title: RNA-Seq analysis reveals the growth of Populus in different light qualities

status: Public on Jun 09 2024

city: Kunming

first: Xiaolin

last: Zhang

address: qingyun street

institute: southwest forestry university

summary: Light plays a key role in plant growth, development and response to adversity. Plants perceive different wavelengths of light in the environment through various photoreceptors and regulate plant growth and development through light signaling. However, there are fewer studies on the effects of different light qualities on the growth and development of tree species at high altitude. In the study, the effects of blue and green light treatments on the growth and development of Populus cuttings were investigated. Blue light treatment significantly increased the high growth of Populus, while green light treatment showed the opposite trend. Consequently, blue light treatment demonstrated growth promotion by increasing the growth hormone content of Populus. This implies that Populus may benefit from blue light therapy in terms of growth and development, which may be helpful for further research into the introduction and cultivation of  poplar species in high altitude regions.

sample_organism:
Populus qamdoensis
Populus schneideri

platform_organism:
Populus qamdoensis
Populus schneideri

overall_design: To investigate the response mechanism of plants to different light bands at high altitude, we evaluated the effects of blue, green and white light on plant growth and physiological traits by treating the cuttings of Populus with white, blue and green light films. We further used RNA-seq technology to investigate the molecular basis of plant responses to different wavelengths of light at the transcriptional level.

first: ChengZhong

last: He

first: Dan

last: Zong

first: Jingmin

last: Wang


title: A Conserved Transcription Factor Regulatory Program Promotes Tendon Fate

status: Public on Jun 13 2024

city: Boston

first: April

middle: M

last: Craft

address: 300 Longwood Ave

country: USA

institute: Boston Children's Hospital

type: Expression profiling by high throughput sequencing

summary: Tendons, which transmit force from muscles to bones, are highly prone to injury. Understanding the mechanisms driving tendon fate would impact efforts to improve tendon healing, yet this knowledge is limited. To find direct regulators of tendon progenitor emergence, we performed a zebrafish high-throughput chemical screen. We established Forskolin as a tenogenic inducer across vertebrates, functioning through Creb1a, which is required and sufficient for tendon fate. Putative enhancers containing cAMP response elements (CRE) in human, mouse and fish, drove specific expression in zebrafish cranial and fin tendons. Analysis of these genomic regions identified motifs for Ebf/EBF transcription factors. Mutation of CRE or Ebf/EBF motifs significantly disrupted enhancer activity and specificity in tendons. Zebrafish ebf1a/ebf3a mutants displayed defects in tendon formation. Notably, Creb1a/CREB1 and Ebf1a/Ebf3a/EBF1 overexpression facilitated tenogenic induction in zebrafish and human pluripotent stem cells. Together, our work reveals functional conservation of two novel transcription factors in promoting tendon fate.

overall_design: Col2a1-egfp or Prg4-tdtomato cells were isolated from the 3xR mouse ESC line and subjected to bulk RNA sequencing

first: Xubo

last: Niu

first: Delmy

last: Melendez

first: Andrew

last: Zhu

first: Lick

last: Lai

last: McMahon

first: Jenna

last: Galloway


title: Single-Cell Transcriptome Analysis Reveals Differential Signatures of Human Left-Sided and Right-Sided Colon

status: Public on Jun 10 2024

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

summary: In our study, we obtained paired normal left-sided and right-sided colon mucosa tissues by colonoscopy, and 9,642 individual cells were analyzed by single-cell RNA-seq, which aims to explore the differennces of cell component between the left and the right colon.

overall_design: This dataset consists of 4 10x Genomics libraries including paired Left colon and right colon tissues from two healthy patients. The first two libraries were obtained from a 48-year-old female by colonoscopy, and the second two libraries were obtained from a 46-year-old male.

first: Jingjing

last: Li

first: Lifenng

last: Sun

first: Xiaoxu

last: Ge

last: Wu

first: Jian


title: Seclidemstat blocks the transcriptional function of multiple FET-fusion oncoproteins

status: Public on Jun 12 2024

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

summary: Genes encoding the RNA-binding proteins FUS, EWSR1, and TAF15 (FET proteins) are involved in chromosomal translocations in several rare sarcomas. FET-rearranged sarcomas are often aggressive malignancies affecting pediatric, adolescent, and young and middle-aged adults, with prognosis depending on the fusion and whether the disease is localized, metastatic, or relapsed. New therapies are needed for these patients. These translocations fuse the 5’ portion of the FET family gene with a 3’ partner gene encoding a transcription factor. The resulting fusion proteins have the intrinsically disordered low complexity domain (LCD) of the FET protein paired with a DNA binding domain and these chimeras function as oncogenic transcription factors. FET fusion proteins have proven stubbornly difficult to target directly and promising new therapeutic strategies target the critical regulators and co-regulators of these proteins. One such protein is the histone lysine specific demethylase 1 (LSD1). LSD1 physically interacts with and is recruited by multiple FET fusions, including EWSR1::FLI1. LSD1 promotes EWSR1::FLI1 gene regulation and prior studies showed that treatment with the noncompetitive inhibitor SP-2509 blocked the transcriptional activity of the fusion. A similar molecule, seclidemstat (SP-2577), was identified as a promising lead for clinical development and is currently in clinical trials for FET-rearranged sarcomas (NCT03600649). However, whether seclidemstat has pharmacological activity against EWSR1::FLI1 or any other FET fusion protein has yet to be demonstrated. In this study, we sought to evaluate the in vitro potency of seclidemstat against multiple cell lines derived from different FET-rearranged sarcomas, including Ewing sarcoma, desmoplastic small round cell tumor, clear cell sarcoma, and myxoid liposarcoma. We also defined the transcriptomic effect of seclidemstat treatment in these diseases and evaluated the activity of seclidemstat against FET fusion transcriptional regulation in multiple cell lines. Seclidemstat showed potent activity in cell viability assays in all four FET-rearranged sarcomas and disrupted the transcriptional function of all the tested fusion proteins. Though epigenetic and targeted inhibitors are unlikely to be effective as a single agents in the clinic, these data suggest seclidemstat remains a promising new treatment strategy for patients with FET-rearranged sarcomas

overall_design: To evaluate the pharmacologic effects of seclidemstat treatment on the transcriptomes of FET-rearranged sarcoma cell lines, we treated 9 cell lines expressing a variety of FET fusion oncogenes with either DMSO or the IC90 dose of seclidemstat for 48 hours, collected RNA, and performed RNA-seq. Additionally, to compare with another sarcoma without a FET-rearrangement, we treated 3 fusion positive rhabdomyosarcoma cell lines with 2 uM SP-2509. RNA from these samples was collected at 48 hours and analyzed by RNA-seq.

first: Galen

last: Rask

first: Ariunaa

last: Bayanjargal

first: Julia

last: Selich-Anderson

first: Emily

middle: R

last: Theisen

first: Benjamin

last: Stanton


title: Prediction of Non-Coding sRNAs and Screening of Virulence-Related sRNAs of Salmonella Pullorum

city: Haikou

first: HE

last: Ting

address: Hainan University, Meilan District, Haikou City, Hainan Province, China

institute: Hainan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: Searching for sRNAs in Salmonella pullorum by RNA sequencing and exploring their functions.Methods: High-throughput sequencing of RNA extracted from Salmonella pullorum under normal growth conditions to detect newly discovered sRNAs, followed by experiments to verify their functions.Results: The proportion of Clean Reads of this sequencing was >65%, and the base Q30s were all above 85%, indicating that the sequencing quality is good and can be used for subsequent analysis. The sRNAscanner software predicted that 148 new sRNAs might exist on the reference genome of Salmonella fowl dysentery, and the reads obtained from sequencing were compared to the genome, and it was found that 110 out of the 148 newly predicted sRNAs could be detected.Conclusions: sRNAs are widely found in bacteria and are involved in many physiological processes. In this study, we detected new sRNAs in Salmonella pullorum by RNA-seq, which lays the foundation for the subsequent investigation of the regulatory functions of sRNAs in bacteria.

sample_organism: Salmonella enterica subsp. enterica serovar Pullorum

overall_design: Salmonella pullorum were cultured to logarithmic growth in LB medium, total RNA was extracted ，in triplicate, and 150 bp bipartite sequencing was performed using an Illumina NovaSeq 6000 high-throughput sequencer.

first: Ting

last: He

first: Tiansen


title: The Mohawk homeobox gene represents a marker and osteo-inhibitory factor in cranial suture stem cells

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

summary: The regeneration of craniofacial bones of the mammalian skeleton necessitates the action of both intrinsic and extrinsic inductive factors from multiple cell types, which function in a hierarchical and temporal fashion to control the differentiation of osteogenic progenitors. Single-cell transcriptomics of developing mouse cranial suture recently identified a suture mesenchymal progenitor population with tendon- or ligament-associated gene expression profile previously uncharacterized. Here, we developed a Mohawk homeobox (MkxCG;R26RtdT) reporter mouse, finding that this teno-ligamentous gene identifies a cranial suture resident cell population within the adult mouse that gives rise to calvarial osteoblasts and osteocytes overtime during homeostatic conditions.  Single cell RNA-Sequencing (scRNA-Seq) demonstrated that Mkx+ suture cells demonstrate a stem-like phenotype with expression of teno-ligamentous genes.  Bone injury with Mkx+ cell ablation showed delayed bone healing.  Remarkably, Mkx gene played a critical role as an osteo-inhibitory factor in cranial suture cells, as knockdown or knockout resulted in increased osteogenic differentiation.  Furthermore, in vivo local deletion of Mkx in Mkx floxed mice resulted in robustly increased calvarial defect repair.  Finally, we observed that mechanical stretch dynamically regulates Mkx expression in turn regulating calvarial cell osteogenesis. Overall, we identify Mkx+ cells within the suture mesenchyme as a progenitor cell population for adult craniofacial bones required for bone repair and Mkx itself as mechanical stretch responsive gene which functions to prevent osteogenic differentiation within the stem cell niche.

overall_design: There are three samples that prepared from uninjured calvarial bone, day 7, and day 30 after calvarial defect  Uninjured is control.

first: Yiyun

last: Wang

first: Qizhi

last: Qin

first: Ziyi


title: Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis [Xenium]

status: Public on Jun 04 2024

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

summary: Large-scale changes in the structure and cellular makeup of the distal lung are a hallmark of pulmonary fibrosis (PF), but the spatial contexts that contribute to disease pathogenesis have remained uncertain. Using image-based spatial transcriptomics, we analyzed the gene expression of 1.6 million cells from 35 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characterized the localization of PF-emergent cell types, established the cellular and molecular basis of classical PF histopathologic features and identified a diversity of distinct molecularly defined spatial niches in control and PF lungs. Using machine learning and trajectory analysis to segment and rank airspaces on a gradient of remodeling severity, we identified compositional and molecular changes associated with progressive distal lung pathology, beginning with alveolar epithelial dysregulation and culminating with changes in macrophage polarization. Together, these results provide a unique, spatially resolved view of PF and establish methods that could be applied to other spatial transcriptomic studies.

overall_design:
Sample names were generated based on their collection site (Vanderbilt University-'VU'; Translational Genomics Research Institute-'T'), disease status (healthy donor-'HD'; interstitial lung disease-'ILD'), unique number assigned to the patient and where applicable, whether the sample was taken from a 'less affected' or 'more affected' tissue section as determined by percent pathology scores. Replicate healthy samples were labeled 'A' and 'B' to distinguish (for example, VUHD116A and VUHD116B), and replicate disease samples with the same 'less affected' or 'more affected' designation were labeled '1' and '2' (for example, VUILD105MA1 and VUILD105MA2).

