A Detailed Overview About the Single-Cell Analyses of Solid Tumors Focusing on Colorectal Cancer

Kothalawala, William Jayasekara; Barták, Barbara Kinga; Nagy, Zsófia Brigitta; Zsigrai, Sára; Szigeti, Krisztina Andrea; Valcz, Gábor; Takács, István; Kalmár, Alexandra; Molnár, Béla

doi:10.3389/pore.2022.1610342

Cited by 6 publications

(7 citation statements)

References 75 publications

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“…This technology offers a better approach for detecting multiple genetic changes with a minimal amount of DNA. What is particularly important is that it is also possible to sequence RNA transcripts from single cells (scRNA-Seq) [ 46 ].…”

Section: Methods To Assess Cell Proliferation In Colorectal Cancermentioning

confidence: 99%

“…The correlation between mRNA expression and protein translation is not always guaranteed, especially in heterogeneous tumors (including CRC), prompting the need for more sophisticated molecular techniques to assess the actual expression of biomarkers. In addition, studying complex interactions between different RNA types requires modern technology (e.g., high-throughput CLIP-Seq, degradome-Seq, and RNA–RNA interactome sequencing methods) [ 46 , 320 ].…”

Section: Methods To Assess Cell Proliferation In Colorectal Cancermentioning

confidence: 99%

“…Several publications have summarized the data on the clinical application of NGS technology in CRC [ 46 , 321 , 322 , 324 , 342 , 343 ]. Additionally, NGS allows for the identification of unknown interactions between genetic variation in CRCs and the relationship of CRCs to the structure of the gut microbiota composition [ 342 ].…”

Section: Methods To Assess Cell Proliferation In Colorectal Cancermentioning

confidence: 99%

“…The presence of CIN in tumors results in the accumulation of mutations in oncogenes and tumor suppressor genes ( APC , TP53, KRAS , and BRAF ). However, more than 24 mutated genes have currently been associated with CRC [ 45 ], with the number possibly higher due to the development of modern testing techniques including single-cell next-generation sequencing (NGS) [ 46 ].…”

Section: Molecular Mechanisms Of Colorectal Cancerogenesismentioning

confidence: 99%

“…The assessment of proliferation in CRC, especially in a prognostic and diagnostic context, has been the focus of scientists and clinicians for a number of years. The difficulty in interpreting many findings in this area is related to the enormous heterogeneity of the tumor in terms of genotype, phenotype, morphology, and cell metabolism [ 46 ]. Interestingly, while epithelial cells in the large intestine have a longer lifespan and proliferate slower than in the small intestine (5–21 days versus 3–4 days) [ 71 , 72 ], colon cancer is far more common than small intestinal cancers (10% versus <1% of all cancers) [ 4 ].…”

Section: Cellular Proliferation Models Versus Colorectal Carcinogenes...mentioning

confidence: 99%

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Prognostic Biomarkers of Cell Proliferation in Colorectal Cancer (CRC): From Immunohistochemistry to Molecular Biology Techniques

Kasprzak

2023

Cancers

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Colorectal cancer (CRC) is one of the most common and severe malignancies worldwide. Recent advances in diagnostic methods allow for more accurate identification and detection of several molecular biomarkers associated with this cancer. Nonetheless, non-invasive and effective prognostic and predictive testing in CRC patients remains challenging. Classical prognostic genetic markers comprise mutations in several genes (e.g., APC, KRAS/BRAF, TGF-β, and TP53). Furthermore, CIN and MSI serve as chromosomal markers, while epigenetic markers include CIMP and many other candidates such as SERP, p14, p16, LINE-1, and RASSF1A. The number of proliferation-related long non-coding RNAs (e.g., SNHG1, SNHG6, MALAT-1, CRNDE) and microRNAs (e.g., miR-20a, miR-21, miR-143, miR-145, miR-181a/b) that could serve as potential CRC markers has also steadily increased in recent years. Among the immunohistochemical (IHC) proliferative markers, the prognostic value regarding the patients’ overall survival (OS) or disease-free survival (DFS) has been confirmed for thymidylate synthase (TS), cyclin B1, cyclin D1, proliferating cell nuclear antigen (PCNA), and Ki-67. In most cases, the overexpression of these markers in tissues was related to worse OS and DFS. However, slowly proliferating cells should also be considered in CRC therapy (especially radiotherapy) as they could represent a reservoir from which cells are recruited to replenish the rapidly proliferating population in response to cell-damaging factors. Considering the above, the aim of this article is to review the most common proliferative markers assessed using various methods including IHC and selected molecular biology techniques (e.g., qRT-PCR, in situ hybridization, RNA/DNA sequencing, next-generation sequencing) as prognostic and predictive markers in CRC.

