PMID- 36949761
OWN - NLM
STAT- MEDLINE
DCOM- 20230324
LR  - 20230430
IS  - 2167-8359 (Electronic)
IS  - 2167-8359 (Linking)
VI  - 11
DP  - 2023
TI  - "In the light of evolution:" keratins as exceptional tumor biomarkers.
PG  - e15099
LID - 10.7717/peerj.15099 [doi]
LID - e15099
AB  - Keratins (KRTs) are the intermediate filament-forming proteins of epithelial 
      cells, classified, according to their physicochemical properties, into "soft" and 
      "hard" keratins. They have a key role in several aspects of cancer 
      pathophysiology, including cancer cell invasion and metastasis, and several 
      members of the KRT family serve as diagnostic or prognostic markers. The human 
      genome contains both, functional KRT genes and non-functional KRT pseudogenes, 
      arranged in two uninterrupted clusters on chromosomes 12 and 17. This 
      characteristic renders KRTs ideal for evolutionary studies. Herein, comprehensive 
      phylogenetic analyses of KRT homologous proteins in the genomes of major 
      taxonomic divisions were performed, so as to fill a gap in knowledge regarding 
      the functional implications of keratins in cancer biology among tumor-bearing 
      species. The differential expression profiles of KRTs in diverse types of cancers 
      were investigated by analyzing high-throughput data, as well. Several KRT genes, 
      including the phylogenetically conserved ones, were found to be deregulated 
      across several cancer types and to participate in a common protein-protein 
      interaction network. This indicates that, at least in cancer-bearing species, 
      these genes might have been under similar evolutionary pressure, perhaps to 
      support the same important function(s). In addition, semantic relations between 
      KRTs and cancer were detected through extensive text mining. Therefore, by 
      applying an integrative in silico pipeline, the evolutionary history of KRTs was 
      reconstructed in the context of cancer, and the potential of using non-mammalian 
      species as model organisms in functional studies on human cancer-associated KRT 
      genes was uncovered.
CI  - (c) 2023 Takan et al.
FAU - Takan, Isil
AU  - Takan I
AUID- ORCID: 0000-0002-0269-6625
AD  - Izmir Biomedicine and Genome Center, Izmir, Turkey.
AD  - Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 
      Izmir, Turkey.
FAU - Karakulah, Gokhan
AU  - Karakulah G
AUID- ORCID: 0000-0001-6706-1375
AD  - Izmir Biomedicine and Genome Center, Izmir, Turkey.
AD  - Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 
      Izmir, Turkey.
FAU - Louka, Aikaterini
AU  - Louka A
AD  - DNA Damage Laboratory, Department of Physics, School of Applied Mathematical and 
      Physical Sciences, National Technical University of Athens, Athens, Greece.
AD  - Section of Cell Biology and Biophysics, Department of Biology, School of 
      Sciences, National and Kapodistrian University of Athens, Athens, Greece.
FAU - Pavlopoulou, Athanasia
AU  - Pavlopoulou A
AD  - Izmir Biomedicine and Genome Center, Izmir, Turkey.
AD  - Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 
      Izmir, Turkey.
LA  - eng
PT  - Journal Article
DEP - 20230317
PL  - United States
TA  - PeerJ
JT  - PeerJ
JID - 101603425
RN  - 68238-35-7 (Keratins)
RN  - 0 (Biomarkers, Tumor)
RN  - 0 (Intermediate Filament Proteins)
SB  - IM
MH  - Humans
MH  - *Keratins/genetics
MH  - Phylogeny
MH  - *Biomarkers, Tumor/genetics
MH  - Intermediate Filament Proteins/genetics
MH  - Biological Evolution
PMC - PMC10026720
OTO - NOTNLM
OT  - Cancer
OT  - Comparative genomics
OT  - Data mining
OT  - Evolution
OT  - Gene expression patterns
OT  - Interaction network
OT  - Natural language processing
OT  - Phylogeny
COIS- Gokhan Karakulah is an Academic Editor for PeerJ.
EDAT- 2023/03/24 06:00
MHDA- 2023/03/25 06:00
PMCR- 2023/03/17
CRDT- 2023/03/23 02:14
PHST- 2022/11/11 00:00 [received]
PHST- 2023/02/28 00:00 [accepted]
PHST- 2023/03/23 02:14 [entrez]
PHST- 2023/03/24 06:00 [pubmed]
PHST- 2023/03/25 06:00 [medline]
PHST- 2023/03/17 00:00 [pmc-release]
AID - 15099 [pii]
AID - 10.7717/peerj.15099 [doi]
PST - epublish
SO  - PeerJ. 2023 Mar 17;11:e15099. doi: 10.7717/peerj.15099. eCollection 2023.