UPDATE [May-08-2025]:
- GSM7990534_output-XETG00048__0003400__TILD117MA__20230313__191400_transcripts.csv.gz
was replaced by
GSM7990534_output-XETG00048__0003400__TILD117MA1__20230313__191400_transcripts.csv.gz
- GSM8505453_TILD117MA_transcripts.csv.gz
was replaced by
GSM8505453_TILD117MA2_transcripts.csv.gz

UPDATE [June-06-2025]: The processed data were updated.

first: Annika

last: Vannan

first: Ruqian

last: Lyu

first: Arianna

middle: L

last: Williams

last: Negretti

first: Evan

middle: D

last: Mee

first: Joseph

last: Hirsh

first: Samuel

first: David

middle: S

last: Nichols

first: Chase

middle: J

last: Taylor

first: Vasiliy

middle: V

last: Polosukhin

first: A

last: McCall

first: Jason

last: Gokey

first: Heejung

last: Shim

first: Lorraine

middle: B

last: Ware

first: Matthew

last: Bacchetta

first: Ciara

last: Shaver

first: Timothy

last: Blackwell

first: Jennifer

last: Sucre

first: Jonathan

middle: A

last: Kropski

first: Davis

last: McCarthy

middle: E


title: Intermittent MEK inhibition with GITR co-stimulation rescues T cell function for increased efficacy with CTLA-4 blockade in solid tumor models

city: NEW YORK

first: LEVI

last: MANGARIN

state: NY

address: 413 E 69TH STREET

department: MEYER CANCER CENTER

institute: WEILL CORNELL MEDICINE

summary: MEK inhibitors (MEKis) have limited success with MAPK/ERK pathway dependent cancers due to various resistance mechanisms tumor cells can employ. CH5126766 (CKI27) is a novel inhibitor that binds to MEK and prevents release of RAF, reducing the relief of negative feedback commonly observed with other MEKis. We observed that CKI27 increased MHC expression on tumor cells and improved T cell mediated killing. Yet, CKI27 also decreased T cell proliferation, activation, and cytolytic activity by inhibiting the MAPK/ERK pathway that is activated downstream of T cell receptor signaling. Therefore, we aimed to balance the positive and negative immunomodulatory effects of MEKis for optimal combination with immunotherapy. Intermittent administration of CKI27 allowed T cells to partially recover and co-stimulation via GITR and OX-40 agonist antibodies completely alleviated inhibition of function. In Kras mutant lung and colon tumor mouse models, intermittent CKI27 and anti-GITR significantly decreased tumor growth and prolonged survival when further combined with CTLA-4 immune checkpoint blockade. Moreover, this triple combination increased CD8+ and CD4+ T cell proliferation, activation, and effector/memory subsets in the tumor draining lymph nodes and tumors and led to intra-tumoral Treg destabilization. These data, collectively, will allow for more informed decisions when optimizing combination regimens by overcoming resistance, reducing toxicity, and generating long-term immune responses.

overall_design: Tumor draining lymph nodes (TDLNs) were isolated from LLC tumor bearing mice treated with different drug regimens. Single cell suspensions of the TDLNs were individually hash-tagged, pooled into treatment groups, labeled with the TotalSeq-C mouse universal cocktail, and fluorescence-activated cell sorting (FACS) was used to sort live CD45+ cells for scRNA-seq.

first: Lauren

last: Dong

first: Levi

last: Mangarin

first: Jedd

last: Wolchok

first: Taha

last: Merghoub


title: ADAT2/3 complex-deposited tRNA inosines drives oncogenic transformation

first: Xushen

last: Xiong

address: Wenyi Road West

department: Medical Center

institute: Zhejiang University

summary: Transfer RNAs (tRNAs) are subject to numerous posttranscriptional modifications that influence their maturation, stability, and function. Adenosine to Inosine (A-to-I) editingin thetRNA anticodon stem loop is an important modification that influences anticodon-codon recognition.However,the implications of tRNA editing in cancer and its potential for diagnostic and therapeutic applicationsare not yet well understood.We showed that the ADAT2/3 enzyme complex, responsible for this modification in humans, is amplified and overexpressed in several tumor types,with a higher amplification rate in sarcoma tumors, particularly liposarcomas. We determine that the ADAT complex works as an oncogene in these tumors and that its inhibition reduces tumor growth, offering a new approach to cancer treatment. In addition, we provided insight into the mechanisms of cancer development and progression, demonstrating that tRNA editing is required for higher mRNA translation of oncogenic proteins enriched with specific ADAT-sensitive codons. Thus, ADAT-mediated tRNA modification drives oncogenic transformation by remodeling the set of mRNAs being actively translated to increase expression of proteins that promote proliferation. Our results explain how cancer cells benefit from increased tRNA A-to-I editing and propose ADATs as potential therapeutic targets for the treatment of cancer.

overall_design: To understand the role of A-to-I editing in tRNA in tumor development, we carried out small RNA-seq in ADAT2 knock-down cells. We identify the editing events deposited by ADAT2 enzyme and monitor their molecular functions on translation as well as physiological roles during tumor growth.

first: Julia

last: Ramírez-Moya

first: Richard

middle: I

last: Gregory


title: Apolipoprotein E2 expression drives increased brain exosome levels during aging to mitigate neuronal endosomal dysfunction

status: Public on Jun 05 2024

city: Orangeburg

first: Paul

last: Mathews

address: 140 Old Orangeburg Rd.

department: Psychiatry

institute: New York University Grossman School of Medicine

summary: The polymorphic APOE gene is the greatest genetic determinant of sporadic Alzheimer’s disease risk: the APOE4 allele increases risk while the APOE2 allele is neuroprotective compared with the risk-neutral APOE3 allele. The neuronal endosomal system is inherently vulnerable during aging, and APOE4 exacerbates this vulnerability by driving an enlargement of early endosomes and reducing exosome release in humans and mice. We hypothesized that the protective effects of APOE2 are mediated through the endosomal pathway during aging. In contrast to Alzheimer’s disease and APOE4 models, we detected normal morphology and abundance of early endosomes within cortical neurons of APOE2 targeted-replacement mice during aging despite decreased rab5b recruitment to early endosomes. Similarly, the morphology and abundance of retromer-associated vesicles was normal in APOE2 mice, despite reduced recruitment of vesicle-associated VPS35. Significantly, we observed increased brain extracellular levels of endosome-derived exosomes in APOE2 compared with APOE3 mice during aging, indicative of an enhanced endosomal cargo clearance to the extracellular space that contributes to a homeostatic balance of endosomal functions. Our findings thus demonstrate that APOE2 effectively offsets endosomal pathway changes during aging to preserve its integrity by enhancing exosome biogenesis, mitigating age-driven endosomal dysfunction that contributes to Alzheimer’s disease risk.

overall_design: Hemibrain genetic profiles of targeted-replacement APOE2, APOE3, and APOE4 mice at 18 months of age

first: Katherine

middle: Y

last: Peng

first: Braison

last: Liemisa

last: Pasato

first: Pasquale

last: D'Acunzo

first: Monika

last: Pawlik

first: Adriana

last: Heguy

first: Sai

last: Penikalapati

first: Amanda

last: Labuza

first: Harshitha

last: Pidikiti

first: Melissa

last: Alldred

first: Stephen

last: Ginsberg

first: Efrat

last: Levy


title: Kentucky assay: C5 ketone (2-pentanone)

status: Public on Jun 01 2024

city: Lexington

first: Tim

last: McClintock

state: KY

address: 780 Rose St.

department: Physiology

institute: University of Kentucky

summary:
Mice have 1,100 odorant receptors.  Nearly all are orphan receptors.  The pattern of receptor responses to odorants is the input that allows the brain to detect and discriminate odors
The Kentucky assay measures the function of each of the 1,100 odorant receptors and 14 TAARs  in vivo.

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or 2-pentanone were subjected to microarray analysis using Clariom S arrays

first: Timothy


title: The penetrant chordoid glioma PRKCA mutation is an oncogenic gain-of-function kinase inactivation eliciting early onset chondrosarcoma in mice

city: DERIO

first: VERONIQUE

middle: FRANÇOISE

last: CALLEJA

state: Vizcaya

address: ASTONDO BIDEA 612

country: Spain

institute: Hawk Biosystems

summary: A highly penetrant heterozygous mutation in PRKCA was found recently in chordoid glioma. To establish whether this mutant of PKCapha was a driver of tumour formation or maintenance in vivo, knock-in mice were generated. The constitutive, heterozygous expression of the Prkca D463H mutant in mice provoked the development of bilateral hindlimb chondrosarcomas and early neonatal mortality. The lack of activity of the D463H mutant was not the trigger of the phenotype as heterozygous knock-in of the related inactivating mutation D463N produced offspring indistinguishable from parental strains. Moreover, this surprising distinction between D463H and D463N mutations did not reflect a selective lack of dominance for the D463N mutation over the wild type (WT) allele since homozygous expression of this mutation was phenotypically WT. In cell culture, the D463H mutant expression, localisation and downregulation behaviours closely mimicked that of the WT, with the D463N mutant displaying some subtle differences. Biochemically, both the D463H and D463N mutants were shown to be inactive, although based on thermal shift assays the D463N mutant had reduced ATP affinity compared to WT or D463H proteins. Using induced transcriptional changes as a functional readout, altered mRNA expression indicates that the D463H acts as a dominant gain-of-function PKC mutant, despite a complete lack of intrinsic kinase activity; transcriptional changes induced by the D463N mutant were distinct from both the WT and D463H mutant. These findings suggest a model in which there is a non-catalytic effector function of PKCalpha which it is presumed operates through protein-protein interactions, as evidenced here by TurboID proximity labelling. The penetrant selection of the specific inactivating D463H mutation in chordoid glioma and the distinction with the D463N mutation indicates that this is conformationally sensitive. The properties characterised suggest this is driven by ATP binding and by inference, in this tissue context, the catalytic activity of this kinase acts as an autoregulatory negative feedback control.

overall_design: RNA sequencing was done using U87MG gliomablastoma cell line stably expressing WT, D463H or D463N mutant of Myc-PKCalpha. The parental U87MG cells were used as control. The condition were done in triplicate.

