc1 can associate with a small group of m6A-tagged mRNAs and participate in their mRNA stability regulation.  Conclusions: Our integrated multi-omic analysis links m6A modification to the diverse fates of maternal and zygotic mRNAs and establishes a key role of m6A mediated RNA metabolism in mammalian MZT.

first: Wencheng

last: Zhu

first: Yufeng

last: Ding

first: Lei

last: Gu

first: Wenjun

last: Liu


title: Transcriptomic profiling of draining lymph nodes from immunized neonatal mice.

status: Public on Mar 24 2023

city: Gothenburg

first: Ali

last: Harandi

address: Box 435

department: Department of Microbiology and Immunology

country: Sweden

institute: University of Gothenburg

summary: Differential gene expression in mouse lymph nodes at 2 different time points following administration of antigen alone or together with adjuvant.

overall_design: Gene expression analysis in lymph node RNA treatment.

first: Malin

last: Östensson

first: Josefine

last: Persson


title: RNA N6-methyladenosine reader YTHDC1 is essential for TGF-beta-mediated metastasis of triple negative breast cancer [m6A-Seq]

overall_design: Immunoprecipitated and input groups were analyzed with two biological replicates for each group for a total of 4 samples.


title: Gene expression profile at single cell level of primary CD4+ T cells, infected with HIV in vitro and activated on plates coated with antiCD3/antiCD28 antibodies.

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary: CD4+ T cells respond differentially to the T cell receptor (TCR) stimulus: some get fully activated and proceed to cell proliferation; others are only minimally activated and remain non-dividing for as long as 7 days following exposure to the TCR stimulus. In this study, we identified genes expressed differentially in cells infected with HIV, compared to uninfected cells, in cell subsets with different proliferative responses to the TCR stimulus. We show common and unique gene expression signatures in HIV-positive cells depending on cellular proliferative response.

overall_design: Primary CD4+ T cells were isolated from peripheral blood of 3 different HIV-seronegative blood donors and viably frozen. On the day of the experiment, cells were thawed, cultured overnight, and then stained with a viable dye carboxyfluorescein diacetate succinimidyl ester to allow tracking of cell proliferation. The next day, cells were infected with HIV NL4-3 for 4-6 hours, and activated on plates coated with antiCD3/antiCD28 antibodies for 4 days. The cells were then removed from plates and incubated for additional 3 days in RPMI medium supplemented with 5% human serum and IL2+IL-15 cytokines. On day 7, cells were collected and processed for single cell RNA-Seq.

first: Xinlian

last: Zhang


title: Single nuclei multiomics of human stem cell-derived islets identifies deficiencies in lineage specification

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We profiled the transcritpome and ATAC profiles of human pancreatic islets generated from pluripotent stem cells. Multiomic profiling was also performed on primary human islets and in vivo matured SC-islets for comparision. We catalogued the ATAC associated signatures for each cell types in SC-islets and compared them to their human primiary islet counterparts. In vivo maturation of SC-islets were also compared with in vitro SC-islets. In this study, we identified key regulators associated with islet identity during differentiation and maturation. Gene manipulation of CTCF affects differentiating SC-islet cell fate to enteroendocrine-like lineage. ARID1B knockdown caueses islet cells to present mature signatures. These gene altered SC-islets were also sequenced.

overall_design: Single nulei multiome (RNA and ATAC) sequencing of human islets and stem cell derived islets.

first: Punn

last: Augsornworawat

middle: R


title: Gene expression profile of peripheral blood mononuclear cells from mild and severe COVID-19 patients, severely ill  COVID-19 patients treated with dexamethasone and healthy controls

status: Public on Mar 23 2023

city: Cincinnati

first: Ameet

last: Chimote

state: Ohio

address: 231 Albert Sabin Way, ML 0585, CARE 6884

department: Internal Medicine- Nephrology

institute: University of Cincinnati

summary:
The objective of this experiment was to compare the transcriptomic profile (NanoString platform)  of peripheral blood mononuclear cells (PBMCs) from COVID-19 patients with mild disease, and patients with severe COVID-19 with and without dexamethasone treatment, and healthy controls.
We analyzed PBMCs from 4 mild COVID patients, 3 severe COVID patients,4 severe COVID patients treated with dexamethasone, and 5 healthy controls

overall_design: Total RNA was isolated from the patient and control PBMCs using the E.Z.N.A. total RNA isolation Kit (Omega Bio-tek).We analyzed 100 ng of RNA from four mild, three severe, and four severe COVID-19 patients treated with dexamethasone, along with five unexposed healthy donors using the human Host Response CodeSet panel (NanoString), which includes 773 genes covering the host immune response to infectious diseases, and 12 internal reference genes for data normalization. The RNA samples were hybridized as per the manufacturer’s instructions, and each sample was read in a multiplexed reaction with the reference (positive, negative controls, and housekeeping genes) probes on the NanoString nCounter Flex instrument.

middle: A

first: Laura

last: Conforti


title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T-cell acute lymphoblastic leukemia

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

summary: Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including MYC, DTX1, HES4, IL7R, and NOTCH3. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.

overall_design: Examination of the epigenetic and transcriptomic changes in T-ALL cell lines following NOTCH1 inhibition and RUNX1 knockdown.


title: Small non-coding vault RNA1-2 modulate expression of cell membrane proteins through nascent RNA silencing

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

country: United Kingdom

institute: University of Oxford

summary: We used sequencing analyses to identify dysregulated genes upon svtRNA1-2 knock-out at the chromatin level in HEK293T cells. We found that svtRNA1-2 sequence KO dysregulated many genes at the chromatin levels indicating an important role of vtRNA1-2 within the cell.

overall_design: Chromatin-associated RNA profiles of HEK293 WT and svtRNA1-2 knockout cells were generated by deep sequencing, in triplicates.

first: J

last: Terenova

first: A

last: Alagia

first: F

last: Ketley

first: I

first: M

last: Gullerova


title: Differentially expressed lncRNAs in hDPSCs between the OCT4A-overexpressing and vector groups.

city: Guangzhou

first: hong

last: hong

address: No.56, Lingyuan West Road

institute: Hospital of Stomatology,,Sun Yat-sen University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To determine whether lncRNAs were involved in the OCT4A-related network that regulates the self-renewal of hDPSCs, human lncRNA microarrays were used to identify the lncRNA expression profiles in OCT4A-overexpressing and vector hDPSCs.  978 lncRNAs (250 of which were upregulated and 728 downregulated) and 404 mRNAs (222 of which were upregulated and 182 downregulated) were potential differentially expressed genes (fold change≥2, P<0.05).

overall_design: Differentially expressed lncRNAs was measured in hDPSCs between the OCT4A- overexpressing and vector groups.Three independent experiments were performed at each group.

first: Hong

last: Hong

first: Wei

last: Xi


title: The role of the Ep400/Kat5 chromatin remodeling complex in the cranial neural crest and orofacial clefting

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

summary: The cranial neural crest plays a fundamental role in orofacial development and morphogenesis. As a pluripotent and dynamic cell population, the cranial neural crest is undergoing vast transcriptional alterations throughout embryogenesis and the formation of facial structures. These transcriptional changes are regulated by several transcription factors and remodeling complexes. Previously, we revealed the relevance of the Ep400/Kat5 histone acetyltransferase complex in the cranial neural crest and showed that the knockout of Ep400 causes neural crest-related malformations such as orofacial clefting. Furthermore, a case study identified three patients carrying missense mutations in Kat5 who showed severe mental impairments as well as orofacial clefts.2 The exact molecular causes and mechanisms, however, are still unknown.   In this study we selectively knocked out Ep400 or Kat5 in the murine cranial neural crest cell line O9-1 to examine its roles in neural crest biology. To understand the regulatory effects of Ep400 and Kat5, knockout neural crest cells were investigated via bulk RNA sequencing to unravel transcriptomic changes in the affected cells. Bioinformatic analyses hinted at the regulation of major cellular functions such as proliferation, ATP generation and protein synthesis by the Ep400/Kat5 complex.   Reduced proliferation was confirmed by crystal violet staining, phospho-histone H3 staining and the determination of mitotic cells with condensed chromatin in vitro. We did not detect increased apoptosis in the knockout cell lines. The energetic profile of the cells was investigated by Seahorse technology. The ATP-rate assay showed a decreased glycolytic activity in Ep400- or Kat5-deficient cells. An O-propargyl-puromycin (OPP) Click-iT assay revealed a significant reduction in protein synthesis. To verify in vivo the discovered in vitro effects, Ep400 and Kat5 were selectively ablated in cranial neural crest using Wnt1-Cre in transgenic mice. The knockout of each of the subunits resulted in severe craniofacial malformations from E12.5 onwards. At E10.5 a significant reduction in neural crest-derived tissue and proliferation rate was evident.   The strong defect in orofacial structures of mice lacking Kat5 or Ep400 completely correspond to the milder orofacial malformations in patients carrying heterozygous missense mutations. Our results furthermore argue that changes of metabolism, protein synthesis and proliferation in cranial neural crest cells are responsible for the orofacial defects observed in patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for O9-1 wildtype cells and CRISPR/Cas9 knockout cell lines for Kat5 or Ep400.

first: Sebastian

last: Gehlen-Breitbach

first: Theresa

last: Schmid

first: Matthias

last: Weider

first: Lina

last: Gölz


title: Determination of MHV virion genome poly(A) tail length and 3' end additions.

city: DURHAM

first: ANKIT

last: GUPTA

address: TW 111 ALEXANDER DRIVE

department: RDBL

institute: NIEHS

summary: The mouse hepatitis virus (MHV) genomic RNA has a poly(A) tail required for replication. Here we investigated the presence of terminal poly(A) tail uridylation and guanylation in the virion RNA. After isolating the viral RNA followed by sequencing, we found a mean poly(A) tail of 66 nucleotides long with a peak of terminal uridylation on tails 55 to 66 nucleotides long.

