title: Emergence of sex-specific transcriptomes in a sexually-dimorphic brain nucleus

status: Public on Jul 14 2022

city: Portland

first: Claudio

middle: V

last: Mello

state: OR

address: 3181 SW Sam Jackson Park Rd, L470

department: Behavioral Neuroscience

institute: Oregon Health & Science University

summary: Sexual dimorphisms in the brain give rise to sex differences in physiology and behavior, yet we have limited understanding of the transcriptomic changes underlying their development. We evaluated developmental transcriptome dynamics for one of the most extreme neuroanatomical sexual dimorphisms in vertebrates - the songbird robust nucleus of the arcopallium (RA). RA is the telencephalic motor output nucleus of the song system. It grows monomorphically for the first few weeks posthatch, then continues growing in males but regresses in females, becoming 5-7 times larger in males. We quantified RA gene expression from monomorphic and dimorphic stages of development in both sexes. Mirroring the morphology, male and female transcriptomes initially resembled one other, then diverged markedly. Thousands of genes showed developmental regulation, corresponding to highly sex-specific biological processes. Males showed enrichments for neuronal growth and morphogenesis, synapse organization, metabolism, and voltage-gated ion channels. Females showed enrichments for cell polarity and differentiation, chemotaxis inhibition, gene silencing, and hormone and immune signaling. Notably, the majority of sex-biased genes in monomorphic RA were sex chromosome Z genes. These findings reveal a profound, sex-specific reorganization of RA’s transcriptome, providing novel insights into potential targets and drivers of sexually dimorphic neurodevelopment.

overall_design: mRNA profiles of brain nucleus RA from 20 DPH and 50 DPH male and female zebra finches

first: Samantha

last: Friedrich

first: Alex

middle: A

last: Nevue

first: Abraao

middle: L

last: Andrade

first: Tarciso

last: Velho


title: Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time

status: Public on Jul 12 2022

city: New Haven

first: Emma

middle: Tung

last: Corcoran

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

country: USA

institute: Yale University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Despite the broad array of roles for epigenetic mechanisms on regulating diverse processes in eukaryotes, no experimental system for the direct assessment of histone function is currently available in plants. In this work, we present the development of a genetic strategy in Arabidopsis thaliana in which modified H4 transgenes can completely replace the expression of endogenous histone H4. Using this strategy, we established a collection of plants expressing different H4 point mutants targeting residues that may be post-translationally modified in vivo. To demonstrate the utility of this new H4 mutant collection, we screened it to uncover substitutions in H4 that alter flowering time. We identified different mutations in the tail (H4R17A) and the globular domain (H4R36A, H4R39K, H4R39A, and H4K44A) of H4 that strongly accelerate the floral transition. Furthermore, we found a conserved regulatory relationship between H4R17 and the ISWI chromatin remodeling complex in plants. Similar to other biological systems, H4R17 regulates nucleosome spacing via ISWI. Overall, this work provides a large set of H4 mutants to the plant epigenetics community that can be used to systematically assess histone H4 function in A. thaliana and a roadmap to replicate this strategy for studying other histone proteins in plants.

overall_design:
Examination of RNA-seq in 9 different backgrounds (Col0, rH4-1, rH4-2, rH4R17A-1, rH4R17A-2, arid5, rlt1/2, chr11/17, and pie1) and MNase-seq in 5 different backgrounds (Col0, rH4-2, rH4R17A-1, arid5, and rlt1/2)
Examination of RNA-seq in 3 different backgrounds (Col0, H4 septuple mutant, and fas1-4)

middle: T

first: Chantal

last: LeBlanc

first: Mia

last: Tsang

first: Anthony

last: Sarkiss

first: Yannick

last: Jacob


title: Single cell sequencing profile of a unique mesenchymal progenitor subset from the developing murine forelimb

status: Public on Jul 15 2022

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

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

overall_design: Refer to individual Series


title: Systems analysis of the female genital tract reveals differential expression of inflammatory and epithelial barrier genes in South African adolescents randomized to injectable, oral or vaginal ring contraception

status: Public on Jul 11 2022

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary:
Use of hormonal contraceptives (HC) could alter the bacterial community, immune response and epithelial barrier integrity of the female genital tract (FGT) mucosal environment, leading to increased susceptibility to sexually transmitted infections (STIs), including HIV. Here, we tested whether use of three types of HCs, injectable Net-En, combined oral contraceptives (COC) and NuvaRing, a combined contraceptive vaginal ring (CCVR), led to distinct patterns in FGT host transcriptomics transcriptome in South African adolescent females.
In an intention-to-treat analysis, we observed few changes in endocervical gene expression in the Net-En and COC groups. Relative to the COC and Net-En arms, samples from the CCVR arm had significant elevation of transcriptional networks driven by IL-6, IL-1 and NFKB, and lower expression of genes supporting epithelial barrier integrity. An integrated multivariate analysis of the cervicovaginal microbiome, transcriptome and cytokines demonstrated that networks of microbial dysbiosis and inflammation accurately discriminated the CCVR arm from the other contraceptive groups, while genes involved in epithelial cell differentiation were predictive of the Net-En and COC arms.

overall_design:
Between September 2015 and June 2017, 130 HIV negative, sexually active adolescent females aged 15-19 years were enrolled into a substudy of UChoose, an open-label randomized crossover study (NCT02404038), comparing acceptability and product preference of contraceptives.
The participants were randomized to injectable Net-En, combined oral contraceptives (COC) or NuvaRing, a combined contraceptive vaginal ring (CCVR) for 16 weeks in a 1:1:1 fashion.
Cervicovaginal samples were collected at baseline and after 16 weeks of randomized HC use for RNA sequencing.
Post RNAseq, low-quality samples were filtered out and the final data set includes n=13 baseline and n=96 follow-up samples.

first: Christina

last: Balle

first: Prachi

middle: M

last: Gupta

first: Sydney

last: Nelson

first: Iyaloo

middle: N

last: Konstantinus

first: Katie

last: Lennard

first: Shameem

middle: Z

last: Jaumdally

first: Anna-Ursula

last: Happel

first: Shaun

last: Barnabas

first: Katherine

last: Gill

first: Linda-Gail

last: Bekker

first: Jo-Ann

middle: S

last: Passmore

first: Heather

middle: B

last: Jaspan

first: Steven

middle: E

last: Bosinger


title: Hematopoietic stem and progenitor cells integrate microbial signals to promote gut tissue repair

status: Public on Jul 07 2022

city: Kumamoto

first: Hitoshi

last: Takizawa

address: 2-2-1 Honjo, Chu-ku

country: Japan

institute: Kumamoto University

summary: This study examines how bone marrow (BM)-resident hematopoietic stem and progenitor cells (HSPCs) are activated by bacterial insults for lineage specification to replenish the host hemato-immune system. We use the dextran sulfate sodium (DSS) colitis model to cause acute gut inflammation and observe molecular changes that occur in MPP2s, which expand both in the BM and MLN upon DSS treatment.

overall_design: One hundred MPP2s (LSKCD48+CD150+) were sorted from the bone marrow and mesenteric lymph nodes after mice were administered with either ddW or 2.5% DSS in the drinking water for 7 days. Samples were subjected to RNA-seq.


title: Role of YAP/TAZ-TEAD in human trophoblast

status: Public on Jul 17 2022

city: Eiheiji

first: Tetsuya

last: Mizutani

state: Fukui

address: 4-1-1 Kenjojima

institute: Fukui Prefectural University

summary:
During placentation, placental cytotrophoblast cells differentiate into syncytiotrophoblast cells and extravillous trophoblast cells. In placenta, the expression of various genes is regulated by the Hippo pathway through the transcriptional coactivator YAP/TAZ-TEAD activity. To examine the effect of YAP/TAZ and/or TEAD on trophoblast differentiation, knockdown experiments were performed.
Microarray analysis were performed to identify YAP/TAZ and/or TEAD target genes in human trophoblast.

overall_design: Observation of gene expression changes in human trophoblast stem cells after treatmet with siRNAs targeting YAP/TAZ or TEAD using microarray.


title: Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley


title: Asymmetrical forward and reverse developmental trajectories determine molecular programs of B cell antigen receptor editing

status: Public on Jul 06 2022

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: During B lymphopoiesis, B cell progenitors progress through alternating and mutually exclusive stages of clonal expansion and immunoglobulin (Ig) gene rearrangements. Great diversity is generated through the stochastic recombination of Ig gene segments encoding heavy and light chain variable domains. However, this commonly generates autoreactivity. Receptor editing is the predominant tolerance mechanism for self-reactive B cells in the bone marrow (BM). B cell receptor editing rescues autoreactive B cells from negative selection through renewed light chain recombination first at Igκ then Igλ loci. Receptor editing depends upon BM microenvironment cues and key transcription factors such as Nuclear factor kappa B, Forkhead box protein O and Transcription Factor 3. The specific BM factor required for receptor editing is unknown. Furthermore, how transcription factors coordinate these developmental programs to promote usage of the λ-chain remain poorly defined. Therefore, we utilized two mouse models that recapitulate pathways by which Igλ light chain positive B cells develop. The first possess deleted J kappa (Jκ) genes and, as such, models Igκ expression resulting from failed Igκ recombination (Igκdel). The second models autoreactivity by ubiquitous expression of a single-chain chimeric anti-Igκ antibody (κ-mac). Here, we demonstrated that autoreactive B cells transit asymmetric forward and reverse developmental trajectories. This imparted a unique epigenetic landscape on small pre-B cells, which opened chromatin to transcription factors essential for Igλ recombination. The consequences of this asymmetric developmental path were both amplified and complemented by CXCR4 signaling. These findings reveal how intrinsic molecular programs integrate with extrinsic signals to drive receptor editing.

overall_design: 63 samples collectively from Kappa-macroself mice (B6.Cg-Pepcb Ptprca Tg(UBC-scFv)2Nemz/J JAX Stock No: 006259), IgK deleted mice (PMID: 8458340), WT (Littermate control from Kappa-macroself mice), Cxcr4fl/fl Mb1-cre+ Kappa-macroself (+) and Cxcr4fl/fl Mb1-cre+ Kappa-macroself (-) mice. Sorted small pre-B (B220+CD19+CD43-IgM-FSClo) and immature B cells (B220loCD19+CD43-IgM+) were subjected to ATAC-seq (20 samples) and RNA-seq (19 samples). Small pre-B cells (B220+CD19+CD43-IgM-FSClo) were sorted from Cxcr4fl/fl Mb1-cre+ Kappa-macroself (+) and Cxcr4fl/fl Mb1-cre+ Kappa-macroself (-) mice, expanded in culture in the presence or absence of IL-7 and CXCL12 then subjected to RNA-seq (24 samples). Sorted small pre-B (B220+CD19+CD43-IgM-FSClo), large pre-B (B220+CD19+CD43-IgM-FSChi), immature B (B220loCD19+CD43-IgM+) from CD45.1 and CD45.2 mice were subjected to RNA-seq(14 samples).

