Basic anatomy and tumor biology of the RPS6KA6 gene that encodes the p90 ribosomal S6 kinase-4

Updating mRNA variants of the human RSK4 gene and their expression in different stressed situations

We determined RNA spectrum of the human RSK4 (hRSK4) gene (also called RPS6KA6) and identified 29 novel mRNA variants derived from alternative splicing, which, plus the NCBI-documented ones and the five we reported previously, totaled 50 hRSK4 RNAs that, by our bioinformatics analyses, encode 35 hRSK4 protein isoforms of 35-762 amino acids. Many of the mRNAs are bicistronic or tricistronic for hRSK4. The NCBI-normalized NM_014496.5 and the protein it encodes are designated herein as the Wt-1 mRNA and protein, respectively, whereas the NM_001330512.1 and the long protein it encodes are designated as the Wt-2 mRNA and protein, respectively. Many of the mRNA variants responded differently to different situations of stress, including serum starvation, a febrile temperature, treatment with ethanol or ethanol-extracted clove buds (an herbal medicine), whereas the same stressed situation often caused quite different alterations among different mRNA variants in different cell lines. Mosifloxacin, an antibiotics and also a functional inhibitor of hRSK4, could inhibit the expression of certain hRSK4 mRNA variants. The hRSK4 gene likely uses alternative splicing as a handy tool to adapt to different stressed situations, and the mRNA and protein multiplicities may partly explain the incongruous literature on its expression and comports.

Differential Expression of RSK4 Transcript Isoforms in Cancer and Its Clinical Relevance

While we previously revealed RSK4 as a therapeutic target in lung and bladder cancers, the wider role of this kinase in other cancers remains controversial. Indeed, other reports instead proposed RSK4 as a tumour suppressor in colorectal and gastric cancers and are contradictory in breast malignancies. One explanation for these discrepancies may be the expression of different RSK4 isoforms across cancers. Four RNAs are produced from the RSK4 gene, with two being protein-coding. Here, we analysed the expression of the latter across 30 normal and 33 cancer tissue types from the combined GTEx/TCGA dataset and correlated it with clinical features. This revealed the expression of RSK4 isoforms 1 and 2 to be independent prognostic factors for patient survival, pathological stage, cancer metastasis, recurrence, and immune infiltration in brain, stomach, cervical, and kidney cancers. However, we found that upregulation of either isoform can equally be associated with good or bad prognosis depending on the cancer type, and changes in the expression ratio of isoforms fail to predict clinical outcome. Hence, differential isoform expression alone cannot explain the contradictory roles of RSK4 in cancers, and further research is needed to highlight the underlying mechanisms for the context-dependent function of this kinase.

ACTB and GAPDH appear at multiple SDS-PAGE positions, thus not suitable as reference genes for determining protein loading in techniques like Western blotting

We performed polyacrylamide gel electrophoresis of human proteins with sodium dodecyl sulfate, isolated proteins at multiple positions, and then used liquid chromatography and tandem mass spectrometry (LC-MS/MS) to determine the protein identities. Although beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are 41.7 and 36 kDa proteins, respectively, LC-MS/MS identified their peptides at all the positions studied. The National Center for Biotechnology Information (USA) database lists only one ACTB mRNA but five GAPDH mRNAs and one noncoding RNA. The five GAPDH mRNAs encode three protein isoforms, while our bioinformatics analysis identified a 17.6 kDa isoform encoded by the noncoding RNA. All LC-MS/MS-identified GAPDH peptides at all positions studied are unique, but some of the identified ACTB peptides are shared by ACTC1, ACTBL2, POTEF, POTEE, POTEI, and POTEJ. ACTC1 and ACTBL2 belong to the ACT family with significant similarities to ACTB in protein sequence, whereas the four POTEs are ACTB-containing chimeric genes with the C-terminus of their proteins highly similar to the ACTB. These data lead us to conclude that GAPDH and ACTB are poor reference genes for determining the protein loading in such techniques as Western blotting, a leading role these two genes have been playing for decades in biomedical research.

Comprehensive characterization of pathological stage-related genes of papillary thyroid cancer along with survival prediction

It is crucial to understand the differences across papillary thyroid cancer (PTC) stages, so as to provide a basis for individualized treatments. Here, comprehensive function characterization of PTC stage‐related genes was performed and a new prognostic signature was developed for advanced patients. Two gene modules were confirmed to be closely associated with PTC stages and further six hub genes were identified that yield excellent diagnostic efficiency between tumour and normal tissues. Genetic alteration analysis indicates that they are much conservative since mutations in the DNA of them rarely occur, but changes of DNA methylation on these six genes show that 12 DNA methylation sites are significantly associated with their corresponding genes' expression. Validation data set testing also suggests that these six stage‐related hub genes would be probably potential biomarkers for marking four stages. Subsequently, a 21‐mRNA‐based prognostic risk model was constructed for PTC stage III/IV patients and it could effectively predict the survival of patients with strong prognostic ability. Functional analysis shows that differential expression genes between high‐ and low‐risk patients would promote the progress of PTC to some extent. Moreover, tumour microenvironment (TME) of high‐risk patients may be more conducive to tumour growth by ESTIMATE analysis.