overall_design: Direct RNAseq of RNA isolated from MHV virion

first: Ankit

last: Gupta

first: Brian

middle: N

last: Papas

first: Marcos

last: Morgan


title: Determination of MHV RNA poly(A) tail length and 3' end additions upon NCTC cells infection

summary: The mouse hepatitis virus (MHV) genomic and sub-genomic RNAs have 3’ poly(A) tails. The terminal addition of uridines to poly(A) tails has been shown to be a widespread modification. Here, we investigated the presence of 3' end additions on the MHV RNA poly(A) tails. To this end, we infected NCTC cells with MHV and isolated RNA at 24-hours post-infection (hpi). While the median poly(A) tail length of the MHV RNAs is around 50 nucleotides, we observed a peak of uridylation in transcripts with poly(A) tails about 40 nucleotides long

overall_design: Direct RNAseq of RNA isolated from MHV-infected NCTC cells at 24 hpi


title: Characterization of human hepatic natural killer cells in end-stage chronic liver diseases

status: Public on Mar 22 2023

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

address: 1450 Biggy Street, NRT 3514

institute: USC

summary: Hepatic Natural Killer (he-NK) cells are innate immune effectors that contribute to immune tolerance and eliminate dangerous “non-self” antigens. He-NK cells fall into two groups, liver resident (rNK) cells, mainly cytokine secretors, and infiltrating conventional NK (cNK) cells, which are cytotoxic. He-NK cell dysfunction and contribution to end-stage liver disease are not fully understood. The present study evaluates the transcriptomes of he-NK subpopulations in chronic hepatic disease of different etiologies, including sterile inflammation (non-alcoholic steatohepatitis - NASH), autoimmunity (primary sclerosing cholangitis - PSC), and viral infection (hepatitis C - HCV).

overall_design: Non-parenchymal cells were isolated from human livers using mechanical and enzymatical dissociation. NK cells (CD56+ CD3-) were FACS sorted and partitioned for scRNAseq using 10x genomics (kit 3’ v3.1) technology. Our analysis included cirrhotic livers from NASH (n=4), HCV (n=4), and PSC (n=4) patients and normal livers from healthy donors (n=4).

first: Matthew

middle: P

last: Salomon

first: Lucy

last: Golden-Mason


title: A nucleolar condensin-recruiting complex that regulates yeast chromosome III structure [ChIP-Seq]

city: charlottesville

first: Jeffrey

middle: S

last: Smith

state: VIRGINIA

address: 1340 jpa pinn hall

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary:
Purpose: To identify cohibin-dependent condensin binding sites throughout the yeast genome.
Conclusions: This ChIP-seq experiment showed that the condensin subunit, Brn1, was depleted from the RDT1 promoter in an lrs4Δ mutant strain. The experiment also showed that the Lrs4 subunit of the cohibin complex is highly enriched at the RDT1 promoter on chromosome III.

overall_design: ChIP-seq profiles of Brn1-myc, Lrs4-myc, Ctf3-myc,and Brn1-myc in lrs4Δ grown in YPD media.

first: Ryan

middle: D

last: Fine

first: Manikarna

last: Dinda

first: Minguang

last: Li


title: Allogenic and Autologous anti-CD7 CAR-T cell Therapies in Relapsed or Refractory T-Cell Malignancies

city: wuhan

first: Yinqiang

last: Zhang

address: Jiefang avenue no.1277

institute: Huazhong university of science and technology

summary: Chimeric antigen receptor-T (CAR-T) therapy remains to be investigated in T-cell malignancies. CD7 is an ideal target for T-cell malignancies but is also expressed on normal T cells, which may cause CAR-T cell fratricide. Donor-derived anti-CD7 CAR-T cells using endoplasmic reticulum retention have shown efficacy in patients with T-cell acute lymphoblastic leukemia (ALL). Here we launched a phase I trial to explore differences between autologous and allogeneic anti-CD7 CAR-T therapies in T-cell ALL and lymphoma. Ten patients were treated and 5 received autologous CAR-T therapies. No dose-limiting toxicity or neurotoxicity was observed. Grade 1-2 cytokine release syndrome occurred in 7 patients, and grade 3 in 1 patient. Grade 1-2 graft-versus-host diseases were observed in 2 patients. Seven patients had bone marrow infiltration, and 100% of them achieved complete remission with negative minimal residual disease within one month. Two-fifths of patients achieved extramedullary or extranodular remission. The median follow-up was 6 (range, 2.7- 14) months and bridging transplantation was not administrated. Patients treated with allogeneic CAR-T cells had higher remission rate, less recurrence and more durable CAR-T survival than those receiving autologous products. Allogeneic CAR-T cells appeared to be a better option for patients with T-cell malignancies.

overall_design: two patients achieved durable remission after receiving CD7 CAR-T cell therapies.To further explore the immune reconstitution after CAR-T cell infusion, we performed single-cell transcriptomic sequencing of PBMCs derived from the two patients. Sample 1 was from patient 1 at 12 months after autologous CAR-T treatment, and sample 2 from patient 5 at 9 months after allogeneic CAR-T therapy.

first: Chenggong

first: Heng

last: Mei

first: Yu

last: Hu


title: Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III [Micro-C seq]

summary:
Purpose: This study was designed to determine the mechanism of condensin and Sir2 recruitment to the RDT1 promoter region of S. cerevisiae chromosome III, and to test whether preventing condensin recruitment by deleting the key factors, Fob1 and Lrs4, significantly alters the conformation of chromosome III.
Conclusions: Conformational changes in chromosome III and loss of CEN12-rDNA looping in chromosome XII observed in lrs4? and fob1? mutants.

overall_design: Micro-C XL profiles of wild type, lrs4?, and fob1?, strains grown in YPD media were generated.

first: Zhenjia

last: Wang

first: Chongzhi

last: Zang


title: Microarray expression profile analysis of tobaccos responding to chilling stress

city: Chongqing

first: Kexuan

last: Deng

address: Tiansheng

institute: Southwest University

summary: To investigate the molecular mechanism of tobacco flower in response to the cold treatment, transcriptomic analysis was performed using Agilent Tobacco Gene Expression Microarrays.

overall_design: The seedling of two ﬂue cured tobacco varieties (Xingyan 1 and YunYan 85) with six true-leaf were grown at 28°C and 12°C for 10 days, and stem tips were collected for microarrays analysis.

first: Xiumei

last: Dai


title: Targeting advanced prostate cancer with STEAP1 chimeric antigen receptor T cell and tumor-localized IL-12 immunotherapy [scRNA-seq]

city: Seattle

first: John

middle: K

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: Six transmembrane epithelial antigen of the prostate 1 (STEAP1) is a compelling tumor-associated cell surface antigen for therapeutic targeting in solid tumors. Here, we identified broad expression of STEAP1 relative to the established theranostic target prostate-specific membrane antigen (PSMA) in a series of lethal metastatic prostate cancers which prompted the development of a STEAP1-directed chimeric antigen receptor (CAR) T cell therapy. STEAP1 CAR T cells demonstrated reactivity in low antigen density, antitumor activity across multiple metastatic human and mouse prostate cancer models, and preliminary safety in a human STEAP1 knock-in mouse model. In human-in-mouse and mouse-in-mouse studies, STEAP1 CAR T cell therapy yielded effective tumor responses, but antigen escape was appreciated as a recurrent mechanism of treatment resistance and STEAP1 antigen loss was associated with diminished tumor antigen processing and presentation. The application of tumor-localized interleukin-12 (IL-12) therapy in the form of a collagen binding domain (CBD)-IL-12 fusion protein as an adjunct to STEAP1 CAR T cell therapy enhanced antitumor efficacy by remodeling the immunologically cold tumor microenvironment of prostate cancer and combating STEAP1 antigen escape through the engagement of host immunity and epitope spreading. In summary, we describe the extent of STEAP1 expression in treatment-refractory metastatic prostate cancer, characterize a STEAP1 CAR T cell therapy with preclinical evidence of potency and safety, and nominate a combinatorial immunotherapy strategy to overcome barriers to the efficacy of CAR T cell therapy in advanced prostate cancer.

overall_design: Single cell RNA-Seq (scRNA-Seq) was performed on RM9 tumors treated with either vehicle (control group) and the tumors treated with collagen binding domain fused with interlukin-12 (CBD-IL-12) that represents the treatment group.

first: Vipul

last: Bhatia

first: Nikhil

middle: V

last: Kamat

first: Tiffany

middle: E

last: Pariva

first: Li-Ting

last: Wu

first: Annabelle

last: Tsao

first: Koichi

last: Sasaki

first: Huiyun

last: Sun

first: Gerardo

last: Javier

first: Ilsa

last: Coleman

first: Lauren

middle: T

last: Wiest

first: Ailin

first: Dmytro

last: Rudoy

first: Roman

last: Gulati

first: Radhika

last: Patel

first: Martine

last: Roudier

first: Lawrence

last: True

first: Michael

last: Haffner

first: Peter

last: Nelson

first: Saul

middle: J

last: Priceman

first: Jun

last: Ishihara


title: Targeting advanced prostate cancer with STEAP1 chimeric antigen receptor T cell and tumor-localized IL-12 immunotherapy

first: John

last: Lee

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: An ancient testis-specific IQ motif containing H gene regulates specific isoform expression during spermatogenesis

city: Madrid

first: Alfonso

last: Gutiérrez-Adán

address: Av. Puerta de Hierro 28

department: Animal Reproduction

country: Spain

institute: INIA

summary: Spermatogenic cells express more alternatively spliced RNAs than most whole tissues; however, the regulation of these events remains unclear. Here we characterize the function of a testis-specific IQ motif containing H gene (Iqch), whose expression has been confirmed to be testis specific in all mammalian species analyzed yet its role remains elusive. Using a mutant mouse model, we found that Iqch is essential for the specific expression of RNA isoforms during spermatogenesis. Through immunohistochemistry of adult mouse testis, we noted that Iqch was localized in somatic and germ cells, including spermatogonia, spermatocytes and round spermatids. Further, Iqch was expressed mainly in the nucleus at the stages spermatocyte and spermatid, where IQCH appeared juxtaposed with SRRM2 and ERSP1, suggesting that interactions among these proteins regulate alternative splicing (AS). By RNA-seq, we noted that mutant Iqch produces alterations in gene expression, including the clear downregulation of testis-specific lncRNAs and protein coding genes at the spermatid stage, and AS modifications, principally increased intron retention, resulting in complete male infertility. Interestingly, the presence of WT Iqch allowed us to identify novel spliced transcripts, while mutant Iqch modified the expression and use of hundreds of RNA isoforms, favoring the expression of the canonical form. This suggests that Iqch is part of a splicing control mechanism, essential in germ cell biology. Our findings reveal the role of Iqch in spermatogenesis and provide clues to the molecular mechanisms controlling the expression of RNA isoforms, mainly in the last stages of spermatogenesis

overall_design: Differential gene expression analysis in mice Iqch knockout testis compared to wild-type testis.

first: Paula

last: Navarrete-López

first: Marta

last: Lombó

first: María

last: Maroto

first: Raúl

last: Fernández-González

first: Eva

last: Pericuesta

first: Priscila

last: Ramos-Ibeas


title: Stochastic 10-cell profiling of an MCF-10A clone expressing chimeric EGFR and Erbb2 receptors

