title: Gene and allele specific expression during electric organ ontogeny in African weakly electric fish and hybrid

first: Feng

last: Cheng

summary: Hybridization can act as a catalyst for rapid phenotypic evolution by introducing novel allelic combinations, which can affect hybrid phenotype through changes in gene expression. The African weakly electric fish use their muscle-derived electric organ to produce electric organ discharge (EOD) for electrocommunication and electrolocation. The EOD in genus Campylomormyrus and cross-species hybrids is usually species-specific and varies during ontogeny. We compared the gene expression patterns and allele specific expression between juvenile and adult individuals in C. compressirostris (EOD duration 0.4 ms in juvenile and 0.4 ms in adult), C. rhynchophorus (EOD duration 5 ms in juvenile and 40 ms in adult) and their hybrid (EOD duration 0.4 ms in juvenile and 4 ms in adult). Differentially expressed genes between juveniles and adults were highly enriched in “membrane”, “plasma membrane” and “cytoplasm” Go Ontogeny terms. We detected several potassium channel-related genes (e.g. KCNJ2, ADCYAP1) that are potentially involved in the EOD development during ontogeny. The alleles from C. compressirostris show dominant expression in the hybrid at juvenile and adult life stages. KCNJ2 is the only gene that exhibits allelic dominance of C. rhynchophorus allele, and has an increasing expression during ontogeny in this allele. This suggests that the EOD development in hybrids could be related to the increasing allelic expression of the C. rhynchophorus allele under the scenario of overall dominance of C. compressirostris alleles. Our study sheds light in the evolution of the electric organ discharge in electric fishes and on the role of introgressive hybridization in complex phenotypic traits.

platform_organism: Campylomormyrus compressirostris x Campylomormyrus rhynchophorus

overall_design: All juvenile samples were artifically bred and raised at the Univerrsity of Potsdam. Those fish were anesthetized by a lethal dose of clove oil, and dissected on cold 99% ethanol.  Electric organ tissue from each specimen were flash frozen in liquid nitrogen, and further preserved in -80°C.

first: Alice

last: Dennis

first: Otto

last: Baumann

first: Marisol

last: Domínguez

first: Frank

last: Kirschbaum

first: Ralph

last: Tiedemann


title: RNA-seq for tumor associated macrophages in hepatocellular carcinoma

status: Public on Jul 10 2023

city: Beijing

first: Yunxi

last: Liao

state: Beijing

address: 38 Xueyuan Rd, Haidian District

country: China

institute: School of Basic Medical Sciences, Peking University

type: Expression profiling by high throughput sequencing

summary: To investigate the relationship between MIF and SPP1, we induced THP-1 cells with lentivirus carrying SPP1 shRNA and negative control virus into HCC-TAMs and 4IPP-treated HCC-TAMs (tumor associated macrophages in hepatocellular carcinoma).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCC-TAMs, its KD derivatives (shSPP1) and 4IPP-treated HCC-TAMs.

first: Dongyu

last: Zhao

first: Jinhua

last: Wen


title: Cross-activation of the FGF, TGF- and WNT pathways constrains BMP4-mediated induction of the Totipotent state in mouse embryonic stem cells.

status: Public on Jun 26 2023

city: Montreal

first: Thulaj

last: Meharwade

state: QC

address: 110 Pine Ave W,

department: Division of Systems Biology

country: Canada

institute: Montreal Clinical Research Institute

summary: Cell signaling induced cell fate determination is central to stem cell and developmental biology. Embryonic stem cells (ESC) are an attractive model for understanding the relationship between cell signaling and cell fates. Cultured mouse ESCs can exist in multiple cell states resembling distinct stages of early embryogenesis, such as Totipotent, Pluripotent, Primed and Primitive Endoderm. The signaling mechanisms regulating the Totipotent state acquisition and coexistence of these states are poorly understood. Here we identify BMP4 as an inducer of the Totipotent state. However, we discovered that BMP4-mediated induction of the Totipotent state is constrained by the cross-activation of FGF, TGF- and WNT pathways. We exploited this finding to enhance the proportion of Totipotent cells in ESCs by rationally inhibiting these cross-activated pathways using small molecules. Single-cell mRNA-sequencing further revealed that induction of the Totipotent state is accompanied by the suppression of both the Primed and Primitive Endoderm states. Furthermore, the reprogrammed Totipotent cells generated in culture have a molecular and functional resemblance to Totipotent cell stages of preimplantation embryos. Our findings reveal a novel BMP4 signaling mechanism in ESCs to regulate multiple cell states, potentially significant for managing stem cell heterogeneity in differentiation and reprogramming.

overall_design: Mouse ESCs grown in LB and LBPXRS were analyzed at 72hours using single cell RNAsequencing.

first: Loïck

last: Joumier

first: Maxime

last: Parisotto

first: Vivian

last: Huynh

first: Edroaldo

middle: L

last: da Rocha

first: Mohan

last: Malleshaiah


title: Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer

status: Public on Jul 15 2023

city: Wuhan

first: Yiqi

last: Wang

state: State...

address: Shizishan Street

institute: Huazhong Agricultural University, China

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Identifying the Role of Zuo1 protein in Saccharomyces cerevisiae

status: Public on Jun 01 2023

city: Istanbul

first: mehmet

last: tardu

address: Beyazit campus

department: Biology

country: Turkey

institute: Istanbul University

summary: The ribosome associated complex (RAC) is a ribosome bound protein chaperone complex reported to surveil the translation of proteins with positively charged regions. It has been posited that RAC might be able to directly regulate translation by coupling co-translational folding with the peptide-elongation cycle. To identify the targets of RAC in cells and test the hypothesis that the complex modulates translation, we performed ribosome profiling on wild- type yeast cells and cells lacking a key component of the RAC that binds near the ribosome active site (zuo1Δ).

overall_design: mRNA-seq and Ribosome profiling of exponentially growing (OD600 = 0.6) Saccharomyces cerevisiae cells were performed by deep sequencing , in two biological replicates, using Illumina HiSeq-4000 platform.

first: Mehmet

last: Tardu

first: Kristin

middle: S

last: Koutmou


title: Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion [bulkRNAseq]

status: Public on Jun 07 2023

city: Houston

first: Jae-Il

last: Park

state: Texas

address: 6565 MD Anderson BLVD

department: Dept. of Experimental Radiation Oncology

country: USA

institute: M.D. Anderson Cancer Center

summary: Accumulated genetic mutations or copy number alterations are frequently observed in esophageal squamous cell carcinoma (ESCC) patients. However, it is still elusive which gene is the driver to initiate ESCC. We identified key genetic determinants for ESCC development using CRISPR/Cas9-based multiple genes KO mouse esophageal organoid model.  Trp53, Cdkn2a, and Notch1 triple KO (PCN) organoid showed the phenotypes of ESCC. These triple genes KO served for cell proliferation through building multiple root cell clusters and remodeling the immune landscape beneficial for tumorigenesis by Ccl2-Ccr2 mediated intercellular interactions. Ccl2-releasing PCN tumors were surrounded by exhausted T cells and M2 macrophages leading to immune evasion. The PCN-type tumor was observed in more than 30% of ESCC patients who express high levels of B2M, CCL2, and NF-kB. Our study unveiled genetic determinants for ESCC development crucial for cell-autonomous growth as well as non-cell autonomous interactions with immune cells.

overall_design: Triplicated organoids from WT, PN, and PCN were collected 7 days after seeding.

first: Kyung-Pil

last: Ko

first: Yuanjian

last: Huang

first: Shengzhe

last: Zhang

first: Gengyi

last: Zou

first: Bong

middle: J

last: Kim

first: Jie

first: Sohee

last: Jun


title: Developmental programming of Kupffer cells by maternal obesity causes fatty liver disease in the offspring I

status: Public on Aug 22 2023

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

country: Germany

institute: University of Bonn

summary: Kupffer cells (KCs) are tissue-resident macrophages which colonize the developing liver early during embryogenesis1. Throughout development and adulthood, KCs have distinct core functions that are essential for liver and organismal homeostasis, such as supporting fetal erythropoiesis as well as postnatal erythrocyte recycling and liver metabolism2. KCs acquire their tissue-specific transcriptional signature immediately after colonizing the liver, mature together with the tissue, and adapt to the tissue’s function1,3,4. However, whether perturbation of macrophage core functions during development may contribute to or cause disease at postnatal stages is poorly understood. Here, we utilize a maternal obesity model to disturb KC functions during gestation. We show that offspring born to obese mothers develop fatty liver disease that is accompanied by a local pro-inflammatory response, a phenotype that is augmented if the offspring is kept on control diet after birth. Further, transcriptional analyses reveal that KCs undergo developmental programming through the maternal high-fat diet, which lasts until adulthood. The offspring’s KC developmental programming is irreversible despite the switch to control diet and leads to increased lipid uptake in hepatocytes mediated via paracrine factors stemming from KCs. The transcriptional programming of KCs and the fatty liver disease phenotype are rescued by genetic depletion of hypoxia-inducible factor alpha (Hif1a) in macrophages during gestation. These results demonstrate that macrophages rely on an undisturbed development to fulfil their core functions and support organ homeostasis during adulthood, and establish developmental programming of KCs as a therapeutic strategy for metabolic disorders, such as fatty liver disease.

overall_design: Three-week-old female Hif1αflox/flox female mice were initially fed with a control diet (CD) for two weeks and were thereafter divided into two groups: one continued on the CD while the other received a high-fat diet (HFD) for eight weeks. The homeostatic model for insulin resistance (HOMA-IR) was used to assess metabolic changes. Mice with higher HOMA-IR on the HFD were selected to create a maternal obesity model and mice fed with CD were used to generated maternal lean offspring. All females were mated with Hif1αflox/flox;LyzMCre/+ CD males to generate Hif1αflox/flox;LyzMCre/+ (KO) or Hif1α flox/flox;LyzM+/+ (WT) offspring. All neonatal mice were cross-fostered by females with the same diet as their mothers. WT or KO male offspring were weaned into CD or HFD postweaning cages. KCs or hepatocytes from 11-12 weeks old male mice were sorted for bulk RNA-sequencing.

