Identification of chemical inhibitors targeting long noncoding RNA through gene signature-based high throughput screening.

Scalable methods for functionally high-throughput screening of RNA-targeting small molecules are currently limited. Here, an RNA knockdown gene signature and high-throughput sequencing-based high-throughput screening (HTS) were integrated to identify RNA-targeting compounds. We first generated a gene signature characterizing the knockdown of the long non-coding RNA LINC00973.

Chromatin accessibility dynamics in colorectal cancer liver metastasis: Uncovering the liver tropism at single cell resolution.

Tumor metastasis causes over 90% of cancer related death and no currently available therapies target it. However, there is limited understanding regarding the epigenetic regulation of genes during this complex process. Here by integrating single-cell ATAC-seq (scATAC-seq), single-cell RNA-seq (scRNA-seq), microarray, bulk RNA-seq, immunohistochemistry (IHC) staining, as well as proteomics datasets from paired primary and liver metastatic colorectal cancer (CRC) patient-derived xenograft (PDX) model and patients, we discovered that liver metastatic CRC cells lose their colon-specific chromatin accessible sites yet gain liver-specific ones.

Long non-coding RNA DARS-AS1 promotes tumor progression by directly suppressing PACT-mediated cellular stress.

Cancer cells evolve various mechanisms to overcome cellular stresses and maintain progression. Protein kinase R (PKR) and its protein activator (PACT) are the initial responders in monitoring diverse stress signals and lead to inhibition of cell proliferation and cell apoptosis in consequence. However, the regulation of PACT-PKR pathway in cancer cells remains largely unknown.

Genetic association and single-cell transcriptome analyses reveal distinct features connecting autoimmunity with cancers.

Autoimmune diseases (ADs) are at a significantly higher risk of cancers with unclear mechanism. By searching GWAS catalog database and Medline, susceptible genes for five common ADs, including systemic lupus erythematosus (SLE), rheumatoid arthritis, Sjögren syndrome, systemic sclerosis, and idiopathic inflammatory myopathies, were collected and then were overlapped with cancer driver genes. Single-cell transcriptome analysis was performed in the comparation between SLE and related cancer.

Oncogenic lncRNA LINC00973 promotes Warburg effect by enhancing LDHA enzyme activity.

Aerobic glycolysis, also known as the Warburg effect, is a hallmark of cancer and essential for metabolism in malignancies, but its regulation and modulation in cancer cells remain poorly understood. Here, using large-scale functional screening, we identified a tumor-associated and broadly expressed oncogenic long noncoding RNA LINC00973. Notably, knocking down LINC00973 significantly inhibits the proliferation of multiple types of cancer cells and reduces tumor growth in vivo.

Tumor immunological phenotype signature-based high-throughput screening for the discovery of combination immunotherapy compounds.

Combination immunotherapy is promising to overcome the limited objective response rates of immune checkpoint blockade (ICB) therapy. Here, a tumor immunological phenotype (TIP) gene signature and high-throughput sequencing-based high-throughput screening (HTS) were combined to identify combination immunotherapy compounds. We firstly defined a TIP gene signature distinguishing "cold" tumors from "hot" tumors.

A large-scale transcriptional study reveals inhibition of COVID-19 related cytokine storm by traditional Chinese medicines.

Coronavirus disease-2019 (COVID-19) has become a major global epidemic. Facilitated by HTS technology, we evaluated the effects of 578 herbs and all 338 reported anti-COVID-19 TCM formulae on cytokine storm-related signaling pathways, and identified the key targets of the relevant pathways and potential active ingredients in these herbs. This large-scale transcriptional study innovatively combines HTS technology with bioinformatics methods and computer-aided drug design.

An immune-related gene signature for predicting survival and immunotherapy efficacy in hepatocellular carcinoma.

Background: Hepatocellular carcinoma (HCC) ranks the fourth in terms of cancer-related mortality globally. Herein, in this research, we attempted to develop a novel immune-related gene signature that could predict survival and efficacy of immunotherapy for HCC patients.

Methods: The transcriptomic and clinical data of HCC samples were downloaded from The Cancer Genome Atlas (TCGA) and GSE14520 datasets, followed by acquiring immune-related genes from the ImmPort database.

Guizhi Fuling Decoction inhibiting the PI3K and MAPK pathways in breast cancer cells revealed by HTS technology and systems pharmacology.

As one of the classical traditional Chinese medicine (TCM) prescriptions in treating gynecological tumors, Guizhi Fuling Decoction (GFD) has been used to treat breast cancer (BRCA). Nonetheless, the potential molecular mechanism remains unclear so far. Therefore, systems pharmacology was used in combination with high throughput sequencing-based high throughput screening (HTS) assay and bioinformatic technologies in this study to investigate the molecular mechanisms of GFD in treating BRCA.

Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer.

Metastasis, the development of secondary malignant growths at a distance from a primary tumor, is the cause of death for 90% of cancer patients, but little is known about how metastatic cancer cells adapt to and colonize new tissue environments. Here, using clinical samples, patient-derived xenograft (PDX) samples, PDX cells, and primary/metastatic cell lines, we discovered that liver metastatic colorectal cancer (CRC) cells lose their colon-specific gene transcription program yet gain a liver-specific gene transcription program. We showed that this transcription reprogramming is driven by a reshaped epigenetic landscape of both typical enhancers and super-enhancers.

A comprehensive evaluation of connectivity methods for L1000 data.

The methodologies for evaluating similarities between gene expression profiles of different perturbagens are the key to understanding mechanisms of actions (MoAs) of unknown compounds and finding new indications for existing drugs. L1000-based next-generation Connectivity Map (CMap) data is more than a thousand-fold scale-up of the CMap pilot dataset. Although several systematic evaluations have been performed individually to assess the accuracy of the methodologies for the CMap pilot study, the performance of these methodologies needs to be re-evaluated for the L1000 data.

Chemical genomics reveals inhibition of breast cancer lung metastasis by Ponatinib via c-Jun.

Metastasis is the leading cause of human cancer deaths. Unfortunately, no approved drugs are available for anti-metastatic treatment. In our study, high-throughput sequencing-based high-throughput screening (HTS) and a breast cancer lung metastasis (BCLM)-associated gene signature were combined to discover anti-metastatic drugs.