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

summary: ErbB2 activation of MCF10A cells gives rise to a multiacinar phenotype that is incompletely penetrant.  To identify candidate upstream regulators of the phenotype, an MCF10A-5E clone was subcloned to express chimeric receptors of human EGFR and rat Erbb2, and this B2B1 subclone was stochastically profiled (PMID: 20228812) after 24 hours of 3D culture with or without synthetic dimerization.

overall_design: B2B1 cells were grown in 3D culture for six days, treated with or without synthetic heterodimerizer (AP21967) for 24 hours, and cryoembedded for frozen sectioning.  10-cell samples or pool-and-split controls were randomly collected by laser-capture microdissection for analysis of transcriptional regulatory heterogeneities by stochastic profiling (Janes et al., Nat Methods 7(4):311-7 [2010]).

first: Lixin

last: Wang


title: Targeting advanced prostate cancer with STEAP1 chimeric antigen receptor T cell and tumor-localized IL-12 immunotherapy [bulk RNA-seq]

overall_design: Bulk RNA-Seq was performed on prostate cancer 22Rv1 control cells (22Rv1-WT), 22Rv1 STEAP1 CRISPR/Cas9 knockout cells (22Rv1-STEAP1-ko), and 22Rv1-STEAP1-ko cells with the rescue of STEAP1 (22Rv1-STEAP1-Ko+Addback). Bulk RNA-Seq was also performed on the 22Rv1 xenograft tumors which showed antigen loss. Formalin fixed paraffin embedded (FFPE) tumor tissues from the untransduced T cells (UT) treated group were used as control and the tumor samples from STEAP1-Bbζ CAR T cells represents the treatment group.

first: Vipul

last: Bhatia

first: Nikhil

last: Kamat

first: Tiffany

last: Pariva

first: Li-Ting

last: Wu

first: Annabelle

last: Tsao

first: Koichi

last: Sasaki

first: Huiyun

last: Sun

first: Gerardo

last: Javier

first: Ilsa

last: Coleman

first: Lauren

last: Wiest

first: Ailin

last: Zhang

first: Dmytro

last: Rudoy

first: Roman

last: Gulati

first: Radhika

last: Patel


title: Gene expression profiling in the puf4∆ (midlog), and gcn4∆ (midlog and oxidative stress) mutants of Cryptococcus neoformans.

city: Buffalo

first: John

middle: C.

last: Panepinto

state: NY

address: 955 Main Street Suite 5240

department: Microbiology and Immunology

institute: University at Buffalo

summary: This study aimed to investigate transcriptomic changes in Cryptococcus neoformans mutants. We report transcriptome wide changes in the puf4∆ under basal growth conditions (30˚C, midlog, YPD). We report transcriptome remodeling following hydrogen peroxide (H2O2) treatment in wildtype (H99) and gcn4∆ cells.

overall_design: Cells were grown to midlog growth stage at 30˚C, then indicated samples were treated with 1 mM H2O2 for 1 hour. Cells were pelleted and total RNA were extracted, DNase treated and sequenced using Illumina HiSeq platform.

first: Murat

last: Kalem


title: Ontogeny and Trophic Factor Sensitivity of Gastrointestinal Projecting Vagal Sensory Cell Types

status: Public on Mar 21 2023

first: Anna

last: Kamitakahara

address: 4661 Sunset Blvd, MS 135

institute: Children's Hospital Los Angeles

summary: Vagal sensory neurons (VSNs) located in the nodose ganglion provide information, such as stomach stretch or the presence of ingested nutrients, to the caudal medulla via specialized cell types expressing unique marker genes. Here, we leverage VSN marker genes identified in adult mice to determine when specialized vagal subtypes arise developmentally and the trophic factors that shape their growth. Experiments to screen for trophic factor sensitivity revealed that brain derived neurotrophic factor (BDNF) and glial cell derived neurotrophic factor (GDNF) robustly stimulate neurite outgrowth from VSNs in vitro. Perinatally, BDNF was expressed by neurons of the nodose ganglion itself, while GDNF was expressed by intestinal smooth muscle cells. Thus, BDNF may support VSNs locally, whereas GDNF may act as a target-derived trophic factor supporting the growth of processes at distal innervation sites in the gut. Consistent with this, expression of the GDNF receptor was enriched in VSN cell types that project to the gastrointestinal tract. Lastly, mapping of genetic markers in the nodose ganglion demonstrates that defined vagal cell types begin to emerge as early as embryonic day 13, even as VSNs continue to grow to reach gastrointestinal targets. Despite the early onset of expression for some marker genes, expression patterns of many cell type markers appear immature in prenatal life and mature considerably by the end of the first postnatal week. Together, the data support location-specific roles for BDNF and GDNF in stimulating VSN growth, and a prolonged perinatal timeline for VSN maturation in male and female mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse nodose ganglion samples at postnatal day 9 and 12 weeks of age.

first: Meaghan

last: McCoy


title: Reprogramming of human peripheral blood mononuclear cells into induced mesenchymal stromal cells

city: Loma Linda

first: Charles

last: Wang

address: 11021 Campus Street

institute: Loma Linda University

type: Methylation profiling by high throughput sequencing

summary: We reported direct reprogramming human PBMCs into induced MSCs using non-integrating episomal vectors, and performed epigenetic analysis, including chromatin openness and methylation status, along with transcriptomic analysis, on functional as well as non-functional induced MSCs from different reprogramming factors combinations, in order to better understand epigenetic signature of functional MSCs.

overall_design: RNA-seq, ATAC-seq, and RRBS methylation profiles of day 28 induced MSCs reprogrammed from human peripheral blood mononuclear cells by three different reprogramming factors combinations.

first: Wanqiu

last: Chen


title: Transcriptome profiling of the Chlamydomonas reinhardtii phot mutant

city: Grenoble

first: Dimitris

last: Petroutsos

address: 17 rue des Martyrs

country: France

institute: 4University of Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV

summary: To investigate the gene regulatory effect of the phototropin receptor PHOT,  RNAseq data of the corresponding knock-out mutant was compared to wt data grown in high and low light.

overall_design: Samples of liquid batch cultures grown autotrophically were analyzed by RNA sequencing prior and after high light exposure. This experiment was conducted in tripicates with CC-125 wt cultures and phot cultures.

first: M

last: Ruiz-Sola

first: Marius

last: Arend

first: YiZhong

last: Yuan

first: Zoran

last: Nikoloski


title: mtRF1 recognises non-canonical stop codons in human mitochondria

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

summary: The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial translation deviates from the standard genetic code which includes the reassignment of two arginine codons into stop codons {Jukes, 1993 #438}. Translation termination at these non-canonical stop codons requires a protein factor to release the newly synthesized polypeptide chain, however, the identity of this factor is not known currently{Nadler, 2021 #406}. Here, we used gene editing and ribo-profiling in combination with cryo-electron microscopy to establish that the unusual mitochondrial release factor 1 (mtRF1) detects the non-canonical stop codons. We show that loss of mtRF1 leads to stalling of mitochondrial ribosomes on non-canonical stop codons and consequent reduced translation of cytochrome C oxidase subunit 1 that results in decreased mitochondrial respiration. We show that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual distortion in the mRNA conformation and that the ribosomal RNA importantly participates in the specific recognition of the non-canonical stop codons.

overall_design: Ribosome profiling (Ribo-Seq) of mtRF1 KO and WT CAL51 cells (n=1)

first: Martin

last: Saurer

first: Marc

last: Leibundgut

first: Hima

last: Priyanka Nadimpalli

first: Alain

last: Scaiola

first: Tanja

last: Schönhut

first: Richard

middle: G

last: Lee

first: Oliver

last: Rackham

first: David

last: Gatfield

first: Aleksandra

last: Filipovska

first: Nenad

last: Ban


title: Determination of MHV RNA poly(A) tail length and 3' end additions upon 17-CL1 cells infection [17-CL1_WT]

first: ANKIT

last: GUPTA

summary: The mouse hepatitis virus (MHV) genomic and sub-genomic RNAs are 3’ polyadenylated. The length of the 3’ poly(A) tail is known to change during infection, but little is known about the molecular mechanisms driving this change. Here, we investigate the presence of terminal uridylation and terminal guanylation on the MHV poly(A) tail during infection. We infected 17-CL1 cells with MHV and isolated RNA at 24- and 48-hour post-infection (hpi). We observed that MHV RNAs poly(A) tails shortened during infection and that short poly(A) tails of about 20 nucleotides are highly uridylated.

overall_design: Direct RNAseq of RNA isolated from mouse hepatitis virus-infected 17-CL1 wildtype cells at 24 and 48 hour post infection (hpi)

first: Ankit

last: Gupta

first: Brian

last: Papas

first: Marcos

last: Morgan


title: Transcriptomic analysis of the pre-optic area and the mediobasal hypothalamus of female rats after perinatal exposure to ketoconazole or diethylstylbestrol

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

summary: Because perinatal exposure to diethylstilbestrol (DES; strong estrogen) or ketoconazole (KTZ; steroidogenesis inhibitor) delayed vaginal opening and GnRH secretion in female rats, we studied the hypothalamic transcriptome to identify their target genes.

overall_design: Female rats were exposed to vehicle or DES or KTZ during the perinatal period (gestation day 7 to postnatal day (PND) 22). Doses for DES were 0; 3; 6; 12 µg/kg bw/day and doses for KTZ were 0; 3; 6; 12 mg/kg bw/day. Expression of hypothalamic genes was analyzed by RNA-seq at PND22, PND42 and PND90. n=5/group

first: Delphine

last: Franssen

first: Anne-Simone

last: Parent


title: Single-cell analyses reveal the dynamic functions of Itgb2+ microglia subclusters at different stages of cerebral ischemia-reperfusion injury in transient middle cerebral occlusion mice model

city: guangzhou

first: Fanning

last: Zeng

state: Guangdong

address: Jingxi Street, Baiyun District

department: Department of Anesthesiology

institute: Nanfang hospital, Southern Medical University

summary: The underlying pathophysiological mechanisms of cerebral ischemia-reperfusion injury (CIRI) is intricate, and current studies suggest that neuron, astrocyte, microglia, endothelial cell, and pericyte all have different phenotypic changes of specific cell types after ischemic stroke. And microglia account for the largest proportion after CIRI. Previous transcriptomic studies of ischemic stroke have typically focused on the 24 hours after CIRI, obscuring the dynamics of cellular subclusters throughout the disease process. Therefore, traditional methods for identifying cell types and their subclusters may not be sufficient to fully unveil the complexity of single-cell transcriptional profile dynamics caused by an ischemic stroke. In this study, to explore the dynamic transcriptional profile of single cells after CIRI, we used scSTAR, a new bioinformatics method, to analyze the single cell transcriptional profile of day 1, 3 and 7 of transient middle cerebral artery occlusion (tMCAO) mice. Combining our bulk RNA sequence and proteomics data, we found that the Itgb2+ subclusters of microglia exhibited specific functions at three different time points after the tMCAO. Our further analysis revealed that the Itgb2+ microglia subcluster was mainly involved in energy metabolism, cell cycle, angiogenesis, neuronal myelin formation and repair at 1, 3 and 7 days after tMCAO, respectively. Our results suggested that Itgb2+ microglia act as a time-specific multifunctional immunomodulatory subcluster during CIRI, and the underlying mechanisms remain to be further investigated.