first: Nora

last: Balzer

first: Iva

last: Splichalova

first: Hao

first: Lea

last: Seep


title: Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stability

status: Public on May 24 2023

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University of Edinburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The SS18-SSX fusion drives oncogenic transformation in synovial sarcoma by bridging SS18, a member of the mSWI/SNF (BAF) complex, to Polycomb repressive complex 1 (PRC1) target genes. Here we show that the ability of SS18-SSX to occupy H2AK119ub1-rich regions is an intrinsic property of its SSX C terminus, which can be exploited by fusion to transcriptional regulators beyond SS18. Accordingly, SS18-SSX recruitment occurs in a manner that is independent of the core components and catalytic activity of BAF. Alternative SSX fusions are also recruited to H2AK119ub1-rich chromatin and reproduce the expression signatures of SS18-SSX by engaging with transcriptional activators. Variant Polycomb repressive complex 1.1 (PRC1.1) acts as the main depositor of H2AK119ub1 and is therefore required for SS18-SSX occupancy. Importantly, the SSX C terminus not only depends on H2AK119ub1 for localization, but also further increases it by promoting PRC1.1 complex stability. Consequently, high H2AK119ub1 levels are a feature of murine and human synovial sarcomas. These results uncover a critical role for SSX-C in mediating gene deregulation in synovial sarcoma by providing specificity to chromatin and further enabling oncofusion binding by enhancing PRC1.1 stability and H2AK119ub1 deposition.

overall_design: Calibrated Native Chromatin immunoprecipitation DNA-sequencing (cChIP-seq) for H2AK119ub1 in human synovial sarcoma cells HS-SY-II after PCGF1 knockout

first: Ana

last: Banito


title: Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer [RNA-seq]

first: Yiqi

last: Wang

summary: In this study, we performed whole-transcriptome sequencing of bladder tumors and their peritumoral tissues to identify differentially expressed circ-, lnc-, mi-, and mRNAs.

overall_design: Whole trascriptome analysis of total RNA data on circRNA, lncRNA and mRNA for bladder cancer tissues and normal tissues.

first: Sanhe

last: Liu

first: Shaozhong

last: Wei

first: Zhiqiang

last: Dong


title: Gene expression profile at single cell level of bulk liver allograft tissue isolated 12 months post-transplant in patients receiving regulatory dendritic cell therapy (STUDY) and reference standard-of-care patients (SOC)

city: Pittsburgh

first: Lillian

last: Tran

state: Pennsylvania

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

summary: Regulatory dendritic cell therapy has shown potential in modulating the effector immune response after liver transplant in precliical models . We used single cell RNA sequencing (scRNA-seq) to analyze the differences in immune cell landscape of liver allograft at 12 months post-transplant in patients infused with regulatory dendritic cell therapy compared to standard-of-care control patients.

overall_design: Non-parenchymal and parenchymal cells from liver allograft biopsy tissue obtained 12 months post-transplant were analyzed using scRNAseq.


title: ADAR1 Zα domain P195A mutation activates the MDA-5 dependent RNA-sensing signaling pathway in the brain enhanced by haploinsufficiency without overall RNA editing level decrease.

status: Public on May 31 2023

first: Shuchang

state: PA

address: 203 Lothrop Street

summary: The A-to-I RNA editing enzyme ADAR1 critically regulates the cellular RNA sensing signaling pathway, as the RNA-sensing signaling pathway recognizes unedited RNAs as “non-self” to activate the innate immune response. Mutations of ADAR1 cause severe inflammatory tissue injury, as shown in Aicardi-Goutières syndrome (AGS), in which severe inflammation occurs in the brain. The most frequent ADAR1 mutation in AGS is the P193A mutation in the Za domain, which exists in the AGS families coupling with an additional ADAR1 mutation. How this mutation alters the cellular RNAs leading to innate immune activation, has not been fully understood. This study analyzed RNA editing status and innate immune activation in the brains of a mouse model that carries the human ADAR1 P193A-equivalent mouse P195A mutation. We found that this mutation alone can cause excessive ISG expression in the brains, especially in the periventricular areas reflecting the pathologic feature of AGS. Furthermore, we found that ADAR1 P195A mutation did not affect the RNA editing activity in the overall RNA editing level; however, it leads to ISG expression in a dose-dependent manner, causing severer innate immune activation in haploinsufficiency status, whereas wildtype ADAR1 is redundant to suppress innate immune activation. The finding from this study indicated that the intact Z-RNA binding activity of ADAR1 plays a critical role in suppressing self-cellular RNA sensing, and innate immune homeostasis requires a minimum Z-RNA binding capacity of ADAR1.

overall_design: WT_WT, WT_d, 195M_195M, 195M_d, with three repeats each

first: Guo

last: Xinfeng

first: Liu

last: Silvia

first: Sheng

last: Yi

first: Zenati

last: Mazen

first: Billiar

last: Timothy

first: Herbert

last: Alan

first: Wang

last: Qingde


title: Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion [scRNAseq]

first: Jae-Il

last: Park

overall_design: organoids from WT, PC, PN, and PCN were collected 7 days after seeding and digested with 0.05% trypsin-EDTA at 37 ℃ for 30 min. After inactivating trypsin with 10% FBS DMEM, single-cell suspension was collected by passing through the 35 m cell strainer. Each group was tagged with 2 CMO tags from CellPlex kit (10x Genomics). The tagged cells of each group were pooled together with same number of cells after counting cells. cDNA library was prepared with the 10x Genomics 3’ v2 kit, cDNA library was sequenced on an Illumina NovaSeq (Novogene) and mapped to GRCm38/mm10 genome and demultiplexed using Cellranger.

first: Kyung-Pil

last: Ko

first: Yuanjian

last: Huang

first: Shengzhe

last: Zhang

first: Gengyi

last: Zou

first: Bong

last: Kim

first: Jie

first: Sohee

last: Jun


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [in_vitro_RNA_seq]

status: Public on May 04 2023

city: Stanford

first: Laura

middle: D

last: Attardi

state: CA

address: 269 Campus Drive

institute: Stanford University

summary: Lung cancer is the leading cause of cancer deaths worldwide. TP53 tumor suppressor gene mutations occur in 50% of lung adenocarcinomas (LUADs) and are linked to poor prognosis, but how p53 suppresses LUAD development remains enigmatic. We show here that p53 suppresses LUAD by governing cell state, by promoting alveolar type 1 (AT1) differentiation. Using mice expressing oncogenic Kras and null, wild-type, or hypermorphic p53 alleles in alveolar type 2 (AT2) cells, we observed graded effects of p53 on LUAD initiation and progression. RNA-sequencing and ATAC-sequencing of LUAD cells uncovered a p53-induced AT1 differentiation program during tumor suppression in vivo through direct DNA binding, chromatin remodeling, and AT1 gene induction. Single-cell transcriptomics analyses revealed that during LUAD evolution, p53 promotes AT1 differentiation through action in a transitional cell state analogous to a transient intermediary seen during AT2-to-AT1 differentiation in alveolar injury repair. Notably, p53 inactivation resulted in the inappropriate persistence of these transitional cancer cells accompanied by upregulated growth signaling and divergence from lung lineage identity, characteristics associated with LUAD progression. Analysis of p53wt and p53-null mice showed that p53 also directs alveolar regeneration after injury, by regulating AT2 self-renewal and promoting transitional cell differentiation into AT1 cells. Collectively, these findings illuminate mechanisms of p53-mediated LUAD suppression, in which p53 governs alveolar differentiation, and suggest that tumor suppression reflects a fundamental role of p53 in orchestrating tissue repair after injury.

overall_design: Lung cancer cell lines were harvested and analyzed using RNA-seq

first: Alyssa

middle: M

last: Kaiser

first: Kathryn

middle: T

last: Bieging-Rolett


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [in_vivo_RNA_seq]

overall_design: Mouse lung cancer cells were isolated via FACS and analyzed via RNA-seq


title: snoRNA-sequencing analysis of liver cancer stem cells from human samples

status: Public on Jun 30 2023

first: Yang

last: gu

address: 15 Datun Road

institute: institute of biophysics

summary: To explore the role of small nucleolar RNA (snoRNA) on self-renewal of liver cancer stem cells (CSCs), we isolated liver CSCs (CD133+CD13+) and Non-CSCs (CD133-CD13-) from huamn liver tumor tissues.

overall_design: Then snoRNA-sequencing analysis were performed and differentially expressed snoRNAs were identified.  Total RNAs were extracted from liver cancer stem cells and subjected to snoRNA-sequencing analysis

last: Gu

first: Zusen

last: Fan


title: Extracellular succinate induces spatially organized biofilm formation in Clostridioides difficile

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

country: France

institute: Institut Pasteur

summary: we report that succinate, a metabolite abundantly produced by the dysbiotic gut microbiota, induces in vitro biofilm formation of C. difficile  strains. We characterized the morphology and spatial composition of succinate- induced biofilms, and compared to non-induced or deoxycholate-induced biofilms, biofilms induced by succinate are significantly thicker, structurally more complex, and poorer in proteins and exopolysaccharides (EPS).

overall_design: Total RNA was extracted from 4 independent biological replicates of 630 C. difficile strains at 4 conditions with 240µM Deoxycholate for the 1687 mutant and the wild type strains and with plasmid empty or that contains the 1687 gene.

first: Emile

last: Auria

first: Juliana

middle: P

last: Da Fonseca


title: A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Motor neurons (MNs) are the cellular targets of multiple adult-onset diseases. Because distinct MN populations differ in disease susceptibility, it is important to define in animal models the degree of diversity within adult MNs. Here, we generated a comprehensive molecular resource of adult MNs in C. elegans. Single-cell RNA-sequencing of 12,603 cells revealed that all eight morphologically defined MN classes of the ventral nerve cord and its flanking ganglia subdivide into 29 distinct subclasses, almost quadrupling the degree of their previously described diversity. We find that four of the six C. elegans Hox genes delineate most, but not all MN subclasses. Strikingly, all 29 subclasses are delineated by unique expression codes of neuropeptide genes and receptors, critical for extra-synaptic (wireless) signaling. Leveraging the C. elegans connectome, we found a strong correlation between molecularly and connectivity defined MN subclasses. Beyond providing a valuable resource and searchable database (spinalcordatlas.com), our study identifies Hox and neuropeptide codes as key molecular descriptors of adult MN diversity, codes likely conserved in MNs across species.

overall_design: Ventral nerve cord MNs were isolated from two strains of worms. Two samples were collected from both CZ631 juIs14 [acr-2::GFP] and KRA257 kasIs2 [lin-39p::RFP] worms. MNs were isolated by FACS and analyzed by 10X Genomics 3' single-cell RNA sequencing.

