Single cell RNA-seq (scRNA-seq) is a powerful tool to reveal the heterogeneity in cancer cells. Cancer heterogeneity would provide crucial information to understand eventual development of drug resistant cells or metastatic disseminations in cancers. In our study, we particularly focused on transcriptomic heterogeneity in response to an anti-cancer drug in five lung adenocarcinoma-derived cell lines. We generated single-cell RNA-seq by the two different platforms, the micro-droplet based platform and the micro-chamber platform, then we attempted to combine those datasets to complete information of datasets.

Combinatory use of the distinct single cell RNA-seq analytical platforms reveals heterogeneous transcriptome response to an anti-cancer drug in lung adenocarcinoma cell lines

Full-Parasites (http://fullmal.hgc.jp/) is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species

Full-parasites: database of full-length cDNAs of apicomplexa parasites, 2014 update

To understand heterogeneous behaviors of individual cancer cells, it should be important to investigate gene expression levels as well as their divergences between individual cells. Here we conducted a single cell RNA Seq analysis of a series of lung adenocarcinoma cell lines. We analyzed a total of 337 RNA Seq libraries of single cells and found gene expression diversities between individual cells are characteristic depending on genes. The genes showing highly variable expressions were enriched in particular pathways. Particularly, the EGFR pathway genes originally showed wider variations and further diversity was induced in response to an anticancer-drug stimulation. We also observed that cancer-related genes, which were identified from recent clinical cancer sequencing projects, showed potential expression variations, which firstly became apparent on the anti-cancer drug stimulation.

Single cell analysis of lung adenocarcinoma cell lines and the response to an anti-cancer drug stimulation

To understand the mutual association of the transcriptomes between host humans and infecting malaria parasites, Plasmodium falciparum (Pf), in vivo, we conducted the RNA-Seq analysis of 116 Indonesian malaria patients. Using RNAs extracted from peripheral blood of the patients as the mixture of the human and Pf transcripts, we generated a total of 3 billion RNA-Seq tags. Analysis of these tags allowed us to identify genes and pathways which were associated with clinical symptoms both on human and parasite sides. Particularly, we observed characteristic expression changes in the human innate immune response pathway genes depending on severity of malaria. We also identified a group of transcription regulatory factors and signaling molecule genes which have positive or negative correlations between humans and Pfs. These genes may change their expression patterns to accommodate the respective organisms to mutually conflicting environments. Furthermore, it was possible to utilize the RNA-Seq data for genotyping of the parasites to identify possible drug resistant genetic variations. By bypassing technical difficulty in preparing samples in field, this approach should provide a practically useful mean to describe mutually interacting transcritpomes of humans and parasites, which should eventually explain diverse malaria symptoms.

Interactive Transcriptome Analysis of Malaria Patients and Infecting Plasmodium falciparum in Indonesia

Although thousands of long noncoding RNAs(lncRNAs) are localized in the nucleus, only a fewdozen have been functionally characterized. Herewe show that nuclear enriched abundant transcript1 (NEAT1), an essential lncRNA for the formation ofnuclear body paraspeckles, is induced by influenzavirus and herpes simplex virus infection as well asby Toll-like receptor3-p38 pathway-triggered polyI:C stimulation, resulting in excess formation ofparaspeckles. We found that NEAT1 facilitates theexpression of antiviral genes including cytokinessuch as interleukin-8 (IL8). We found that splicingfactor proline/glutamine-rich (SFPQ), a NEAT1-bindingparaspeckle protein, is a repressor of IL8 transcription,and that NEAT1 induction relocates SFPQfrom the IL8 promoter to the paraspeckles, leadingto transcriptional activation of IL8. Together, ourdata show that NEAT1 plays an important role inthe innate immune response through the transcriptionalregulation of antiviral genes by the stimulusresponsivecooperative action of NEAT1 and SFPQ.

Long Noncoding RNA NEAT1-Dependent SFPQRelocation from Promoter Region to ParaspeckleMediates IL8 Expression upon Immune Stimuli

Global gene expression patterns were compared among wild-type Col-0, teb, atr, teb atr of A. thaliana using shoot apices.


Transcription profiling of shoot apices from Arabidopsis wild type, teb, atr, and teb atr mutant plants

Comparison of Arabidopsis wild-type developing seeds grown under sulfur-deficient condition vs Arabidopsis wild-type developing seeds grown under control condition.


Transcription profiling of Arabidopsis wild type seeds grown under sulfur-deficient conditions

Next Generation Sequencing Facilitates Quantitative Analysis of sunitinib resistant cells and its HIF2a knock out cells.

Examination of gene expression in sunitinib resistant cells and its HIF2a knock out cells

IL28B genotype was shown to be associated with treatment outcome of antiviral thearpy for HCV infection. We tried to clarify the molecular feature that was asocciated with IL2B genotype by comparing Hepatic gene expression of HCV related Hepatocellular carcinoma and non-cancerous tissue with Il28B rs8099917 TT genotype and TG/GG genotype.

Association of interleukin-28B genotype and hepatocellular carcinoma recurrence in patients with chronic hepatitis C.

Hepatic gene expression of HCV related Hepatocellular carcinoma and non-cancerous tissue with Il28B rs8099917 TT genotype and TG/GG genotype

Muscle atrophy F-box (MAFbx/atrogin-1), an E3 ubiquitin ligase, is a crucial mediator of skeletal muscle atrophy and cardiac hypertrophy in response to pressure overload and exercise.