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Section: Methods To Assess Cell Proliferation In Colorectal Cancermentioning

confidence: 99%

Section: Methods To Assess Cell Proliferation In Colorectal Cancermentioning

confidence: 99%

Section: Methods To Assess Cell Proliferation In Colorectal Cancermentioning

confidence: 99%

Section: Molecular Mechanisms Of Colorectal Cancerogenesismentioning

confidence: 99%

Section: Cellular Proliferation Models Versus Colorectal Carcinogenes...mentioning

confidence: 99%

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Prognostic Biomarkers of Cell Proliferation in Colorectal Cancer (CRC): From Immunohistochemistry to Molecular Biology Techniques

Kasprzak

2023

Cancers

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Whole genome sequencing resolves 10 years diagnostic odyssey in familiar myxoma

Pálla,

Tőke,

Bozsik

et al. 2023

Sci Rep

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Carney complex (CNC) is an ultrarare disorder causing cutaneous and cardiac myxomas, primary pigmented nodular adrenocortical disease, hypophyseal adenoma, and gonadal tumours. Genetic alterations are often missed under routine genetic testing. Pathogenic variants in PRKAR1A are identified in most cases, while large exonic or chromosomal deletions have only been reported in a few cases. Our aim was to identify the causal genetic alteration in our kindred with a clinical diagnosis of CNC and prove its pathogenic role by functional investigation. Targeted testing of PRKAR1A gene, whole exome and whole genome sequencing (WGS) were performed in the proband, one clinically affected and one unaffected relative. WGS identified a novel, large, 10,662 bp (10.6 kbp; LRG_514t1:c.-10403_-7 + 265del; hg19, chr17:g.66498293_66508954del) deletion in the promoter of PRKAR1A in heterozygous form in the affected family members. The exact breakpoints and the increased enzyme activity in deletion carriers compared to wild type carrier were proved. Segregation analysis and functional evaluation of PKA activity confirmed the pathogenic role of this alteration. A novel deletion upstream of the PRKAR1A gene was proved to be the cause of CNC. Our study underlines the need for WGS in molecular genetic testing of patients with monogenic disorders where conventional genetic analysis fails.

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Droplets microfluidics platform—A tool for single cell research

Cheng

et al. 2023

Front. Bioeng. Biotechnol.

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Cells are the most basic structural and functional units of living organisms. Studies of cell growth, differentiation, apoptosis, and cell-cell interactions can help scientists understand the mysteries of living systems. However, there is considerable heterogeneity among cells. Great differences between individuals can be found even within the same cell cluster. Cell heterogeneity can only be clearly expressed and distinguished at the level of single cells. The development of droplet microfluidics technology opens up a new chapter for single-cell analysis. Microfluidic chips can produce many nanoscale monodisperse droplets, which can be used as small isolated micro-laboratories for various high-throughput, precise single-cell analyses. Moreover, gel droplets with good biocompatibility can be used in single-cell cultures and coupled with biomolecules for various downstream analyses of cellular metabolites. The droplets are also maneuverable; through physical and chemical forces, droplets can be divided, fused, and sorted to realize single-cell screening and other related studies. This review describes the channel design, droplet generation, and control technology of droplet microfluidics and gives a detailed overview of the application of droplet microfluidics in single-cell culture, single-cell screening, single-cell detection, and other aspects. Moreover, we provide a recent review of the application of droplet microfluidics in tumor single-cell immunoassays, describe in detail the advantages of microfluidics in tumor research, and predict the development of droplet microfluidics at the single-cell level.

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A Detailed Overview About the Single-Cell Analyses of Solid Tumors Focusing on Colorectal Cancer

Cited by 6 publications

References 75 publications

Prognostic Biomarkers of Cell Proliferation in Colorectal Cancer (CRC): From Immunohistochemistry to Molecular Biology Techniques

Prognostic Biomarkers of Cell Proliferation in Colorectal Cancer (CRC): From Immunohistochemistry to Molecular Biology Techniques

Whole genome sequencing resolves 10 years diagnostic odyssey in familiar myxoma

Droplets microfluidics platform—A tool for single cell research

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