overall_design: Single-cell sequencing of the ipsilateral cerebral hemispheres of mice at 1, 3, 7 days after tMCAO and at day 7 of sham group.

first: Jun

last: Cao

first: Zexuan

last: Hong

first: Yujun

last: Liu

first: Jie

last: Hao

first: Zaisheng

last: Qin

first: Xin

last: Zou

first: Tao

last: Tao


title: Acetate and light stress timecourse expression profiling in C. reinhardtii

first: Dimitris

last: Petroutsos

summary: To investigate how acetate and high light stress affect gene expression in Chlamydomonas reinhardtii, RNAseq data from a timeline of cultures subjected to high light and different carbon sources was analyzed.

overall_design: Samples of liquid batch cultures grown auto or mixotrophically were analyzed by RNA sequencing prior and after high light exposure.

first: Marius

last: Arend

first: YiZhong

last: Yuan

first: M

last: Ruiz-Sola

first: Zoran

last: Nikoloski


title: Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion [ATAC-seq]

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

summary: This study comprehensively profiles the mSWI/SNF complexes throughout acute and chronic T cell stimulation, with and without small molecular inhibitors and degraders. Specifically, we find pan SWI/SNF and complex specific roles in both activation and exhaustion.

overall_design: Assay for transposase-accessible chromatin with sequencing of human primary CD8 positive T cells after acute or chronic stimulation using CD3/CD28 dynabeads at 0, 3, 24, 48, 72 hours, 6 days, and 9 days, with and without treatment and of mouse primary CD8 positive T cells after acute or chronic stimulation using CD3/CD28 dynabeads at 0, 48, 72 hours, 6 days, and 9 days, with and without treatment with mSWI/SNF inhibitors.

first: Dawn

last: Elena

first: Elena

last: Battistello

first: Kimberlee

last: Hixon

last: Comstock

first: Clayton

last: Collings

first: Iannis

last: Aifantis


title: Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion [RNA-seq]

summary:
This study comprehensively profiles the mSWI/SNF complexes throughout acute and chronic T cell stimulation, with and without small molecular inhibitors and degraders.
Specifically, we find pan SWI/SNF and complex specific roles in both activation and exhaustion.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of CD3/CD28 activated Human Primary CD8 positive T cells with and without treatment of mSWI/SNF inhibitors or degraders and of CD3/CD28 activated Mouse Primary CD8 positive T cells with and without treatment with mSWI/SNF inhibitors.


title: Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion [Cut&Tag]

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) for BAF subunits SMARCA4, SS18, ARID1A, Brd9, and PBRM1 as well as the histone modification H3K27ac in activated Primary Human and Mouse CD8 positive T cells with and without compound treatment.


title: Small RNA sequencing identified miR-3180 as a potential prognostic biomarker for Chinese hepatocellular carcinoma patients

status: Public on Mar 20 2023

city: beijing

first: Wang

last: Yan

address: 16# Lincui street,Chaoyang

institute: CAS

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) and their target genes are aberrantly expressed in many cancers and are linked to carcinogenesis and metastasis, especially among hepatocellular carcinoma (HCC) patients. This study sought to identify new biomarkers related to HCC prognosis using small RNA sequencing from the tumor and matched normal adjacent tissue of 32 patients with HCC. Eight miRNAs were downregulated and 61 were upregulated more than twofold. Of these, five miRNAs, hsa-miR-3180, hsa-miR-5589-5p, hsa-miR-490-5p, hsa-miR-137, and hsa-miR-378i, were significantly associated with 5-year overall survival (OS) rates. Differential upregulation of hsa-miR-3180 and downregulation of hsa-miR-378i in tumor samples supported the finding that low and high concentrations of hsa-miR-3180 (p = 0.029) and hsa-miR-378i (p = 0.047), respectively, were associated with higher 5-year OS. Cox regression analyses indicated that hsa-miR‑3180 (HR = 0.08; p = 0.013) and hsa-miR‑378i (HR = 18.34; p = 0.045) were independent prognostic factors of poor survival. However, high hsa-miR‑3180 expression obtained larger AUCs for OS and progression-free survival (PFS) and had better nomogram prediction than hsa-miR‑378i. These findings indicate that hsa-miR‑3180 may be associated with HCC progression and could serve as a potential biomarker for this disease.

overall_design: Tumor tissue from 32 patients who were diagnosed with HCC and the matched adjancent tissue was performed miRNA sequencing.

first: Libo

last: Sun

first: Yan

last: Wang

first: Guangming

last: Li


title: Temporal multimodal single-cell profiling of native hematopoiesis illuminates altered differentiation trajectories with age

city: Lund

first: Anna

last: Konturek-Ciesla

state: Skane

address: Klinikgatan 26, BMC B12

department: Laboratory Medicine

institute: Lund University

summary: Aging impacts negatively on hematopoiesis, with consequences for immunity and acquired blood cell disorders. While impairments in hematopoietic stem cell (HSC) function contribute to this, the in vivo dynamics of such changes remain obscure. Here, we integrate extensive longitudinal functional assessments of HSC-specific lineage tracing with single-cell transcriptome and epitope profiling. In contrast to recent suggestions from single-cell RNA sequencing alone, our data favor a defined structure of HSC/progenitor differentiation that deviates substantially from HSC-derived hematopoiesis following transplantation. Native age-dependent attrition in HSC differentiation manifests as a drastically reduced lymphoid output via an early lymphoid-primed progenitor (MPP Ly-I). While in vitro activation fails to rescue lymphoid differentiation from most aged HSCs, robust lymphopoiesis can be achieved by culturing elevated numbers of candidate HSCs. Therefore, our data position rare chronologically aged HSC clones, fully competent at producing lymphoid offspring, as prime target for approaches aimed to improve lymphopoiesis in the elderly.

overall_design: Single cell profiling and lineage tracing from murine hematopoietic stem and progenitor cells during normal development and upon aging.

first: Parashar

last: Dhapola

first: Qinyu

last: Zhang

first: Petter

last: Säwén

first: Haixia

last: Wan

first: Göran

last: Karlsson

first: David

last: Bryder


title: PRMT1 suppresses anti-tumor immunity

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

summary: PRMT1 is known as a regulator of immune function by directly interacting with interferon receptors, methylating STAT1, and promoting B cell and macrophage differentiation by methylating CDK4 or B cell antigen receptor  However, the function of PRMT1 as a therapeutic target of cancer remains largely elusive, particularly for its role in cancer immunosurveillance. Here, we performed bulk RNA-seq for CT26, a mouse tumor cell line, after either knocking down of endogeneous Prmt1 or blocking PRMT1 by two specific inhibitors, namely MS023 and GSK3368715.

overall_design: Two series of experiments were included, namely Prmt1 knockdown and PRMT1inhibition. For Prmt1 knockdown, there are two groups (shControl and shPrmt1) with 3 biological replicates for each group. For PRMT1 inhibition, there are three groups (Control, MS023 and GSK3368715) with 3 biological replicates for each group.

first: Jing

last: Liu

first: Wenyi

last: Wei


title: Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion

first: Cigall

last: Kadoch

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

overall_design: Refer to individual Series


title: Chimeric EGFR ChIP-seq of an MCF-10A clone expressing chimeric EGFR and Erbb2 receptors

first: Kevin

last: Janes

summary: Synthetic activation of chimeric EGFR-Erbb2 receptors causes nuclear translocation of the heterodimers at long time scales.  To identify genomic loci bound by nuclear EGFR-Erbb2, chromatin from an MCF10A-5E clone coexpressing chimeric EGFR and Erbb2 was prepared with or without synthetic activation and immunoprecipitated for chimeric EGFR by its GluGlu epitope tag.

overall_design: The EGFR-Erbb2 MCF10A-5E clone (B2B1) was grown in overlay culture for six days, stimulated with or without 0.5 µM AP21967 for 24 hours, and prepared for chromatin immunoprecipitation with GluGlu antibody (RRID:AB_2191052) or naïve rabbit IgG as described (Wang et al., Proc. Natl. Acad. Sci. 108:E803-12 [2011]).

first: B

middle: B

last: Paudel


title: HK-2 cells: control and Substance P (SP)-treated

city: Shenzhen

first: Enyi

last: Zhu

address: no.628 Zhenyuan Road

institute: the Seventh Affiliated Hospital,Sun yat-sen university

summary: NK-1R axis in HK-2 cells by treated HK-2-overexpressed NK-1R cells with or without SP.

overall_design: S) under 5% CO2 and 37 °C conditions. For experiment,we added 20 μM SP or PBS to NK-1R-overexpressed HK-2 cells for a 48-h incubation period, followed by harvesting for RNA isolation using Trizol reagent.

first: Yang

first: Ming

last: Zhong


title: The m6A reader YTHDC1 and the RNA helicase DDX5 control the production of rhabdomyosarcoma-enriched circRNAs

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

summary: N6-Methyladenosine (m6A) is well-known for controlling different processes of linear RNA metabolism. Conversely, its role in the biogenesis and function of circular RNAs (circRNAs) is still poorly understood. Here, we characterize circRNA expression in the pathological context of rhabdomyosarcoma (RMS), observing a global increase when compared to wild-type myoblasts. For a set of circRNAs, such an increase is due to the raised expression of the m6A machinery, which we also find to control the proliferation activity of RMS cells. Furthermore, we identify the RNA helicase DDX5 as a novel mediator of the back-splicing reaction and as a co-factor of the m6A regulatory network. DDX5 and the m6A reader YTHDC1 are shown to interact and to promote the production of a common subset of circRNAs in RMS. In line with the observation that YTHDC1/DDX5 depletion reduces RMS proliferation, our results provide proteins and RNA candidates for the study of rhabdomyosarcoma tumorigenicity.

overall_design: Comparative circRNA expression profiling analysis of Ribo-minus Total RNA-seq data for wild-type myoblasts and RD (ERMS) or RH4 (ARMS) cell lines, either in control conditions (si-SCR) or depleted for YTHDC1 or DDX5.