first: Seth

middle: R

last: Taylor

first: Jayson

last: Smith

first: Paschalis

last: Kratsios


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression


title: Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion

first: Jae-Il

last: Park


title: Generation of thymus reconstituting T cell progenitors from genetically unmodified human pluripotent stem cells

city: Dolgoprudny

first: Eugene

last: Albert

address: Institutskiy Pereulok, 9

country: Russia

institute: MIPT

summary: Derivation of transplantable T cell progenitors from human pluripotent stem cells is the key step towards regenerative therapy of hereditary and acquired immunodeficiencies. Here, we describe an original methodology for differentiation of genetically non-modified human pluripotent stem cells (hPSCs) that yields T cell progenitors capable for direct and unmediated reconstitution of mouse thymus. The hPSC-derived T cell progenitors exhibited a strong thymus and spleen homing potential and developed into single positive human T cells that could enter circulation. Detailed single cell transcriptome analysis confirmed the similarity of hPSC-T cell progenitors with their in vivo counterparts. The transcription profiling attested the emergence of cells that displayed the transcription signature of early T cell progenitors.

overall_design: Invitro differentiation of hPSCs into T cell progenetors

first: Elena

last: Filonenko


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [10x_multiome_ATAC]

overall_design: Mouse lung cancer cells were isolated via FACS and analyzed via 10x single cell multiomics ATAC

last: Hanson


title: Integration of a multi-omics stem cell differentiation dataset using a dynamical model

status: Public on Apr 25 2023

city: Leiden

first: Stefan

last: Semrau

address: Einsteinweg 55

department: Physics

country: Netherlands

institute: Leiden University

summary: Stem cell differentiation is a highly dynamic process involving pervasive changes in gene expression. The large majority of existing studies has characterized differentiation at the level of individual molecular profiles, such as the transcriptome or the proteome. To obtain a more comprehensive view, we measured protein, mRNA and microRNA abundance during retinoic acid-driven differentiation of mouse embryonic stem cells. We found that mRNA and protein abundance are typically only weakly correlated across time. To understand this finding, we developed a hierarchical dynamical model that allowed us to integrate all data sets. This model was able to explain mRNA-protein discordance for most genes and identified instances of potential microRNA-mediated regulation. Overexpression or depletion of microRNAs identified by the model, followed by RNA sequencing and protein quantification, were used to follow up on the predictions of the model. Overall, our study shows how multi-omics integration by a dynamical model could be used to nominate candidate regulators.

overall_design: Time-course multi-omics experiment measuring mRNA (total poly(A) RNA-seq and fractionated cytoplasmic/nuclear RNA-seq), microRNA (small RNA-seq), and protein (TMT-based mass spectrometry) abundance at 8 time points (0, 6, 12, 24, 36, 48, 72, 96 h) during retinoic acid-induced differentiation of E14 mouse embryonic stem cells (mESCs), with 2–3 biological replicates per modality. A follow-up perturbation experiment assessed the effect of miRNA mimic and inhibitor transfections (14 miRNAs + controls, 3 biological replicates) on mRNA abundance by RNA-seq.

first: Patrick

last: van den Berg

first: Noémie M L P

last: Bérenger-Currias

first: Bogdan

last: Budnik

first: Nikolai

last: Slavov


first: Nezha

last: Benabdallah

overall_design: RNA sequencing of human mesenchymal stem cells expressing various oncofusions

first: Ana

last: Banito


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [scRNA-Seq]

first: Laura

last: Attardi

overall_design: Mouse lung cells during injury were isolated via FACS and analyzed via 10x scRNA-seq

first: Alyssa

last: Kaiser

first: Kathryn


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [in_vivo_ATAC_seq1]

overall_design: Mouse lung cancer cells were isolated via FACS and analyzed via ATAC-seq


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [10x single cell multiomics RNA-Seq]

overall_design: Mouse lung cancer cells were isolated via FACS and analyzed via 10x single cell multiomics gene expression


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [in_vivo_ATAC_seq2]


title: Gene Expression Profiling of leukemic blasts/ mesenchymal stem cells (MSC) derived from bone marrow of Indian patients with Acute Myeloid Leukemia (AML) and profiling of AML xenograft post-treatment with human MSC in mice model

status: Public on May 02 2023

city: Navi Mumbai

first: Jyoti

middle: Anand

last: Kode

state: Maharashtra

address: Kharghar

department: Kode Lab

country: India

institute: Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre

summary:
Heterogeneity and variable survival outcomes of Acute Myeloid Leukemia (AML), suggest that yet undiscovered genes and pathways contribute to AML. Mesenchymal stem cells (MSC), an important component of bone marrow/ stromal microenvironment has been shown to contribute to development and progression of various cancers. Current study was aimed at characterizing MSC from AML bone marrow (BM) and evaluate their therapeutic potential in controlling survival of AML leukemic blasts. MSCs were isolated and cultured from BM of high-risk AML patients. MSC were also obtained from BM of bi-lineage leukemia (ETP-ALL) patients as control MSC from precursor stage of leukemia. MSC derived from uninvolved BM (UnBM) of lymphoma patients were used as normal MSC control. Leukemic blasts were derived from BM of AML and ETP-ALL patients. Patient derived AML-MSC exhibited characteristic profile of MSC Type-II CD90+CD45lo expressing high percent of TLR3 than TLR4 receptors, indicating pro-tumorigenic nature. Gene expression profiles of freshly derived leukemia blasts, AML cell line and AML MSC exhibited deregulated and overactivated Aurora Kinase pathway and inflammasome innate immune pathway. These two pathways are known to be upregulated in many solid and hematological cancers. Further we observed few tumor suppressor genes were downregulated in these groups. In vitro, AML MSC supported survival of leukemic blasts and increased chemoresistance to standard anticancer drugs. Hence AML MSC and ETP-ALL MSC were treated with immunomodulatory drug cocktail (IMiD) containing TLR3 antibody, TLR4 ligand and CXCR4 antagonist peptide (Gift from Kyoto University, Japan), designated as MSC-IMiD. It was observed that MSC-IMiD reduced chemoresistance of leukemic blasts to certain extent in vitro. Further we evaluated if leukemia BM derived MSC, MSC culture supernatant or MSC-IMiD can provide therapeutic benefit to control growth of AML xenograft in mouse model. Human gene expression profile was mapped in human-mouse xenograft made as subcutaneous tumor in immunodeficient NOD-SCID mice model from AML cell line KG1. Comparison was done of all treated groups with tumor bearing control gene expression data. It was interesting to note that MSC and MSC-IMiD could reduce tumor growth in 50% of mice tested. Mice treated with MSC culture supernatant exhibited reduction in tumor growth at par with that seen in Adriamycin treated positive control group. Deregulation of Aurora kinase pathway, inflammasome pathway genes and tumor suppressor genes was found to be reversed in residual tumor tissue of mice treated with MSC and MSC culture supernatant. This gene expression profiling study has helped understanding pathways involved in chemoresistance and immune suppression observed in AML. Moreover, this study has provided leads that MSC or its conditioned media can be explored further to control abnormal myelopoiesis in AML and develop targeted therapy.

Funding source:
Grant ID:  53/13/2013/CMB/BMS.
Grantee:  Jyoti Kode
Grant title: Understanding the cross-talk between mesenchymal stromal cells and leukemic stem cells in Acute Myeloid Leukemia: Implications in disease biology and therapy.
Name of the funding source: Indian Council of Medical Research, Government of India, India.

first: Manasi

last: Nagare

first: Manju

last: Sengar

first: Navin

last: Khattry

first: Sachin

last: Punatar

first: Anant

last: Gokarn

first: Shubhada

last: Chiplunkar


title: Plant recognition by Trichoderma harzianum elicits upregulation of a novel secondary metabolite cluster required for colonization

status: Public on Apr 11 2023

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

summary: The plant recognition specific PCA cluster mediates early chemical communication between plant and fungus, is required for colonization and it is likely responsible for the high potential of T. harzianum and closely related species for biocontrol applications.

overall_design: Strains of this study were grown on plates with Mandels Andreotti Minimal Medium containing 0.1 % w/v glucose as  carbon source

first: Guofen

last: Li

first: Miriam

last: Schalamun


title: Retapamullin and Chloramphenicol treated mRNA half-life profiling.

status: Public on Apr 03 2023

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

institute: Indiana University

summary: mRNA half-life profiling in the bacterium Caulobacter crescentus was performed in cells that were inhibited in translation initiation (retapamullin) or elongation (chloramphenicol) by shutting of transcription with the antibiotic rifampicin, and following mRNA abundance at 1, 2, 4, 8, and 15 minutes post rifampicin. All RNA measurements were performed on cells grown to mid-log in M2G minimal growth medium. Two biological replicates time coursees were collected from independent starter cultures.

overall_design: WT NA10000 cells were treated with Chloramphenicol or Retapamullin, then globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq.  Total RNA samples were collected just prior to rifampicin addition, and after 1, 2, 4, 8, or 15 minutes incubation with 100ug/mL rifampicin. Each total RNA sample was depleted of rRNA using the ribozero kit (Illumina) for gram negative bacteria, and subjected to total RNA-seq libraries as in (Ingolia et al. Science 2009). tRNA was left in each sample as an internal control for stable RNA.


title: Reactivity-Based RNA Profiling (RBRP) determined transcriptome interactions of small molecule drugs

status: Public on Apr 13 2023

first: Linglan

last: Fang

state: California

address: 369 N-S AXIS STAUFFER I, RM-107-CHEMISTRY-KOOL LAB

summary: We developed Reactivity-Based RNA Profiling (RBRP) approach to determine the off-target transcriptome interactions of small molecule drugs. Deep sequencing was used to locate and quantify drug-promoted acylation of RNA 2´-hydroxyl groups as a proxy of RNA-drug interaction in HEK293.

overall_design: The sequencing experiments were performed in two biological replicates. Comparative analysis of deep sequencing data using a customized pipeline identifies drug binding events.

first: Eric

last: Kool


title: Olfactory and neuropeptide inputs to appetite neurons in the arcuate nucleus

status: Public on Mar 27 2023

city: Seattle

first: Linda

last: Buck

state: Washington

address: 1100 fairview ave North

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Centre

summary: We report RNA sequencing of single Agrp neurons isolated from the arcuate nucleus of the hypothalamus. Analyses of Agrp neuron transcriptomes reveals differential expression of receptors for multiple neuromodulators. Neuroanatomical mapping of known ligands of the receptors define subsets of neurons directly upstream of AgRP neurons in specific brain areas.

overall_design: Isolation of fluorescently labelled individuals cells disociated from the mouse arcuate nuclues. Cells were visualized and isolated using a micropipette under a microscope, followed by cell lysis, RT, and cDNA synthesis.