first: Véronique

last: Calleja

first: Stefan

last: Boeing

first: Jack

middle: C

last: Henry


title: Kentucky assay: C5 alcohol (1-pentanol)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or pentanol were subjected to microarray analysis using Clariom S arrays


title: Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Guangdong Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Sus scrofa
Mus musculus

platform_organism:
Sus scrofa
Mus musculus

overall_design: Refer to individual Series


title: Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation [ATAC-seq]

summary: Granulosa cells (GCs) are the most dynamically responsive cell lineage to encourage continuous folliculogenesis; however, developmental dynamics and interplay with downstream transcription circuitry remain unclear. Here, we unravel the redistribution of genome-wide chromatin areas that drive broad developmental-related transcriptomic alterations during follicular maturation in murine and porcine GCs. Distinct GC-activated accessibility regions (GAAs) at the ovulatory phase are responsible for augmenting flanking GC-involved developmental gene (GDG) expression, which are essential for transcriptional responses to developmental cues. Mechanistically, the transcription factor (TF) Fosl2 is strongly recruited to GAAs, facilitating chromatin accessibility state transition. Elevated GAA signals driven by Fosl2 loading induce a significant upregulation of adjacent GDG expression. Additionally, GC-specific Fosl2 deletion in mice perturbs GC cellularity, leading to subfertility related to reproductive aging. Together, we highlight a dynamic chromatin accessibility landscape during follicular maturation, revealing the indispensable Fosl2 function not only controls transcriptional activation via a reconfigured chromatin state, but also orchestrates intricate signaling pathways that are fundamental for ovulation and reproduction.

overall_design: Paired-end ATAC-seq of oocytes and GCs in pig and mouse to sought the accessible chromatin spanning follicular stages.


title: Kentucky assay: C5 acid (pentanoic acid)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or pentanoic acid were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C6 acid (hexanoic acid)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or hexanoic acid were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C7 alcohol (heptanol)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or heptanol were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C7 ketone (2-heptanone)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or 2-heptanone were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C7 acid (heptanoic acid)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or heptanoic acid were subjected to microarray analysis using Clariom S arrays


title: Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation [CUT&Tag]

overall_design: CUT&Tag assays in pig GCs to investigate the genome-wide Fosl2, H3K27ac and H3K4me3 occupancy spanning follicular stages.


title: Bacteria can anticipate and adaptively respond to the seasons

city: Nashville

first: Carl

middle: Hirschie

last: Johnson

state: Tennessee

address: 465 21st Avenue South, U-8215 BSB/MRBIII

department: Biological Sciences

institute: Vanderbilt University

summary: Photoperiodic Time Measurement (PPTM) is the ability of plants and animals to measure differences in day/night-length (photoperiod, PP) and use that information to anticipate seasonal changes in key environmental factors such as annual changes in average temperature. This timekeeping phenomenon, which is well documented for higher organisms, enables processes such as gonadal growth/regression, flowering, hibernation, and diapause to optimally adapt to annual transformations of the environment. We discovered PPTM capability in cyanobacteria, which is unexpected since cyanobacteria are unicellular prokaryotes with generation times as short as 5-6 hours. Therefore PPTM is not confined to eukaryotes with long generation times. Here we show that cyanobacteria can distinguish between short and long daylengths (photoperiods) and respond to short winter-like days by developing an enhanced resistance to cold. This capability develops over several cycles of photoperiod, and therefore they harbor a “photoperiodic counter” that is a common characteristic of PPTM in higher organisms. These photoperiodic responses are dependent on the presence of the kaiABC genes that encode the central circadian clockwork in cyanobacteria. Short days that herald winter stimulated desaturation of membrane lipids, which is a seasonally adaptive response to lower temperatures. Long vs. short days evoke differential programs of gene transcription, including differential expression of stress response genes, suggesting that PPTM originally evolved from stresses that recur seasonally. Therefore, PPTM is a property of much simpler organisms than previously appreciated, with important implications for the evolution of biological timekeeping mechanisms.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: In our recent work, we describe that cyanobacteria are capable of anticipating seasonal changes and exhibit photoperiodic responses. To investigate what genes and pathways could be involved in the establishment of this response, we performed RNAseq in 1) wild-type and 2) circadian clock knock-outs (∆kaiABC) strains of the cyanobacterial model Synechococcus elongatus PCC 7942. We used two different photoperiods, 1) short-day (LD8:16, 8h of dark, 16h of darkness), which we demonstrate to be inducible of a photoperiodic resistance to cold, and 2) long-day (LD16:8), which does not induce increased cold resistance. As we observed that the photoperiodic response takes multiple cycles of LD to develop, we performed the RNAseq in samples collected after 1) 1 LD cycle, which is not sufficient to induce the response, 2) 4 LD cycles, which is sufficient to induce a complete response, and 3) 8 LD cycles, which is the condition most used throughout our manuscript. All samples were collected at their respective middays, and had been exposed to ~60h of light of 40µE m-2 s-1 intensity prior to collection.

first: Maria

last: Jabbur

middle: H


title: Microarray data, 4 week HFD/NCD, nostim or 16hrstim

status: Public on May 24 2024

city: Toronto

first: Brendan

last: Cordeiro

state: Ontario

address: 209 Victoria St.

department: Keenan Research Center

country: Canada

institute: St-michael's hospital

summary: How autoimmunity is initiated in Multiple Sclerosis (MS) is unknown, but both genetic and environmental factors have been implicated. Female physiology is associated with a three times higher risk of MS and the ratio of woman to men diagnosed with MS has been increasing over time, suggesting that environmental factors are interacting with female sex to initiate this disease. One MS risk factor that has been increasing that interacts with female sex is obesity. Being overweight or obese as an adolescent increases one’s risk of MS by 2-fold and this risk increases if one is female. To explore how obesity and female sex interact to control T helper autoimmunity, we conducted a proteomic screen on the serum of male and female healthy weight and obese participants that were affected or not affected by MS. We found that obese individuals, regardless of disease status, exhibited a prominent upregulation of proteins in pathways associated with the damage-associated S100 protein pathway, T helper 1 (Th1), IL-17 pathways and RIG-I/Interferon pathways and that this increase was more prominent in women. To explore the mechanisms of how female sex interacts with increased adiposity to regulate CNS autoimmunity, we modeled a diet-induced overweight (DIO) state in mice by placing animals on high fat diet for 4 weeks and then inducing experimental autoimmune encephalomyelitis (EAE), a model of MS. We found that DIO enhanced EAE severity in mice of both sexes compared to controls and this effect was more pronounced in female mice. The increased severity in the female DIO mice associated with a greater accumulation of pathogenic IFN-+IL-17+ CD4+ cells in the CNS and more severe tissue damage.  Further studies of mice at steady-state revealed that DIO increased the frequency of CD44hiCD4+ T cells and enhanced the potential of naïve CD4+ T cells to produce IFN-This phenotype of higher T cell IFN-was also observed in female humans who were overweight. Furthermore, IFN-α was detected at significantly increased levels in the serum of the DIO-female compared to DIO-male or sex-matched control mice. Loss of IFN-α receptor in T cells negated the increases in Th1 inflammation and EAE severity caused by DIO in female mice.  These results highlight that an overweight state may interact with female sex to selectively enhance Th1 responses and CNS autoimmunity by increasing type I and type I IFN signalling in T cells.

overall_design: C57BL6 mice were placed on a normal chow diet (NCD) or a High fat-diet (HFD) for 4 weeks, then naïve CD4+ T cells (CD4+ CD44low-int) were magnetically isolated by negative selection from spleens and lymph nodes and stimulated with 2ug/ml plate-bound anti-CD3 and anti-CD28 antibodies for 16hrs. Total RNA was then isolated (RNEAsy, Qiagen). Total RNA quality was analyzed by RNA 6000 Pico LabChip on a 2100 BioAnalyzer (Agilent). RNA integrity numbers for samples were > 5.2. 10 ng of total RNA was reverse transcribed using GeneChip WT Pico Kit (Affymetrix). Each sample was hybridized to a GeneChip Mouse Gene 2.0 ST array (Affymetrix) for 16- 18 h at 45 °C. The arrays were scanned using a GeneChip Scanner 3000 (Affymetrix).RNA integrity analysis  and microarray probing and detection were performed by the Microarray Facility of the Centre for Applied Genomics at the Hospital for Sick Children, Toronto, Canada.

first: Jeeyoon

last: Ahn

first: Saurabh

last: Gawde

first: Carmen

last: Ucciferri

first: Nuria

last: Alvarez-Sanchez

first: Xavier

last: Revelo

first: Natalie

last: Stickle

first: Kaylea

last: Massey

first: David

middle: G

last: Brooks

first: Joel

last: Guthridge

first: Gabriel

last: Pardo

first: Daniel

last: Winer

first: Robert

last: Axtell

first: Shannon

last: Dunn


title: A NAD + Metabolic Checkpoint Regulates Hematopoietic Stem Cell Activation and Aging

status: Public on May 28 2024

city: Berkeley

first: Danica

last: Chen

state: California

address: 130 Hilgard Way,

department: NST

institute: UC Berkeley

summary: How hematopoietic stem cells (HSCs) maintain metabolic homeostasis to support tissue repair and regeneration throughout the lifespan is elusive. Here we show that CD38, a NAD+ metabolic enzyme, promotes HSC proliferation by inducing mitochondrial Ca2+ influx and mitochondrial metabolism at young age. Conversely, aberrant CD38 upregulation during aging is a driver of HSC deterioration due to compromised mitochondrial stress management. Pharmacological inactivation of CD38 reverses HSC aging and the pathophysiological changes of the aging hematopoietic system. Blocking mitochondrial Ca2+ influx inhibits HSC proliferation at young age yet prevents HSC aging. Our study highlights a NAD+ metabolic checkpoint that balances mitochondrial activation to support HSC proliferation and mitochondrial stress to enhance HSC self-renewal throughout the lifespan, and links aberrant Ca2+ signaling to HSC aging.

overall_design: To investigate the function of CD38 in regulating HSC fate decisions under homeostasis, ex vivo cytokine stimulation, and chronological aging, freshly isolated HSCs (Lin-ckit+scal1+) from 2-month-old or 24-month-old WT or CD38 KO mice were subjected to 3' Tag RNA sequencing directly or after ex vivo stimulation for 24 hours.