first: Setti

last: Adriano

first: Dattilo

last: Dario

first: Di Timoteo

last: Gaia

first: Bozzoni

last: Irene


title: Immune Activation and Exhaustion Marker Expression on T-cell Subsets in Perinatal HIV-1 Infection as Correlates of Viral Persistence

city: ABINGDON

first: Adit

last: Dhummakupt

state: MD

address: 349 SPRUCE PINE ROAD,

institute: Johns Hopkins University, School of Medicine

summary: HIV-1 infection of resting memory CD4+ T cells forms a barrier to curing HIV-1. Identification of immune biomarkers that correlate with HIV-1 reservoir size could aid with assessing efficacy of HIV-1 eradication strategies, especially in pediatric infections where blood sampling is limited. In adults, the immune exhaustion marker PD-1 on central memory CD4+ T cells (Tcm) correlates with HIV-1 reservoir size. Immune correlates of HIV-1 reservoir size are less defined in perinatal infection. Using multi-parameter flow cytometry, we examined immune activation (CD69, CD25, HLA-DR), and exhaustion (PD-1, TIGIT, LAG-3 and TIM-3) markers on CD4+ T cell subsets (naïve (Tn), central memory (Tcm), and a combination (Ttem) of transitional (Ttm) and effector memory (Tem) in 10 children living with HIV-1 (median age 15.9 years; median duration of virologic suppression 7.0 years), in whom HIV-1 reservoir size was determined with both the Intact Proviral HIV-1 DNA assay (IPDA) and the Tat/Rev limiting dilution assay (TILDA). Total HIV-1 DNA in CD4+ T cells was also measured. Correlations between immune activation, and exhaustion markers on T cell subsets with the various markers of proviral reservoir size, and baseline CD4+ T cell transcriptomes were examined. The median total HIV-1 DNA concentration was 211.9 copies per million CD4+ T cells, with a median intact proviral load in individuals with HIV-1 subtype B of 8.0 copies per million CD4+ T cells. Levels of HLA-DR and TIGIT on Ttem were strongly correlated with total HIV-1 DNA (r=0.758, p=0.015) and (r=0.721, p=0.023), respectively, but not with intact proviral load or inducible reservoir size. HIV-1 DNA load was also positively correlated with transcriptional clusters associated with HLA-DR. In contrast, PD-1 expression on Tcm was inversely correlated with both total HIV-1 DNA (r=-0.67, p=0.039) and HLA-DR in Ttem (r=-0.89, p=0.060). Gene expression profiles for HLA-DR and PD-1 were also inversely correlated.  In conclusion, with virologically suppressed perinatal HIV-1 infection, HLA-DR and TIGIT on Ttem CD4+ T cells correlate with total HIV-1 DNA, and may serve as immune biomarkers for transcriptionally active proviruses, including defectives persisting on ART.

overall_design: RNA-seq from CD4+ T cells, from individuals with perinatally-acquired HIV-1.

first: Yuyang

last: Huang

first: Weiqiang

last: Zhou

first: Hongkai

last: Ji

first: Deborah

last: Persaud


title: Kidney gene expression in response to high phosphate diet

first: Eugene

last: Rhee

address: 165 Cambridge Street

department: Endocrinology

institute: MGH

summary: Phosphate homeostasis is a known critical function performed by the mammalian kidneys.  However, changes to the transcriptome of the mammalian kidney in response to phosphate loading is unclear.  The goal of this study was to examine kidney gene expression in response to high phosphate diet, compared to normal phosphate diet.  RNA-seq was performed on the kidneys of C57BL/6J mice who were fed a high phosphate diet and in mice who received a normal phosphate diet for three days.

overall_design: C57Bl/6J mice were placed on experimental diets (Envigo) containing normal phosphate (0.6%) or high phosphate (1.2%) diets for three days (n=4 in each group). mRNA was prepared from kidney cortex samples acquired on day 3

first: Onica

last: Washington

first: Wen


title: TWIST2-Mediated Chromatin Remodeling Promotes Fusion-Negative Rhabdomyosarcoma [RNA-seq Xenograft]

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

summary: Sarcomas are derailed in pathways that specify mesenchymal lineages during embryogenesis, causing tumor cells to stall at early stages of differentiation. Among them, rhabdomyosarcoma (RMS) is a pediatric soft tissue sarcoma of skeletal muscle origin. A key feature of RMS is their inability to terminally differentiate despite the high expression of master myogenic regulator MYOD. The bHLH transcription factor TWIST2, which governs mesenchymal stem cell identity and restricts myogenesis, is overexpressed in patient fusion-negative RMS (FN-RMS) tumors. We show that knockdown of TWIST2 enables FN-RMS cells to exit the cell cycle and undergo myogenic differentiation, thereby reducing the growth of FN-RMS xenograft tumors. ChIP-seq analysis revealed that most TWIST2-mediated gene regulation occurs independent of changes in MYOD binding in FN-RMS cells. Instead, TWIST2 controls the deposition of H3K27 acetylation at distal enhancers by interacting with the chromatin remodelers, SMARCA4 and CHD3, to activate growth-related and repress myogenesis-related TWIST2 target genes. Our findings provide new insights into the role of TWIST2 in maintaining an undifferentiated and tumorigenic state of FN-RMS and highlight the clinical potential of reversing the TWIST2-regulated phenotype.

overall_design: RNA was isolated from Doxycycline (Dox)-inducible shTWIST2 RD xenograft tumors treated with +Dox (TWIST2 KD) or -Dox (Control) for 52 days. Stranded mRNA-seq was performed to profile gene expression changes upon TWIST2 knockdown.

first: Akansha

last: Shah

first: Kenian

last: Chen

first: Lin

last: Xu

first: Ning

last: Liu

first: Eric

last: Olson


title: TWIST2-Mediated Chromatin Remodeling Promotes Fusion-Negative Rhabdomyosarcoma [RNA-seq FN-RMS Cells]

overall_design: RNA was isolated from Doxycycline (Dox)-inducible shTWIST2 RD or SMS-CTR cells treated with +Dox (TWIST2 KD) or -Dox (Control) for 4 days. Stranded mRNA-seq was performed to profile gene expression changes upon TWIST2 knockdown.


title: Comparison of different T cell differentiation states by RNA-seq analysis identifies BX-795 induced Th-IL-2 cells

status: Public on Mar 17 2023

city: Vienna

first: Winfried

middle: F

last: Pickl

address: Lazarettgasse 19

country: Austria

institute: Medical University of Vienna

summary: We here report RNA-seq data on CD4+ T cells from double transgenic allergy-mice (Neunkirchner A. et al.) expressing a humanized T cell receptor (TCR) specific for the major mugwort pollen allergen Art v 1 peptide 23-36 in combination with a humanized HLA-DR molecule at time-point zero (FACS sorted naive CD4+ T cells from murine spleen) and after 120 h of stimulation of such FACS sorted naive T cells with bone-marrow derived dendritic cells (BMDCs) from these mice plus recombinant Art v 1 (rArt v 1) protein and either DMSO (T effector), BX-795 (Th-IL-2) or a mix of TGF-b, anti-IL-4 and anti-IFN-g (iTreg). T cells cultured for 120 h were FACS sorted before RNA extraction to exclude BMDCs (purity > 90 %). These data is supposed to characterize the expression phenotype of T cells differentiated in the presence of BX-795 (Th-IL-2) and extract specific features by comparing it to control phenotypes (naive, T effector, iTreg).

overall_design: RNA-seq of murine naive CD4+ T cells at time point 0 and after 120 h of stimulation at various differentiation conditions

first: Peter

last: Tauber


title: TWIST2-Mediated Chromatin Remodeling Promotes Fusion-Negative Rhabdomyosarcoma.

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus


title: Host-specific differences in top-expanded TCR clonotypes correlate with divergent  outcomes of anti-PD-L1 treatment in responders versus non-responders

city: Pittsburgh

first: Jing

middle: Hong

last: Wang

email: jhw51@pitt.edu, wangj28@upmc.edu

state: PA

address: 5117 Centre Avenue, Suite 2.35

department: Department of Medicine

institute: University of Pittsburgh

summary: Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment; however, the responses to ICI treatment are highly variable in different individuals and the underlying mechanisms remain poorly understood.

overall_design:
Here, we employed a mouse squamous cell carcinoma (SCC) model where tumor-bearing recipients diverged into responders (R) versus non-responders (NR) upon anti-PD-L1 treatment. We performed in-depth TCRβ sequencing with immunoSEQ platform to delineate the differences in CD8 tumor-infiltrating lymphocytes (TILs).  We found that R and NR CD8 TILs both exhibited evidence of clonal expansion, suggesting activation regardless of response status.  We detected no differences in clonal expansion or clonal diversity indexes between R vs. NR.  However, the top expanded (>1%) TCRβ clonotypes appeared to be mutually exclusive between R and NR CD8 TILs, showing a preferential expansion of distinct TCRβ clonotypes in response to the same SCC tumor in R vs. NR.  Notably, the mutual exclusivity of TCR clonotypes in R vs. NR was only observed when top TCRβ clonotypes were counted, because such top-expanded clonotypes are present in the opposite outcome group at a much lower frequency.  Many TCRβ sequences were detected in only one recipient at a high frequency, implicating highly individualized anti-tumor immune responses.  We conclude that differences in the clonal frequency of top TCR clonotypes between R and NR CD8 TILs may be one of the factors underlying differential anti-PD-L1 responses. This notion may offer a novel explanation for variable ICI responses in different individuals, which may substantially impact the development of new strategies for personalized cancer immunotherapy.