title: The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile

status: Public on Apr 19 2023

first: Marc

last: Monot

summary: The ability of bacterial pathogens to establish recurrent and persistent infections is frequently associated with their ability to form biofilms. Clostridioides difficile infections have a high rate of recurrence and relapses and it is hypothesised that biofilms are involved in its pathogenicity and persistence. Biofilm formation by C. difficile is still poorly understood. It has been shown that specific molecules such as deoxycholate (DCA) or metronidazole induce biofilm formation, but the mechanisms involved remain elusive. In this study, we describe the role of the lipoprotein CD1687 in the DCA-induced biofilm formation of C. difficile. We showed that the expression of CD1687, which is part of an operon within the CD1685-CD1689 gene cluster, is controlled by multiple transcription starting sites induced for some of them in response to DCA. Only CD1687 is required for biofilm formation and the overexpression of CD1687 is sufficient to induce biofilm formation. Using RNAseq analysis, we showed that CD1687 affects the expression of transporters and metabolic pathways and we identified several potential binding partners by pull-down assay, including transport-associated extracellular proteins. We then demonstrated that CD1687 is surface exposed in C. difficile, and this localization is required for DCA-induced biofilm formation. Given this localization and that C. difficile forms eDNA-rich biofilms, we confirmed that CD1687 binds DNA in a non-specific manner. We thus hypothesize that CD1687 is a component of the downstream response to DCA leading to biofilm formation by promoting interaction between the cells and the biofilm matrix by binding eDNA.

first: Emile

last: Auria

first: Juliana

last: Da Fonseca


title: Transcriptional profile regulated by 1,25-dihydroxyvitamin D (Calcitriol) in primary Human Monocyte-Derived Macrophages infected by zika virus

status: Public on Mar 15 2023

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

summary: ZIKA virus (ZIKV) infection is characterized by alterations in gene expression profile on host cells that consequently lead to an immune response. Here, we used RNA sequencing to analyze the mRNA and miRNA expression profile in human monocyte-derived macrophages (MDMs) differenitated in presenece of 1,25-dihydroxyvitamin D (Calcitriol) and infected with a Zika virus strain COL345Si-Asian at MOI of 5 and analized 24 hpi.

overall_design: Human peripheral blood mononuclear cells (PBMCs) from blood samples of 4 healthy donors mixed with 2% EDTA, were isolated through density gradient with Lymphoprep. Monocytes-derived Macrophages (MDM) were obtained from total PBMCs by adherence to the plastic and differentiation to macrophages was allowed to occur for 6 days in RPMI-1640 medium supplemented with 10% (v/v) FBS, 4 mM L-glutamine, 0.3% (v/v) NaCO3, and 1% (v/v) antibiotic-antimycotic solution 100X (complete medium), at 37 °C and 5% CO2, without growth factors. Additionally, MDMs were differentiated in presence of 1,25 di-hydroxyvitamin D3 to obtain D3-MDM. 1,25 di-hydroxyvitamin D3 was added to the culture media at a final concentration of 1 nM and replenished every 24 h for six days. MDM and D3-MDM monolayers were washed with warm PBS and were infected with  Zika virus strain COL345Si-Asian at MOI of 5. Three hpi, the cells were washed with warm PBS to remove unbound virus. Then 24 hpi, macrophage monolayers were used for sample collection.

first: Geysson

last: Fernandez

first: Silvio

last: Urcuqui-Inchima


title: A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea [Synchronization RNA-seq]

status: Public on Mar 08 2023

city: Qingdao

first: yunfeng

last: Yang

state: Shandong

address: 72 Binhaidadao, Aoshanwei, Jimo

institute: Shandong University

summary: Cell cycle regulation is of paramount importance for all forms of life. Here we report that a conserved and essential cell cycle-specific transcription factor (designated as aCcr1) and its viral homologs control cell division in Sulfolobales. We show that the transcription level of accr1 reaches peak during active cell division (D-phase) subsequent to the expression of CdvA, an archaea-specific cell division protein. Cells over-expressing the 58-aa-long RHH (ribbon-helix-helix) family cellular transcription factor as well as the homologs encoded by large spindle-shaped viruses Acidianus two-tailed virus (ATV) and Sulfolobus monocaudavirus 3 (SMV3) display significant growth retardation and cell division failure, manifested as enlarged cells with multiple chromosomes. aCcr1 over-expression results in downregulation of 17 genes (>4-folds) including cdvA. A conserved motif, aCcr1-box, located between the TATA-binding box and the translation initiation site in the promoters of 13 out of the 17 highly repressed genes, is critical for aCcr1 binding. The aCcr1-box is present in the promoters of cdvA genes across Sulfolobales, suggesting that aCcr1-mediated cdvA repression is an evolutionarily conserved mechanism by which archaeal cells dictate cytokinesis progression, whereas their viruses take advantage of this mechanism to manipulate the host cell cycle.

overall_design: S. islandicus REY15A cells were synchronized as previously described with slight modifications. Briefly, cells were first grown aerobically at 75°C with shaking (145 rpm) in 30 ml of STV medium. When the OD600 reached 0.6-0.8, the cells were transferred into 300 ml STV medium with an initial estimated OD600 of 0.05. When the OD600 reached 0.15-0.2, acetic acid was added at a final concentration of 6 mM and the cells were blocked at G2 phase of the cell cycle after 6h treatment.6 mM acetic acid can synchronize S. islandicus REY15A in the G2 phase. Then, the cells were collected by centrifugation at 3,000 g for 10 min at room temperature to remove the acetic acid and washed twice with 0.7% (w/v) sucrose. Finally, the cells were resuspended into 300 ml of pre-warmed STV medium and cultivated as above for RNA-seq analysis.

first: Yunfeng

first: Junfeng

last: Liu

first: Mart

last: Krupovic

first: Yulong

last: Shen


title: Transcription Factor Network Reveals New Treatments for Prostate Cancer Docetaxel Drug Resistance

status: Public on Apr 01 2023

city: Ann Arbor

first: Evan

last: Keller

state: MI

address: 2800 Plymouth Rd

institute: University of Michigan

summary: Overcoming drug resistance is critical increasing the survival rate for prostate cancer (PCa).  In this study, we modeled docetaxel resistance using two PCa cell lines, DU145 and PC3.  We conducted both single cell and bulk RNA sequencing.  We constructed a transcription factor (TF) network for the docetaxel sensitive and resistant variants for all cell lines and sequencing methods resulting in 8 networks.  We identified shared edges and nodes that represent a shared TF network for PCa that modeled the changes after acquiring drug resistance.  Using this shared TF network, we identified drivers of the resistant phenotype.  Interestingly, the network constructed from the bulk sequencing dataset revealed different TF drivers of resistance compared with the network constructed from the single cells.  We validated the results constructed from the single cells to demonstrate the validity of the single cell sequenced TF network.  We targeted GABPA (only identified in the single cell constructed network) and successfully re-sensitized both cell lines to docetaxel treatment.  Additionally, we conducted connectivity map analysis to identify potential drugs that disrupt the resistant networks.  We identified trichostatin A as a potential combination treatment using the single cell sequenced network.  Combination treatment of trichostatin A and docetaxel, both in vitro and in vivo PCa models decreased tumor growth.  These results suggest by analyzing a population of resistant cells, identification of drivers and novel treatments is possible.

overall_design: RNA sequencing of DU145 and PC3 sensitive and docetaxel resistant cell lines

first: Patricia

last: Schnepp

first: Aqila

last: Ahmed

first: June

last: Escara-Wilke

first: Greg

last: Shelley

first: Atsushi

last: Mizokami


title: The effect of TRPM7 kinase inactivation on expression levels of the genes involved in insulin production and cell cycle regulation in pancreatic islets

city: Muenchen

first: Noushafarin

last: Khajavi

state: Bavaria

address: Goethestr. 33

department: Walther-Straub-Institut für Pharmakologie und Toxikologie

institute: LMU

summary:
To investigate the function of TRPM7 kinase in the regulation of insulin production and beta cell proliferation, we used a mouse model harboring a single point mutation at the active site of the enzyme Trpm7tm1.1Mkma (K1646R, Trpm7R/R)
We then performed gene expression profiling analysis using data obtained from RNA-seq of isolated islets of Trpm7R/R mice and their control littermates after 16 weeks exposure to the obesogenic diet

overall_design: Comparative gene expression profiling analysis of RNA-seq data for isolated islets of Trpm7R/R mice and their control littermates (3 mice per genotype)

first: Khajavi

last: Noushafarin

first: Beyerle

last: Philipp

first: Thomas

last: Gudermann


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

status: Public on Mar 13 2023

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

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

institute: Tomsk State University

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

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

first: Pavel

last: Iamshchikov

first: Tatiana

last: Gerashchenko

first: Denis

last: Piankov

first: Philipp

last: Koshkin

first: Sergei

last: Korostelev

first: Evgeny

last: Denisov


title: Single-cell transcriptomics of resected human traumatic brain injury tissues reveals acute activation of endogenous retroviruses in oligodendroglia

status: Public on Mar 03 2023

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

summary: Traumatic brain injury (TBI) is a leading cause of chronic brain impairment and results in a robust, but poorly understood, neuroinflammatory response that contributes to the long-term pathology. We used snRNA-seq to study transcriptomic changes in different cell populations in human brain tissue obtained acutely after severe, life-threatening TBI. This revealed a unique transcriptional response in oligodendrocyte precursors and mature oligodendrocytes, including the activation of a robust innate immune response, indicating an important role for oligodendroglia in the initiation of neuroinflammation. The activation of an innate immune response correlated with transcriptional upregulation of endogenous retroviruses in oligodendroglia. This observation was causally linked in vitro using human glial progenitors, implicating these ancient viral sequences in human neuroinflammation. In summary, this work provides a unique insight into the initiating events of the neuroinflammatory response in TBI, which has new therapeutic implications.

overall_design:
To investigate changes in cell-type composition and cell-type specific transcriptional responses after severe, acute TBI in humans, we performed single-nucleus RNA sequencing (snRNA-seq) from fresh frozen human brain tissue. We recruited 12 severe TBI patients, defined as post resuscitation Glasgow Coma Scale (GCS) score ≤ 8. The mean age of TBI patients (10 males, 2 females) was 49.5 ± 18.2 years. In these patients decompressive surgery was a life-saving measure to remove injured and swollen space-occupying brain tissue causing marked mass effect or increased intracranial pressure (ICP) refractory to conservative, medical neurointensive care treatment. The injured and contused brain regions (typically the injured part of a temporal or frontal lobe) were surgically removed between 4 hours and 8 days after injury 20. The raw data of these patients is not included in the GEO repository as these are alive individuals protected by GDPR, processed files are available. As control tissue, we used five fresh-frozen post-mortem samples from the frontal and temporal lobe obtained from three non-neurological deaths aged 69, 75 and 87 years. We isolated nuclei from frozen human brain tissue using ultracentrifugation and FACS (see methods for details) and performed snRNA-seq using the 10X Genomics pipeline.

