THE HUMAN CELL


Intermediate filaments are one of the three types of cytoskeletons in the cell. Their main role lies in providing mechanical support to the cell, as well as participating in organization of the chromatin in the cell nucleus. The latter is achieved by anchoring the chromatin to the nuclear lamina that lines the inner part of the nuclear membrane. Intermediate filaments may also be involved in other cellular processes such as adhesion, migration and tumor invasion (Leduc C et al, 2015). For examples of proteins localizing to the intermediate filaments, see Figure 1.

Of all human proteins, 180 (1%) have been experimentally shown to localize to the intermediate filaments in the Cell Atlas (Figure 2). A Gene Ontology (GO)-based analysis shows molecular functions related to intermediate filament binding and cytoskeleton structural component are highly enriched in the intermediate filament proteome. Many of the proteins localized to intermediate filaments are also detected in additional cellular compartments, the most common ones being the cytosol and the nucleus.

GFAP - U-2 OS
GFAP - HEK 293
NES - U-2 OS


KRT13 - A-431
KRT19 - RT4
DES - RH-30

Figure 1. Examples of proteins localized to the intermediate filaments.
GFAP (detected in U-2 OS and HEK 293 cells) and NES (detected in U-2 OS cells). KRT13 (detected in A-431cells), KRT19 (detected in RT-4 cells) and DES (detected in RH-30 cells).

  • 1% (180 proteins) of all human proteins have been experimentally detected in the intermediate filaments by the Human Protein Atlas.
  • 36 proteins in the intermediate filaments are supported by experimental evidence and out of these 8 proteins are validated by the Human Protein Atlas.
  • 122 proteins in the intermediate filaments have multiple locations.
  • 63 proteins in the intermediate filaments show a cell to cell variation. Of these 58 show a variation in intensity and 6 a spatial variation.
  • Proteins are mainly involved in providing mechanical support to cells.

Figure 2. 1% of all human protein-coding genes encode proteins localized to the intermediate filaments. Each bar is clickable and gives a search result of proteins that belong to the selected category.

The structure of the intermediate filaments


Intermediate filaments are homologous across species, and known proteins are often well studied. Unlike the other cytoskeletons in the cell (microtubules and actin filaments), intermediate filaments consist of non-polar filaments, which are approximately 10 nm in diameter. Although it has been demonstrated that intermediate filaments are continually undergoing a dynamic assembly/disassembly in the cell, the mechanism of this turnover has yet to be further characterized. This dynamic remodeling is necessary for intermediate filaments to adjust to the cell's needs, in terms of mechanical support, flexibility or attachment to the surrounding matrix (Robert A et al, 2016).

Intermediate filament proteins are classified into subgroups, although an agreement has not yet been reached whether there are five or six subgroups, based on their structure and homology: Keratins are categorized into type I and II (acidic and basic), whereas vimentin (VIM), desmin (DES), glial fibrillary acidic protein (GFAP) and peripherin (PRPH) are categorized as type III. Neurofilaments are categorized as type IV and lamins as type V (Fuchs E et al, 1994). The sixth subgroup would contain nestin (NES) and synemin (SYNM) (Leduc C et al, 2015), but they are often also categorized as type IV (Robert A et al, 2016, Fuchs E et al, 1994). For a curated list of protein markers for intermediate filaments, see Table 1. Figure 3 shows immunofluorescent stainings of keratins in different cell types.

Table 1. Selection of proteins suitable as markers for the intermediate filaments or its substructures.

Gene

Description

Substructure

KRT19 Keratin 19, type I Intermediate filaments
KRT4 Keratin 4, type II Intermediate filaments
DES Desmin Intermediate filaments
NES Nestin Intermediate filaments
KRT17 Keratin 17, type I Intermediate filaments
KRT13 Keratin 13, type I Intermediate filaments

KRT17 - U-2 OS
KRT19 - MCF7
KRT14 - HaCaT

Figure 3. Examples of the morphology of intermediate filaments in different cell lines, represented by immunofluorescent staining of keratins: KRT17 in U-2 OS cells, KRT19 in MCF-7 cells and KRT14 in HaCaT cells.

The function of the intermediate filaments


In human cells and tissue, intermediate filaments are crucial in providing physical support and stabilizing the cell structure, enabling them to withstand mechanical stress and tension. A subgroup of intermediate filaments, VIM, has been shown in vitro to exhibit different properties when exposed to increasing levels of strain. When increasing the strain the filaments are exposed to, the structures stiffen, resisting breakage (Janmey PA et al, 1991, Köster S et al, 2015). There may be a dynamic rearrangement of intermediate filaments, responding to changes in cell motility, as it has been show that they are organized closer to the nuclear membrane in immobile cells, whereas in migrating cells they are aligned with lamella in the cell's leading edge (Leduc C et al, 2015). There are more than 70 genes known to be coding for intermediate filaments (Lowery J et al, 2015), and the UniProtKB database lists approximately 200 proteins in humans as localized to the intermediate filaments. In Table 2, the 10 most highly expressed genes coding for intermediate filament proteins are summarized. Although most intermediate filament proteins are cytoplasmic, there is a smaller group, known as lamins, localizing to the nucleus. In the Human Protein Atlas, nuclear lamins show staining of the nuclear membrane. Both mutations in genes coding for cytoplasmic intermediate filaments such as keratins, as well as genes coding for nuclear lamins have been linked to severe diseases. The review article by Herrmann et al gives an overview of the field (Herrmann H et al, 2007). A Gene Ontology (GO)-based analysis of the enriched genes localized to the intermediate filament proteome shows terms for both biological processes (Figure 4a) and molecular function (Figure 4b) that are well in-line with the known functions of the intermediate filaments.