title: RORA proximal enhancer regulates its expression during early human Th17 cell differentiation [ChIP]

status: Public on May 23 2024

city: Turku

first: Sini

last: Junttila

address: Tykistökatu 6 A

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

summary: Distal regulatory elements, such as enhancers, play a pivotal role in dictating cell identity by controlling the transcriptional status of specific cells. The comprehensive understanding of the epigenetic landscape, encompassing enhancer establishment and chromatin accessibility, during the differentiation of human Th17 cells remains incomplete. Leveraging ATAC-seq based chromatin accessibility profile along with the profiling of key histone marks we identified potential enhancers crucial for fate specification of Th17 cells. We found that 24 single nucleotide polymorphisms (SNPs) associated with autoimmune diseases were located near Th17-enhancers. Interestingly, these SNPs overlapped the binding sites of transcription factor active in Th17 cells. Among the Th17 specific enhancers, we identified an enhancer in the intron of RAR-related orphan receptor alpha (RORA) that was earlier predicted to regulate RORA expression. Functional validation through luciferase reporter assays confirmed that this enhancer positively regulate the transcription. Moreover, employing CRISPR-Cas9-mediated deletion of a transcription factor binding site-rich region within the identified RORA enhancer, we demonstrated its role in regulating RORA transcription. These findings provide insights into the potential mechanism by which the RORA enhancer modulates Th17 differentiation and into the role of regulatory SNPs within noncoding regions in conferring resistance or susceptibility to Th17 cell-mediated autoimmune pathologies.

overall_design: Human CD4+ T cels are isolated from cord blood. Cells were activated under Th0 and Th17 condition for 0.5 and 72 h. ChIP assay was performed using H3K4me1, H3K4me3, and H3K27ac, antibodies following protocol described earlier (Ullah et al., 2018).

first: Mohd

last: Moin Khan

first: Subhash

last: Tripathi

first: Ubaid

last: Ullah Kalim

first: Omid

last: Rasool

first: Riitta

last: Lahesmaa


title: Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation [RNA-seq]

first: Yiting

last: Guan

overall_design: RNA sequencing  spanning follicular stages to sought the transcriptome developmental changes of oocytes and GCs in pig and mouse.


title: Kentucky assay: C6 alcohol (hexanol)

first: Tim

last: McClintock

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or hexanol were subjected to microarray analysis using Clariom S arrays

first: Timothy


title: Deconstruction of cellular dynamics after treatment of volumetric muscle loss injury with extracellular matrix

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2800 Plymouth Rd.

department: Biomedical Engineering

institute: University of Michigan

summary: Volumetric muscle loss (VML) is an acute loss of a critical volume of skeletal muscle that results in inflammation, fibrotic scarring in muscle tissue, and permanent muscle defects. The cellular and molecular processes that underlie fibrosis induced from VML injury need to be evaluated in larger animal models. Therefore, we used a canine model of VML alongisde treatment with an extracellular matrix (ECM) hydrogel. Treatment with the ECM hydrogel improved muscle regenerative responses and decreased proportions and spatial signatures of fibrotic and inflammatory cell populations.

overall_design: For single-nuclear RNA sequencing, samples were collected from biopsy samples of untreated canine skeletal muscle tissues at  0, 7, and 14 days post volumetric muscle loss (VML) injury. Canine tissues from animals at 0, 7, and 14 days post VML were collected for spatial gene expression profiling. Samples wereflash-frozen, OCT embedded, muscle tissue. Canine tissues were collected in different wound locations (mid or edge) in treated samples. There were a total of 4 replicates for untreated samples, 3 untreated samples at 7 days post injury, 3 untreated samples at 14 days post injury, and 4 ECM-treated samples at 14 days post injury.

first: Adrienne

last: Giannone

first: Jacqueline

last: Larouche

first: Grace

last: Kenny

first: Paula

middle: M

last: Fraczek


title: Immunotherapeutic targeting of surfaceome heterogeneity in AML

status: Public on May 21 2024

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: Immunotherapy remains underexploited in AML compared to other hematological malignancies. Currently, gemtuzumab ozogamicin is the only therapeutic antibody approved for this disease. To identify potential targets for immunotherapeutic intervention, we analyzed the surface proteome of 100 genetically diverse primary human AML specimens for the identification of cell surface proteins and conducted single-cell transcriptome analysis on a subset of these specimens to assess antigen expression at the sub-population level. Through this comprehensive effort, we successfully identified numerous antigens and markers preferentially expressed by primitive AML cells. Many identified antigens are targeted by therapeutic antibodies currently under clinical evaluation for various cancer types, highlighting the potential therapeutic value of the approach. Importantly, this initiative led to the uncovering of AML heterogeneity at the surfaceome level, identifying several antigens and potential LSC markers characterising AML subgroups and positioning immunotherapy as a promising approach to target AML subgroup specificities.

overall_design: Single-cell RNA sequencing of 20 primary human AML specimens for antigen and marker identification

first: Vincent-Philippe

last: Lavallée

first: Véronique

last: Lisi

first: Azer

last: Farah

first: Banafsheh

last: Khakipoor

first: Jalila

last: Chagraoui

first: Nadine

last: Mayotte

first: Isabel

last: Boivin

first: Arnaud

last: Métois

first: Éric

last: Audemard

first: Marie-Eve

last: Bordeleau

first: Louis

last: Theret

first: Jean-François

last: Spinella

first: Léo

last: Aubert

first: Ossama

last: Moujaber

first: Laure

last: Mallinger

first: Azadeh

last: Hajmirza

last: Bonneil

first: François

last: Béliveau

first: Sybille

last: Pfammatter

first: Albert

last: Feghaly

first: Geneviève

last: Boucher

first: Patrick

last: Gendron

first: Pierre

last: Thibault

first: Frédéric

last: Barabé

first: Sébastien

last: Lemieux

first: Guillaume

last: Richard-Carpentier

first: Josée

last: Hébert

first: Philippe

middle: P

last: Roux


title: Synergically enhanced anti-tumor immunity of in vivo CAR by vaccination-elicited antibody-mediated cellular cytotoxicity boosting

status: Public on May 22 2024

city: Shenzhen

first: Chengzhi

last: Zhao

address: No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong

institute: Southern University of Science and Technology

summary: Chimeric Antigen Receptor (CAR) T cell therapy has shown promise in treating hematologic malignancies. However, it is limited to individualized cell therapy and faces challenges, including high costs, extended preparation time, and limited efficacy against solid tumors. Here, we generated circular RNAs (circRNAs) encoding Chimeric Antigen Receptor (CAR) transmembrane proteins, referred to as circRNACAR, which mediated remarkable tumor killing in both T cells and macrophages. In addition, macrophages exhibited efficient phagocytosis of tumor cells and pro-inflammatory polarization induced by circRNACAR in vitro. We demonstrated that circRNACAR, delivered with immunocyte-tropic lipid nanoparticles (LNPs), significantly inhibited tumor growth, improved survival rates and induced a pro-inflammatory tumor microenvironment in mice. Importantly, the combination of circRNAAnti-HER2-CAR and circRNA-based cancer vaccines encoding the corresponding transmembrane HER2 antigen, termed circRNAHER2, exhibited synergistically enhanced anti-tumor activity. Notably, we found that circRNACAR could boost the level of circRNAHER2-elicited antibodies, which could mediate effective killing of HER2+ tumor cells by macrophages, indicating the potential of vaccination-elicited antibodies in developing novel immunotherapy. This proof-of-concept study demonstrated that the combination of circRNA-based in vivo CAR and vaccines, termed in vivo CAR-VAC, holds the potential to become an upgraded off-the-shelf immunotherapy, and also sheds light on the huge potential of vaccination-elicited antibodies in cancer immunotherapy.

overall_design: comparative gene expression profiling analysis of RNA-seq data for tumor-infiltrating immune cells after PBS, circRNAEV or circRNACAR treatment.

first: Yanyan

last: Wang

first: Xinyue

first: Yichi

last: Xu

first: Liang

last: Qu


title: RORA proximal enhancer regulates its expression during early human Th17 cell differentiation [ATAC]

first: Sini

last: Junttila

overall_design: Human CD4+ T cels are isolated from cord blood. Cells were activated under Th0 and Th17 condition for 2 h, 4 h, 24 h, 48 h, and 72 h and ATAC-seq was performed on harvested nucleii.

first: Mohd

last: Moin Khan

first: Ubaid

last: Ullah Kalim

first: Omid

last: Rasool

first: Riitta

last: Lahesmaa


title: An age specific platelet differentiation path from hematopoietic stem cells causes thrombocytosis and exacerbated thrombosis

city: Santa Cruz

first: Camilla

last: Forsberg

address: 1156 High Street

institute: Institute for the Biology of Stem Cells, University of California Santa Cruz

summary: Here we reveal a direct differentiation pathway from hematopoietic stem cells into platelets that is unique to aging. We used single cell RNA sequencing (scRNA-seq) to analyze age specific platelet pathway at the clonal level.

overall_design:
Cell preparation and sorting: Cells were harvested and c-Kit-enriched from the long bones and hips of the hind legs of young and old mice as described above. Cc-Kit-enriched cells were then stained for lineage markers via a purified rat-anti-mouse antibody cocktail (CD3, CD4, CD5, CD8, CD11b, B220, Gr-1, and Ter119) on ice for 30 minutes. Cells were washed three times followed by incubation with goat-anti-rat Alexa Fluor 680 secondary on ice in the dark for 20 minutes. Cells were washed three times then resuspended in blocking solution (10% bovine calf serum (BCS), 10% normal mouse serum (Invitrogen), and 10% normal rat serum (Invitrogen) in 1X PBS (Cytiva). Cells were blocked for 10 minutes on ice in the dark. Following block, directly conjugated antibodies were directly added to the cells (CD117/cKit and CD150) and incubated on ice in the dark for 45 minutes, gently mixing the cells at the 30-minute mark. A small aliquot of cells was also used to perform a CD150 fluorescence minus one (FMO) control. Cells were washed three times, resuspended in 10% BCS in 1X PBS (wash buffer), with three drops of propidium iodide (diluted 1:5000 in wash buffer) added. Live, lineage-c-Kit+CD150- and live, lineage-c-Kit+CD150+ young and old cells were sorted on a BD FACSAria IIu (BD Biosciences) (Figure S6). The CD150- and CD150+ gates were touching to ensure a continuum of cells across CD150 expression were sorted. Cells were sorted into chilled 1X PBS (without Mg2+) containing 20% BCS and checked for sort purity. Following sorting, cells were washed and each of the four sorted populations (young CD150-, young CD150+, old CD150-, and old CD150+) were split into three aliquots for Cell Multiplexing Oligo (CMO) labeling (10X Genomics) following manufacturer’s instructions, with each individual group of cells receiving a single unique CMO tag. Cells were washed three times with wash buffer and manually counted via a hemocytometer. When possible, equal numbers of cells from each of the 12 CMO labeled aliquots were combined to artificially inflate the numbers of rare CD150+ cells and to equalize numbers between young and old mice. The pooled cells were then split into two replicates for further processing.
Sample sequencing and preparation: Both pooled replicates were used in parallel in the Chromium Next GEM single Cell 3’ v3.1 protocol (10X Genomics) following manufacturer’s directions. GEM generation and barcoding was performed immediately post-sorting, with resulting samples stored at -20ºC per manufacturer’s instructions. All other steps were performed simultaneously for all samples from each of the two independent experiments. Following library construction, samples were assessed via an Agilent Bioanalyzer with a High Sensitivity chip (Agilent Technologies). Final sample libraries were sequenced on a Novaseq P100 at the University of California Davis DNA Technologies and Expression Analysis Core, targeting 50,000 read pairs per cell for the gene expression libraries and 5,000 reads per cell for the CMO libraries.
Data analysis – quality control and data processing. Sequencing data was initially processed via the 10X Genomics Cell Ranger Cloud pipeline, using the mouse genome (mm10) modified to allow for detection of reporter transgene RNA expression. For the downstream analysis, cells with expression of fewer than 200 genes were excluded, and genes detected in fewer than three cells were removed from subsequent analysis steps. Mitochondrial and ribosomal gene transcripts, as well as Malat1 transcripts, were removed to reduce technical bias. This resulted in a dataset of 22,790 cells and 22,870 genes. Additionally, 13 cells with absent Kit RNA were filtered out. Doublets identified by DoubletDetection 2.4.0 (p_thresh=1e-16, voter_thresh=0.5) removed 157 cells in total (Gayoso et al. 2018).  The UMI counts for each cell were normalized by the total counts across all genes (target_sum=1e4), and log-transformed with an added pseudo count of 1.