To investigate a mechanistic link between interferon activation and ERV expression we decided to perform in vitro experiments in human glial progenitor cells (hGPCs). We differentiated human embryonic stem cells (hESCs) into hGPCs using a 135-day differentiation protocol. The hGPCs were treated with interferon gamma (IFN?, 5ng/ml) for 48 hours before harvested for 2×150 bp paired-end, strand-specific bulk RNA-seq analysis.

***Raw data not provided for GSM6376811-GSM6376826 due to patient privacy concerns***

The records have been updated with the following files on Sep 5, 2023:
TBI_gene_count_matrix_2.csv
hGPC_gene_count_matrix_2.csv

first: Raquel

last: Garza

first: Yogita

last: Sharma

first: Diahann

last: Atacho

first: Arun

last: Thiruvalluvan

first: Sami

middle: A

last: Hamdeh

first: Marie

last: Jönsson

first: Vivien

last: Horvath

first: Anita

last: Adami

first: Martin

last: Ingelsson

first: Patric

last: Jern

first: Molly

middle: G

last: Hammell

first: Elisabeth

last: Englund

first: Agnete

last: Kirkeby

first: Niklas

last: Marklund


title: RNAseq analysis on metastatic Colorectal Cancer

status: Public on Mar 01 2023

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

summary:
In this study we want present a bank of metastatic colorectal cancer (mCRC) Patient Derived Organoids (PDOs) obtained from Patient Derived Xenografts (PDXs).
These models are annotated with different omics to advance our understanding of CRC.
We wanted to create a resource for the scientific community to assess the predictive reliability of these preclinical models.
We performed comparative analyses between PDOs and matched PDXs to assess the similarities of these two platforms regarding molecular profiles and transcriptional classification.
Moreover, we analyzed how these models respond to Cetuximab, a chimeric monoclonal antibody, normally given to patients after chemotherapy, that inhibits EGFR.
After having assessed models’ reliability with Cetuximab, we aimed at identifying potential synergistic drugs to individuate new possible therapeutic prospects.

overall_design:
Transcriptional profiles were obtained with RNA sequencing – we aligned reads with STAR on a hybrid human-mouse genome, in order to remove the mouse derived reads without requiring a pre-filtering step.
Reads were assigned to human genes with FeatureCounts, then we used DESeq2 to obtain normalized expression values and perform differential expression analyses.
All analytical pipelines have been implemented with Snakemake as a workflow management system, to ensure portability and reproducibility.
----------------------------------------------
Authors state the following "Raw data with reads from our samples need controlled access, since they derive from human tumors."
----------------------------------------------
Clarification for columns “cell type”, “cell line” and “treatment”.
The column “cell type” defines the type of samples
LM: liver metastasis
PR: primary (from colon)
The column “cell line” defines the origin of samples
H: patients
X: xenografts
O: organoids
The column “treatment” describes the experiments done with cetuximab
cetuxi: treated samples (72h (written as h) or 6w for xenografts)
NT: non-treated control
The word “basale” indicates xenografts or organoids grown in normal conditions. They are not the non-treated control of the cetuximab experiments.

first: Elena

last: Grassi

first: Simonetta

last: Leto

first: Martina

last: Ferri

first: Marco

last: Viviani

first: Eugenia

last: Zanella

first: Francesca

last: Cottino

first: Valentina

last: Vurchio

first: Claudio

last: Isella

first: Enzo

last: Medico

first: Andrea

last: Bertotti


title: Coordinated local overexpression of complement induced by interferon gamma in myositis

status: Public on Feb 08 2023

city: Bethesda

first: Iago

last: Pinal-Fernandez

state: MARYLAND

address: 50 South Drive, Room 1142, Building 50, MSC 8024

department: NIAMS

institute: NIH

summary: Complement proteins are deposited in the muscles of patients with myositis. However, the local expression and regulation of complement genes within myositis muscle have not been well characterized. In this study, bulk RNA sequencing (RNAseq) analyses of muscle biopsy specimens revealed that complement genes are locally overexpressed and correlate with markers of myositis disease activity, including the expression of interferon-gamma (IFN𝛾)-induced genes. Single cell and single nuclei RNAseq analyses showed that most local expression of complement genes occurs in macrophages, fibroblasts, and satellite cells, with each cell type expressing different sets of complement genes. Biopsies from immune-mediated necrotizing myopathy patients, who have the lowest levels of IFN𝛾-induced genes, also had the lowest complement gene expression levels. Furthermore, data from cultured human cells showed that IFN𝛾 upregulates complement expression in macrophages, fibroblasts, and muscle cells. Taken together, our results suggest that in myositis muscle, IFN𝛾 coordinates the local overexpression of complement genes that occurs in several cell types.

overall_design: Gene expression profiling analysis of RNA-seq data for patients with different types of myositis (DM, AS, IMNM, IBM) and histologically normal muscle biopsies (NT).

first: Andrew

last: Mammen


title: Histopathologic and transcriptome profiling identify novel trophoblast lineage-specific defects in preeclampsia

status: Public on Jan 10 2023

city: La Jolla

first: Mariko

last: Horii

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: Preeclampsia (PE) is a heterogeneous disease which lacks pathophysiology-based subclassification. Current clinical classification is based on gestational age at diagnosis and severity of disease. However, PE placentas have heterogeneous findings on pathologic exam. We combined clinical, pathological, immunohistochemical (IHC), and transcriptomic profiling to better subclassify this disease. 303 PE and 1388 non-hypertensive controls were included, with subgroups of samples used for each analysis. Detailed clinical and placental pathologic data were abstracted from our Obstetric Registry. Tissue studio (Definiens) was used for IHC analysis. RNAseq was performed using Illumina-NovaSeq using our standard pipeline. We found that maternal vascular malperfusion (MVM) in the placenta is associated with preterm PE and small-for-gestation neonates, with further subclassification into groups with and without fetal vascular malperfusion (FVM). Interestingly, MVM with FVM was further characterized by loss of proliferative cytotrophoblast, as confirmed by p63 IHC. Finally, transcriptomic analysis identified pathways associated with hypoxia and reduced cell-proliferation in PE-MVM placentas, and further subclassified this group into syncytiotrophoblast (STB)hi and extravillous trophoblast (EVT)hi PE, confirmed by IHC for trophoblast lineage-specific markers. Our findings suggest that PE can be subclassified based on underlying pathophysiologic changes, allowing identification of pathways which can be targeted for diagnostic and therapeutic purposes.

overall_design: Total RNA-seq of placental RNA from non-hypertensive control and severe preeclampsia.

first: Mana

last: Parast

first: Louise

middle: C

last: Laurent

first: Cuong

last: To

first: Robert

middle: E

last: Morey


title: Influenza A virus modulation of Streptococcus pneumoniae infection using ex vivo transcriptomics in a human primary lung epithelial cell

status: Public on Feb 16 2023

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Deep sequencing of cDNA from Streptococcus pneumoniae EF3030 bacteria and normalized human broncial epithelial cells (nHBEC), alone, together, and after coincubation with Influenza A virus pH1N1.

sample_organism:
Streptococcus pneumoniae
Homo sapiens
Influenza A virus

overall_design: Total RNA was isolated from EF3030 and nHBEC, alone and after co-culture with pH1N1 over time. Ribosomal RNA was depleted and the remaining RNA was reverse-transcribed into a cDNA library for Illumina sequencing. Reads were mapped to the EF3030,and the human genome.

first: Kevin

last: Harrod

first: Jennifer

last: Tipper

first: Carlos

last: Orihuela

first: Adonis

last: D'Mello

first: Jessica

last: Lane

first: Eriel

last: Martínez

first: Holly

middle: N

last: Roussey

first: Hervé

last: Tettelin


title: Transcriptional profiling of fetal forebrain using single cell/nuclei RNAseq, bulk RNAseq and CUT&RUN

first: Johan

last: Jakobsson

summary: This study aims to profile transposable element expression in human fetal forebrain

overall_design: We performed 10x single cell/nuclei RNAseq of fetal forebrain to characterize transcriptional changes of gene and transposable elements in different cell types of the fetal human forebrain. We complimented our analysis using bulk RNAseq and H3K4me3 CUT&RUN.

first: Raquel

last: Garza


title: Different expression of ceRNAs (lncRNAs, circRNAs and mRNAs) in peripheral blood exosomes from idiopathic short stature patients and healthy controls

status: Public on Jan 31 2023

city: Nanchang

first: xijuan

last: liu

state: Jiangxi

address: No. 1 Minde Road

institute: The Second Affiliated Hospital of Nanchang University

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

summary: Idiopathic short stature is diagnosed by a standing height of less than two standard deviation scores in a specific population adjusted for age and gender and the exclusion of identifiable diseases. A series of studies have confirmed that noncoding RNAs can regulate the chondrocyte proliferation, hypertrophy, and endochondral ossification in the growth plate. In order to analyze and find differentially expressed ceRNAs (lncRNAs, circRNAs and mRNAs in peripheral blood exosomes of idiopathic short stature and healthy controls, we aimed to explore whether differentially expressed ceRNAs (lncRNAs, circRNAs and mRNAs) in peripheral blood exosomes of idiopathic short stature. Three pairs of peripheral blood exosomes samples were subjected to microarray analysis using the SBC human ceRNA Microarray.

overall_design: Three pairs of peripheral blood exosomes specimens from idiopathic short stature patients and healthy controls were used for SBC human ceRNA microarray analysis. RNA samples were prepared for microarray hybridization using Eastep Super RNA simple Total RNA Kit according to the manufacturer’s protocol.