first: Michael

last: Okoreeh

first: Domenick

last: Kennedy

first: Akinola

middle: O

last: Emmanuel

first: Margaret

last: Veselits

first: Azam

last: Moshin

middle: H

last: Ladd

last: Erickson

first: Kaitlin

last: McLean

first: David

last: Nemazee

first: Malay

last: Mandal

first: Marcus

middle: R

last: Clark


title: RNA polymerase II is necessary for enhancer-promoter interactions.

status: Public on Jul 05 2022

city: goettingen

first: Shu

last: Zhang

address: Robert-Koch-Strasse 40

department: Institute of Pathology

country: Germany

institute: University Medical Center Göttingen

summary: Enhancer-promoter interactions and their interplay between CTCF-cohesin are assumed that regulate gene expression. Here, we use Micro-C sequencing instead of Hi-C sequencing to explore whole-genome E-P interactions in an auxin-mediated degradation of RNA polymerase II cell line.

overall_design: Micro-C and Cut&Tag sequencing in DLD1 cells.

first: Argyris

last: Papantonis

first: Nadine

last: Übelmesser


title: Transcriptomic analysis of VBNC cells of osmostressed Bacillus subtilis 168

status: Public on Jul 02 2022

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: Characterization of the putative genetic determinants of the VBNC state in a known spore-forming Gram-positive organism Bacillus subtilis 168. The VBNC state was induced under osmotic stress and aminoglycoside treatment. The transcriptome landscape of VBNC cells was compared to the viable, antibiotic sensitive B. subtilis cells and to the viable cells with no antibiotic treatment.

overall_design: 9 samples, 3 biological replicates for each studied condition

first: Luiza

middle: P

last: Morawska

first: Oscar

last: Kuipers


title: Chromosome silencing in vitro reveals trisomy 21 causes cell-autonomous deficits in angiogenesis and early dysregulation in Notch signaling

city: Worcester

first: Jennifer

middle: Eunmi

last: Moon

state: MA

address: 55 Lake Ave N

institute: University of Massachusetts Medical School

summary: Despite the prevalence and clinical importance of Down syndrome, little is known as to the specific cell pathologies that underlie this multi-system disorder. To understand which cell types and pathways are more directly impacted by trisomy 21, we used an inducible-XIST system to silence the extra chromosome 21 in a panel of patient-derived iPSCs. Transcriptomic analysis showed significant dysregulation of potentially impacting programming of multiple cell-types as well as Notch. Analysis revealed prominent dysregulation in two major cell type processes: neurogenesis and angiogenesis. Angiogenesis is important for many systems impacted in Down syndrome but has been understudied. An in vitro assay for microvasculature formation used in a tightly controlled system reveals a novel cellular pathology that showed impairment in angiogenic response during tube formation. Results demonstrate that this is a cell-autonomous effect of trisomy 21 and transcriptomic analysis of differentiated endothelial cells shows deficits in known angiogenesis regulators. This study reveals a major unknown cell pathology caused by trisomy 21 and highlights the importance of endothelial cell function for Down syndrome pathologies, with wide reaching implications for development and disease progression.

overall_design: Four trasgenic clones with an inducible XIST transgene, isogenic trisomic and disomic control cell lines (no XIST transgene) were grown with or without doxycycline (500 ng/ml). RNA was extracted and sequenced.

first: Jeanne

last: Lawrence


title: Comparison of the Translatome of normal alveolar type 2 organoids and lung adenocarcinoma organoids

status: Public on Jul 08 2022

city: Tampa

first: Alex

last: Jaeger

state: FL

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: Moffitt Cancer Center

summary: In an effort to understand the differences between the presented repertoire of MHC-I peptides in healthy lung tissue and tumor bearing lung, we evaluated the translatome of AT2 cells and tumor cells.

overall_design: Examination of 2 independent AT2 cultures and 3 independent tumor derived organoids

first: Tyler

last: Jacks


title: Retinoic Acid Receptor Gamma is Required for Proliferation of  Pancreatic cancer cells

status: Public on Jul 01 2022

city: Guangzhou

first: Kaiyuan

last: Ji

address: No.9 Jinsui Road, Guangzhou, China

department: Guangzhou Women and Children’s Medical Center

country: China

institute: Guangzhou Medical University

summary: Despite of the expectation that retinoic acid receptor could be the potential therapeutic targets for pancreatic cancers, there has been the lack of information about the role and the impact of Retinoic acid receptor gamma (RARγ, RARG) on pancreatic cancer, unlike other two RARs.RARG is commonly over-expressed in human pancreatic cancer and is an independent diagnostic marker predicting the poor prognosis of pancreatic cancer patients. In addition, we demonstrated that the reduction in the expression of RARG in human pancreatic cancer cells dramatically suppress their proliferation and tumor growth in vivo, partially attributable to the down-regulation of tumor-supporting biological processes such as glucose transport and the decreased expression of various oncogenes like MYC and STAT3.

overall_design: Crispr-cas9 was used to construct RARG-Knockout PANC1 cells lines. Transcriptome analysis was performed in wildtype and RARG-Knockout PANC1.

first: Jingfeng

last: Liu


title: Genome-wide expression profiling of Octopus Arm and Hatchlings

status: Public on Jun 30 2022

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: This study was carried out to investigate the gene expression profile from arm and hatchlings transcriptome across multiple individual Octopus bimaculoides .

overall_design: 3 different arm sections from an adult male Octopus bimaculoides were collected (containing all tissues, including skin, sucker, muscle and nerve).  2 arm tips were collected from a different adult male and one adult female. One whole-body 30 day old hatchling was removed from chorion and anesthetized. All animals were anesthetized in ethanol, all samples were dissected in sea water and flash frozen. RNA was extracted using Trizol and DNAse treated to carry out Ribo-Zero library preparation.

first: Filippo

last: Macchi

middle: C

last: Sadler


title: Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [Cut&Run]

first: Robert

last: Tjian

summary: Transcription factors (TFs) are classically attributed a modular construction, containing well-structured sequence specific DNA-binding domains (DBDs) paired with disordered activation domains (ADs) responsible for protein-protein interactions targeting cofactors or the core transcription initiation machinery. However, this simple division of labor model struggles to explain why TFs with identical DNA binding sequence specificity determined in vitro exhibit distinct binding profiles in vivo. The family of Hypoxia-Inducible Factors (HIFs) offer a stark example: aberrantly expressed in several cancer types, HIF-1α and HIF-2α subunit isoforms recognize the same DNA motif in vitro – the hypoxia response element (HRE) – but only share a subset of their target genes in vivo, while eliciting contrasting effects on cancer development and progression under certain circumstances. To probe the mechanisms mediating isoform-specific gene regulation, we used live cell single particle tracking (SPT) to investigate HIF nuclear dynamics and how they change upon genetic perturbation or drug treatment. We found that HIF-α subunits and their dimerization partner HIF-1β exhibit distinct diffusion and binding characteristics that are exquisitely sensitive to concentration and subunit stoichiometry. Using domain-swap variants, mutations, and a HIF-2α specific inhibitor, we found that although the DBD and dimerization domains are important, a major determinant of chromatin binding and diffusion behavior is dictated by the AD-containing intrinsically disordered regions (IDR). Using orthogonal genomic approaches such as Cut-and-Run and RNA-seq, we also confirmed IDR-dependent binding and activation for a specific subset of HIF-target genes. These findings reveal a previously unappreciated role of IDRs in regulating the TF search process that may play a role in selective functional target site binding on chromatin.

overall_design: Cut&Run: WT 786-O cells (anti-V5 antibody, IgG control), 786-O cells with either HIF-2a (anti-V5 antibody, IgG control) endogenously tagged with a V5-Halo moiety, and 786-O cells exogenously expressing HIF-1a (anti-V5 antibody, IgG control), HIF-2a (anti-V5 antibody, IgG control) or chimeric HIF-2a/1a (anti-V5 antibody, IgG control) or HIF-1a/2a (anti-V5 antibody, IgG control) transcription factors. 3 biological replicates for each condition.

first: Claudia

last: Cattoglio

first: Yu

last: Chen

first: Gina

last: Dailey

first: Qiulin

last: Zhu

first: Xavier

last: Darzacq


title: Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [RNA-seq]

overall_design: Poly-A RNA-seq batch1: WT 786-O cells (n = 3), 786-O cells with either HIF-1b (n = 3) or HIF-2a (n = 3) endogenously tagged with a V5-Halo moiety, and 786-O cells exogenously expressing wild type HIF-1a (n = 3), R30E HIF-1a (n = 3), R170A/V191D HIF-1a (n = 3), wild type HIF-2a (n = 3), R27E HIF-2a (n = 3) or R171A/V192D HIF-2a (n = 3). Poly-A RNA-seq batch2: WT 786-O cells (n = 3), 786-O cells exogenously expressing HIF-1a (n = 3), HIF-2a (n = 3) or chimeric HIF-2a/1a (n = 3) or HIF-1a/2a (n = 3) transcription factors.


title: Adult hippocampal neurogenesis in aged macaques and humans

status: Public on Jun 29 2022

city: Beijing

first: Qiang

last: Ma

address: Datun Road, #15

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: We performed snRNA-seq of macaque hippocampal formation sample to investigate whether there is the existence of adult neural stem cells and adult hippocampal neurogenesis.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Single-nucleus RNA-seq for 3 macaque hippocampus (4, 11 and 23 years old) and 4 human hippocampus (67, 85, 87 and 92 years old) samples

first: Bo

last: Zeng

first: Qianqian

last: Zhang

first: Wei

last: Wang

first: Xiaoqun

first: Qian

last: Wu


title: Functional Portrait of Irf1 (Orf19.217), a Regulator of Morphogenesis and Iron Homeostasis in Candida albicans [RNA-Seq]

city: Paris

first: Lasse

middle: van

last: Wijlick

address: 25-28 Rue du Dr Roux

department: Mycology

country: France

institute: Institut Pasteur

summary: The fungus Candida albicans is part of the human microbiome and mainly colonises the GI tract of healthy individuals. However, when the balance in the GI tract is disturbed, the fungus can switch from a commensal to a virulent lifestyle and can turn into a life-threatening pathogen. Life in the host is characterised by a constant struggle for nutrients, essential trace elements such as iron, copper and zinc are particularly important. To protect itself from pathogens, the human host has developed a strategy to limit the availability of trace elements, this strategy is also described as nutritional immunity. C. albicans has developed a whole range of counter-strategies to obtain sufficient trace elements. In this manuscript, we have characterised the transcription factor Orf19.217, which acts at the interface between trace element scavenging and acquisition and is therefore particularly important in adaptation to life in the host. According to its identified function, we named the transcription factor Irf1, Iron-dependent Regulator of Filamentation. The transcription factor was previously identified in a systematic screen of genes whose overexpression contributes to morphological changes in C. albicans. We have comprehensively investigated the function of Irf1 using state-of-the-art functional genomics approaches, including ChIP-seq, transcriptomics and bioinformatics analyses. Analysis of the Irf1 gene-regulatory network indicates that the transcription factor is involved in the regulation of genes important for iron uptake. Using phenotypic analysis, we confirmed that Irf1 acts in a pathway parallel to known iron uptake regulators and is also required for hyphal formation induced by iron deficiency, a process that allows the fungus to access more viable body niches. Through epistasis experiments, we were also able to identify downstream effectors of Irf1 that are involved in this process. Our study provides new insights into how C. albicans adapts to iron deficiency and establish a direct functional link between hyphal formation and iron uptake.