first: Donna

last: Poscablo

first: Paloma

last: Medina


title: RORA proximal enhancer regulates its expression during early human Th17 cell differentiation

overall_design: Refer to individual Series


title: An age-specific differentiation path from hematopoietic stem cells contributes to exacerbated thrombosis

summary: To investigate the transcriptome of age-specific MkPs compared to canonical MkPs

overall_design: mRNA levels were examined in Young or Old Lin-cKit+Sca1-CD150+CD41+GFP+ or Tom+ cells, or  Old Lin-cKit+Sca+-CD150+Flk2-Tom+ cells FACS sorted from the bone marrow of Young or Old FlkSwitch mice

first: D

first: E


title: Gene expression profile at single cell level of non-malignant cells in KRAS syngeniec mouse tumor models harboring STK11 and/or KEAP1 co-muation

status: Public on May 20 2024

city: Houston

first: Yu

last: Qian

address: 1515 Holcombe blvd

institute: MDACC

summary: STK11/LKB1 and KEAP1 mutations are associated with immunotherapy resistance. We employed KRAS syngeneic mouse cells (K) and generated KEAP1 loss (KK) or STK11/KEAP1 loss (KLK) by CRISPR/KO. Then we injected these tumor cells and collected the tumor for single-cell RNA-seq. Our aim is to analyze the impact of STK11 and/or KEAP1 deficiency on the immune microenvironment.

overall_design:
LKR13K, LKR13KK and LKR13KLK tumor cells were injected into 129SV mice. The tumors were collected and performed scRNAseq at the Univerisity of Texas MD Anderson Cancer Center Sequencing Core.

UPDATE: [Feb-12-2026] The processed data file was corrected.

first: Ferdinandos

last: Skoulidis

first: John

last: Heymach


title: Transciptomic changes in Mycobacterium tuberculosis (Mtb) infected hepatocytes at early and late time points of infection

status: Public on May 17 2024

city: New Delhi

first: Debasisa

last: Mohanty

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Imunology

summary: Mycobacterium tuberculosis (Mtb), although primarily a pulmonary pathogen, can disseminate to various other organs of the body causing extra pulmonary tuberculosis (EPTB). In the present study, we have shown that hepatocytes, the major parenchyma cells of the liver, get robustly infected by Mtb. Using a combination of in-vitro, ex-vivo and animal models; we demonstrate that Mtb utilizes hepatocytes as a replicative niche, modulates its various biological functions like lipid metabolism and shields itself against the common anti-TB drugs. Hepatocytes, being a key cell type having both immune and metabolic functions, controls and coordinates various aspects of the physiology in both health and disease. In case of a multifactorial chronic infection like TB, we are curious to know whether hepatocyte infection plays any major role in the systemic outcome of this age-old disease.

overall_design: HepG2 cell lines were infected with Mtb-H37Rv-mCherry at a multiplicity of infection of 10 (MOI:10) . Two time points were selected:- early time point of 0 hour post infection ( i.e., 5 hours of incubating the cells with Mtb) and late time point of 48 hours post infection (i.e., 48 hours ). After infection, a single cell suspension was made and only the mCherry positive HepG2 cells (infected) were sorted.

first: Rajesh

last: Gokhale

first: Vinay

middle: K

last: Nandicoori

first: Binayak

last: Sarkar

first: Jyotsna

last: Singh


title: Transthyretin orchestrates vitamin B12-induced stress resilience [II]

status: Public on May 18 2024

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: Background: Chronic stress significantly contributes to mood- and anxiety disorders. Previous data suggest a correlative connection between vitamin B12 supplementation, depression, and stress resilience. However, the underlying mechanisms are still poorly understood.  Methods: Using the chronic variable stress mouse model coupled with RNA-sequencing, we determined vitamin B12-induced transcriptional changes related to stress resilience. By viral-mediated gene transfer and in vivo epigenome editing, we reveal a functional pathway linking vitamin B12, DNA methylation, and depressive-like symptoms. Results: We identified Transthyretin (Ttr) as a sex-specific key target of vitamin B12 action in chronic stress. Accordingly, TTR expression was increased postmortem in the prefrontal cortex of male, but not female, depressed patients. Virally altered Ttr in the prefrontal cortex functionally contributed to stress- and depression-related behaviors, changes in dendritic spine morphology, and gene expression. In stressed mice, vitamin B12 reduced DNAme in the Ttr promoter region. Importantly, using in vivo epigenome editing to alter DNAme in the brains of living mice for the first time, we establish a direct causal link between DNAme on Ttr and stress-associated behaviors.  Discussion: In summary, using state-of-the-art techniques, this study uncovers a mechanistic link between cobalamin supplementation, Ttr, and markers of chronic stress and depression, encouraging further studies into dietary interventions for mood disorders.

overall_design: PolyA selected mRNA sequenced for 16 brain (prefrontal cortex) samples from 10 weeks old, male mice in four groups: under naive condition or after 21 days of induced chronic variable stress and saline (control) or vitamin B12 injected afterwards.

first: Gregor

last: Stein

first: Janine

middle: S

last: Aly

first: Annamaria

last: Manzolillo

first: Lisa

last: Lange

first: Iqra

last: Hussain

first: Elizabeth

last: Heller

first: Susana

last: Cubillos

first: Thomas

last: Ernst

first: Christian

last: Hübner

first: Gustavo

last: Turecki

first: Steve

last: Hoffmann

first: Olivia

last: Engmann


title: Gene expression profiles at single-cell level of human post-mortem brain tissue from the orbitofrontal cortex

status: Public on May 15 2024

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: The human cortex consists of a variety of different cell types. We used single-nuclei RNA sequencing to characterize cell-type specific gene-expression profiles in a cohort of psychiatrically healthy controls and individuals diagnosed with psychiatric disease.

overall_design: Fresh-frozen post mortem orbitofrontal cortex tissues of Brodmann area 11 (BA 11) was obtained from the NSW Brain Tissue Resource Centre in Sydney, Australia. Single-nucleus RNA sequencing from tissue samples from 35 psychiatrically healthy donors and 57 donors diagnosed with a psychiatric disease was performed.

first: Anna

last: Fröhlich

first: Nathalie

last: Gerstner

first: Miriam

last: Gagliardi

first: Maik

last: Ködel

first: Natalie

last: Matosin

first: Simone

last: Roeh

first: Vanessa

last: Murek

last: Knauer-Arloth

first: Michael

middle: J

last: Ziller


title: Transthyretin orchestrates vitamin B12-induced stress resilience

status: Public on May 13 2024

first: Konstantin

last: Riege

overall_design: Total mRNA sequenced for 12 brain (prefrontal cortex) samples from 14 weeks old, male mice, 4 weeks after stereotaxic surgery to infect PFC by 1) empty Adeno-associated virus constructs (GFP control), 2) AAVs to overexpress (OE) Ttr, 3) AAVs or knockdown (KD) Ttr.

first: Gregor

last: Stein

first: Janine

last: Aly

first: Annamaria

last: Manzolillo

first: Lisa

last: Lange

first: Iqra

last: Hussain

last: Heller


title: A chromosome region linked to neurodevelopmental disorders acts in distinct neuronal circuits in males and females to control locomotor behavior

status: Public on May 10 2024

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 169 Newton Road

department: Neuroscience and Pharmacology

institute: University of Iowa

summary: We report a single nuclei RNA-seq of mouse total striatum to identify gene expression changes in males and female between WT and 16p11.2 hemideletion.

overall_design: We performed single nuclei RNA-sequencing from total striatum of 4 groups: WT males (sample 795 and 809), 16p11.2 del/+ males (sample 796 and 807), WT females (sample 798 and 803), and 16p11.2 del/+ females (sample 806 and 811).

first: Jaekyoon

last: Kim

first: Felicia

last: Davatolhagh

first: Benjamin

last: Kelvington

first: Joseph

middle: F

last: Lynch III

first: Snehajyoti

last: Chatterjee

first: Sarah

middle: L

last: Ferri

first: Christopher

last: Angelakos

first: Alea

last: Mills

first: Marc

last: Fuccillo

first: Thomas

last: Nickl-Jockschat

first: Ted

last: Abel


title: Viral and host network analysis of the human cytomegalovirus transcriptome in latency

city: Tucson

middle: Dare

last: Goodrum

address: 1657 E Helen St

department: Immunobiology

institute: University of Arizona

summary:
To investigate HCMV (and human host) gene expression profile during latency and reactivation, we infected THP-1 cells with the wildtype HCMV-TB40E or with recombinant viruses that cannot establish latency (UL138stop) or cannot reactivate (UL135stop).
After the establishment of viral latency, we treated cells with TPA to induce cellular differentiation and viral reactivation. We then performed gene expression profiling analysis using data obtained from RNA-seq over a timecourse of undifferentiated and differentiated cells
that are infected with each virus. Uninfected cells are included as a control for gene expression changes that are virally induced.

overall_design: Temporal gene expression profiling analysis of RNA-Seq data for THP1 cells infected with HCMV wildtype or recombinant viruses

first: Donna

last: Collins-McMillen

first: Diogo

last: de Oliveira Pessoa


title: Cell-type transcriptomes for the choanoflagellate Salpingoeca rosetta

city: San Francisco

first: David

last: Booth

state: CA

department: Biochemistry and Biophysics

institute: UCSF

summary: Transcriptome profiles of four cell types from the choanoflagellate Salpingoeca rosetta : Slow Swimmers, Rosettes, Fast Swimmers, and Thecate

overall_design: Slow Swimmer, Rosette, and Thecate cell type were grown to mid-log phase at 22°C before harvesting mRNA. Rosettes were induced from slow swimmers with outer membrane vesicles from the bacterium Algoriphagus machipongonensis. Fast swimmers were derived from Slow Swimmers by growing to stationary phase and heat shocking at 37°C for 2.75 h.