first: Xijuan

last: Liu

first: Jingyu

last: Jia

first: Jinghong

last: Yuan


title: SIRT6 is a key regulator of mitochondrial function in the brain

status: Public on Feb 03 2023

city: Beersheba

first: Dmitrii

middle: Nikolaevich

last: Smirnov

address: David Ben Gurion Blvd 1

department: Department of Life Sciences

country: Israel

institute: Ben-Gurion University of the Negev

summary: The SIRT6 deacetylase has been implicated in DNA repair, telomere maintenance, glucose and lipid metabolism and, importantly, it has critical roles in the brain ranging from its development to neurodegeneration. Here, we combined transcriptomics and metabolomics approaches to characterize the functions of SIRT6 in mouse brains. Unexpectedly, our analysis reveals that SIRT6 is a central regulator of mitochondrial activity in the brain. SIRT6 deficiency in the brain leads to mitochondrial deficiency with a global downregulation of mitochondria-related genes and pronounced changes in metabolite content. We suggest that SIRT6 affects mitochondrial functions through its interaction with the transcription factor YY1 that, together, regulate mitochondrial gene expression. Moreover, SIRT6 target genes include SIRT3 and SIRT4, which are significantly downregulated in SIRT6-deficient brains. Our results demonstrate that the lack of SIRT6 leads to decreased mitochondrial gene expression and metabolomic changes of TCA cycle byproducts, including increased ROS production, reduced mitochondrial number, and impaired membrane potential that can be partially rescued by restoring SIRT3 and 4 levels. Importantly, the changes we observed in SIRT6 deficient brains are also occurring in aging human brains and particularly in patients with Alzheimer's, Parkinson's, Huntington's, and Amyotrophic lateral sclerosis disease. Overall, our results suggest that the reduced levels of SIRT6 in the aging brain and neurodegeneration initiate mitochondrial dysfunction by altering gene expression, ROS production and mitochondrial decay.

overall_design: We performed comparative transcriptomic analysis of 4 WT and 4 brain-specific SIRT6-KO mouse brain profiles.

first: Ekaterina

last: Eremenko

first: Daniel

last: Stein

first: Shai

last: Kaluski

first: Weronika

last: Jasinska

first: Claudia

last: Consetino

first: Barbara

last: Martinez-Pastor

first: Yariv

last: Brotman

first: Raul

last: Mostoslavsky

first: Debra

last: Toiber

last: Khrameeva


title: A next generation three-dimensional hydrogel-based culture system for studying host-pathogen interaction and drug efficacy in tuberculosis

status: Public on Jan 30 2023

city: Bengaluru

first: Rachit

last: Agarwal

state: Karnataka

address: CV Raman road

department: Biosystems Science and Engineering

institute: Indian Institute of Science, Bangalore

summary: An accessible, simple, reliable, next-gen in-vitro platform to further the screening for Mtb drugs and understand TB host-pathogen interaction.

sample_organism:
Homo sapiens
Mycobacterium tuberculosis H37Rv

overall_design:
Dual RNA sequencing to dissect the host-pathogen interaction mechanisms by identifying their transcriptomic differences in the collagen gels 14 days post-infection.
Please note that the 'Dual_Mtb3' sample was not considered for analysis.

first: Vishal

last: Gupta


title: Gene expression profiling of Mycobacterium tuberculosis-infected THP-1 cells with/without treatment with Vitamin C

status: Public on Feb 01 2023

city: Bangalore

first: Genotypic

last: technology

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: Transcriptional response of THP-1 cells infected with Mycobacterium tuberculosis utilizing ‘Active’ Mtb and ‘Dormant’ Mtb infection models at different time points. Analysis of the transcriptomic data deciphered the perturbation of gamut of host cellular pathways that are common and differentially manifested in the ‘Active’ Mtb and ‘Dormant’ Mtb infection models.

overall_design: Agilent one-color experiment,Organism: Homo sapiens  Agilent Microarray Gene Expression 8x60K Arrays AMADID: 27114

first: Sakshi

last: Dhingra Batra

first: Kiran

last: Kumari

first: Jaya

middle: S

last: Tyagi


title: Epigenomic profiling of human postmortem cortical samples

status: Public on Feb 10 2023

first: Johan

last: Jakobsson

summary: CUT&RUN was used to profile the epigenetic status of cells in human adult neurons (n=3) by measuring enirchment of H3K4me3 and H3K9me3 epigenetic marks over a non-targeting (IgG) control.

overall_design: CUT&RUN experiments (IgG, H3K4me3 and H3K9me3) were performed in nuclei of human adult NeuN+ nuclei (n=3)

first: Raquel

last: Garza


title: Early onset colorectal cancer tissues and late onset colorectal cancer tissues

city: Deajeon

first: YunJae

last: Shin

state: Deajeon

address: 125, Gwahak-ro, Yuseong-gu, 34141 Daejeon, South Korea

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary:
To identify the gene expression of early-onset colorectal cancer, we sampled early-onset colorectal cancer patients (age < 50) and late-onset colorectal cancer paitients (age > 70)
We then performed gene expression profiling analysis using data obtained from RNA-seq of early-onset colorectal cancer tissues and late-onset colorectal cancer tissues.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for early-onset colorectal cancer tissues and late-onset colorectal cancer tissues.

first: Chan

middle: W

last: Kim

first: Ye

middle: J

last: Ha


title: Functional implications of polygenic risk for schizophrenia in human neurons

city: New York

first: Kayla

last: Townsley

state: New York

address: 240 E. 89th Street, Apt. #1C

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: We predicted that eGenes linked to schizophrenia would share substantial downstream transcriptomic changes with a common direction of effect (termed “convergence”). Although convergence has been described in the context of loss-of-function autism spectrum disorder risk genes, these rare mutations almost never co-occur in the same individual. The convergent impact of common variants which are frequently inherited together, and the impacts of which are apparent only in aggregate remain unknown. We targeted twenty-one schizophrenia eGenes in iGLUTs using pooled and arrayed CRISPR-based approaches, significantly perturbing seventeen (CALN1, CLCN3, DOC2A, FES, FURIN, GATAD2A, NAGA, PCCB, PLCL1, THOC7, TMEM219, SF3B1, SNAP91, SNCA, UBE2Q2L, ZNF823, ZNF804A), and resolving convergent impacts robust to experimental and donor effects. To test if convergence influenced the outcome when eGenes were inherited in combination (i.e. if eGene effects sum linearly according to the additive model), we compared manipulation of eGenes one at a time and in groups defined by annotated functions at the synapse (“synaptic”: SNAP91, CLCN3, PLCL1, DOC2A, SNCA), or regulating transcription (“regulatory”: ZNF823, INO80E, SF3B1, THOC7, GATAD2A), or with un-related non-synaptic, non-regulatory biology (“multi-function”: CALN1, CUL9, TMEM219, PCCB, FURIN), and random combinations thereof. Altogether, with broad relevance across complex polygenic disease our work begins to experimentally determine answers to the long-standing question of how risk variants interact in human neurons.

overall_design:
Pooled CRISPR screening combined single-cell RNA sequencing readouts and direct detection of sgRNAs. Two independently designed, constructed, and validated pooled CRISPRa libraries were transduced into iGLUTs from two donors in independent experiments at unique developmental time-points (DIV7 or DIV21). To identify groups of genes with similar expression patterns across eGene perturbations we define “convergent networks” as relationships between genes that are co-regulated by shared biological mechanisms. To study the strength and composition of convergent networks, we define “network convergence” as the sum of the network connectivity score (i.e., networks with fewer nodes and more interconnectedness have increased convergence). We endeavored to identify the biological factors (e.g., number of eGenes, functional similarity of eGenes, and eGene co-expression) that influenced network convergence. eGene number tested the number of eGenes used to generate a convergent network.  Functional similarity (i.e., the degree of shared biological functions amongst eGenes) was calculated two ways: Gene Ontology semantic similarity scoring (within biological pathway, cellular component, and molecular function), and synaptic/signaling score (proportion of eGenes with annotated function as either “signaling” for pooled or “synaptic” for arrayed)

We next manipulated eGenes in combination to approximate the polygenic nature of schizophrenia and test if convergence between eGenes influences observed effects. Given that genes implicated in synaptic biology and epigenetic/transcriptional regulation are enriched for the schizophrenia risk we sought to generate three groups of eGenes, linked to synaptic biology, gene regulation, or neither (Fig. 1A, arrayed experiment). Unconstrained by the unidirectionality of pooled CRISPR screens, we did not restrict our list to eGenes with a single direction of effect. From the 18 coding genes prioritized by the intersection of transcriptomic imputation and colocalization, eGenes were separated into discrete functional categories based on gene ontology annotations. Our final gene list included five synaptic genes (SNAP91, CLCN3, PLCL1, DOC2A, SNCA), five regulatory genes (ZNF823, INO80E, SF3B1, THOC7, GATAD2A), and five genes with non-synaptic, non-regulatory functions, termed “multi-function” (CALN1, CUL9, TMEM219, PCCB, FURIN).
We then applied an arrayed design (i.e., distinct conditions in each well) to manipulate schizophrenia eGenes alone and in combination, allowing us to capture cell autonomous and non-cell autonomous effects in a manner not possible in the pooled design. Three to five vectors per gene were tested in 7-day-old (D7) iGLUTs, identifying the single vector that best achieved the level of significant perturbation predicted by eQTL analyses as confirmed by qPCR. Each eGene was perturbed in 21-day-old (D21) iGLUTs for 72 hours, individually and jointly, including appropriate vector and scrambled controls, from two neurotypical donors with average polygenic risk scores (one experimental batch per donor). Three groups of five random genes, one group of ten random genes, and one group of all fifteen genes were also included. Significant (p<0.05) changes in eGene expression in iGLUTs were confirmed by RNAseq in 13/15 eGenes (SNAP91, CLCN3, PLCL1, DOC2A, SNCA, ZNF823, SF3B1, THOC7, GATAD2A, CALN1, TMEM219, PCCB, FURIN) (SI Fig. 1G, SI Fig. 19A); we validated the magnitude and direction of experimental eGene perturbation relative to the dosage effects of the top predicted causal SNPs (e.g. eQTL effect size) and predicted eGene expression changes.

last: Retallick-Townsley

first: Peter

last: Deans

first: Aiqun

last: Li

first: Carina

last: Seah

first: Jessica

last: Johnson

first: Judit

last: Garcia Gonzalez

first: Sam

last: Cartwright

first: Georgios

last: Voloudakis

first: Wen

last: Zhang

first: Minghui

last: Wang

first: John

last: Fullard

last: Girdhar

first: Eli

last: Stahl

first: Panos

last: Roussos

first: Schahram

last: Akbarian

first: Bin

first: Paul

last: O'Reilly

first: Laura

last: Huckins

first: Kristen

last: Brennand

first: Nadine

last: Schrode

first: Evan

last: Cao


title: Limited cross-variant immune response from SARS-CoV-2 Omicron BA.2 in naïve but not previously infected outpatients

status: Public on Dec 20 2022

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Omicron is currently the dominant SARS-CoV-2 variant and several sublineages have emerged. Questions remain about the impact of previous SARS-CoV-2 exposure on cross-variant immune responses elicited by the SARS-CoV-2 Omicron sublineage BA.2 compared to BA.1. Here we show that without previous history of COVID-19, BA.2 infection induces a reduced immune response against all variants of concern (VOC) compared to BA.1 infection. The absence of ACE2 binding in sera of previously naïve BA.1 and BA.2 patients indicates a lack of meaningful neutralization. In contrast, anti-spike antibody levels and neutralizing activity greatly increased in the BA.1 and BA.2 patients with a previous history of COVID-19. Transcriptome analyses of peripheral immune cells showed significant differences in immune response and specific antibody generation between BA.1 and BA.2 patients as well as significant differences in the expression of specific immune genes. In summary, prior infection status significantly impacts the innate and adaptive immune response against VOC following BA.2 infection.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) of COVID-19 patients infected by SARS-CoV-2 Omicron subvarients (BA.1 and BA.2).

