Detection of rare cell types and patient prognosis in liver cancer

2022-10
Şengül Babal, Simge
Yıldız, Cemal
Pır, Pınar
Show full item record
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
105
views
31
downloads
Cancer is a disease that emerges as a result of complex aberrant processes involving cells that grow and divide uncontrollably and has many patient-specific characteristics. Mutations in genes or changes in the expression of transcripts produce cellular heterogeneity, cancer cells, and tumors, and finally invade other healthy tissues [1]. Primary liver cancer is the second most lethal malignancy worldwide and comprises many molecularly unique subtypes and a highly diverse microenvironment [2]. Among this diversity (immune cells, malignant cells, non-malignant cells, hepatic cells, etc.) the rarest and difficult to define cell types are dormant and cancer stem cells. Dormant cells are in the dormancy state that have stopped dividing but are ready to reproduce under proper environmental conditions, while cancer stem cells are stem cells with self-renewal, differentiation, and tumorigenicity features [3]. Identification of cellular heterogeneity in liver tumors is an important step toward the prevention of the failure of treatments. In addition, rare cells in liver cancer affect the overall survival, therefore their identification is also crucial. The single-cell transcriptomic landscape of liver cancer can identify the biodiversity of single cells in the tumor. Within the scope of this work, the focus was on the detection of cell types that rarely appear in liver cancer. First, rare cell-specific markers were determined and the tools used for the detection of these cells were compared. The noise and heterogeneity of single-cell cancer data have been important considerations in the analysis pipeline. Following the identification of rare cells in single-cell data, their proportions in the bulk data were analyzed and their effects on overall survival analysis were examined [4]. With the survival models we established, survival times were analyzed and cell types with prognostic characteristics were determined.
Liver cancer, Single-cell analysis, Rare cells, Prognosis
https://hibit2022.ims.metu.edu.tr
https://hdl.handle.net/11511/101996
Graduate School of Informatics, Conference / Seminar

Suggestions

Identification of rare cell types in lung cancer and investigation of their use in prognosis
Yıldız, Cemal; Şengül Babal, Simge; Pir, Pınar (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10)
Cancer is a complex, dynamic and heterogeneous disease. Identification of tumor heterogeneity holds a significant promise not only on tumor classification but also on predicting the prognosis and choosing the right treatment. Therefore, it is essential to investigate tumor heterogeneity in a regular diagnosis procedure. Tumors contain variety of cell types such as malignant cells, non-malignant cells, immune cells, and rare cells (i.e., dormant cells (DRM) and cancer stem cells (CSC))....
Identification of gene mutations involved in drug resistance in liver cancer using RNA-SEQ data analysis
Shojaei, Mona; Atalay, Rengül; Acar, Aybar Can; Department of Bioinformatics (2016)
A significant concern in cancer research is the detection of cancer associated somatic mutations. Liver cancer is the 5th most common and 2nd deadliest cancer in the world. Several somatic mutations were previously reported in liver cancer but their relations to chemotherapeutic response was not studied in detail. In this study, the relationship between mutation status and drug treatment response of well-differentiated Huh7 and poorly-differentiated Mahlavu liver cancer cells were analyzed. The RNA-Seq data...
Effects of novel compound derived from vitamin e on prostate cancer cell line
Ergen, Nuri; Severcan, Feride; Department of Biology (2016)
Cancer is a complex disease characterized by uncontrolled cell proliferation, invasion and metastasis. It is known that vitamins having high antioxidant capacity, like vitamin A, C and E, play important roles in adjuvant therapy and as cancer protective agents. Vitamin E is a group of fat soluble antioxidant nutrients consisting of tocopherols and tocotrienols. Various research has been performed on the utility of vitamin E derivatives on cancer treatment. Energy metabolism of cells alters during cancer pro...
Capture of circulating tumor cells from blood on modified gold surfaces inside the microfluidic channels
Çetin, Didem; Külah, Haluk; Department of Biomedical Engineering (2019)
Detection of circulating tumor cells (CTCs) from the bloodstream has a critical role in diagnosing and treatment of cancer. However, the number of CTCs in blood compared to other blood cells are extremely rare. In this thesis, various surface modifications strategies for detection of CTCs are studied in order to be used in the microfluidic detection systems. Functionalizing the gold surface with Self Assembled Monolayers (SAMs) used for attaching the EpCAM antibodies, which made possible to immobilize EpCAM...
Analysis of 3'UTR shortening events in breast cancer
Baloğlu, Onur; Can, Tolga; Department of Bioinformatics (2013)
Cancer is the collective term used to describe a diverse group of diseases that share certain hallmarks, which in turn enables the affected cells to sustain an uncontrolled cell growth. Despite the increasing efforts and advances in cancer therapies, cancers are still responsible for approximately 10% of all the deaths worldwide. Furthermore, the increase in the average human lifespan will further contribute to the cancer incidences. This brings the necessity to focus our efforts on early detection and effe...
Citation Formats
S. Şengül Babal, C. Yıldız, and P. Pır, “Detection of rare cell types and patient prognosis in liver cancer,” Erdemli, Mersin, TÜRKİYE, 2022, p. 3015, Accessed: 00, 2023. [Online]. Available: https://hibit2022.ims.metu.edu.tr.
METU IIS - Integrated Information Service open@metu.edu.tr