Transcriptomics of Single Cell: New Discoveries to Become Basis for Future Studies

Single-cell transcriptome profiling to determine cell type, transcriptomic signatures, and single cell transcriptomics of ncRNAs are some of the research areas gaining momentum and can become the basis for further studies.

Transcriptomes play a crucial part in studying human tissues at a single cell level. This information can be very helpful in determining details about cell differentiation in health, development, and diseases. Determining the importance of making new breakthroughs, private organizations such as Thermo Fisher Scientific, Inc. have taken significant steps. Thermo Fisher launched Ion Torrent Transcriptome Profiling Grant Program to focus on the importance of a gene-level expression analysis. This analysis can help in discovering novel biomarkers that would play a crucial part in prognostics, cancer diagnostics, and experimental therapy. Research and development activities focusing on the role of transcriptomes in single cells are gaining momentum in recent times. According to the research firm Allied Market Research, the global transcriptomics market would reach $7.95 billion by 2023. Moreover, the funding by private and government organizations would grow in coming years. The current breakthroughs from the major research activities conducted in the field of transcriptomics would become the basis for future research.

Single-cell transcriptome profiling for cell type & cell lineages:

According to two new studies published in Science journal, it was found that single-cell transcriptome profiling can be used to determine cell type and form cell lineages in a whole complex animal. In both studies, researchers used Drop-seq, a high-throughput transcriptome-profiling platform developed in collaboration between Harvard University and the Broad Institute. They studied cell types in a model organism, Schmidtea mediterranea.

A team of researchers from the Massachusetts Institute of Technology and the Whitehead Institute for Biomedical Research was able to identify the transcriptomes from each cell type of S. mediterranea. In addition, they were able to sequence nearly 50,000 single cells along with determining nearly 44 distinct major cell clusters and nearly 150 sub-clusters.

"Much like the genome of an animal, we propose this atlas-like dataset of cell-type transcriptomes can serve as a resource fueling an immense amount of research, not only in planarians, but in other bilaterians with similar cell types," wrote researchers.

In the other study, researchers from Berlin’s Max-Delbrück Center for Molecular Medicine, Germany were able to create a cell type atlas for S. mediterranea along with forming a lineage tree. They were able to sequence nearly 20,000 individual cells along with determining nearly 51 cell clusters and 23 cell lineages.

Transcriptomic signatures change with aging:

As organisms age, they develop a relationship between cancer and degenerative chronic diseases at the transcriptome level. The dominance of cancer in elderly people reduce as they age, and its place is taken by degenerative chronic diseases. Researchers at Christian-Albrechts-University, Kiel, Germany speculated that this change occurs due to a shift in gene transcription. They researched the transcriptomes of four vertebrate species with an aim of determining a transcriptomic signature of aging. They found different regulated processes occurring with age. They used two aging time points for the development of transcriptomic signature associated with aging.

These signatures outlined the upregulation of the immune system along with the down-regulation of the cell cycle. Moreover, they represented processes of cell differentiation in the elderly people. As reported in Nature Communications, they discovered that the transcriptomic signatures change with age and become more like those found in degenerative diseases and less like those found in cancer. “These results reveal a fundamental trade-off between cancer and degenerative aging diseases that sheds light on the pronounced shift in their epidemiology during aging,” wrote Kaleta and his colleagues, in their paper.

Single cell transcriptomics of ncRNAs:

It was recently found that single cell within tissues is heterogeneous in nature. Researchers conducted a study to determine the functionality of this heterogeneity through single-cell variation of non-protein coding RNA expression. Non-coding RNAs (ncRNAs) play a crucial role in genomic regulatory functions, so studying variation in them would offer insights on single cell expression variation. In the review published in WIREs RNA, a group surveyed the research studies on ncRNA expression at single cell level. It outlined that ncRNA show as much variability as protein-coding RNA. Some of the classes of ncRNA may show more single cell variability than others.

Many studies focus on the expression of long non-coding RNAs (lncRNA) which are molecules having more than 200 or longer base pairs playing a significant role in development and association with various diseases in humans such as cancer and other cardiovascular diseases. Some studies outline the cell-specific restriction of lncRNA expression, indicating that these molecules influence differentiation in cell lineages. It has been also found that patterns of cell-specific expression are labeled for species-specific lncRNAs. These research studies outline that cell-specific lncRNAs might have developed to control the fates of species-specific cells. Further studies regarding the development of technologies for measurement of a broad spectrum in ncRNAs and profiling them in research of single cell would play a crucial part in various studies in the future.

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