>>>Comment from submitter: "Files are from Adaptive Biotech ImmunoSeq", which does not make its raw data files available.

first: Jessy

last: John

middle: H


title: The identification and characterization of a plant height and grain length related gene hfr131 in rice

city: Shanghai

first: Dengyong

last: Lan

address: Yangpu district

institute: Fudan University

summary: Plant height and grain size are important agronomic traits affecting rice yield. Various plant hormones participate in the regulation of plant height and grain size in rice. However, how these hormones cooperate to regulate plant height and grain size is poorly understood. In this study, we identified a brassinosteroid-related gene, hfr131, from an introgression line constructed using Oryza longistaminata, that caused brassinosteroid insensitivity and reduced plant height and grain length in rice. Further study showed that hfr131 is a new allele of OsBRI1 with a single-nucleotide polymorphism (G to A) in the coding region, leading to a T988I conversion at a conserved site of the kinase domain. An auxin response factor, OsARF17, could bind to the promoter region of HFR131 and positively regulated HFR131 expression, thereby regulating the plant height and grain length, and influencing brassinosteroid sensitivity. Haplotype analysis showed that the consociation of OsAFR17Hap1/HFR131Hap6 conferred an increase in grain length. Overall, this study identified hfr131 as a new allele of OsBRI1 that regulates plant height and grain length in rice, revealed that brassinosteroid and auxin might coordinate through OsARF17–HFR131 interaction, and provided a potential breeding target for improvement of rice yield.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 187R and NIL-hfr131.

first: Liming

last: Cao

first: Mingyu

first: Fuying

last: Ma

first: Peiwen

last: Yan

first: Xinwei

last: Zhang

first: Jian

last: Hu

first: Fuan

last: Niu

first: Shicong

last: He

first: Jinhao

last: Cui

first: Xinyu

last: Yuan

first: Jinshui

last: Yang

first: Ying

first: Xiaojin

last: Luo


title: TWIST2-Mediated Chromatin Remodeling Promotes Fusion-Negative Rhabdomyosarcoma [ChIP-seq]

first: Lei

last: Guo

overall_design: NOT PROVIDED; REQUESTED

first: Akansha

last: Shah

first: Kenian

last: Chen

first: Lin

last: Xu

first: Ning

last: Liu

first: Eric

middle: N

last: Olson


title: Lysine Degradation Reprograms Tumour Immunity through Histone Crotonylation [RNA-seq]

status: Public on Mar 16 2023

first: Huairui

address: 4200 Fifth Ave

summary: To understand how GCDH enhances the oncogenic traits in GSCs, we carried out comparative transcriptomic analysis in two patient-derived GSCs (GSC23, GSC3028) with or without GCDH depletion to identify the driving events. To further examine the connection between lysine catabolism and GSC functions, we controlled L-lysine culture concentrations (0.2 and 2 mM) of GSCs in lysine-deprived media and performed RNA-seq. To address the functional significance of ECHS1 loss in tumour biology, we carried out RNA-seq in two early-passage DGCs (DGC23, DGC3028) with or without ECHS1 depletion. Kcr, H3K27ac or H3K9me3 ChIP-seq was performed in GSC23 to understand the molecular basis of how GCDH loss or lysine restriction affects chromatin landscape.

overall_design: Total RNA was extracted and used for library construction using the Illumina TruSeq Stranded Total RNA Library Prep Kit, which was performed by Novogene. The library was sequenced as a paired-end 150bp read. The chromatin from GSC23 with or without lysine catabolism disruption was prepared according to a ChIP kit (cat: 17-10085; Millipore) and followed by ChIP-seq analysis by Novogene.

first: Jeremy

last: Rich


title: Lysine Degradation Reprograms Tumour Immunity through Histone Crotonylation [ChIP-seq]


title: 10x Single-cell Sequencing for Smad3 wild-type and knockout neutrophils

city: New Territories

first: Patrick Ming-Kuen

last: Tang

address: Cancer center, Prince of Wales Hospital,30-32 Ngan Shing Street, Shatin

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: The role of neutrophils in tumor is still controversial and largely unknown. We previously   identified an anticancer tumor microenvironment from mice lacking Smad3, but the underlying   mechanism is still largely unclear. Interestingly, depletion of neutrophils largely suppressed the   anticancer phenotype of Smad3-KO mice against syngeneic murine Lewis lung carcinoma (LLC).   Here, we discovered that Smad3 is essential for promoting N1/N2 polarization of the tumor_x0002_associated neutrophils (TANs) in lung carcinoma. We found that Smad3 deficiency dramatically   increased N1 TANs associated with an anticancer phenotype in mice and detected a negative   correlation between Smad3 activation and anticancer N1 associated with a higher mortality of   NSCLC. By conducting a neutrophil-specific single-cell RNA-sequencing, we uncovered that   Smad3 is essential for completing the N1/N2 polarization of TANs, whereas N1 will be the   dominated phenotype in the Smad3-KO TME by analyzing the developmental pathways of TANs   with pseudo-time at transcriptome level. Mechanistically, direct binding of Smad3 on the   developmental genes in neutrophils under cancer condition was evidenced by ChIP-sequencing at   genomic level. Importantly, both neutrophil-specific and pharmaceutical inhibition of Smad3   effectively enhanced the anticancer activity of human and murine TANs, thereby suppressing the   progression of lung carcinoma in vivo. Thus, Smad3 may represent a precision therapeutic target   for enhancing the anticancer activity of TANs via blocking N1/N2 polarization in NSCLC.  in C57BL6 (wild-type) and Smad3-deficient (Smad3-/-  ) mice and submitted for cell encapsulation   and library construction by Chromium controller with 5’ expression kit (10x genomics)

overall_design: CD11b+Ly6G TANs were FACS-sorted from the single-cell digestion of s.c LLC tumor inoculated in C57BL6 (wild-type) and Smad3-deficient (Smad3-/-) mice and submitted for cell encapsulation and library construction by Chromium controller with 5’ expression kit (10x genomics). Libraries were sequenced by illumina NovaSeq 6000 platform (PE151bp, 660M raw read).

first: Patrick

middle: M


title: A VEL3 histone deacetylase complex establishes a maternal epigenetic state controlling progeny seed dormancy

city: Norwich

first: Xiaochao

address: Norwich Research Park, Colney Ln

department: Crop Genetics

institute: John Innes Centre

summary: Mother plants play an important role in the control of dormancy and dispersal characters of their progeny. In Arabidopsis seed dormancy is imposed by the embryo-surrounding tissues of the endosperm and seed coat. Here we show that the VERNALIZATION5/VIN3-LIKE 3 (VEL3) gene maintains maternal control over progeny seed dormancy by establishing an epigenetic state early in endosperm development that primes the depth of primary seed dormancy later established during seed maturation. VEL3 relocates MSI1 to the nucleolus and associates with other components of the histone deacetylase complex (HDAC). Furthermore VEL3 preferentially associates with pericentromeric chromatin and is required for deacetylation  and H3K27me3 deposition and is required for gene repression via PRC2 and HDAC at pericentromeric regions established in the central cell. Interestingly, the epigenetic state established by the maternal VEL3 is retained trans-generationally in mature seeds, and controls seed dormancy in part through the repression of programmed cell death-associated gene ORE1. Our data demonstrates a novel mechanism by which maternal control of progeny seed physiology persists post-shedding, maintaining parental control of seed behaviour.

overall_design: RNA-seq was performed in globular seeds, mature endosperm and 24 hours water imbibed endosperm (24HAI) for Col0 and vel3. H3K27me3 and H3K9ac ChIP-seq was performed in mature endosperm for Col0 and vel3. VEL3 ChIP-seq was performed in VEL3-GFP siliques.

first: Steven

last: Penfield


title: mRNA sequencing of lung cancer cell lines before and after stimulation with IFNγ

city: Badalona

first: Pablo

last: Navajas Chocarro

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Josep Carreras Leukaemia Research Institute

summary: We performed RNA sequencing to assess changes in gene expression in lung cancer cell lines. Total RNA was extracted from the cells, before and after stimulation with IFNγ, using standard approaches. RNA-sequencing data performed in this work was performed and analyzed at the CNAG-CRG.

overall_design: We performed RNA-Seq at 0 and at 6 after stimulated with IFNγ (30nM), in a panel of Lung Cancer cell lines

first: Montse

last: Sanchez-Cespedes

first: Juan

last: Alburquerque-Bejar

last: Navajas-Chocarro


title: Lung cancer cell lines before and after stimulation with IFNγ


title: Efficient engineering of human and mouse primary cells using peptide-assisted genome editing

city: Philadelphia

first: Shelley

middle: L.

last: Berger

address: 3400 Civic Center Blvd

department: Penn Epigenetics Institute

institute: University of Pennsylvania

summary:
Simple and efficient delivery of CRISPR genome editing systems in primary cells remains a major challenge. Here, we describe an engineered Peptide-Assisted Genome Editing (PAGE) CRISPR-Cas system for rapid and robust editing of primary cells. PAGE couples a cell-penetrating Cas protein with a cell-penetrating endosomal escape peptide in a 30-minute incubation that yields up to ~98% editing efficiency in primary human and mouse T cells. PAGE provides a broadly generalizable platform for next generation genome engineering in primary cells.

CITATION INFORMATION:
Zhang Zhen, Baxter Amy E, Ren Diqiu, Qin Kunhua, Chen Zeyu, Collins Sierra M., Huang Hua, Komar Chad A., Bailer Peter F., Parker Jared B., Blobel Gerd A., Kohli Rahul M., Wherry E. John*, Berger Shelley,*, and Shi Junwei*. Peptide-assisted genome editing permits efficient CRISPR engineering of primary T cells.

overall_design: The purpose of this experiment is to compare the gene expression changes following opCas12a-CPP RNP delivery by PAGE or electroporation on CAR19 T cells. 0.5 ~ 2 million CAR19 T cells were collected at 6 hours and 3 days post PAGE and electroporation.. Cells were washed once with PBS and resuspend in 0.5 ml of TRIzol (Thermo 15596018) and stored at -80°C. RNA was extracted using RNA Clean & Concentrator-5 (ZYMO R1013) following manufacture?s instruction. mRNA was isolated from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L) to prepare libraries with NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760L) following manufacture?s instruction. RNA libraries were pooled and sequenced with NextSeq 500/550 High Output Kit (75 cycles) v2.5 kit (illumina 20024906) on NextSeq 550 platform (illumina) using paired-end sequencing (42:6:0:42).

first: Zhen

last: Zhang

first: Junwei

last: Shi


title: Multi-omics analysis revealed the pathogenetic mechanisms of Mechanical allodynia in type 1 diabetes

status: Public on Mar 15 2023

city: shanghai

first: Hongjin

address: NO.639 Shanghai Zhizaoju Road, Huangpu District, Shanghai, China.