overall_design: RNA-Seq of irf1 mutant strains or IRF1 overexpression strains, in triplicate including respective control strain samples (matching parental strain)

last: van Wijlick

first: Sadri

last: Znaidi

first: Sophie

last: Bachellier-Bassi

first: Christophe

last: d’Enfert


title: Functional Portrait of Irf1 (Orf19.217), a Regulator of Morphogenesis and Iron Homeostasis in Candida albicans


title: Type I IFNs promote cancer cell stemness by triggering the epigenetic regulator KDM1B

city: Rome

first: Antonella

last: Sistigu

state: Rome

address: Viale Francesco Vito, 1

department: Translational Medicine and Surgery

country: Italy

institute: University of Rome Tor VergataUniversità Cattolica del Sacro Cuore

summary: Cancer stem cells (CSCs) are immature, immortal cells within tumors, adept at resisting therapeutic pressure and responsible for local and distant disease recurrence. Non-genetic mechanisms of acquired resistance are increasingly being described, however molecular insights into this evolutionary process still lack. Here, we showed that Type I interferons (IFNs-I) act as molecular hubs of resistance during immunogenic chemotherapy, as they trigger the epigenetic regulator KDM1B, responsible for an adaptive, yet reversible, transcriptional rewiring of cancer cells towards stemness and immune escape. Accordingly, KDM1B pharmacological inhibition antagonizes the appearance of IFN-I-adapted CSCs, both in vitro and in vivo. Notably, IFN-I-adapted CSCs are heterogeneous in terms of multidrug resistance, plasticity, invasiveness and immunogenicity. Moreover, in breast cancer patients receiving anthracycline-based chemotherapy, IFN-I and KDM1B signatures positively correlate with CSC and immune evasion markers. Our study identifies IFN-I→KDM1B axis as a potent engine of cancer cell reprogramming and recommends KDM1B targeting an attractive adjunctive to immunogenic drugs to prevent CSC expansion and increase the long-term benefit of therapy.

overall_design: ATAC-seq: 3 samples (CD44LOW, CD44HIGH and their PARENTAL) with 2 replicates for each sample; 2 samples (MCA Kdm1bOVER and MCA Kdm1bKD) with 1 replicate for each sample; RNA-seq: 3 samples (CD44LOW, CD44HIGH and their PARENTAL), with 2 replicates for each sample. CHIP-seq: 1 sample (CD44HIGH), with 2 replicates.

first: Martina

last: Musella

first: Andrea

last: Guarracino

first: Nicoletta

last: Manduca

last: Galassi

first: Eliana

last: Ruggiero

first: Alessia

last: Potenza

first: Ester

last: Maccafeo

first: Gwenola

last: Manic

first: Luca

last: Mattiello

first: Sara

last: Soliman Abdel Rehim

first: Michele

last: Signore

first: Marco

last: Pietrosanto

first: Manuela

last: Helmer-Citterich

first: Matteo

last: Pallocca

first: Maurizio

last: Fanciulli

first: Tiziana

last: Bruno

first: Francesca

last: De Nicola

first: Giacomo

last: Corleone

first: Anna

last: Di Benedetto

first: Cristiana

last: Ercolani

first: Edoardo

last: Pescarmona

first: Laura

last: Pizzuti

last: Guidi

last: Sperati

last: Vitale

first: Giovanna

last: Schiavoni

first: Fabrizio

last: Mattei

first: Adele

last: De Ninno

last: Businaro

first: Valeria

last: Lucarini

last: Bracci

first: Eleonora

last: Aricò

last: Ziccheddu

first: Francesco

last: Facchiano

first: Stefania

last: Rossi

first: Massimo

last: Sanchez

first: Alessandra

last: Boe

first: Mauro

last: Biffoni

first: Ruggero

last: De Maria

first: Ilio


title: Consticted migration is associated with stable 3D genome structure differences in cancer cells

city: Knoxville

first: Rosela

last: Golloshi

state: TN

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

first: Christopher

last: Playter

first: Trevor

middle: F

last: Freeman

first: Priyojit

last: Das

first: Thomas

middle: I

last: Raines

first: Joshua

last: Garretson

first: Delaney

last: Thurston

first: Rachel

last: McCord


title: Blocking ActRIIB signaling and restoring appetite reverses cachexia and improves survival in mice with lung cancer

status: Public on Jul 09 2022

city: New York

first: Charles

last: Murphy

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Cancer cachexia is a common, debilitating condition with limited therapeutic options. The defining feature of cachexia is weight loss, which suggests a state of negative energy balance. Using an established genetically engineered mouse model of lung cancer, we found that cachexia is characterized by reduced food intake, spontaneous activity, and energy expenditure accompanied by muscle metabolic dysfunction and atrophy. Calorie restriction in wild-type mice does not recapitulate this phenotype, suggesting that reduced food intake is not the only driver of weight loss in this model. Using unbiased RNA-sequencing of the muscle and tumor, we identified Activin A as a purported driver of the peripheral metabolic dysfunction. To reverse anorexia and muscle dysfunction, we treated the mice with anamorelin (Ana), a ghrelin receptor agonist, alone or in combination with the ActRIIB-Fc, a decoy ligand for TGF-β/activin family members. Ana effectively increased food intake but only the combination of drugs increased lean mass, restored spontaneous activity, and improved overall survival. These beneficial effects were limited to female mice and were dependent on ovarian function. In agreement, we found that high expression of Activin A in human lung adenocarcinoma correlates with unfavorable prognosis only in female patients, even though expression levels are similar in both sexes. Overall, our study suggests that multimodal, sex-specific, therapies are needed to reverse CACS.

overall_design: We sequenced 51 RNA-seq samples from mice. Nineteen samples were from gonadal white adipose tissue (with or without lung-cancer induced cachexia), 22 were from tumors, and ten samples from the gastrocnemius muscle (with or without lung cancer-induced cachexia). Replicates were included for all conditions.

first: Andre

middle: L

last: Queiroz

first: Marcus

middle: D

last: Goncalves

first: Ezequiel

last: Dantas


title: Consticted migration is associated with stable 3D genome structure differences in cancer cells (Hi-C)

summary: We investigated the effect of constricted migration (using transwell assays with 5-μm or 12-μm in diameter) on the organization of the 3D genome in melanoma and breast cancer cells.

overall_design: Hi-C was performed to investigate changes in 3D genome organization after constricted migration. This experiment was performed on all sub-populations of A375 with two biological replicates per condition.


title: Identification of Pathogenic Immune Cell Subsets in Checkpoint Inhibitor-induced Myocarditis

city: Stanford

first: Han

last: Zhu

address: G1105, 265 Campus Drive

department: Cardiovascular Medicine

institute: Stanford University

summary: Immune checkpoint inhibitors (ICIs) are monoclonal antibodies used widely to activate the immune system against tumor cells. Despite their therapeutic benefits, ICIs are known to cause immune-related adverse events (irAE) such as myocarditis, a rare but serious side effect with up to 50% mortality. To identify pathogenic immune subset(s) responsible for ICI myocarditis and other irAE, we performed single cell mass cytometry (CyTOF) on peripheral blood mononuclear cells from 40 patients and controls with irAE including four patients with ICI myocarditis. We also profiled 15 patients/controls using single cell RNA sequencing (scRNA-seq) with feature barcoding for surface marker expression confirmation. In both CyTOF/scRNAseq analyses, we found expansions of cytotoxic CD8+ T effector cells re-expressing CD45RA (Temra CD8+ cells) in ICI myocarditis patients compared to controls. Using T cell receptor sequencing, we demonstrated a significant clonal expansion of CD8+ Temra cells in myocarditis patients. Transcriptomic profiling of these Temra CD8+ clones confirmed their highly activated and cytotoxic phenotype with expression of granzyme/perforin. Longitudinal data revealed the progression of these Temra CD8+ cells into an exhausted phenotype two months after diagnosis of myocarditis and after treatment with glucocorticoids. Differential expression of several proinflammatory chemokines (CCL4/CCL4L2/CCL5) was uncovered in the clonally expanded Temra CD8+ cells and ligand-receptor analysis implicated their regulation of other inflammatory cells such as monocytes and NK cells. These data suggest that the therapeutic modulation of these chemokines may serve as an attractive strategy for reducing life-threatening irAE in ICI-treated cancer patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
PBMCs were collected and isolated from three main patient groups: Group A - patients on immune checkpoint inhibitors without any known immune adverse events (irAEs), Group B - patients on immune checkpoint inhibitors with non-myocarditis irAEs, Group C - patients on immune checkpoint inhibitors with myocarditis. High-throughput sequencing in the form of scRNA-seq, single cell TCR sequencing, and feature barcoding were then performed. CyTOF (mass cytometry) data was also obtained on samples (not included on this record).

The processed data for the CITE-seq component are included in the single-cell RNA-seq sample data matrices..

first: Sean

last: Wu


title: Single-cell multi-omics in human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation.

first: Neville

last: Dusaj

type: Methylation profiling by high throughput sequencing

summary: Clonal hematopoiesis (CH) reflects clonal expansion of blood stem and progenitor cells with somatic mutations. We leveraged multi-modality single-cell sequencing to capture mutation status together with the transcriptome and methylome of CD34+ hematopoietic progenitor cells from five individuals with DNMT3A R882-mutated CH.

overall_design:
We profiled CD34+ enriched cells from GCSF mobilized bone marrow samples (n = 4) using single-cell RNA sequencing (10X) with targeted genotyping, and single-cell DNA methylation (RRBS) with single-cell RNA sequencing (Smart-Seq2) and targeted genotyping.
A 5th CH bone marrow aspirate sample was obtained to validate observed results.