first: Ludwig

last: Knabl


title: Human iPSC Derived Enamel Organoid Guided by Single Cell Atlas of Human Tooth Development

status: Public on Jan 11 2023

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: UW Medicine at South Lake Union, 850 Republican Street

department: Department of Biochemistry

institute: University of Washington

summary: Tooth enamel secreted by ameloblasts is the hardest material in the human body, acting as a shield protecting the teeth. However, enamel is gradually damaged or partially lost in over 90% of adults and cannot be regenerated due to a lack of ameloblasts in erupted teeth. Here we use sci-RNA-seq to establish a spatiotemporal single cell atlas for the developing human tooth and identify regulatory mechanisms controlling the differentiation process of human ameloblasts. We reveal key signaling pathways involved between the support cells and ameloblasts during fetal development and recapitulate those findings in a novel human ameloblast in vitro differentiation from iPSCs. We furthermore develop a mineralizing enamel organ-like 3D organoid system. These studies pave the way for future regenerative dentistry and therapies toward genetic diseases affecting enamel formation.

overall_design:
To understand how the early differentiation processes of tooth and salivary gland differ and how the epithelial and mesenchymal cell lineages acquire the odontogenic competence, we analyzed the developmental gene expression profiles of human fetal stages by single cell sequencing approach. Tooth germ and salivary gland samples were collected from five fetal age groups. These age groups represented the following developmental stages for tooth differentiation: the bud stage (9-11gw), the cap stage (12-13gw), the early bell stage (14-16gw), and the late bell stage (17-19gw and 20-22gw). We also collected submandibular salivary glands from three matched timepoints (12-13gw, 14-16gw, 17-19gw) that cover the pseudo-glandular and canalicular stages for salivary gland development. A total of 12 samples were prepared for sci-RNA sequencing that consisted of specific tissue from multiple fetuses. For young fetuses, 9-11gw, dissecting individual tooth germs or salivary glands that were in the bud stage was not feasible due to the large number of cells required to perform sci-RNA-seq protocol, instead whole jaw segments were prepared for sequencing. Ten anterior segments (which span from canine tooth to canine tooth region) were pooled as the anterior jaw sample, and 12 posterior jaw segment pairs were pooled as the posterior jaw sample. For older fetuses from 12-22gw, individual tooth germs and salivary glands were dissected. The numbers of pooled samples varied per stage and tooth type, ranging from 40-66 for anterior teeth (including incisors and canines), and 17-51 for molar teeth, as molar teeth are generally larger in size. The salivary gland pooled samples ranged from 3-7 in the three age groups collected.
We utilized the inferred signaling pathways from the sci-RNA-seq data to develop a novel in vitro differentiation protocol that recapitulated the early stages of human ameloblast development from hiPSCs (iAM differentiation); To analyze the efficiency of the differentiation we performed sci-RNA-seq on the two time points of iPSC derived ameloblast differentiation (day10-OE and day16-Early-ameloblasts) and compared the gene expression data to the fetal tissue gene expression data. Bulk RNA-seq was also performed for day0 and day16 of the differentiation .

first: Ammar

last: Alghadeer

first: Sesha

last: Hanson-Drury

first: Devon

last: Ehnes

first: Yang

last: Zhao

first: Anjali

last: Patni

first: Diana

last: O'Day

first: Cailyn

last: Spurrell

first: Aishwarya

last: Gogate

first: Ashish

last: Phal

first: Hai

first: Arikketh

last: Devi

first: Yuliang

first: Lea

last: Starita

first: Daniel

last: Doherty

first: Ian

last: Glass

first: Jay

last: Shendure

first: David

last: Baker

first: Mary

last: Regier

first: Julie

last: Mathieu


title: Effects of Chemotherapy on Human Pancreatic Adenocarcinoma and its Tumor Microenvironment

status: Public on Jan 09 2023

city: San Diego

first: Diane

last: Simeone

state: CA

address: 3855 Health Sciences Drive

institute: UCSD Health

summary: Single-cell RNA-seq analysis of primary and metastatic (liver) human PDAC tumors, some pre-treatment and some post-chemotherapy. (Please note that although the file has "RAW" in the name these are the filtered results from CellRanger.)

first: Gregor

last: Werba

last: Weissinger

first: Emily

last: Kawaler

first: Aristotelis

last: Tsirigos


title: Transcriptome analysis of sweet1 seeds upon treatments during germination

status: Public on Jan 01 2023

city: Urbana

first: Xueyi

last: Xue

state: Illinois

address: 1201 W. Gregory Dr.

department: Department of Plant Biology

institute: University of Illinois at Urbana-Champaign

summary:
Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination.
Methods: After 3-day imbibition, sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads.
Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. Candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function.
Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.

overall_design: Seed transcript profiles in sweet1 under glucose, ABA and ABA+glucose treatments in 30 hours after imbibition.

first: Li-Qing

last: Chen


title: Igh repertoire analysis in primary pro-B cells from  WT, NE1-/- , Site1.3 -/-  mice (VDJ-seq)

status: Public on Dec 22 2022

city: Chicago

first: Amy

last: Kenter

state: IL

address: 835 S Wolcott

institute: UIC

summary: Analysis of the antibody repertoire composition is now possible using VDJ-seq. We used this recently developed method for unbiased amplification from genomic DNA (gDNA) to directly compare the Igh repertoire of C57Bl/6 (WT), NE1-/- and Site1.3 -/- pro-B cells. We find that a group of contiguous proximal and intermediate VH genes are under-utilized in V->DJ rearrangement in the absence of NE1 revealing a NE1 zone of influence. We report the VH gene usage profile from WT, NE1-/- and Site1.3 -/-   primary pro-B cells from the VDJ-seq data.

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design: VDJ-seq of WT, NE1-/- and Site 1.3-/-  primary pro-B cells

middle: L

first: Eden

last: Kleiman

first: Xue

last: Lei

first: Sarah

last: Naiyer

first: Khalid

middle: H

last: Bhat

first: Ann

last: Feeney


title: Transcriptomic and epigenomic analyses of transposable elements in the healthy and diseased human brain

first: Johan

last: Jakobsson

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

overall_design: Refer to individual Series


title: Human derived and patient derived xenografts epigenome analysis of primary and metastasis colorectal cancer

first: Livio

last: Trusolino

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation profiling of primary (PR) and liver metastasis (LM) colorectal cancer (CRC).
The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in human and xenogratfs derived samples.
Raw data were processed using R minfi package. The main goal of this study is to develop a methylation-based classifier and predictor for metastatic CRC (mCRC),
in order to find specific patients stratification for anti-EGFR targeted therapy (cetuximab) and bring the promise to shed new light on the role of methylation in driving colorectal cancer progression in different groups of patients.

first: Marco

last: Viviani

first: Elena

last: Grassi

first: Andrea

last: Bertotti


title: HuR-dependent expression of Wisp1 is necessary for TGFbeta-induced cardiac myofibroblast activity

status: Public on Nov 01 2022

city: Columbus

first: Michael

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

summary: We show that activity of the RNA binding protein HuR is necessary for myofibroblast activation. This data set identifies directly bound HuR target genes in quiescent cardiac fibroblasts and active myofibroblasts.

overall_design: RNA-sequencing of eluted HuR-bound targets following photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) in primary isolated murine cardiac fibroblasts treated with vehicle control or 10 ng/ml TGFbeta


title: A Cdh3 - b-Catenin - Laminin signaling axis by a subset of breast tumor leader cells controls leader cell polarization and directional collective migration

status: Public on Nov 25 2022

city: St. Louis

first: Greg

last: Longmore

state: MO

address: BJCIH, South Euclid Ave.

department: Medicine

institute: Washington University, St. Louis

summary: Carcinoma dissemination can occur when heterogeneous tumor and tumor stromal cells clusters migrate together via collective migration. Cells at the front lead and direct collective migration, yet how these leader cells form and interact with the microenvironment to direct migration are not fully appreciated. From live videos of primary mouse and human breast tumor organoids in a 3D microfluidic system that mimics native breast tumor microenvironment, we developed 3D computational models which hypothesize that leader cells generate high protrusive forces and overcome extracellular matrix (ECM) resistance. Using single cell sequencing, we reveal leader cells are heterogeneous, and we identify and isolate a unique Cadherin-3 (Cdh3) positive leader cell subpopulation necessary and sufficient to lead migration. Cdh3 controls leader cell protrusion dynamics and local production of Laminin-332 which is required for integrin/focal adhesion function. Our findings highlight how a subset of leader cells interact with the microenvironment to direct collective migration.

overall_design: Primary tumor organdoids from K14-Actin.GFP; MMTV-PyMT mice (pure FVB/n background) were isolated, cultured in a microphysiological system, migration was induced (biochemical or biomechanical), organoids were isolated and analyzed using scRNAseq.

first: Gregory

middle: D

first: Priscilla

middle: Y

last: Hwang


title: Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways (DECAMP bronchial brushings)

status: Public on Oct 25 2022

city: Boston

first: Adam

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: SARS-CoV-2 infection and disease severity are influenced by viral entry (VE) gene expression patterns in the airway epithelium. The similarities and differences of VE gene expression (ACE2, TMPRSS2, and CTSL) across nasal and bronchial compartments have not been fully characterized using matched samples from large cohorts. Gene expression data from 793 nasal and 1673 bronchial brushes obtained from individuals participating in lung cancer screening or diagnostic workup revealed that smoking status (current versus former) was the only clinical factor significantly and reproducibly associated with VE gene expression. The expression of ACE2 and TMPRSS2 was higher in smokers in the bronchus but not in the nose. AQ1 scRNA-seq of nasal brushings indicated that ACE2 co-expressed genes were highly expressed in club and C15orf48 secretory cells while TMPRSS2 co-expressed genes were highly expressed in keratinizing epithelial cells. In contrast, these ACE2 and TMPRSS2 modules were highly expressed in goblet cells in scRNA-seq from bronchial brushings. Cell-type deconvolution of the gene expression data confirmed that smoking increased the abundance of several secretory cell populations in the bronchus, but only goblet cells in the nose. The association of ACE2 and TMPRSS2 with smoking in the bronchus is due to their high expression in goblet cells which increase in abundance in current smoker airways. In contrast, in the nose, these genes are not predominantly expressed in cell populations modulated by smoking. In individuals with elevated lung cancer risk, smokinginduced VE gene expression changes in the nose likely have minimal impact on SARS-CoV-2 infection, but in the bronchus, smoking may lead to higher viral loads and more severe disease.