Figure 4a. Gene Ontology-based enrichment analysis for the intermediate filaments proteome showing the significantly enriched terms for the GO domain Biological Process. Each bar is clickable and gives a search result of proteins that belong to the selected category.

Figure 4b. Gene Ontology-based enrichment analysis for the intermediate filaments proteome showing the significantly enriched terms for the GO domain Molecular Function. Each bar is clickable and gives a search result of proteins that belong to the selected category.

Table 2. Highly expressed single localizing intermediate filaments proteins across different cell lines.

Gene

Description

Average TPM

VIM Vimentin 1771
KRT8 Keratin 8, type II 849
KRT17 Keratin 17, type I 484
KRT19 Keratin 19, type I 360
KRT14 Keratin 14, type I 104
KRT13 Keratin 13, type I 67
NES Nestin 59
PJA2 Praja ring finger 2, E3 ubiquitin protein ligase 44
KRT80 Keratin 80, type II 28
S100A8 S100 calcium binding protein A8 13

Intermediate filament proteins with multiple locations


Approximately 68% (n=122) of the intermediate filament proteome detected in the Cell Atlas also localize to other compartments in the cell. The cytoscape network plot (Figure 5) shows that the most common locations shared with intermediate filaments are the nucleus and cytosol. This could possibly indicate that some of the stainings are of soluble intermediate filament subunits, that have not assembled into filaments, or proteins that are connecting intermediate filaments to other cellular structures.

Figure 5. Interactive network plot of intermediate filament proteins with multiple localizations. The numbers in the connecting nodes show the proteins that are localized to intermediate filaments and to one or more additional locations. Only connecting nodes containing more than one protein and at least 0.5% of proteins in the intermediate filament proteome are shown. The circle sizes are related to the number of proteins. The cyan colored nodes show combinations that are significantly overrepresented, while magenta colored nodes show combinations that are significantly underrepresented as compared to the probability of observing that combination based on the frequency of each annotation and a hypergeometric test (p≤0.05). Note that this calculation is only done for proteins with dual localizations. Each node is clickable and results in a list of all proteins that are found in the connected organelles.

Expression levels of intermediate filament proteins in tissue


The transcriptome analysis (Figure 6) shows that intermediate filament proteins are significantly less likely to be expressed at RNA level in all tissue types, compared to the background of all genes with protein data in the Cell Atlas. Instead, they show a statistically significant distribution of being tissue enriched, or having mixed expression patterns. This is well in-line with the known cell type dependent expression pattern of intermediate filaments (Herrmann H et al, 2007).

Figure 6. Bar plot showing the distribution of expression categories, based on the gene expression in tissues, for intermediate filaments-associated protein-coding genes compared to all genes in the Cell Atlas. Asterisk marks statistically significant deviation(s) (p≤0.05) from all other organelles based on a binomial statistical test. Each bar is clickable and gives a search result of proteins that belong to the selected category.

Relevant links and publications


Fuchs E et al, 1994. Intermediate filaments: structure, dynamics, function, and disease. Annu Rev Biochem.
PubMed: 7979242 DOI: 10.1146/annurev.bi.63.070194.002021

Herrmann H et al, 2007. Intermediate filaments: from cell architecture to nanomechanics. Nat Rev Mol Cell Biol.
PubMed: 17551517 DOI: 10.1038/nrm2197

Janmey PA et al, 1991. Viscoelastic properties of vimentin compared with other filamentous biopolymer networks. J Cell Biol.
PubMed: 2007620 

Köster S et al, 2015. Intermediate filament mechanics in vitro and in the cell: from coiled coils to filaments, fibers and networks. Curr Opin Cell Biol.
PubMed: 25621895 DOI: 10.1016/j.ceb.2015.01.001

Leduc C et al, 2015. Intermediate filaments in cell migration and invasion: the unusual suspects. Curr Opin Cell Biol.
PubMed: 25660489 DOI: 10.1016/j.ceb.2015.01.005

Lowery J et al, 2015. Intermediate Filaments Play a Pivotal Role in Regulating Cell Architecture and Function. J Biol Chem.
PubMed: 25957409 DOI: 10.1074/jbc.R115.640359

Robert A et al, 2016. Intermediate filament dynamics: What we can see now and why it matters. Bioessays.
PubMed: 26763143 DOI: 10.1002/bies.201500142