**Submitter declares that the raw data are being deposited in EGA due to patient privacy concerns**

first: Anna

last: Nam

first: Franco

last: Izzo

first: Rekha

last: Murali

first: Ronan

last: Chaligne

first: Irene

last: Ghobrial

first: Dan

middle: A

last: Landau


title: Expression profiling of Cellvibrio japonicus using plant mannans

status: Public on Jun 28 2022

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Plant mannans are a component of lignocellulose that may possess diverse compositions changing both in terms of its backbone and side-chain substitutions.  Consequently, the degradation of mannan substrates requires a cadre of enzymes for complete reduction to substituent monosaccharides, specifically mannose, galactose, and/or glucose. One bacterium that possesses this suite of enzymes is the Gram-negative saprophyte Cellvibrio japonicus, which has ten predicted mannanases from the Glycoside Hydrolase (GH) families 5, 26, and 27. Here we describe a systems biology approach to identify and characterize the essential components of the mannan degradation apparatus in this bacterium. Transcriptomic analysis uncovered significant changes in gene expression for most mannanases, as well as many genes that encode Carbohydrate Active Enzymes (CAZymes) when mannan substrates were actively being degraded. A comprehensive mutational analysis characterized 54 CAZyme genes in the context of mannan utilization. Growth analysis of the mutant strains indicated that the man26C, aga27A, and man5D genes, which encode a mannobiohydrolase, α-  galactosidase, and mannosidase, respectively, were influential to the deconstruction of galactomannan. Furthermore, our updated model of mannan degradation in C. japonicus proposes that the removal of galactose sidechains from substituted mannans constitutes a crucial step for the efficient and complete degradation of this hemicellulose by bacteria.

overall_design: One carbon condition (glucomannan); Two sample points (exponential phase, stationary phase); Data collected in biological triplicate; Total of 6 samples; Data from GSE90955 (glucose) was used in data analysis

middle: G


title: Expression profiles of lncRNAs in 3D cultures.

status: Public on Jun 24 2022

city: CDMX

first: Stephanie Iraiz

last: Nuñez Olvera

address: Circuito, Mario de La Cueva s/n

country: Mexico

institute: Universidad Nacional Autónoma de México

summary:
Breast cancer cells reprogram the oncogenic lncRNAs/mRNAs co-expression networks in three- dimensional microenvironment
To have a more functional approach, organotypic 3D cell cultures that more accurately mimic the characteristics of solid tumors in vivo and the tumor microenvironment are required. In this study, DNA microarrays were employed to deline the changes in lncRNAs expression patterns of breast cancer cells, cultured in 3D and 2D conditions from BT-474 cell line. Furthermore, potential lncRNAs/mRNAs pairs co-expressed in 3D cultures exhibit a high degree of similarity with those found in luminal B breast cancer patients suggesting that they could be adequate pre-clinical tools to identify, not only biomarkers related to endocrine therapy response and PCR, but to understand the biological behavior of cancer cells in 3D microenvironments, which point towards an important contribution of the roles of lncRNAs in organotypic 3D cultures.

overall_design: We analyzed 3D culture samples compared to 2D cultures of the BT-474  luminal B cell line, using the human Clariom D array plataform. Array data were processed with the Affymetrix GeneChip command console software v4.0 computational tool. Samples were run in triplicate.

first: S

last: Nuñez-Olvera

first: L

last: Aguilar-Arnal

first: A

last: Marchat

first: M

last: Cisneros-Villanueva

last: Hidalgo-Miranda

last: Mauricio-Dorantes

middle: Y

last: Salinas-Vera

first: R

last: Ramos-Payán

first: C

last: Pérez-Plasencia

last: Carlos-Reyes

first: J

last: Puente-Rivera

last: López-Camarillo


title: High nucleotide substitution rates associated with retrotransposon proliferation drive dynamic secretome evolution in smut pathogens

city: Cologne

first: Jasper

middle: Robert Lisette

last: Depotter

address: Zülpicher Straße 47a

institute: University of Cologne

summary: Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest in U. hordei and are positively correlated to the mating-type locus sizes, which is up to ~560 kb in U. hordei. Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these occur in specific genome regions of smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more accessory nature results that substitutions often lead to amino acid alterations.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of Ustilago hordei grown in axenic culture and barley.

first: Bilal

last: Ökmen

first: Malaika

middle: K

last: Ebert

first: Jens

last: Beckers

first: Julia

last: Kruse

first: Marco

last: Thines

first: Gunther

last: Doehlemann


title: Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [RNAseq mESC]

status: Public on Jun 27 2022

city: Parkville

first: Natalia

last: Benetti

state: Victoria

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: Parents transmit genetic and epigenetic information to their offspring. Maternal effect genes regulate the offspring epigenome to ensure normal development. Here we report that the epigenetic regulator SMCHD1 has a maternal effect on Hox gene expression and skeletal patterning. Maternal SMCHD1, present in the oocyte and preimplantation embryo, prevents precocious activation of Hox genes post-implantation. Without maternal SMCHD1, highly penetrant posterior homeotic transformations occur in the embryo. Hox genes are decorated with Polycomb marks H2AK119ub and H3K27me3 from the oocyte throughout early embryonic development; however, loss of maternal SMCHD1 does not deplete these marks. Therefore, we propose maternal SMCHD1 acts downstream of Polycomb marks to establish a chromatin state necessary for persistent epigenetic silencing and appropriate Hox gene expression later in the developing embryo. This is a striking role for maternal SMCHD1 in long-lived epigenetic effects impacting offspring phenotype.

overall_design: Our overall design it to compare between Smchd1 control and Smchd1 maternally deleted samples. We have performed RNA-seq in a differentiation timecourse in 4 replicate mESC of each genotype with 6 timepoints (timepoints are missing for three samples across two replicate differentiation experiments; wt day 1 line 1 rep 3, mat del DME LIF line 2 rep 4, mat del day 2.5 line 2 rep 4), comparing the Smchd1 maternally deleted to the control, at the matched timepoint.

first: Marnie

middle: E

last: Blewitt


title: RNA sequencing of undifferentiated and differentiated SH SY5Y cells

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

summary: DNA topoisomerase IIB has an important role in ligand mediated transcriptional regulation of gene expression. SH-SY5Y  is a neuroblastoma cell line that can be induced to differentiate into neuronal-like cells in response to retinoic acid. In this study TOP2B has been knocked out using crispr-cas9 to determine the role of TOP2B in the transcriptional response to retinoic acid. RNA was prepared from untreated wild type and TOP2B null SH-SY5Y cells and from cells exposed to 10 uM All Trans Retinoic Acid (ATRA) for 24 hours.

overall_design: 4 replicates of each of  untreated WT, untreated TOP2B-/- , ATRA treated WT and ATRA treated TOP2B-/-

first: Caroline

last: Austin

first: Mushtaq

last: Khazeem


title: AFF1-HEXIM1 cooperation suppresses rapid-response differentiation initiators to enforce epidermal progenitor maintenance

city: Evanston

first: Xiaomin

last: Bao

address: 633 Clark Street

department: Molecular Biosciences

institute: Northwestern University

summary: In this study we identified an essential role of the SEC, a crucial regulator of Pol II dynamics, in repressing differentiation for epidermal progenitor maintenance. This repression of differentiation is specifically mediated by the scaffold protein AFF1, but not AFF4. Mechanistically, we find that AFF1-SEC associates with the HEXIM1-containing inactive-PTEFb to directly repress a group of rapid-response genes, which feature robust Pol II pausing near their promoters in the progenitor state. De-repression of these genes occurs within 3 hours of SEC-PTEFb disruption by the peptidomimetic inhibitors. These rapid-response genes include the transcription factor ATF3. Increased ATF3 level is sufficient to promote the expression of key differentiation activators, such as PRDM1, OVOL1, GRHL3 and ZNF750. Furthermore, we find that the dissociation of inactivate P-TEFb from SEC mediates the earliest events of PKC signaling, in triggering epidermal differentiation.

overall_design: We performed ChIP-seq for Pol II in progenitors and in differentiated keratinocytes. We additionally performed ChIP-seq for AFF1 and HEXIM1 in progenitors. We completed RNA-seq for AFF1 knockdown (KD), AFF4 KD, and HEXIM1 KD. We also performed RNA-seq after TPA and KL drug treatments.

first: Sarah

middle: M

last: Lloyd

first: Daniel

middle: B

last: Leon

first: Mari

middle: O

last: Brady

first: Deborah

last: Rodriguez

first: Madison

last: McReynolds

first: Junghun

last: Kweon

first: Amy

last: Neely

first: Laura

last: Blumensaadt

first: Patric

middle: J

last: Ho


title: Analysis of time series gene expression and DNA methylation reveals the molecular features of myocardial infarction progression (MeDIP-seq)

status: Public on Jun 23 2022

city: Shanghai

first: Han

last: Yuru

state: Shanghai

address: 279 Zhouzhu Rd. Pudong New District, Shanghai

institute: Shanghai University of Medicine and Health Sciences

summary: Myocardial infarction (MI) is one of the deadliest diseases in the world, and the changes at the molecular level after MI and the DNA methylation features are not clear. Understanding the molecular characteristics of the early stages of MI is of significance for the treatment of the disease. In this study, RNA-seq and MeDIP-seq were performed on heart tissue from mouse models at multiple time points (0 h, 10 min,1 h, 6 h, 24 h and 72 h) to explore genetic and epigenetic features that influence MI progression. Analysis based on a single point in time, the number of differentially expressed genes (DEGs)and differentially methylated regions (DMRs)increased with the time of myocardial infarction, using 0 h as a control group. Moreover, within 10 minutes of MI onset, the cells are mainly in immune response, and as the duration of MI increases, apoptosis begins to occur. Analysis based on time series data, the expression of 1012 genes was specifically downregulated, and these genes were associated with energy metabolism. The expression of 5806 genes was specifically upregulated, and these genes were associated with immune regulation, inflammation and apoptosis. 14 transcription factors were identified in the genes involved in apoptosis and inflammation, which may be potential drug targets. Analysis based on MeDIP-seq combined with RNA-seq methodology, focused on methylation at the promoter region. GO revealed that the downregulated genes with hypermethylation at 72 h were enriched in biological processes such as cardiac muscle contraction. In addition, the upregulated genes with hypomethylation at 72 h were enriched in biological processes, such as cell-cell adhesion, regulation of the apoptotic signalling pathway and regulation of angiogenesis. Among these genes, the Tnni3 gene was also present in the downregulated model. Hypermethylation of Tnni3 at 72 hours after MI may be an important cause of exacerbation of MI.

overall_design: Eighteen 12-week-old male C57BL/6JR mice were included in the experiment. The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (50 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately. The mice in the control group received the same operation, sutured through the inferior artery, but not ligated. Complete anaesthesia of mice with 1-3% isoflurane after specific time of MI, followed by euthanasia by cervical dislocation. DNA fragments methylated on the genome were specifically enriched by 5-methylcytosine antibodies, and then the DNA methylation levels in the samples were examined by high-throughput sequencing.

first: Yanfei

last: Li


title: Analysis of gene expression in lung adenocarcinoma cells following ectopic expression of proliferation-suppressive lncRNAs (PSLR).