overall_design: Bronchial brushings were obtained from subjects enrolled in the DECAMP (Detection of Early lung Cancer Among Military Personnel) cohorts.

first: Ke

last: Xu

first: Xingyi

last: Shi

first: Joshua

last: Campbell

first: Jennifer

last: Beane


title: Paired bulk and single-cell RNA-seq on high-grade serous ovarian cancer (HGSOC) samples

status: Public on Nov 13 2022

city: Philadelphia

first: Ariel

last: Hippen

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We have sequenced ovarian tumors in several different ways: 1) poly-A captured scRNA-seq, 2) poly-A captured pooled scRNA-seq in pools of 4 samples each 3) Bulk RNA-seq on ribo-depleted tumor chunks 4) Bulk RNA-seq on poly-A captured dissociated cells 5) Bulk RNA-seq on ribo-depleted dissociated cells

overall_design:
Gene expression was measured at both the bulk and single-cell level for HGSOC samples from separate, unrelated individuals. The initial dataset contains 34 samples from 8 individuals.
***Raw data are being deposited in dbGaP due to patient privacy concerns***

first: Dalia

middle: K

last: Omran

first: Lukas

middle: M

last: Weber

last: Doherty

first: Stephanie

last: Hicks

first: Casey

last: Greene


title: Dissection of obesity-exercise axis in adipose-muscle tissues

status: Public on Oct 13 2022

city: Piscataway

first: Jiekun

last: Yang

state: NJ

address: 145 Bevier Rd

institute: Rutgers University


title: Single-cell dissection of obesity-exercise axis in adipose-muscle tissues

summary: We studied the opposing effects of exercise training and high-fat diet at single-cell resolution to reveal changes in cell type abundance, cell-type-specific gene expression/pathway/regulatory network changes, and changes in cell-cell communication both within and across tissues. We profiled scRNA-seq in 204,883 cells, grouped into 53 distinct cell sub-types/states across 22 major cell types, from subcutaneous white adipose tissue, visceral white adipose tissue, and skeletal muscle across 16 lean and 15 obese mice with both diet and exercise interventions. Changes in both cell proportion and transcriptional state were most strongly pronounced in adipose stem cells in fat, consistent with roles of adipogenesis in thermogenesis-vs-lipogenesis and hyperplasia-vs-hypertrophy in obesity. For immune cells, exercise training decreases obesity-associated inflammatory tissue-resident cell populations, including myeloid and regulatory T cells, and promotes beige-cell-inducing populations, including NKT cells. These changes clustered in common pathways across tissues for both exercise and obesity, including extracellular matrix remodelling and circadian rhythm in mesenchymal stem cells and cell activation/migration in immune cells.

overall_design: Single-cell mRNA profiles of three metabolic tissues from 6-week old C57BL/6JN mice with 6-week high-fat diet and 3-week exercise training interventions

first: Maria

last: Vamvini

first: Pasquale

last: Nigro

first: Laurie

last: Goodyear

first: Manolis

last: Kellis


title: Structural adaptations of epidermal stem cells to mechanical stress

status: Public on Nov 10 2022

first: Brian

middle: C.

last: Capell

address: 421 Curie Boulevard Biomedical Research Building 1020 Biomedical Research Building 1020

department: Dermatology

summary: To elucidate the cellular mechanisms of keratinocytes in response to an acute mechanical force

overall_design:
p63CreER; Piezo1fl/fl ; R26-mTmG (Piezo1 cKO) mice were administered tamoxifen injections (3 times, 20ug/dose) at P45-P52 to activate cre recombination and delete Piezo1 gene expression in basal layer keratinocytes. Basal epidermal cells were isolated from Piezo1 cKO and control mouse back skin using flow sorting.

On Monday June 16, all processed and raw data files were replaced.

first: Sijia

last: Huang

first: Paola

last: Kuri

first: Jonathan

last: Zou

first: Maxwell

last: Marshall

first: Gabriella

last: Rice

first: Stephen

last: Prouty

first: Tzvete

last: Dentchev

first: Miriam

last: Doepner

first: Joel

last: Boerckel

first: Todd

last: Ridky

first: Pantelis

last: Rompolas


title: Targeting Integrated Stress Response by ISRIB combined with Imatinib attenuates STAT5 signaling and eradicates therapy-resistant Chronic Myeloid Leukemia cells

status: Public on Nov 04 2022

city: Warsaw

first: Katarzyna

last: Piwocka

address: Pasteur 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary:
Integrated Stress Response (ISR) facilitates cellular adaptation to a variable environmental conditions by reprogramming cellular response. Activation of ISR was reported in neurological disorders and solid tumours, but its function in hematological malignancies remains largely unknown. Previously we showed that ISR is activated in chronic myeloid leukemia (CML) CD34+ cells, and its activity correlates with disease progression and imatinib resistance. Here we demonstrate that inhibition of ISR by small molecule ISRIB, but not by PERK inhibitor GSK2656157, restores sensitivity to imatinib and eliminates CML-BP CD34+ resistant cells. We found that In PDX mouse model bearing CD34+ imatinib/dasatinib-resistant CML blasts with PTPN11 gain-of-function mutation, combination of imatinib and ISRIB decreases leukemia engraftment. Furthermore, genes related to SGK3, RAS/RAF/MAPK, JAK2 and IFN pathways were downregulated upon combined treatment. Remarkably, we confirmed that ISRIB and imatinib combination decreases STAT5 phosphorylation and inhibits expression of STAT5-target genes responsible for proliferation, viability and stress response. Thus, our data point to a substantial effect of imatinib and ISRIB combination, that results in transcriptomic deregulation and eradication of imatinib-resistant cells. Our findings suggest such drug combination might improve therapeutic outcome of TKI-resistant leukemia patients exhibiting constitutive STAT5 activation.

Generation of this dataset  was funded by National Science Centre grant OPUS (2021/41/B/NZ5/04077) to Katarzyna Piwocka

overall_design: Comparative polyA mRNA profiling (RNA-sequencing – stranded, single-end) of chronic myeloid leukemia (CML) cells from patient derived xenograft (PDX) model mice either untreated (control) or treated with a) Imatinib only, b) ISRIB only, and c) both Imatinib and ISRIB.

first: Wioleta

last: Dudka

first: Shamba

last: Mondal


title: Tissue-level dissection of obesity-exercise axis in adipose-muscle tissues

first: Jiekun

last: Yang

summary: We studied the opposing effects of exercise training and high-fat diet at tissue-level resolution to reveal gene expression and pathway changes in subcutaneous white adipose tissue, visceral white adipose tissue, and skeletal muscle. We revealed gene modules consistently up-regulated by exercise training, which include fatty acid biosynthesis/beta-oxidation/metabolism, oxidative phosphorylation, TCA cycle, and ROS response. Modules down-regulated by exercise training in all three tissues are antigen presentation, neutrophil degranulation, immune cell migration, phagosome-related genes, ECM-related genes, proliferation, and ribonucleotide biosynthesis. Taken together, exercise training improves fatty acid metabolism and cellular respiration similarly across the three metabolic tissues, and represses immune, ECM, proliferation and tissue-specific pathways.

overall_design: Bulk mRNA profiles of three metabolic tissues from 6-week old C57BL/6JN mice with 6-week high-fat diet and 3-week exercise training interventions

first: Maria

last: Vamvini

first: Pasquale

last: Nigro

first: Laurie

last: Goodyear


title: Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways

first: Adam

last: Gower


title: HRasV12-induced senescence with WSTF overexpression

status: Public on Oct 05 2022

first: Zhixun

last: Dou

address: 185 Cambridge Street, CPZN 4-234

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital


title: ATAC-seq of HRasV12-induced senescence with WSTF overexpression

summary: We discovered that WSTF is downregulated in senescent cells by autophagy degradation. Forced expression of WSTF inhibits senescence-associated secretory phenotype, via inhibition of chromatin accesibility over inflammatory genes.

overall_design: Primary IMR90 cells were stably expressing vector control or WSTF. The cells were then infected by HRasV12 retrovirus to induce senescence. Three replicates each were included in each conditon for ATAC-seq analyses.

first: Murat

last: Cetinbas

first: Ruslan

middle: I

last: Sadreyev


title: RNA-seq of HRasV12-induced senescence with WSTF overexpression

overall_design: Primary IMR90 cells were stably expressing vector control or WSTF. The cells were then infected by HRasV12 retrovirus to induce senescence. Three replicates each were included in each conditon for RNA-seq analyses.


title: Defining the spatial-molecular map of fibrotic tendon healing and the drivers of Scleraxis-lineage cell fate and function

city: Rocheser

first: Jessica

last: Ackerman

state: NY

address: 665 Elmwood Ave

institute: University of Rochester

summary: Spatial transcriptomic analysis of murine FDL tendons following acute injury and repair to evaluate spatiotemporal programming of tendon healing

overall_design: Hindpaws from Scx-Ai9 mice (Scx-lin+ cells labeled with tdTomato fluorescence prior to surgery) were collected at D0, 14, 21, and 28 post-injury (in duplicate) for ST analysis of healing tendons using the 10X Visium platform

first: Katherine

last: Best

first: Samantha

last: Muscat

first: Anne

last: Nichols

first: Elizabeth

last: Pritchett

first: Chia-Lung

last: Wu

first: Alayna

last: Loiselle


title: Human and rodent cell susceptibility and response to different orthohantaviruses uncovers various levels of cellular restriction

status: Public on Sep 30 2022

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

institute: Institut Pasteur

summary: This study highlighted the complexity of host/virus relationship, showed that viruses are restricted at different levels of the viral cycle, and provided multiple levels of analysis to understand how these viruses differ in their interactions with cells to escape innate immunity, depending on the tissue and host origin

overall_design: Total RNA was extracted from 4 independent biological replicates of bank vole cells upon infection with PUUV or PHVs and non infected (12 samples).

first: Myriam

last: Ermonval


title: 3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice

status: Public on Sep 28 2022

city: Wuhan

first: yue

last: li

address: Shizishan Street

country: China

institute: HUAZHONG Agriculture University

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group