first: Fredrick

last: Leon


title: RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing  II

status: Public on May 07 2024

city: Zürich

first: Giulia

middle: Arianna

last: Moro

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

summary: Many scRNAseq-based methods suffer from a high number of non-detects and a bias towards the 3' or 5' end of transcripts. We developed a method termed RoCK and ROI to address these two biases. RoCK and ROI leads to the enrichment of the transcriptome profile of cells with information on transcripts of interest

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RoCK and ROI is based on barcoded beads of the BD Rhapsody platform. For RoCKseq specific capture, TSO oligos on BD Rhapsody beads are modified with a/ multiple capture sequence(s) specific to transcripts of interest. ROIseq, on the other hand, is based on specific primers which are spiked in during library generation, directing reads to regions of interest (ROIs). Multiple scRNAseq experiments were performed on several biological samples to validate RoCK and ROI. To validate RoCK and ROI library generation, scRNAseq experiments were performed on a mix of murine and human cell lines expressing eGFP or tdTomato respectively. As a further validation of RoCK and ROI, epithelial and mesenchymal cells from a transgenic mouse strain (B6.129S4-Pdgfratm11(EGFP)Sor/J) were used.

first: Izaskun

last: Mallona

first: Mark

middle: D

last: Robinson

first: Erich

last: Brunner

first: Konrad

last: Basler


title: RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing I


title: MATRIN3 deficiency leads to cGAS-STING activation

city: Bethesda

first: Markus

last: Hafner

address: 50 South Drive

institute: NIAMS/NIH

summary: To determine the direct targets of MATR3 in human HAP1 cells, we performed PAR-CLIP.

overall_design: PAR-CLIP was performed with MATR3 antibody. Upon getting the binding sites we intersected with RNAseq data.


title: RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing III


title: Glycine max Jumonji C domain-containing proteins JMJ19/20 exhibit endopeptidase activity and interact with LUXs to mediate flowering time [CUT&Tag]

status: Public on May 05 2024

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

summary: Histone demethylases serve essential functions in plant growth and development across various species. However, their roles in Glycine max remain largely unexplored. This study identified GmJMJ19 and GmJMJ20, encoding JmjC domain-containing proteins. They exhibit circadian rhythmic expression patterns and interact with LUX ARRHYTHMO 2 (GmLUX2) both in vitro and in vivo. Although GmJMJ19/20 bind to histones, they lack conventional histone demethylase activity. Rather, GmJMJ19/20 function as endopeptidases that specifically cleave histone H3 peptides at unmethylated lysine 27 residues, in a manner independent of Fe²⁺ and α-ketoglutarate (α-KG), the cofactors required for typical JmjC enzymes. Structural modeling supports the occlusion of the catalytic pocket that prevents access to methylated substrates. The simultaneous knockout of GmJMJ19/20 significantly delays flowering time. Comparative transcriptomic analyses reveal that the GmJM19/20-GmLUX2 module enhances GmFULc expression via independent of the canonical evening complex. Haplotype analysis suggests that GmJMJ19 underwent selection during domestication, potentially contributing to soybean geographical adaptation.

overall_design:
Genomic occupancy of H3K4me3, H3K27me3 and H3K36me3 in soybean leaves at ZT12 in Williams 82 and gmjmj1920-2

UPDATE: [Feb-04-2026] Samples GSM7305536, GSM7305537, GSM7305546, and GSM7305547 are not included in the associated manuscript and have been removed.

first: Yapeng

last: Han

first: Yingxiang

last: Wang


title: A promising clinical treatment for EGFRI-induced rash by targeting the early pathological alteration revealed by transcriptome analysis

first: qing

last: you

address: 800 Dongchuan

institute: Shanghai Jiao Tong University

summary: In order to investigate the early pathological alteration of EGFRI-induced rash, we treated rat with vehicle or afatinib for 3 days. We then performed gene expression profiling analysis using data obtained from RNA-Seq of 3 different rat skins in each group

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control rat skins (vehicle treated) and afatinib-treated rat skins, in triplicate.

first: Shiyi

last: Zhang

first: Qing

first: Leying

last: Chen

first: Liangyong

last: Xia


title: Designing Molecular RNA Switches with Restricted Boltzmann Machines

status: Public on May 06 2024

city: Paris

first: Pierre

last: HARDOUIN

state: France

address: 4 avenue de l'observatoire

department: CiTCoM

country: France

institute: Faculté de pharmacie UMR 8038

summary: Riboswitches are structured allosteric RNA molecules that change conformation in response to a metabolite binding event, eventually triggering a regulatory response. Computational modelling of the structure of these molecules is complicated by a complex network of tertiary contacts, stabilized by the presence of their cognate metabolite. In this work, we focus on the aptamer domain of SAM-I riboswitches and show that Restricted Boltzmann machines (RBM), an unsupervised machine learning architecture, can capture intricate sequence dependencies induced by secondary and tertiary structure, as well as a switching mechanism between open and closed conformations. The RBM model is then used for the design of artificial allosteric SAM-I aptamers. To experimentally validate the functionality of the designed sequences, we resort to chemical probing (SHAPE-MaP), and develop a tailored analysis pipeline adequate for high-throughput tests of diverse homologous sequences. We probed a total of 476 RBM designed sequences in two experiments, showing between 20% and 40% divergence from any natural sequence, obtaining ≈ 30% success rate of correctly structured aptamers that undergo a structural switch in response to SAM.

sample_organism:
Bacteria
synthetic construct

platform_organism:
Bacteria
synthetic construct

overall_design: DNA oligonucleotides representing the 206 SAM-I aptamer natural sequences, and the two batches (100 and 450) of artificial sequences, preceded by the T7 promoter (5’CGGCGAATCTAATACGACTCACTATAGG3’) and followed by a tag sequence representing a 10 nucleotide bar code unique for each aptamer and a primer binding site, were purchased as an oligonucleotide pool (Twist bioscience®). The Tag sequence was designed to avoid interference with the aptamer secondary structure using RNAFold. The oligo pool was PCR amplified using the T7 promoter as forward primer and and five different reverse primers. RNAs were in vitro transcribed by using the T7 RNA polymerase and were checked for the absence of aberrant products on a 1% agarose gel. SHAPE chemical probing was performed as described previously [1]. Then, RNAs were then reverse transcribed with the Superscript III reverse transcriptase (Invitrogen®) and NGS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs®). Final products were sequenced by using the illumina technology (NextSeq 500/500 Mid 2x150 flowcell). Sequencing data were analyzed and reactivity maps were derived using ShapeMapper2.  [1] N. A. Siegfried, S. Busan, G. M. Rice, J. A. Nelson, and, K. M. Weeks. Rna motif discovery by shape and mutational profiling (shape-map). Nature methods, 11(9):959–965, 2014.

first: Jorge

last: Fernandez-de-Cossio-Diaz

last: Hardouin

first: Francois-Xavier

last: Lyonnet du Moutier

first: Andrea

last: DiGioacchino

first: Bertrand

last: Marchand

first: Yann

last: Ponty

first: Bruno

last: Sargueil

first: Remi

last: Monasson

first: Simona

last: Cocco


title: PRICKLE4 Underlies IDH mutant Tumors Resistance against PARP Inhibition

status: Public on May 01 2024

city: shanghai

first: Giero

address: dong an road

institute: Fudan university

summary: Mutations in isocitrate dehydrogenase (IDH) genes render affected gliomas sensitive to PARP inhibition due to epigenetic reprogramming of the DNA damage repair circuits. However, PARPi treated tumor eventually relapse. We report in this study that anti-angiogenetic agent lenvatinib efficiently cooperate with PARPi and the combination therapy induces marked tumor regression and significant extension of survival time. Genomic study with PARPi and lenvatinib treated tumor samples uncovered that PARPi evokes global transcriptome changes that are overall pro-inflammatory, thus inducing tumor angiogenesis. We identified that prickle planar cell polarity protein 4 (Prickle4) as the specific mediator for PARPi induced neovascularization. Suppression of Prickle4 efficiently overcomes PARPi resistance in these tumors. Overall, multimodality therapy combining PARPi and anti-angiogenetic agents represents a feasible treatment that is of excellent potential for clinical applications.

overall_design: Veliparib and lenvatinib together displayed prominent tumor regressive activity that neither of the two administrated alone achieved. We reasoned that this activity may be linked to molecular changes post one drug treatment that render tumor cells sensitive to another, rather than a simple combinatory effect of drugs. It is also possible that the resistent mechanisms that one drug treatment stimulated is overcome by its corresponding blockade agent. And information of these changes can only be broadly captured by genomic studies to elaborate these mechanisms. To determine this, we subjected fresh tumor samples 9 days post treatment regimens to transcriptional profiling with bulk RNA sequencing.


title: Semaglutide Exacerbates Stunting in Growth-Impaired Juvenile Male Mice via Reduced Energy Metabolism

city: Lyon

first: Filipe

last: De Vadder

address: 32-34 Avenue Tony Garnier

institute: Institut de Génomique Fonctionnelle, ENS de Lyon, CNRS UMR5242, Université Claude Bernard Lyon 1

summary: Animals rely on linear growth to attain their full adult size. The regulators of this multifactorial process, including environmental and endocrine cues, are still incompletely understood. Notably, GLP-1, glucagon-like peptide 1 (GLP-1) has emerged as a potential player in this process. Here, we employ semaglutide, a pharmaceutical GLP-1R agonist as a tool to mechanistically dissect the interplay between GLP-1 receptor activation, energy metabolism, and linear growth during the juvenile period, independent of its clinical applications. Using a juvenile mouse model, we show that chronic semaglutide treatment lowers blood glucose without affecting food intake or weight gain in juveniles with a normal growth pattern. However, in growth-stunted juveniles, semaglutide treatment exacerbates linear growth impairment through at least 2 concomitant mechanisms: a moderate reduction in food intake, and a decreased catabolic activity incompatible with tissue growth. These data suggest a complex interplay between GLP-1 signaling, energy metabolism, and growth during juvenile development. Overall, these findings highlight the value of semaglutide as a mechanistic tool for understanding how GLP-1 receptor activation modulates growth and metabolism in juveniles, emphasizing the importance of developmental context for interpreting its effects.

overall_design: To investigate the effect of semaglutide treatment on undernourished juveniles males, we analyzed the liver of those mice at 8 weeks (after a 5 weeks dietary challenge with low-protein diet, 5% in kcal). Bulk RNA sequencing was performed after RNA isolation from the tissue. We used vehicle-treated animals as the reference (5 mice), and semaglutide-treated animal as the experimental condition (5 mice).