status: Public on Jun 22 2022

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

summary: RNA-sequencing was performed to gain insight into the transcriptome-wide molecular changes induced by FAM198B-AS1 (PSLR-1) or SEPTIN9-DT (PSLR-2) ectopic expression in lung adenocarcinoma cells. Following expression of PSLR-1 or PSLR-2 lncRNA or control RNA, RNA-sequencing was performed. This high-throughput data revealed elevated expression of these lncRNAs reduced the expression of genes and pathways known to induce proliferation in lung adenocarcinoma cells.

overall_design: PSLR-1 or PSLR-2 expressed in lung adenocarcinoma cells and gene expression profiles were generated using RNA-sequencing.

first: Christine

last: Eischen

first: Clare

last: Adams


title: Analysis of time series gene expression and DNA methylation reveals the molecular features of myocardial infarction progression

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

overall_design: Refer to individual Series


title: Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [H3K27me3 CUT&RUN]

first: Natalia

last: Benetti

overall_design: H3K27me3 CUT&RUN-sequencing comparing Smchd1 wildtype and maternally deleted samples in 3 mESC lines grown in 2i+LIF medium for each genotype, and a differentiation timecourse with 2 replicate mESC of each genotype, each with 1-2 technical replicates.

first: Marnie

last: Blewitt


title: Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [H2AK119ub CUT&RUN]

sample_organism:
Drosophila melanogaster
Mus musculus

overall_design: H2AK119ub CUT&RUN-sequencing comparing Smchd1 wildtype and maternally deleted samples in 3 mESC lines grown in 2i+LIF medium for each genotype, and a differentiation timecourse with 2 replicate mESC of each genotype, each with 1-2 technical replicates. Note that no Ab control files are in H3K27me3_CUT_RUN_differentiation folder. Please add to current geo entry GSE183739 and update the experimental design with this description.


title: Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo


title: Integrated multiomic characterization of congenital heart disease [ATAC-Seq]

city: Cambridge

first: Matthew

middle: C

last: Hill

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: The heart, the first organ to develop, undergoes complex morphogenesis that when defective results in congenital heart disease (CHD). With current therapies, more than 90% of CHD patients survive into adulthood but often suffer premature death from heart failure (HF) and non-cardiac causes 1. To gain insight into poorly understood disease progression, we performed single nuclear RNA sequencing (snRNA-seq) and analyzed more than 157,000 nuclei from donors and CHD patients, including hypoplastic left heart syndrome (HLHS) and Tetralogy of Fallot (TOF), two common forms of cyanotic CHD lesions, as well as, dilated (DCM) and hypertrophic (HCM) cardiomyopathies. We observed CHD specific cell states in cardiomyocytes (CMs) which had evidence of insulin resistance and increased FOXO and CRIM1 expression. Cardiac fibroblasts (CFs) in HLHS had enrichment for a low HIPPO and high YAP cell state characteristic of activated CFs. Imaging Mass Cytometry (IMC) uncovered the spatially resolved perivascular microenvironment consistent with an immunodeficient state in CHD. Peripheral immune cell profiling suggested deficient monocytic immunity in CHD in agreement with CHD predilection to infection and cancer 2. Our comprehensive CHD phenotyping provides a roadmap for future personalized medicine in CHD.

overall_design: ATAC-seq was performed on cardiac tissue from patients and donors

first: Thomas

last: Martin


title: Integrated multiomic characterization of congenital heart disease


title: Genome wide DNA methylation profiling of whole blood samples from C57BL/6 and DBA/2J healthy mice

status: Public on Jun 21 2022

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Aging of mice can be tracked by DNA methylation changes at specific sites in the genome. In this study, we used the Infinium Mouse Methylation BeadChip to compare such epigenetic modifications in C57BL/6 (B6) and DBA/2J (DBA) mice. There were marked differences in age-associated DNA methylation in these commonly used mouse strains. In B6 the age-associated DNA methylation revealed general age-associated hypomethylation with focused hypermethylation at CpG islands, whereas this was hardly observed in DBA mice. The CpGs with highest age-correlation were overlapping in B6 and DBA and included the genes Hsf4, Prima1, Aspa, and Wnt3a. Notably, Hsf4, Prima1 were also top candidates in previous studies based on whole genome deep sequencing approaches. Furthermore, Hsf4, Aspa, and Wnt3a revealed highly significant age-associated DNA methylation in the homologous regions in human. Taken together, age-associated DNA methylation differs between B6 and DBA, but the most prominent regions are conserved, even in humans.

overall_design: Bisulphite converted DNA from the 35 whole blood samples were hybridised to the Illumina Infinium MouseMethylation BeadChip

first: J

last: Pérez-Correa

first: W


title: The neurons that restore walking after paralysis

status: Public on Jun 20 2022

city: Vancouver

first: Jordan

middle: W

last: Squair

state: BC

address: 818 West 10th Avenue

institute: University of British Columbia


title: Oxidative stress alters transcript localization of disease-causing genes in the retinal pigment epithelium

city: Buffalo

first: Michael

last: Farkas

address: 3495 Bailey Ave, Bldg 20, Mail Stop 151

department: Ophthalmology

institute: State University of New York at Buffalo

summary: To evaluate the effect of oxidative stress on transcript localization in the retinal pigment epithelium (RPE), we performed poly-A RNA sequencing on nuclear and cytoplasmic fractions from induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) cells exposed to hydrogen peroxide, as well as untreated controls.

overall_design: RNASeq analysis of nuclear and cytoplasmic fractions from control iPSRPE cells and iPSRPE cells subjected to hydrogen peroxide

first: Tadeusz

last: Kaczynski

first: Elizabeth

last: Au

middle: H


title: Anole ocular patterns of gene expression

city: Athens

first: Douglas

last: Menke

address: 500 DW Brooks Drive

institute: University of Georgia

summary: For the purpose of facilitating gene annotation, a transcriptome profile of the developing anole eye was used to identify coding and non-coding regions in the Anolis genome. RNA datasets were generated by collecting samples from three subregions of the anole posterior globe (central, temporal, and nasal) which was comprised of nerual retina, retinal pigmented epithelium, choriod, and scleral tissues. A total of five sample replicates were made. Each replicate incorporated pooled tissues collected from three stage 16.5 developing anole embryos.

overall_design: Five RNA-seq datasets of three different subregions of the anole posterior globe (central, temporal, and nasal) were generated using embryos of mixed sexes collected at stage 16.5 that were obtained from random populations of wild-caught anoles that originated from south Florida.

first: Ashley

last: Rasys

first: Sungdae

last: Park

first: James

last: Lauderdale


title: Integrated multiomic characterization of congenital heart disease [RNA-Seq]

overall_design: Single nuclei RNA-seq was performed on cardiac tissue from patients and donore, and single cell rna-seq was performed on isolated PBMCs.


title: The neurons that restore walking after paralysis [spatial transcriptomics]

summary: Here, we show that epidural electrical stimulation (EES) of the lumbar spinal cord applied during neurorehabilitation (EESREHAB) restored walking in nine people with chronic spinal cord injury (SCI). This recovery involved a reduction of the metabolic activity in the lumbar spinal cord during walking. We hypothesized that this unexpected reduction reflects activity-dependent selection of specific neuronal subpopulations that become essential to walk after SCI. To identify these putative neurons, we modelled the technological and therapeutic features underlying EESREHAB in mice. We applied single-nucleus RNA sequencing and spatial transcriptomics to the spinal cord of these mice to chart a spatially-resolved molecular atlas of recovery from paralysis. We then employed cell type and spatial prioritization to uncover the neurons involved in the recovery of walking. A single population of excitatory interneurons nested within intermediate laminae emerged. Although these neurons were not necessary to walk before SCI, we demonstrate that they are essential to regain walking following SCI. In turn, augmenting their activity instantly phenocopied the recovery of walking enabled by EESREHAB. We thus identified a recovery-organizing neuronal subpopulation that is necessary and sufficient to regain walking after SCI. Moreover, our methodology establishes a framework to identify the neurons producing complex behaviours using molecular cartography.

overall_design:
We used single-nucleus RNA sequencing (snRNA-seq) to profile the lumbar spinal cord of mice. We devised a progression of eight experimental conditions that captured the key therapeutic features of EESREHAB. We obtained high-quality transcriptomes from 82,093 nuclei that were evenly represented across 24 mice from all eight conditions.

Mice were divided in three experimental groups: uninjured, SCI (no neurorehabilitation), and EESREHAB. At the end of the experimental period, mice were terminated to harvest fresh tissues or perfused and dissected. Half of the groups of mice underwent a terminal experimental condition immediately before being terminated, which is denoted by     final_condition. If more than one component was integrated in the terminal experimental condition, the additional component is denoted by  ::. Group 1 (uninjured) consisted of uninjured mice that did not perform a terminal behavioral task. Mice in Group 2 (SCI) received a contusion SCI and did not perform a terminal behavioral task. Mice in Group 3 (EESREHAB) received a contusion SCI and followed EESREHAB  for four weeks, but did not perform a terminal behavioral task.  Mice in Group 4 (SCI   EES::walking) received a contusion SCI and walked with EESON  for 30 minutes immediately before being terminated. Mice in Group 5 (EESREHAB   EES::walking) received a contusion SCI and followed EESREHAB  for four weeks, and walked with EESON  for 30 minutes immediately before being terminated. Mice in Group 6 (EESREHAB   EES) received a contusion SCI and and followed EESREHAB  for four weeks, and were stimulated for 30 minutes with EES just below motor threshold immediately before being terminated. Mice in Group 7 (EESREHAB   EES::cortex) received a contusion SCI and followed EESREHAB  for four weeks, and walked with optogenetic stimulation of the motor cortex for 30 minutes immediately before being terminated. Mice in Group 8 (EESREHAB   EES::cortex::walking) received a contusion SCI and followed EESREHAB  for four weeks, and walked with EESON  and optogenetic stimulation of the motor cortex for 30 minutes immediately before being terminated.

first: Claudia

last: Kathe

last: Skinnider

last: Hutson

first: Nicola

last: Regazzi

first: Matthieu

last: Gautier

first: Robin

last: Demesmaeker

first: Salif

last: Komi

first: Steven

last: Ceto

first: Nicholas

last: James

first: Newton

last: Cho

first: Laetitia

last: Baud

first: Katia

last: Galan

first: Kaya

last: Matson

first: Andreas

last: Rowald

first: Kyungjin

last: Kim

first: Ruijia

last: Wang

first: John

last: Prior

first: Leonie

last: Asboth

first: Quentin

last: Barraud

first: Stephanie

middle: P

last: Lacour

first: Ariel

last: Levine

first: Fabien

first: Jocelyne

last: Bloch

first: Grégoire

last: Courtine


title: Cancer-specific deficiency of SMARCE1, a module-linking subunit, generates a targetable chromatin regulatory dependency in clear cell meningioma

status: Public on Jun 16 2022

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: Mammalian SWI/SNF (mSWI/SNF) ATP-dependent chromatin remodeling complexes are critical for establishing and maintaining chromatin accessibility and gene expression and are frequently perturbed in human disease. Select rare cancer types are characterized uniformly by mSWI/SNF subunit perturbations, underscoring their driving roles. Clear cell meningioma (CCM), an aggressive CNS tumor, is driven by loss of the SMARCE1 subunit, found in ~100% of cases. Here we identify an unexpected and evolutionarily conserved structural role for SMARCE1 in selectively stabilizing the cBAF complex core -ATPase module interaction. SMARCE1 is required for stable docking of cBAF complexes to nucleosomes via ATPase rigidification. In CCM, cBAF complexes selectively fail to stabilize on nucleosome substrates and chromatin and residual cores increase the formation of BRD9-containing ncBAF complexes. Combined attenuation of cBAF complex function and ncBAF complex activity generate the CCM-specific gene expression profile, which is distinct from NF2 loss. Importantly, SMARCE1-deficient cells exhibit heightened sensitivity to small molecule inhibition of ncBAF complexes. These data inform on the function of a previously elusive subunit and suggest new therapeutic approaches for highly aggressive SMARCE1-deficient CCM.

overall_design:
ChIP-seq, Cut & Tag, RNA-seq, and ATAC-seq in BT549 (SMARCE1-null breast cancer cell), AC7 (Human meningeal cell), and fresh frozen primary CCM tumors to investigate the genomic ramification of SMARCE1 loss.