institute: Shanghai Ninth People's hospital

summary: To understand the differences in gene expression profiles between MA rats and other groups of rats, we examined the gene expression profiles of different groups of rats by RNA-seq.（n=3）

overall_design: Comparative gene expression profiling analysis of RNA-seq data for diabetic group with mechanical allodynia (in raw data: P1,P2,P3) and other groups (diabetic group without mechanical allodynia (in raw data: NP1,NP2,NP3), control group (in raw data: con1,con2,con3))

first: Chenlong

last: Liao

first: Xiaosheng

last: Yang

first: Han

last: Zhou


title: Modular oxidation of cytosine modifications and their application in direct and quantitative sequencing of 5-hydroxymethylcytosine

city: Oxford

first: Linzhen

last: Kong

address: University of Oxford Old Road Campus Research Building

department: Nuffield Department of Medicine

institute: Ludwig Institute for Cancer Research

summary: Selective, efficient, and controllable oxidation of cytosine modifications is valuable for epigenetic analyses, yet only limited progress has been made. Here, we present two modular chemical oxidation reactions: conversion of 5-hydroxymethylcytosine (5hmC) into 5-formylcytosine (5fC) utilizing 4-acetamido-2,2,6,6-tetramethylpiperidine-1-oxoammonium tetrafluoroborate (ACT+ BF4–) and further transformation of 5fC into 5-carboxycytosine (5caC) through Pinnick oxidation. Both reactions are mild and efficient on double-stranded DNA. We integrated these two oxidations with borane reduction to develop chemical-assisted pyridine borane sequencing plus (CAPS+), for direct and quantitative mapping of 5hmC. Compared with chemical-assisted pyridine borane sequencing (CAPS), CAPS+ improved the conversion rate and false-positive rate. We applied CAPS+ to mouse embryonic stem cells (mESCs) DNA, human normal brain and glioblastoma DNA samples, and demonstrated its superior sensitivity in analyzing the hydroxymethylome

overall_design: Whole genome sequencing of 5 hydroxymethylcytosine applying CAPS+ in mESCs (two replicates) and human brain samples (normal brain and glioblastoma).

first: Haiqi

first: Jinfeng

last: Chen

first: Jingfei

last: Cheng

first: Xiufei

first: Masato

last: Inoue

first: Yibin

first: Meiping

last: Zhao

first: Chun-Xiao

last: Song


title: A nucleolar condensin-recruiting complex that regulates yeast chromosome III structure

city: charlottesville

first: Jeffrey

middle: S

last: Smith

address: 1340 jpa pinn hall

institute: University of Virginia

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

overall_design: Refer to individual Series


title: DNA Methylation Explains a Subset of Placental Gene Expression Differences Based on Ancestry and altitude

city: Tampa

first: Derek

last: Wildman

state: FL

address: 3720 Spectrum Blvd

institute: University of South Florida

summary: Investigation of how gene expression and epigenetics contribute to conservation of birth weight at high altitudes by examining mRNA and DNA methylation differences between placentas of indigenous Andeans and placentas of European descent residing at high and low altitude

overall_design: Gene Expression analyisis of RNA from 45 villous placentas

first: William

last: Gundling Jr


title: Inhibition of lysine-specific demethylase 1 inhibition in glioblastoma

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

summary: Investigate transcriptome effects of LSD1 inhibiton via genetic knockdown and small molecule inhibition

overall_design: To assess concordance between knockdown of LSD1 and inhibition of LSD1 using a prototype inhibitor in GBM, we performed RNA-seq to identify genes and biological processes associated with inhibition.

first: Joya

last: Chandra


title: Lysine Catabolism Reprograms Tumour Immunity through Histone Crotonylation.

first: Huairui

last: Yuan


title: ChIP-sequencing of the IRF1 transcription factor in lung cancer cell lines after stimulation with IFNγ

first: Pablo

last: Navajas Chocarro

summary: We performed chromatin immnoprecipitation followed by sequencing (ChIP-Seq) of IRF1 in different LC cell lines.

overall_design: ChIP-Seq of human: we performed ChIP-Seq in a panel of LC cells after stimulation (30nM, 6 hours) with IFNγ in LC cell lines.

first: Montse

last: Sanchez-Cespedes

first: Juan

last: Alburquerque-Bejar

last: Navajas-Chocarro


title: Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids [Bisulfite-seq]

status: Public on Mar 14 2023

city: Wuhan

first: Hao

last: Wang

address: No. 1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: To investigate the expression and methylation patterns of hybrid embryo development in Brassica napus, we performed pattern analysis on different developmental stages of parental and hybrid embryos

overall_design:
Methylation profiling using Bisulfite-seq data from parents and offspring at three developmental stages

Grant ID: 31861133016
Grant title: Genome-wide patterns of heterotic vigour associated with allopolyploid chromosome collision
Funding source: National Science Foundation project (NSFC)

Grant ID: SN14/22-1
Grant title: Genome-wide patterns of heterotic vigour associated with allopolyploid chromosome collision
Funding source: German Research Foundation (DFG)

first: Mauricio

last: Orantes-Bonilla

first: HueyTyng

last: Lee

first: Wenwen

last: Li

first: Dandan

last: Hu

first: Jun

last: Zou

first: Rod

last: Snowdon


title: Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids [miRNA-seq]

overall_design:
sRNA expression profiling using sRNA-seq data from parents and offspring at three developmental stages

Grant ID: 31861133016
Grant title: Genome-wide patterns of heterotic vigour associated with allopolyploid chromosome collision
Funding source: National Science Foundation project (NSFC)

Grant ID: SN14/22-1
Grant title: Genome-wide patterns of heterotic vigour associated with allopolyploid chromosome collision
Funding source: German Research Foundation (DFG)


title: The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells

first: David

last: Klein

address: 4249 Fifth Ave

department: Biological Sciences

summary: Nucleosome remodeling factors regulate the occupancy and positioning of nucleosomes genome-wide through ATP-driven DNA translocation. While many nucleosomes are well- and consistently positioned, some nucleosomes and nucleosome-like structures are more sensitive to nuclease digestion or transitory in nature. To better understand the role of nucleosome remodeling factors in generating and clearing these alternative nucleosome structures, we depleted murine embryonic stem cells of the remodeler ATPases BRG1 and SNF2H then performed MNase-seq in murine embryonic stem cells. We performed MNase-seq under high- and low-MNase conditions to assess the effects of nucleosome remodeling factors on nuclease-sensitive or “fragile” nucleosome occupancy. In parallel, we gel-extracted MNase-digested fragments to enrich for another alternative nucleosome structure, the overlapping dinucleosome. Overlapping dinucleosomes are composed of two canonical nucleosomes, asymmetrically lacking one H2A:H2B dimer and wrapped by ~250 bp of DNA. In vitro studies of nucleosome remodeling have suggested that the collision of adjacent nucleosomes by nucleosome sliding can stimulate formation of overlapping dinucleosomes. Using these methods, we were able to identify fragile nucleosomes and overlapping dinucleosomes near transcription start sites and gene-distal DNaseI hypersensitive sites  in mouse embryonic stem cells, among other loci. We find that BRG1 consistently stimulates occupancy of fragile nucleosomes but represses occupancy of overlapping dinucleosomes through its nucleosome remodeling function, while SNF2H expression slightly increases fragile nucleosome occupancy.

overall_design:
36 MNase-seq samples are included, comprised of three independent replicates with knockdown of EGFP (control, unexpressed), Smarca4, and Smarca5. Independent knockdowns were split into gel-extracted libraries to enrich for overlapping dinucleosomes and unextracted libraries for traditional MNase-seq (no size selection). Each experiment was performed in triplicate under both high (60U) and low (10U) MNase digestion conditions.

MNase-ChIP-seq samples. Two replicates are included for wildtype samples and one replicate is included for EGFP KD samples. Digestion was performed with high- and low-MNase treatments (30U and 5U, respectively). Input samples digested with low MNase are provided for all samples, as are IgG- and H3-ChIP samples.

middle: C

first: Kris

last: Troy

first: Sarah

middle: A

last: Tripplehorn

last: Hainer


title: Rhinovirus-induced epithelial RIG-I inflammasome suppresses antiviral immunity and promotes inflammation in asthma and COVID-19

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary:
Balanced immune responses in airways of patients with asthma are crucial to succesful clearance of viral infection and proper asthma control.
We used microarrays to detail the global programme of gene expression data from bronchial brushings from control individuals and patients with asthma after rhinovirus infection in vivo.

overall_design: Bronchial brushings from control individuals and patients with asthma around two weeks before (day -14) and four days after (day 4) experimental in vivo rhinovirus infection were used for RNA isolation and hybrydyzation with Affymetric microarrays.

first: Sebastian

last: Johnston

last: Jackson

first: Michael

last: Edwards

first: Tatiana

last: Kebadze

first: Rick

last: Williamson

first: Milena

last: Sokolowska


title: Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids [RNA-seq]

last: Wang

overall_design:
Gene expression profiling using RNA-seq data from parents and offspring at three developmental stages

Grant ID: 31861133016
Grant title: Genome-wide patterns of heterotic vigour associated with allopolyploid chromosome collision
Funding source: National Science Foundation project (NSFC)

Grant ID: SN14/22-1
Grant title: Genome-wide patterns of heterotic vigour associated with allopolyploid chromosome collision
Funding source: German Research Foundation (DFG)

last: Orantes-Bonilla


title: Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics

status: Public on Mar 13 2023

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

summary: The Illumina sequencing systems demonstrate high efficiency and power and remain the most popular platforms. Platforms with similar throughput and quality profiles but lower costs are under intensive development. In this study, we compared two platforms Illumina NextSeq 2000 and GeneMind Genolab M for 10x Genomics Visium spatial transcriptomics.

overall_design: We performed comparison of GeneMind Genolab M and Illumina NextSeq 2000 sequencing platforms using three ovarian cancer 10x Genomics Visium libraries. We evaluate performance of both platforms in terms of sequencing quality and detection of UMI, spatial barcode, and probe sequence. We compared raw read mapping and read counting efficiency. Additionally, downstream analysis was performed in order to reveal concordance of dimension reduction, clusterization, and differential gene expression results between the Genolab M and NextSeq 2000 platforms. The study was carried out according to Declaration of Helsinki and was approved by the local committee of Medical Ethics of Tomsk Cancer Research Institute; all patients signed informed consent for the study.

first: Pavel

last: Iamshchikov

last: Gerashchenko

first: Denis

last: Piankov

first: Philipp

last: Koshkin

first: Sergei

last: Korostelev

first: Evgeny

last: Denisov


title: Galectin-3 expression in donor T cells reduces GvHD severity and lethality after allogeneic hematopoietic cell transplantation

city: Buffalo

first: Hemn

last: Mohammadpour

address: Elm and Carlton Sts.

institute: Roswell Park Comprehensive Cancer Center

summary: Abundant donor cytotoxic T cells that attack normal host organs remain a major problem for patients receiving allogeneic hematopoietic cell transplantation (Allo-HCT). Despite an increase in our knowledge of the pathobiology of acute graft versus host disease (aGvHD), the mechanisms regulating the proliferation and function of donor T cells remain unclear. Here, we show that activated donor T cells express galectin-3 (Gal-3) after allo-HCT. In both major and minor histocompatibility–mismatched models of murine aGvHD, expression of Gal-3 is associated with decreased T cell activation and suppression of the secretion of effector cytokines including IFN-γ and GM-CSF. Mechanistically, Gal-3 results in activation of NFAT signaling which can induce T cell exhaustion. Gal-3 overexpression in human T cells prevents severe disease by suppressing cytotoxic T cells in xenogeneic aGvHD models.  Together these data identify the Gal-3-dependent regulatory pathway in donor T cells as a critical component of inflammation in aGvHD.