first: Amélie

last: Joly

first: Lucas

last: Rebiffé

first: Yves

last: Dusabyinema

first: Julien

last: Dellinger

first: François

last: Leulier

first: Karine

last: Gauthier

first: Estelle

last: Caillon


title: Evaluating the effects of polyoma small T antigen on gene expression

city: Boston

first: Cherubin

last: Manokaran

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary: We developed an inducible degradation system for murine polyoma small T antigen (PyST) to study the effects of PyST on gene expression. We examined changes in expression following ectopic expression of tagged antigen and following their degradation in the MCF10A human mammary epithelial cell line.

overall_design: Examination of the effects of murine polyoma small T expression and degradation in mammary epithelial cells

first: Yubao

last: Wang

first: Thomas

last: Roberts


title: Interleukin-15-armored GPC3-CAR T cells for patients with solid cancers

first: Antonino

last: Montalbano

state: TX

address: 1102 Bates Ave

institute: Baylor School of Medicine

summary: Interleukin-15 (IL15) enhances the antitumor properties of CAR T cells in preclinical solid tumor models but its effects on CAR T cells in humans are not known. Here, we report the first-in-human evaluation of IL15 co-expression in CAR T cells in two cohorts of a total of 24 patients with glypican-3 (GPC3) expressing solid neoplasms. In cohort 1, GPC3-CAR T cells were safe, no objective antitumor responses were detected. In cohort 2, co-expression of IL15 in GPC3-CAR T cells was associated with increased peak expansion in blood and measurable antitumor responses. Cytokine release syndrome was controlled with immunomodulation or with the inducible caspase 9 safety switch. Single cell transcriptomic analyses identified gene expression of tumor infiltrating CAR T cells associated with antitumor responses.

overall_design: scRNA-seq from patients' samples.

first: David

last: Steffin

first: Nishta

last: Ghatwai

first: Purva

last: Rathi

first: Amy

last: Courtney

first: Azlann

middle: B

last: Arnett

first: Ramy

last: Sweidan

first: Tao

first: Huimin

last: Zhang

first: Prakash

last: Masand

first: John

last: Maris

first: Daniel

last: Martinez

first: Jennifer

last: Pogoriler

first: Navin

last: Varadarajan

first: Sachin

last: Thakkar

first: Deborah

last: Lyon

first: Natasha

last: Lapteva

first: Zhuyong

last: Mei

first: Kalyani

last: Patel

first: Dolores

last: Lopez-Terrada

first: Carlos

last: Ramos

first: Premal

last: Lulla

first: Tannaz

last: Armaghany

first: Bambi

last: Grilley

first: Gianpietro

last: Dotti

first: Leonid

last: Metelitsa

first: Helen

last: Heslop

first: Malcolm

last: Brenner

first: Pavel

last: Sumazin

first: Andras

last: Heczey


title: RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing

first: Giulia

last: Moro

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

overall_design: Refer to individual Series


title: 20S Proteasome Hyperactivation enhances translation, lipid metabolism, proteostasis and longevity: a Proteo-transcriptimic analysis

city: Morgantown

first: David

middle: Rodrigo

last: Salcedo

state: WV

address: 64 Medical Center Drive

department: Biochemistry and Molecular Medicine

institute: West Virginia University

summary: Our study elucidates the broad-spectrum effects of proteasome hyperactivation on the proteome, demonstrating its substantial influence on the proteostasis network. Through comprehensive analyses, we identified a significant reorganization of the transcriptome, enhanced mRNA processing, and increased translation activity. The study further reveals the hyperactivation's impact on intrinsically disordered proteins, lipid synthesis, and biogenesis, evidenced by major changes in lipid droplets and peroxisome proliferation. Notably, we uncovered protective phenotypes against oxidative stress, primarily mediated by Super Oxide Dismutases (SODs), indicating an elevated stress response readiness. Additionally, our research highlighted the hyperactive proteasome's selective targeting of vitellogenins, crucial for lipid metabolism and implicated in the aging process of C. elegans. Enhanced ERAD-dependent degradation was observed, facilitating the clearance of senescent VIT-2 protein aggregates and promoting healthier aging. The α3ΔN mutant significantly reduced the quantity of human alpha-1 antitrypsin (ATZ) aggregates and delayed their formation in a C. elegans model for ATZ disease, suggesting its potential as an ERAD enhancer. These findings propose proteasome hyperactivation as a promising strategy for treating aggregation-prone diseases, offering novel avenues for drug development and therapeutic interventions against neurodegeneration.

overall_design: Total mRNA was extracted from age synchronized C.elegans populations . In total 5 replicates Wild types and 5 replicates  Hyperactive proteasome mutants from Day 8 adults were used for sequencing.

last: Salcedo Tacuma

first: Nadeem

last: Asad

first: Giovanni

last: Howells

first: Raymond

last: Anderson

last: Smith


title: XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [RNA-seq]

status: Public on Apr 24 2024

first: Claire

last: Rougeulle

address: 35 rue Helene Brion

department: Epigenetics and Cell Fate

institute: Université Paris Cité, CNRS

summary: XIST long non-coding RNA is responsible for X chromosome inactivation (XCI) in placental mammals, yet it accumulates on both X chromosomes in human female pre-implantation embryos without triggering X chromosome silencing. The long non-coding RNA XACT co-accumulates with XIST on active Xs and may antagonize XIST function. Here we used human ES cells in a naïve state of pluripotency to assess the function of XIST and XACT in shaping the X chromosome chromatin and transcriptional landscapes during pre-implantation development. We show that XIST triggers the deposition of polycomb-mediated repressive histone modifications and attenuates transcription of most X-linked genes in a SPEN-dependent manner, while XACT deficiency does not significantly affect XIST activity or X-linked gene expression. Our study demonstrates that XIST is functional prior to XCI, confirms the existence of a transient process of X chromosome dosage compensation, and reveals that X chromosome inactivation and dampening rely on the same set of factors.

overall_design: RNA-seq on 3 independent clones of XIST CRISPRi naïve hESCs treated with doxycyclin. Untreated clones were used as controls. Also RNA-seq on 3 replicates of 1 XIST KO clone and WT. RNA-seq on 3 independent clones of XACT KO (naïve) and WT (primed). RNA-seq after siRNA knockdown of SPEN protein using two different mixes of siRNAs.

first: Charbel

last: Alfeghaly


title: XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [RAP-seq]

overall_design: RAP-seq for XIST in naïve and primed hESCs. 2 independent replicates per condition were used.


title: Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean.

first: Chenjiang

last: You


title: XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [MeD-seq]

type: Methylation profiling by high throughput sequencing

overall_design: MeD-seq on 3 independent replicates of naïve hESCs


title: XIST dampens X chromosome activity in a SPEN-dependent manner during early human development


title: Immunotyping of microglia and macrophages in the CNS during acute SIV infection: a single-cell study of rhesus macaque brains

city: Omaha

first: Howard

last: Fox

state: Nebraska

address: 42nd and Emile

institute: University of Nebraska Medical Center

summary: Human immunodeficiency virus (HIV) is widely recognized for its striking impact on the immune system. Even though HIV is primarily known for the impairment of the peripheral CD4 T cells, its influence on the central nervous system (CNS) also cannot be neglected. The main immune constituents in the brain, microglia and macrophages, are the target for HIV in the brain, as well as for the simian immunodeficiency virus (SIV) in nonhuman primates. This infection can lead to neurological effects as well as the establishment of a virus reservoir. Given the gaps in our knowledge on how these cells respond in vivo to CNS infection, we performed single-cell RNA sequencing (scRNA-seq) on myeloid cells from the brains of 3 rhesus macaque with 12-day SIV infection as well as 3 uninfected controls. We identified six microglial clusters and two macrophage clusters by transcriptomic profiling. Intriguingly, there were two microglial clusters populated with the cells from infected animals. These two infection-specific clusters had significantly higher expression (p < 0.05) of MHC class I molecules, interferon-induced proteins, chemokines, and cytokines than did the other clusters. Although only a low proportion of SIV-infected cells were detected in microglia and macrophages (~0.14%), almost all the microglia and macrophages in infected animals were activated to certain extents. In addition, the clusters with higher expression of cytotoxic molecules increased their populations during the infection, suggesting their potential to cause HIV-associated neurological disorders.

overall_design: 92T, 104T, 111T were non-infected control samples and other three (93T, 94T, 95T) were in acute-infected group. The rhesus macaques in the acut-infected group were infected with Simian Immunodeficiency Virus (SIV) for 12 days

first: Xiaoke

last: Xu

first: Meng

last: Niu

first: Benjamin

last: Lamberty

first: Katy

last: Emanuel


title: Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts

status: Public on Apr 26 2024

city: Chicago

first: D Allan

last: Drummond

state: IL

address: 929 E 57th Street

institute: University of Chicago

summary: Stress-induced condensation of mRNA and proteins into stress granules is conserved across eukaryotes, yet the function, formation mechanisms, and relation to well-studied conserved transcriptional responses remain largely unresolved. Stress-induced exposure of ribosome-free mRNA following translational shutoff is thought to cause condensation by allowing new multivalent RNA-dependent interactions, with RNA length and associated interaction capacity driving increased condensation. Here we show that, in striking contrast, virtually all mRNA species condense in response to multiple unrelated stresses in budding yeast, length plays a minor role, and instead, stress-induced transcripts are preferentially excluded from condensates, enabling their selective translation. Using both endogenous genes and reporter constructs, we show that translation initiation blockade, rather than resulting ribosome-free RNA, causes condensation. These translation initiation-inhibited condensates (TIICs) are biochemically detectable even when stress granules, defined as microscopically visible foci, are absent or blocked. TIICs occur in unstressed yeast cells, and, during stress, grow before the appearance of visible stress granules. Stress-induced transcripts are excluded from TIICs primarily due to the timing of their expression, rather than their sequence features. Together, our results reveal a simple system by which cells redirect translational activity to newly synthesized transcripts during stress, with broad implications for cellular regulation in changing conditions.

overall_design: S. cerevisiae cells were stressed, and their RNA was fractionated either using Sed-Seq (to identify RNA which sediments in a non-ribosome dependent fashion) or Polysome-Seq (to identify the ribosome association of RNA).