**Raw data for the primary meningioma tumor samples were not provided due to patient privacy concerns and will be submitted to dbGaP**

first: Roodolph

last: St. Pierre

first: Clayton

last: Collings


title: Chromatin profiling of HUVECs

status: Public on Jun 15 2022

first: Bettina

middle: Maria

last: Fuglerud

address: 675 W 10th Ave

institute: BC Cancer

summary: We analyzed SOX9 binding and the global effect of SOX9 overexpression on chromatin accessibility and enrichment of histone modifications (H3K4me1, H3K27ac, H3K27me3, H3S28P) by CUT&RUN, CUT&Tag, and ATAC-seq of HUVECs transduced with SOX9 expression plasmid or an empty vector control.

overall_design: Cells were transduced with plasmids and 4 days after they were harvested for CUT&RUN, CUT&Tag, or ATAC-seq. For the time-course SOX9 CUT&RUN and ATA-seq, cells were harvested at the indicated times after transduction. 500 000 cells were used per CUT&RUN and CUT&Tag experiment and 100 000 cells were used per ATAC-seq experiment.  Sample quality control was performed using the Agilent 2100 Bioanalyzer. CUT&RUN samples were prepped following the standard protocol for the NEBnext DNA Ultra ii (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 with Paired End 42bp × 42bp reads and Illumina NextSeq 2000 with Paired End 61bp x 61bp.

first: Sibyl

last: Drissler

first: Pamela

last: Hoodless


title: Control of bladder peripheral clock and diurnal micturition pattern by glucocorticoids

city: tsukuba

first: Ichiro

last: Chihara

state: Ibaraki

address: 1-1-1 tennodai

department: Urology

institute: University of TSUKUBA

summary: Peripheral clocks function to regulate each organ and are synchronized though various molecular and behavioral signals. However, signals that entrain the bladder clock remain elusive. Here, we show that glucocorticoids are a key cue for the bladder clock in vitro and in vivo. A pBmal1-dLuc human urothelial cell line showed significant shifts in gene expression after cortisol treatment while, in vivo, rhythmic bladder clock gene expression was not influenced by bilateral-adrenalectomy (ADx) but shifted 4 hours forward by corticosterone administration at the inactive phase (CORT). Moreover, the bladder clock shifted 8-12 hours in ADx+CORT mice. These mice saw decreases in the diurnal rhythm of volume voided per micturition, while maintaining diurnal activity rhythm. These results indicate that the diurnal rhythm of glucocorticoid signaling is a zeitgeber that overcomes other entrainment factors for the bladder clock and coordinates the diurnal rhythm of volume voided per micturition. (145 words)

overall_design: Examination of changes over time in total bladder RNA in mice with bilateral adrenalectomy and corticosterone administration or contol.

first: C

last: Ichiro

first: N

last: Hiromitsu

first: K

last: Jin

last: Yoshiyuki

first: T

last: Haruki

last: Kosuke

first: S

last: Masanobu

last: Ken

last: Shyuya

first: B

last: Mathis

first: M

last: Masafumi

last: Hiroyuki


title: A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours

status: Public on Jun 14 2022

city: Toronto

first: Akram

last: Hamed

institute: University of Toronto

summary: We map the development of mouse cerebrum across the developmental time-course, from embryonic day 12.5 to postnatal day 365, performing single-cell transcriptomics on >100,000 cells. By comparing this reference atlas to single-cell data from >100 glial tumours of the adult and pediatric human cerebrum, we find that tumour cells have an expression signature that overlaps with temporally restricted, embryonic radial glial precursors (RGPs) and their immediate sublineages. Further, we demonstrate that transformation of early RGPs in a genetic mouse model gives rise to adult cerebral tumours that show an embryonic/juvenile RGP identity. Together, these findings implicate the acquisition of embryonic-like states in the genesis of adult glioma, providing insight into the origins of human glioma, and identifying specific developmental cell types for therapeutic targeting.

overall_design: 1) scRNA-seq of the mouse cerebrum from 11 developmental timepoints - mouse model: Sox2eGFP - # of GFP+ve samples: 11 samples - # of GFP-ve samples: 11 samples. 2) scRNA-seq of mouse cerebral tumours - mouse model: Nestin-Cre; P53 f/f; Pten f/+; R26 tdTomato/+ - # of samples: 2 samples.

first: Daniel

last: Kunz

first: Ibrahim

last: El-Hamamy

first: Quang

last: Trinh

first: Omar

middle: D

last: Subedar

first: Laura

last: Richards

first: Warren

last: Foltz

first: Garrett

last: Bullivant

first: Matthaeus

last: Ware

first: Maria

last: Vladoiu

first: Jiao

last: Zhang

first: Antony

last: Raj

first: Trevor

last: Pugh

first: Michael

last: Taylor

first: Sarah

last: Teichmann

first: Lincoln

last: Stein

first: Benjamin

last: Simons

first: Peter

last: Dirks


title: Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (ChIP-seq and Hi-C data)

city: New York

first: Jun

last: Kim

address: 100 Washington Square East 1009 Silver Center

institute: NYU

summary: Inspection of Hi-C and ChIP-seq data suggests that condensin DC is an X-chromosome enriched loop extruder that stalls at rex sites. Insertion of rex site on X-chromosome suggests orientation independent barrier function of rex sites. Insertion of rex site on chromosome-II results in recruitment and spreading of condensin DC that coincides with TAD formation.

overall_design: ChIP-seq and Hi-C data in WT, XV fusion, rex insertion conditions . All experiments were performed in two or more biological replicates. Embryo and L2/L3 larvae were used.

first: Jimenez

middle: S

last: David

first: Kim

last: Jun

first: Ragipani

last: Bhavana

first: Zhang

last: Bo

first: Albritton

last: Sarah

first: Street

middle: A

last: Lena

first: Kramer

last: Maxwell

first: Morao

last: Ana

first: Ercan

last: Sevinc


title: The molecular role of CBX2 in acute myeloid leukemia (AML)

status: Public on Jun 11 2022

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

institute: Erasmus University Medical Center Rotterdam

summary: The dynamic epigenome and proteins specialized in the interpretation of epigenetic marks critically contribute to leukemic pathogenesis but also offer opportunities for alternative therapeutic avenues. Targeting novel chromatin readers involved in leukemogenesis may thus provide new anticancer strategies. Accumulating evidence suggests that the PRC1 complex member CBX2 is overexpressed in solid tumors and promotes cancer cell survival. However, its role in leukemia is unclear.  We found CBX2 overexpressed in leukemia both in vitro and ex vivo samples compared to CD34+ cells. Decreased CBX2 RNA levels prompted a robust reduction in cell proliferation and induction of apoptosis. Similarly, sensitivity to CBX2 silencing was observed in primary acute myeloid leukemia samples. CBX2 suppression also led to increased genome-wide chromatin accessibility followed by alteration of leukemic cell transcriptional programs, resulting in enrichment of cell death pathways and downregulation of survival genes. Intriguingly, CBX2 silencing induced epigenetic reprogramming at p38 MAPK-associated regulatory sites with consequent deregulation of gene expression. Our results identify CBX2 as a crucial player in leukemia progression and unveil a potential druggable CBX2-p38 MAPK route in AML.

overall_design: shRNA knockdown of CBX2 in U937 cells, followed by ATAC-seq and RNA-seq experiment.

first: Ning

middle: Q

first: Nunzio

last: Del Gaudio

first: Lucia

last: Altucci


title: Biochemically distinct states of cohesin mediate formation of loop and TAD domains

status: Public on Jul 24 2022

city: Worcester

first: Yu

address: 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

summary: We established an in vitro system to cleave cohesin in purified nuclei and this system allows us to analyze biochemcial states of cohesin in distinct chromosome structures.

overall_design: Using CRISPR, we inserted 3x TEV sites to RAD21 to estalbish HAP1-RAD21-TEV cells, from which we purified nuclei and cleaved RAD21 to examine chromosome structure changes. This in vitro system allows us to examine cohesin biochemical states in different chromosome structures.

first: Job

last: Dekker


title: The neurons that restore walking after paralysis [snRNA-seq]

first: Jordan

last: Squair

first: Claudia

last: Kathe

first: Michael

last: Skinnider

first: Thomas

last: Hutson

first: Nicola

last: Regazzi

first: Matthieu

last: Gautier

first: Robin

last: Demesmaeker

first: Salif

last: Komi

first: Steven

last: Ceto

first: Nicholas

last: James

first: Newton

last: Cho

first: Laetitia

last: Baud

first: Katia

last: Galan

first: Kaya

last: Matson

first: Andreas

last: Rowald

first: Kyungjin

first: Ruijia

last: Wang

first: John

last: Prior

first: Leonie

last: Asboth

first: Quentin

last: Barraud

first: Stephanie

last: Lacour

first: Ariel

last: Levine

first: Fabien

last: Wagner

first: Jocelyne

last: Bloch

first: Grégoire

last: Courtine


title: Gene expression in donor kidney biopsies prior to kidney transplantation

status: Public on Jun 13 2022

city: Columbus

first: Kellie

middle: J.