overall_design: At day 7 after allo-HCT, CD4+ or CD8+ T cells (live, H-2Kb+CD45+CD3+) were sorted from single-cell suspensions of spleens from BALB/c recipient mice for gene expression (Immunology Panel, Nanostring) using BD FACSAria (BD Bioscience) in the Roswell Park Flow and Image Cytometry Shared Resource. After sorting, the total T cells ranged from 0.5×106 to 1×106 cells. Cells were immediately frozen in liquid nitrogen and then stored at -80°C or on dry ice. Samples were sent to the Roswell Park Genomic Shared Resource for gene expression profiling. Nanostring analysis was performed with the nCounter® Analysis System from NanoString Technologies utilizing the nCounter Mouse Immunology Kit, which includes 561 immunology-related mouse genes according to manufacturer’s protocols.

first: Takemasa

last: Tsuji

first: Cameron

middle: R

last: MacDonald

first: Joseph

middle: L

last: Sarow

first: Hanna

last: Rosenheck

first: Saeed

last: Daneshmandi

first: JeeEun

last: Choi

first: Jingxin

last: Qiu

first: Junko

last: Matsuzaki

first: Agnieszka

middle: K

last: Witkiewiz

first: Kristopher

last: Attwood

first: Bruce

last: Blazar

first: Kunle

last: Odunsi

first: Elizabeth

last: Repasky

first: Philip

last: McCarthy


title: Transcriptomic profiling of breast cancer cells on hydrogels with different stiffness [array]

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

institute: Karolinska Institutet

summary:
Remodeling and increased stiffness of the extracellular matrix is a hallmark of solid cancers and contributes to tumor progression through increased proliferation, survival and migration. Mechanotransduction, the process in which cells sense and transduce mechanical signals, can result in transcriptional changes that in turn alter cellular behavior. In vitro culturing of MCF10ACA1a (CA1a) breast cancer cells on polyacrylamide-based hydrogels of variable stiffness revealed drastic changes in morphology, indicating a stiffness dependent induction of a malignant phenotype.
We used DNA microarray to characterize the transcriptome of CA1a cells on low (400 Pa) and high (5000 Pa) stiffness, corresponding to the stiffness of normal breast and breast cancer, respectively.

overall_design: In vitro cultures of MCF10CA1a cells on polyacrylamide-based hydrogels of variable stiffness revealed drastic stiffness-dependent morphology.  To elucidate how this phenotypic switch is reflected by changes in mRNA levels, we used DNA-microarrays (initially) and RNA sequencing (later) and studied MCF10CA1a cells cultured for five days on stiffness mimicking normal breast tissue or breast cancer.

first: Shan

last: Chen


title: Transcriptomic profiling of breast cancer cells on hydrogels with different stiffness


title: Transcriptomic profiling of breast cancer cells on hydrogels with different stiffness [sequencing]

summary: Remodeling and increased stiffness of the extracellular matrix is a hallmark of solid cancers and contributes to tumor progression through increased proliferation, survival and migration. Mechanotransduction, the process in which cells sense and transduce mechanical signals, can result in transcriptional changes that in turn alter cellular behavior. In vitro culturing of MCF10ACA1a (CA1a) breast cancer cells on polyacrylamide-based hydrogels of variable stiffness revealed drastic changes in morphology, indicating a stiffness dependent induction of a malignant phenotype. We used two different techniques, DNA microarray and RNA sequencing, to characterize the transcriptome of CA1a cells on low (500 Pa) and high (8000 Pa) stiffness, corresponding to the stiffness of normal breast and breast cancer, respectively.

overall_design: 3 biological replicates of MCF10CA1a cells  cultured on low (500 pa) or high (8000 pa) stiffness.


title: Lung-specific MCEMP1 acts as an adaptor for KIT to promote SCF-mediated mast cell proliferation [PCMC RNA-seq]

city: Cleveland

first: Youn Jung

email: choiy4@ccf.org, younjung514@gmail.com

state: OH

address: 9500 Euclid Ave, NE2-251

department: Cancer biology

institute: Cleveland Clinic Lerner Research Institute

summary: We analyzed transcriptomic changes in Mcemp1-/- Peritoneal cell-derived mast cells (PCMC) versus Mcemp1 wild-type PCMC cultured with SCF and IL-3 for 9-days.

overall_design: Peritoneal cells of wild-type mice and Mcemp1-/- mice were cultured with SCF and IL-3 for 9 days.

first: Youn

middle: J

first: Jae

middle: U

last: Jung


title: Lung-specific MCEMP1 acts as an adaptor for KIT to promote SCF-mediated mast cell proliferation [Lung RNA-seq]

summary: We analyzed the lung transcriptome of Mcemp1-/- mice versus wild-type mice in ovalbumin (OVA)-induced asthma model by RNA sequencing.

overall_design: 6-8 weeks old wild-type mice or Mcemp1-/- C57BL/6 mice were immunized via intraperitoneal injection of ovalbumin (OVA) on days 1, 4, and 7. 5 days after the third sensitization, mice were challenged with intranasal instillation of OVA weekly for a total of 8 weeks. Control mice received saline for both sensitization and challenge.


title: Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

first: Hao

last: Wang

overall_design:
Refer to individual Series

Grant ID: 31861133016
Grant title: Genome-wide patterns of heterotic vigour associated with allopolyploid chromosome collision
Funding source: National Science Foundation project (NSFC)

Grant ID: SN14/22-1
Grant title: Genome-wide patterns of heterotic vigour associated with allopolyploid chromosome collision
Funding source: German Research Foundation (DFG)


title: Lung-specific MCEMP1 acts as an adaptor for KIT to promote SCF-mediated mast cell proliferation


title: Next-generation sequencing facilitates quantitative analysis of wild-type peritoneal murine mast cells (PMCs) and their comparison to PMC lines

city: Aachen

first: Sandro

last: Capellmnn

address: Pauwelsstrasse 30

department: Institute of Biochemistry and Molecular Immunology

institute: University Hospital RWTH Aachen

summary: Spontaneously developed murine PMC lines were compared to naive murine PMCs to elucidate genomic changes and correlate those to phenotypes observed with respect to mast cell effector functions, characteristics and activation of siganling pathways. Moreover, control PMCs will be used to analyze gender differences.

overall_design: mRNA profiles of untreated peritoneal mast cells (PMCs) of wild-type (WT) mice (cell lines and naive) were generated by deep sequencing, in triplicate

last: Capellmann

first: Lin

last: Gan

first: Michael

last: Huber


title: Treatment with HKMTI-1-005, a dual inhibitor of EZH2 and G9a/GLP histone methyltransferases, promotes differentiation of acute myeloid leukaemialeukemia

status: Public on Mar 10 2023

city: Plovdiv

first: Yordan

last: Sbirkov

address: 15 A Vassil Aprilov Blvd

department: Medical Biology

country: Bulgaria

institute: Medical University of Plovdiv

summary:
The canonical function of EZH2 is methylation of H3K27, although important non-canonical roles have recently been described. EZH2 mutation or deregulated expression has been conclusively demonstrated in the pathogenesis and response to treatment of acute myeloid leukemia (AML), thus making it an attractive therapeutic target. In this study, we therefore investigated whether inhibition of EZH2 might also improve the response of non-APL AML cells to ATRA-based therapy. We focused on GSK-343, a pyridone-containing S-adenosyl-L-methionine (SAM) cofactor-competitive EZH2 inhibitor that is representative of its class, and HKMTI-1-005, a substrate-competitive dual inhibitor targeting EZH2 and the closely related G9A/GLP H3K9 methyltransferases. We found that treatment with HKMTI-1-005 phenocopied EZH2 knockdown and was more effective in inducing myeloid differentiation (both in the absence and presence of ATRA) than GSK-343, despite the efficacy of GSK-343 in terms of abolishing H3K27 trimethylation. Furthermore, transcriptomic analysis revealed that in contrast to treatment with GSK-343, HKMTI-1-005 upregulated the expression of myeloid differentiation pathway genes with and without ATRA, while downregulating genes associated with a hematopoietic stem cell phenotype.
Expression data (by HuGene 1.0 ST Affymetrix arrays) from HL-60 AML cells treated for 3 days with EZH2 inhibitors (10µM GSK343 or 2.5µM HKMTI-1-005) with or without AtRA (0.1µM) as well as data from HL-60 cells stabelly transduced with EZH2 KD (shEZH2#1 and shEZH2#2) or control (Scr) lentiviruses, selected and expanded for ~20 days with or without treatment with 0.1µM AtRA for 3 days.

overall_design: Data from biological triplicates from each of the following conditions: GSK343, HKMTI-1-005, EZH2 KD shA, EZH2 KD shC, non-targeting control Scr and control cells (untreated and untransduced) +/- AtRA was normalised (GC-RMA and batch effect remove with Partek) and differentially expressed genes were identified in all conditions compared to control (-AtRA). The top 40th percentile of expressed genes according to normalised values was taken and an FDR or 0.05 was used as a cut-off between all conditions. Genes with at least 1.3 fold change in expression were taken for further GO and GSEA analysis.

first: Y

first: K

last: Petrie


title: Gene expression profile at single cell level of murine neural stem cells (NSCs) subjected to bulk electroporation (BEP) and localized electroporation (LEP)

city: Evanston

first: Prithvijit

last: Mukherjee

state: IL

address: 2145 Sheridan Road

institute: Northwestern University

summary: Localized Electroporation (LEP) has emerged as an effective tool for intracellular delivery and non-destructive analysis of cells. However, little is known about the effects of LEP on cellular gene expression which may adversely impact their downstream phenotype. Here we use single cell RNA sequencing to dissect the effects of LEP on murine neural stem cell (NSC) gene expression and compare it to Bulk Electroporation (BEP).

overall_design: Postnatal murine neural progenitors subjected to BEP or LEP were analyzed using scRNAseq 4 hours post treatment and compared to a control.

first: Chian-Yu

last: Peng

first: Tammy

last: McGuire

first: Jin

middle: W

last: Hwang

first: Connor

last: Puritz

first: Nibir

last: Pathak

first: Cesar

last: Patino

first: Rosemary

last: Braun

first: John

last: Kessler

first: Horacio

middle: D

last: Espinosa