first: Jared

middle: A

last: Bard

first: D

first: Edward

middle: W

last: Wallace

first: Hendrik

last: Glauninger


title: RYBP coordinates with Trithorax complex and selectively recruits Polycomb complex for cell fate control

city: Guangzhou

first: Chao

last: Wei

address: No.74 Zhongshan Rd.2

institute: Sun Yat-Sen University

summary: The selective expression is pivotal in orchestrating human development, with the Trithorax Group (TrxG) and Polycomb Group (PcG) complexes playing crucial roles in transcriptional activation and repression, respectively. However, mechanism underlying selective regulation of transcription by TrxG and PcG remains poorly understood. In this study, RYBP was observed to interact with TrxG and PcG components. RYBP and TrxG co-localized loci selectively enriches RING1B. STAT3 enriches at RYBP-TrxG co-localized loci devoid of RING1B, while displaying minimal enrichment at RING1B-enrichred loci. Introduction of STAT3 at RYBP loci disrupted RING1B aggregation and chromatin binding. RYBP-deficiency impairs TrxG deposition at DNA repair genes in RYBP-TrxG loci, consequently diminishing their expression and inducing DNA damage. These results facilitate the transition of embryonic stem cells to 2-cell-like cells. Additionally, RYBP-deficiency attenuates PcG deposition at lineage-specific genes within RYBP-TrxG-RING1B loci, thereby promoting ESC differentiation. Collectively, these results provide novel insights into the selective regulation of gene expression.

overall_design: RYBP KO for ChIP seq and RNA-seq

first: Jun

last: Sun

first: Mulan

last: Wang

first: Zhuoyan

last: Liu

first: Jin

last: Tan

first: Xiaona

last: Huang

first: Ranran

last: Dai

first: Junjun

last: Ding


title: XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [CUT&RUN]

first: Claire

last: Rougeulle

overall_design: CUT&RUN for active (H3K4me3, H3K27ac) and repressive (H3K27me3, H2AK119Ub, and H3K9me3) histone modifications in naïve and primed hESCs. For naïve hESCs, 3 independent clones of XIST CRISPRi doxycycline treated cells and 2 replicates of 1 XIST KO clone were used.

first: Charbel

last: Alfeghaly


title: XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [ATAC-seq]

overall_design: To investigate the chromatin accessibility in naïve hESCs, we performed ATAC-seq on 3 independent naïve hESCs replicates.


title: Functional Interaction between APOE4 and mutant APP promotes cerebrovascular changes in young animals

status: Public on Apr 30 2024

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

summary: The Apolipoprotein E4 (ApoE4) allele is one of the strongest risk factors for late-onset Alzheimer’s disease (AD) and is associated with a breakdown of the blood-brain barrier and vascular dysfunction (Nation et al 2019; Liu and Bu 2022). Importantly, these vascular pathologies are exacerbated when APOE4 is coexpressed with familial mutations in APP or components of the γ-secretase complex (Montagne and Zlokovic 2021), suggesting that the interactions between APOE4 and AD mutations can drive progression of the disease. However, most studies have been done in aging animals and few look at the impact of APOE4 expression in young animals and how that potentially contributes toward late-stage disease susceptibility. Here, we examined the potential functional interaction between APP mutations and ApoE4 in the progression of AD pathophysiology by comparing the hippocampal transcriptomes of 3-month-old female mice of 4 different genotypes: AppNL-G-F/NL-G-F , which harbours three knock-in mutations in the humanised Aβ region of APP  (APP-TKI; Saito et al., 2014), mice with a single allele of human ApoE4 knocked-in, ApoE4+/wt (ApoE4), crosses of these two mouse lines, to create AppNL-G-F/NL-G-F;Apoe4+/wt (double-mutant or DM) mice, and wild-type (WT) mice that served as controls. RNAseq revealed nascent microglial activation signatures in both APP-TKI and double mutant datasets, as well as subtle but significant differences between APP-TKI and double mutant in expression of a subset of vascular remodeling genes.

overall_design: Hippocampal transcriptomes of 3-month-old female wild-type, APP knock-in, ApoE4 and double mutant mice

first: Toh

middle: H

last: Ch'ng

first: George

last: Augustine


title: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer

status: Public on Apr 22 2024

city: Baltimore

first: Michael

last: Beer

state: MD

address: 733 N. Broadway

department: Biomedical Engineering and Genetic Medicine

institute: Johns Hopkins University

summary: We performed ATAC-seq in a set of 25 gastric cancer cell lines to detect differential activation of regulatory programs.

overall_design:
ATAC-seq chromatin accessibility profiling of 25 gastric cancer cell lines.

UPDATE: [Feb-12-2026] For GSM8219921, SNU84 was changed to AGS in the title, source name, and cell line.

first: Shamaine

last: Ho

first: Patrick


title: Human long noncoding RNA, VILMIR, is induced by major respiratory viral infections and modulates the host interferon response

status: Public on Apr 17 2024

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: NC State

summary: Long noncoding RNAs (lncRNAs) are a newer class of noncoding transcripts identified as key regulators of biological processes. Here we aimed to identify novel lncRNA targets that play critical roles in major human respiratory viral infections by systematically mining large-scale transcriptomic datasets. Using bulk RNA-sequencing (RNA-seq) analysis, we identified a previously uncharacterized lncRNA, named virus inducible lncRNA modulator of interferon response (VILMIR), that was consistently upregulated after in vitro influenza infection across multiple human epithelial cell lines and influenza A virus subtypes. VILMIR was also upregulated after SARS-CoV-2 and RSV infections in vitro. We experimentally confirmed the response of VILMIR to influenza infection and interferon-beta (IFN-β) treatment in the A549 human epithelial cell line and found the expression of VILMIR was robustly induced by IFN-β treatment in a dose and time-specific manner. Single cell RNA-seq analysis of bronchoalveolar lavage fluid (BALF) samples from COVID-19 patients uncovered that VILMIR was upregulated across various cell types including at least five immune cells. The upregulation of VILMIR in immune cells was further confirmed in the human T cell and monocyte cell lines, SUP-T1 and THP-1, after IFN-β treatment. Finally, we found that knockdown of VILMIR expression reduced the magnitude of host transcriptional responses to IFN-β treatment in A549 cells. Together, our results show that VILMIR is a novel interferon-stimulated gene (ISG) that regulates the host interferon response and may be a potential therapeutic target for human respiratory viral infections upon further mechanistic investigation.

overall_design: To investigate the functional role of VILMIR during the human interferon response, VILMIR expression was repressed using CRISPR interference. A549 cells expressing dCas9-KRAB and GFP were transduced with two guide RNAs (gRNAs) targeting the 5’ end of VILMIR (VILMIRg1 and VILMIRg2) along with a negative control gRNA targeting GFP expression (Ctrl). In addition, a STAT1 knockdown cell line (STAT1g1) was included for comparison, as STAT1 is well-known to impact the host IFN response. All cell lines were treated with or without human IFN-β at 1 ng/mL or 10 ng/mL for 6 hours in triplicate. RNA-sequencing and differential expression analysis was then performed to identify the impact of VILMIR knockdown on the host transcriptional response to IFN-β treatment.

first: Kristen

last: John

first: Ian

last: Huntress

first: Ethan

last: Smith

first: Hsuan

last: Chou

first: Tammy

last: Tollison

first: Sergio

last: Covarrubias

first: Elisa

last: Crisci

first: Susan

last: Carpenter


title: Condensin I folds the C. elegans genome [Hi-C]

status: Public on Apr 18 2024

city: Bern

first: Peter

last: Meister

state: Schweiz

address: Baltzerstrasse 4

department: Institute of Cell Biology

institute: University of Bern

summary: Structural Maintenance of chromosomes (SMC) complexes, cohesin and condensins, have been named after their roles during meiosis and mitosis. Recent data in mammalian cells and Drosophila have described the additional role of cohesin for genome folding into loops and domains during interphase. However, determinants of genome folding in holocentric species remain unclear. Using high resolution chromosome conformation capture, we show that overlapping large-scale nuclear localization and small-scale epigenomic states compartmentalize the C. elegans genome. By systematically and acutely inactivating each SMC complex, we observe that in contrast to other studied systems, cohesin creates small loops, while condensin I has a major role in genome folding: its inactivation causes genome-wide decompaction, chromosome mixing, loss of loops and TAD structures and reinforcement of fine-scale epigenomic compartments. Counter-intuitively, removal of condensin I and its X-specific variant condensin IDC from the X chromosomes led to the formation of a loop compartment coinciding with a subset of previously characterized loading sites for condensin IDC and bound by the X-targeting complex SDC. While transcriptional changes were limited for all autosomes upon cohesin and condensin II inactivation, removal of condensin I/IDC from the X chromosome led to transcriptional up-regulation of X-linked genes demonstrating that a sustained role for condensin IDC in gene regulation. Finally, while condensin I inactivation leads to reduced lifespan, we show that this reduction is due to X-specific gene upregulation rather than global genome decompaction.

overall_design:
To optimise the protocol, wild type strains were tested first. Once the protocol was established, Hi-C was performed on 6 different strains including the control. All the strains used in this study have two biological replicates.
HiC on entire animals, following cleavage of cohesin's kleisins COH-1 and SCC-1. Two biological repeats, sequenced on a iSeq and Novaseq

first: Moushumi

last: Das

first: Jennifer

last: Semple

first: Anja

last: Haemmerli

first: Janik

last: Scotton

first: Todor

last: Gitchev

first: Julien

last: Mozziconacci

first: Julie

last: Campos


title: Germinal Center Dark Zone harbors ATR-dependent determinants of T-cell exclusion that are also identified in aggressive lymphoma – Visium_FFPE_Spatial_Trasciptomics_project

city: Palermo

first: Claudio

last: Tripodo

address: Corso Tukory 211

department: PROMISE

country: Italy

institute: Univerisity of Palermo

summary: The germinal center (GC) dark zone (DZ) and light zone (LZ) regions spatially separate  expansion and diversification from selection of antigen-specific B-cells to ensure antibody affinity maturation and B cell memory. How GC polarity is established is poorly understood.  This study provides novel insights into signals controlling asymmetric T-cell distribution between DZ and LZ regions. We identify spatially-resolved DNA damage response and chromatin compaction molecular features precluding DZ T-cell infiltration. The DZ spatial transcriptional signature linked to T-cell immune evasion clustered aggressive Diffuse Large B-cell Lymphomas (DLBCL) for differential T cell infiltration. We reveal the dependence of the DZ transcriptional core signature on the ATR kinase and dissect its role in restraining inflammatory responses contributing to estabslish an immune-repulsive imprint in DLBCL. These insights may guide ATR-focused treatment strategies bolstering immunotherapy in tumors marked by DZ transcriptional and chromatin-associated features.

overall_design:
Whole-genome transcriptomic profiling was performed on formalin-fixed tissue sections of mouse FFPE mesenteric lymph nodes from two samples: one with a knocked Aicda gene (B6.129P2-Aicdatm1(cre)Mnz/J, Jackson, RRID no 007770) and the other under wild-type conditions for Aicda gene (B6N;129-Ilktm1Star/J, Jackson, RRID no 023310).

grant ID : *22145*
grant title: *Linking genetic evolution, stromal and immune contextures to
unravel tumor heterogeneity in aggressive B-cell lymphomas*
name of the funding source:* A.I.R.C. (Associazione Italiana Ricerca
Cancro) *

first: Valeria

last: Cancila

first: Gaia

last: Morello

first: Giorgio

last: Bertolazzi