last: Archer

state: OH

address: 1841 Neil Ave

department: Division of Biostatistics

institute: Ohio State University

summary:
Donor organ shortage, growing waiting lists and organ discard rates are key problems in kidney transplantation. Donor organ quality is a critical factor determining post-transplant graft outcomes. However, organ quality is difficult to predict. Balancing the use of marginal donors without affecting outcomes is a main issue in the transplant field. The decision of acceptance of a kidney organ for transplantation is mainly based on donor organ biopsy findings, even though there are recognized limitations. The lack of better measures of organ quality at the time of transplantation as a predictor of performance graft outcome is a serious clinical challenge. Herein, we propose the use of a limited set of genes that captures intrinsic biology of kidney donor organs to improve available scoring systems.
We studied gene expression in 192 deceased donor kidney biopsies and evaluated short-term outcomes which included delayed graft function and eGFR (high versus low) at 24 months for 168 kidney transplant recipients.

overall_design: Biopsies from 192 deceased donor kidneys were obtained prior to a recipient undergoing kidney transplantation. For each sample, RNA was extracted and hybridized to an Affymetrix HG-133Av2 GeneChip.

first: Elissa

last: Bardhi

first: Daneil

middle: G

last: Maluf

first: Jennifer

last: McDaniels

first: Thomas

last: Rousselle

first: Anne

last: King

first: James

last: Eason

first: Lorenzo

last: Gallon

first: Enver

last: Akalin

middle: F

last: Mueller

first: Valeria

middle: R

last: Mas


title: Transcriptional Response to Inducers for E. coli and B. subtilis

city: Austin

first: Joshua

last: Urrutia

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

summary: Sequencing technologies, in particular RNASeq, have become critical tools in the design, build, test, learn cycle for synthetic biology. They provide a better understanding of synthetic designs and they help identify ways to improve and select designs. While this data is beneficial to design, its collection and analysis is a complex, multi-step process that has implications both on discovery and reproducibility of experiments. Additionally, tool parameters, experimental metadata, and normalization of data and standardization of file formats present challenges that are computationally intensive. This calls for high-throughput pipelines expressly designed to handle the combinatorial and longitudinal nature of synthetic biology. In this paper, we present a pipeline to maximize analytical reproducibility of RNASeq for synthetic biologists. We also explore the impact of reproducibility on the validation of machine learning models.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: 1,344 samples were collected in quadruplicate, and there are non-induced controls for each organism.

first: Mohammed

last: Eslami

first: Benjamin

last: Garcia


title: Distinct translatome changes in specific neural populations precede electroencephalographic changes in prion-infected mice

city: Linköping

first: Lech

middle: Tadeusz

last: Kaczmarczyk

address: Campus US

department: Cell Biology

country: Sweden

institute: Linköping University

summary: Selective vulnerability is an enigmatic feature of neurodegenerative diseases (NDs), whereby a widely expressed protein causes lesions in specific cell types and brain regions. Using the RiboTag method in mice, translational responses of five neural subtypes to acquired prion disease (PrD) were measured. Pre-onset and disease onset timepoints were chosen based on longitudinal electroencephalography (EEG) that revealed a gradual increase in theta power between 10- and 18-weeks after prion injection, resembling a clinical feature of human PrD. At disease onset, marked by significantly increased theta power and histopathological lesions, mice had pronounced translatome changes in all five cell types despite appearing normal. Remarkably, at a pre-onset stage, prior to EEG and neuropathological changes, we found that 1) translatomes of astrocytes indicated reduced synthesis of ribosomal and mitochondrial components, 2) glutamatergic neurons showed increased expression of cytoskeletal genes, and 3) GABAergic neurons revealed reduced expression of circadian rhythm genes. These data demonstrate that early translatome responses to neurodegeneration emerge prior to conventional markers of disease and are cell type-specific. Therapeutic strategies may need to target multiple pathways in specific populations of cells, early in disease.

overall_design: RiboTag translatome profiling data demonstrating that early translatome responses to neurodegeneration emerge prior to other signs of disease and are unique to different cell types.

first: Walker

last: Jackson


title: FoxA1 and FoxA2 regulate growth and cellular identity in NKX2-1-positive lung adenocarcinoma (bulk RNA-Seq)

status: Public on Jun 08 2022

city: Salt Lake City

first: Eric

last: Snyder

state: UT

address: 2000 Circle of Hope Drive

department: Pathology

institute: University of Utah, Huntsman Cancer Institute

summary: Changes in cellular identity (also known as histologic transformation or lineage plasticity) can drive malignant progression and resistance to therapy in multiple types of cancer, including lung adenocarcinoma (LUAD). The lineage specifying transcription factors FoxA1 and FoxA2 (FoxA1/2) regulate identity in NKX2-1/TTF1-negative LUAD. However, their role in NKX2-1-positive LUAD has not been systematically investigated. We find that Foxa1/2 knockout severely impairs tumorigenesis in KRAS-driven genetically engineered mouse models and human cell lines. Foxa1/2 deletion leads to collapse of a dual-identity state, marked by co-expression of pulmonary and gastrointestinal transcriptional programs, that has been implicated in LUAD progression. Mechanistically, loss of FoxA1/2 leads to aberrant NKX2-1 activity and genomic localization, which inhibits tumorigenesis and drives alternative cellular identity programs associated with non-proliferative states. This work demonstrates that FoxA1/2 expression is a novel lineage-specific vulnerability in NKX2-1-positive LUAD and identifies mechanisms of response and resistance to targeting FoxA1/2 in this disease.

overall_design: RNAseq in murine lung adenocarcinoma organoids (WT and FoxA1/2-negative)

middle: L

first: Grace

last: Orstad

first: Brian

last: Lohman


title: FoxA1 and FoxA2 regulate growth and cellular identity in NKX2-1-positive lung adenocarcinoma

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

overall_design: Refer to individual Series


title: Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

summary: mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent manner. While cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5’UTRs impacts protein synthesis at the level of initiation. 5’UTR acetylation promotes initiation at upstream sequences, competitively inhibiting annotated start codons. Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results, and in vitro utilizing substrates with site-specific ac4C incorporation. Cryo-EM of mammalian 80S initiation complexes revealed ac4C in the -1-position adjacent to an AUG start codon disrupts an interaction between C and hypermodified t6A at nucleotide 37 of the initiator tRNA. These findings demonstrate the impact of RNA modifications on nucleobase function at a molecular level and introduce mRNA acetylation as a factor regulating translation in a location-specific manner.

sample_organism:
Homo sapiens
Oryctolagus cuniculus

platform_organism:
Homo sapiens
Oryctolagus cuniculus

overall_design: Detection of acetylated cytidine in RNA with a novel method (RedaC:T-seq), via chemical reduction of ac4C with sodium borohydride.  Ribo-Seq after Harringtonine treatment to analyze effects on translation initation. RNA sequencing of polysome fractions.

first: Daniel

last: Arango

middle: M

first: Renbin

last: Yang

first: Tapan

last: Kanai

first: Paulina

last: Bauer

first: Jyothi

last: Roy

first: Ziqiu

last: Wang

first: Masaki

last: Hosogane

first: Sarah

last: Schiffers

first: Shalini

last: Oberdoerffer


title: PD-L1 mediates IFNγ-regulation of glucose but not of tryptophan metabolism in clear cell renal cell carcinoma

status: Public on Jun 05 2022

city: Rockville

first: Alexis

last: Norris

address: 7500 Standish Place

institute: US FDA

summary: The immune checkpoint programmed death-ligand 1 (PD-L1) is expressed on the cell surface of tumor cells and is key for maintaining an immunosuppressive microenvironment through its interaction with the programmed death 1 (PD-1). Clear cell renal cell carcinoma (ccRCC) is a highly immunogenic cancer characterized by an aberrant aerobic glycolytic metabolism and is known to overexpress PD-L1. Multiple immunotherapies have been approved for the treatment of ccRCC, including cytokines and immune checkpoint inhibitors. Recently the intrinsic role of PD-L1 and interferon gamma (IFNγ) signaling have been studied in several types of tumor cells, yet it remains unclear how they affect the metabolism and signaling pathways of ccRCC. Using metabolomics, metabolic assays and RNAseq, we showed that IFNγ enhanced aerobic glycolysis and tryptophan metabolism in ccRCC cells in vitro and induced the transcriptional expression of signaling pathways related to inflammation, cell proliferation and cellular energetics. These metabolic and transcriptional effects were partially reversed following transient PD-L1 silencing. Aerobic glycolysis, as well as signaling pathways related to inflammation, were not induced by IFNγ when PD-L1 was silenced, however, tryptophan metabolism and activation of Jak2 and STAT1 were maintained. Our data demonstrate that PD-L1 expression is required to mediate some of IFNγ’s effect in ccRCC cells and highlight the importance of PD-L1 signaling in regulating the metabolism of ccRCC cells in response to inflammatory signals.

overall_design: The mRNA profiling of PD-L1 knockout and interferon gamma treated clear cell renal cell carcinoma cells.

first: Mamatha

last: Garige

first: Carole

last: Sourbier


title: Role of N-cadherin in epithelial-to-mesenchymal transition and chemosensitivity of colon carcinoma cells

status: Public on Jun 01 2022

city: Prague 10

first: Veronika

last: Boušková

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

summary: Increased N-cadherin expression is a pivotal hallmark and step in epithelial-to-mesenchymal transition (EMT), a trans differentiation process activated by colonic tumor cells to increase their spread and survival in a host organism. Although known to be associated with a considerable tumor aggressiveness and worse patient prognosis, exact mechanism(s) linking N-cadherin expression, EMT and aggressive biological phenotype of tumor cells are not entirely clear. In this study we used and compared two different in vitro cell models with varying N-cadherin expression, i.e. colon cancer cell lines HCT8 and SW480 with artificially upregulated expression of N-cadherin, and colon cancer cells with differing N-cadherin levels obtained from patients. Moreover, we have attempted to investigate the relationship between mesenchymal phenotype of cells (here represented by an increased expression of N-cadherin) and the degree of their chemoresistance. We report that although enforced N-cadherin expression changes select morphological and behavioral characteristics of exposed cells, it fails to successfully reprogram cells to the aggressive, chemoresistant phenotype both in vitro as well as in vivo upon implantation into athymic mice. Conversely, primocultures of patient-colonic cells with naturally high levels of N-cadherin expression show fully aggressive and chemoresistant phenotype pertinent to EMT (in vitro and in vivo), with a potential to develop new mutations and in the presence of dysregulated regulatory pathways as represented by investigated miRNA profiles. These results bring new facts concerning the functional axis of N-cadherin expression and related biological features of colon cancer cells and highlight the colon cancer primocultures as useful models for such studies.

overall_design: Array 1: Human epithelial adenocarcinoma colon cancer cell lines HCT8 (HCT8_CTRL_T, 4 replicates) xenograft model, HCT8 colon cancer cell line with overexpression of N-cadherin (HCT8_N-cad_T, 4 replicates) xenograft model, Array 2: plasma samples obtained from the same mice (HCT8_CTRL_P, HCT8_N-cad_P, both in 4 replicates); Array 3: colorectal cancer primocultures T47B and T48B grown in mice (both in 2 replicates).

last: Skarkova

first: Barbora

last: Vitovcova

first: Petra

last: Matouskova

first: Monika

last: Manethova

last: Kazimirova

first: Adam

last: Skarka

last: Brynychova

first: Pavel

last: Soucek

first: Hana

last: Vosmikova

first: Emil

last: Rudolf


title: Effect of overexpressing a constitutively active human NHE1 (SLC9A1) on gene expression of NK-92 natural killer cell line

status: Public on Jun 02 2022

city: Philadelphia

first: Yao-Yu

last: Gong

address: University of Pennsylvania

institute: University of Pennsylvania

summary: To investigate how the overexpression of a constitutively active human NHE1 may affect cytotoxicity-related gene expression in NK-92 cells, we established NK-92 cell lines stably express the NHE1 or empty vector (EV) control by lentiviral transduction.

overall_design: Gene expression profiling analysis of QuantSeq 3' mRNA-sequencing data for NK-92 cells expressing a constitutively active human NHE1 or EV control.


title: Functional Immunophenotyping of Children with Critical Status Asthmaticus Identifies Differential Gene Expression Responses in Neutrophils Exposed to a Poly(I:C) Stimulus

city: Atlanta

first: Milad

last: Rad

state: GA

address: 266 Ferst Dr NW

department: School of Electrical and Computer Engineering

institute: Georgia Institute of Technology

summary:
We determined whether we could identify clusters of children with critical asthma by functional immunophenotyping using an intracellular viral analog stimulus.
We performed a single-center, prospective, observational cohort study of 43 children ages 6 – 17 years admitted to a pediatric intensive care unit for an asthma attack between July 2019 to February 2021.

overall_design: Neutrophils were isolated from children, stimulated overnight with LyoVec poly(I:C), and mRNA was analyzed using a targeted Nanostring immunology array. Network analysis of the differentially expressed transcripts for the paired LyoVec poly(I:C) samples was performed.

first: Jocelyn

last: Grunwell

first: Rishikasan

last: Kamaleswaran


title: FoxA1 and FoxA2 regulate growth and cellular identity in NKX2-1-positive lung adenocarcinoma (ChIP-Seq)

first: Eric

last: Snyder

overall_design: NKX2-1 ChIPseq in murine lung adenocarcinoma organoids (WT and FoxA1/2-negative)

first: Grace

last: Orstad

first: Timothy

middle: J

last: Parnell


title: Next Generation Sequencing in A375 and SK-MEL-28 cell lines

city: Changsha

first: MEI

last: LUO

state: Hunan

address: Kaifu District

department: Dermatology

institute: Xiangya Hospital

overall_design: RNA was extracted from 12 samples from two melanoma cell lines using MagZol reagent with standard protocol.  We conducted drug sensitivity assays on selected drugs in two different melanoma cell lines (A375 and SK-MEL-28) under a rapamycin-induced autophagy condition versus a control condition.

first: Ruimin

last: Chang

first: Lin

last: Ye

first: Mei

last: Luo


title: The function of Wtap in N6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells

status: Public on Jun 03 2022

city: Planegg-Martinsried

first: Taku

last: Kureha

address: Grosshaderner Str. 9

department: Institute for Immunology

institute: Ludwig-Maximilians-Universität


title: Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites

status: Public on Jun 07 2022

city: Boston

first: Roberto

last: Chiarle

address: 300 Longwood Avenue

department: Department of Pathology

institute: Children’s Hospital Boston and Harvard Medical School

summary: CRISPR/Cas9-based genome editing has revolutionized experimental molecular biology and entered the clinical world for targeted gene therapy. Identifying DNA modifications occurring at CRISPR/Cas9 target sites is critical to determine efficiency and safety of editing tools. Here we show that insertions of LINE-1 (L1) retrotransposons can occur frequently at CRISPR/Cas9 editing sites. Together with PolyA-seq and an improved amplicon sequencing, we characterize more than 2,500 de novo L1 insertions at multiple CRISPR/Cas9 editing sites in HEK293T, HeLa and U2OS cells. These L1 retrotransposition events exploit CRISPR/Cas9-induced DSB formation and require L1 RT activity. Importantly, de novo L1 insertions are rare during genome editing by prime editors (PE), cytidine or adenine base editors (CBE or ABE), consistent with their reduced DSB formation. These data demonstrate that insertions of retrotransposons might be a potential outcome of CRISPR/Cas9 genome editing and provide further evidence on the safety of different CRISPR-based editing tools.

overall_design: To fully appreciate L1 insertions, we first employed the improved amplicon sequencing at multiple target sites for canonical CRISPR/Cas9 system and multiple advanced genome editing technologies such as prime editors (PE) enabling precise base editing including PE2, PE3 and PE3b system, cytosine base editors (CBEs) including BE2, BE3, BE4-Gam and AncBE4max, as well as adenine base editors (ABE8e) system. We also performed polyA L1 insertion location sequencing developed based on HTGTS as described previously (Chiarle et al., 2011), the polyA approach is particularly designed for capturing the canonical TPRT L1 retrotransposition.

first: Jianli

last: Tao

first: Qi

last: Wang


title: The function of Wtap in N6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells [m6A-CLIP]

summary: T cell antigen receptor (TCR) signaling controls the development, activation and survival of T cells by involving several layers and numerous mechanisms of gene regulation. N6-methyladenosine (m6A) is the most prevalent mRNA modification affecting splicing, translation and stability of transcripts. Here, we describe the Wtap protein as essential for m6A methyltransferase complex function and reveal its crucial role in TCR signaling. Wtap and m6A methyltransferase functions were required for the differentiation of thymocytes, control of activation-induced death of peripheral T cells and prevention of colitis by enabling gut RORγt+ regulatory T cell function. Transcriptome and epitranscriptomic analyses reveal that m6A modification destabilizes Orai1 and Ripk1 mRNAs. Lack of post-transcriptional repression of the encoded proteins correlated with increased store-operated calcium entry (SOCE) activity and diminished survival of T cells. These findings uncover how m6A modification impacts on TCR signal transduction and determines activation and survival of T cells.

overall_design: Examination of transcriptome in WT or Wtap KO CD4+ T cells. m6A-CLIP or YTHDF2-iCLIP experiments were performed on polyA+ RNA from mouse CD4+ cells with 3 or 2 biological replicates, respectively.

last: Ito-Kureha

first: Vigo

last: Heissmeyer


title: CRISPR modeling reveals transcriptional and functional changes associated with structural variant disruption to MEF2C and 5q14.3 topological organization in neuronal lineages

status: Public on Jun 10 2022

first: Rachita

last: Yadav

state: MA

address: 185 Cambridge street

department: Neurology

institute: MGH

summary: Chromosome 5q14.3 harbored an unusual but genome-wide significant excess of noncoding BCA breakpoints that did not directly disrupt MEF2C. This distribution of breakpoints in proximity but not directly disruptive to MEF2C was further supported by microdeletions in NDD cases reported in DECIPHER34. In considering the landscape of de novo SVs across the 5q14.3 locus in NDD cases, the primary unifying thread appears to be distal boundary disruption. Taken together, these data provide compelling clinical genetic and statistical genomics evidence suggesting that both direct disruption of MEF2C and alterations to this gene’s encompassing 3D regulatory architecture may result in comparable molecular mechanisms in NDD cases. Motivated by these findings, we have performed a systematic molecular dissection of the 5q14.3 locus to quantify the transcriptomic and electrophysiological effects of MEF2C LoF in human neural derivatives. Through the generation of an allelic series of CRISPR-engineered human induced pluripotent stem cell (hiPSC)-derived neural stem cells (NSCs) and glutamatergic neurons (iNs), we interrogated the impact of enhancer, TAD boundary, and loop boundary deletion on local genome organization, local expression effects on MEF2C, and global transcriptional signatures. Our analyses reveal that direct MEF2C alteration results in both transcriptional and functional changes to the synapse. Moreover, we find that disruption of the distal boundary of the MEF2C-containing loop is insufficient to produce indirect MEF2C haploinsufficiency. By contrast, disruption of the proximal boundary of the same 3D structure results in haploinsufficiency of MEF2C that is comparable to direct gene disruption. Overall, these data suggest that the effects of direct and indirect MEF2C disruption contribute to cell type-specific alterations on neuronal functions that converge on synaptic deficits in neurodevelopment.

overall_design: RNASeq based transcriptomics analyses of NSC and iNs and 4C data for regional contacts

first: Michael

middle: E

last: Talkowski

first: Kiana

last: Mohajeri

first: Eva

last: D’haene


title: Hematopoietic differentiation of human iPSC is hardly affected by knockouts in DNMT3A exons despite loss of de novo DNA methylation [DNA methylation]

status: Public on May 31 2022

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

institute: RWTH Aachen University

summary: DNA methyltransferase 3A (DNMT3A) is the most frequently mutated gene in clonal hematopoiesis, indicating that it may be essential for hematopoietic differentiation. We therefore addressed the functional relevance of DNMT3A for hematopoietic differentiation of human induced pluripotent stem cells (iPSCs) by knocking out either exon 2, 19, or 23. Directed differentiation towards mesenchymal stromal cells or hematopoietic progenitor cells (iHPCs) was only slightly reduced in exon 19-/- lines. Notably, exon 19-/-  and exon 23-/- lines revealed absence of almost the entire de novo DNA methylation during differentiation. Despite the drastic effects on DNA methylation, there was no significant impact on gene expression of iHPCs. Notably, DNA methylation differences in acute myeloid leukemia with/without DNMT3A are related to iHPCs with/without DNMT3A knockout. Our results demonstrate that de novo DNA methylation during hematopoietic differentiation of iPSCs is almost entirely dependent on DNMT3A, while it has little impact on early cell-fate decisions.

overall_design: DNA was isolated from iPSCs, from iPSC-derived mesenchymal stromal cells after 35 days of mesenchymal differentiation, and from iPSC-derived hematopoietic progenitor cells after 16 days of hematopoietic differentiation. DNA was bisulfite converted and hybridized to the Illumina Infinium MethylationEPIC BeadChip.

first: Olivia

last: Cypris

first: Julia

last: Franzen

first: Joana

last: Frobel

first: Chao-Chung

last: Kuo

first: Stephani

last: Schmitz

first: Selina

last: Nüchtern

first: Martin

last: Zenke


title: Hematopoietic differentiation of human iPSC is hardly affected by knockouts in DNMT3A exons despite loss of de novo DNA methylation [RNA-seq]

overall_design: RNA from iPSC-derived hematopoietic progenitor cells was isolated after 16 days of hematopoietic differentiation and sequenced on a HiSeq2500v4 sequencer.