At elevated temperatures, heat shock protein genes show altered ratios of different RNAs and expression of new RNAs, including several novel HSPB1 mRNAs encoding HSP27 protein isoforms

Heat shock proteins (HSP) serve as chaperones to maintain the physiological conformation and function of numerous cellular proteins when the ambient temperature is increased. To determine how accurate the general assumption that HSP gene expression is increased in febrile situations is, the RNA levels of the HSF1 (heat shock transcription factor 1) gene and certain HSP genes were determined in three cell lines cultured at 37˚C or 39˚C for three days. At 39˚C, the expression of HSF1, HSPB1, HSP90AA1 and HSP70A1L genes demonstrated complex changes in the ratios of expression levels between different RNA variants of the same gene. Several older versions of the RNAs of certain HSP genes that have been replaced by a newer version in the National Center for Biotechnology Information database were also detected, indicating that the older versions are actually RNA variants of these genes. The present study cloned four new RNA variants of the HSP27-encoding HSPB1 gene, which together encode three short HSP27 peptides. Reanalysis of the proteomics data from our previous studies also demonstrated that proteins from certain HSP genes could be detected simultaneously at multiple positions using SDS-PAGE, suggesting that these genes may engender multiple protein isoforms. These results collectively suggested that, besides increasing their expression, certain HSP and associated genes also use alternative transcription start sites to produce multiple RNA transcripts and use alternative splicing of a transcript to produce multiple mature RNAs, as important mechanisms for responding to an increased ambient temperature in vitro.

Ribosomal S6 protein kinase 4 promotes radioresistance in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive cancers and is highly resistant to current treatments. ESCC harbors a subpopulation of cells exhibiting cancer stem-like cell (CSC) properties that contribute to therapeutic resistance including radioresistance, but the molecular mechanisms in ESCC CSCs are currently unknown. Here, we report that ribosomal S6 protein kinase 4 (RSK4) plays a pivotal role in promoting CSC properties and radioresistance in ESCC. RSK4 was highly expressed in ESCC CSCs and associated with radioresistance and poor survival in patients with ESCC. RSK4 was found to be a direct downstream transcriptional target of ΔNp63α, the main p63 isoform, which is frequently amplified in ESCC. RSK4 activated the β-catenin signaling pathway through direct phosphorylation of GSK-3β at Ser9. Pharmacologic inhibition of RSK4 effectively reduced CSC properties and improved radiosensitivity in both nude mouse and patient-derived xenograft models. Collectively, our results strongly suggest that the ΔNp63α/RSK4/GSK-3β axis plays a key role in driving CSC properties and radioresistance in ESCC, indicating that RSK4 is a promising therapeutic target for ESCC treatment.

Overexpression of RSK4 reverses doxorubicin resistance in human breast cancer cells via PI3K/AKT signalling pathway

Doxorubicin (DOX) is one of the most effective chemotherapy drugs for the treatment of metastatic breast cancer (BC), but drug resistance becomes an obstacle to treatment. This study aims to investigate the role of Ribosomal S6 protein kinase 4 (RSK4) in regulating BC resistance to DOX. We first used Kaplan-Meier Plotter to identify the prognostic roles of RSK4 in BC. DOX-resistant BC cells (MCF-7/DOX) were constructed and the expression of RSK4 was determined by reverse transcript polymerase chain reaction and western blot. Subsequently, we overexpressed the RSK4 in MCF-7/DOX cells, and measured drug resistance, colony formation, cell migration, invasion ability and cell apoptosis after transfection. In addition, western blot was used to explore the expression of apoptosis-related proteins and BC-resistance protein. Effects of RSK4 on activation of the PI3K/AKT signalling pathway were also tested. Furthermore, tumour xenograft in nude mice was constructed to observe the effect of RSK4 overexpression on tumour growth in vivo. In conclusion, RSK4 was positively correlated with survival rate in BC patients, which is lowly expressed in MCF-7/DOX. Meanwhile, the overexpression of RSK4 may inhibit drug resistance, cell migration, invasion, apoptosis and tumour growth. RSK4 may effectively attenuate DOX resistance in BC by inhibiting the PI3K/AKT signalling pathway.

MiR-548d-3p Promotes Gastric Cancer by Targeting RSK4

Purpose

Previous studies have demonstrated that RSK4 inhibits the proliferation of gastric cancer cells and the occurrence of tumors. However, to date, studies involving microRNAs (miRNAs) that target RSK4 have rarely been reported. Thus, this study aimed to investigate the miRNAs that target RSK4.

Materials and Methods

We screened miRNAs related to RSK4 in miRDB, microT-CDS, TargetScan, and mirDIP databases and found 18 miRNAs. We chose miR-548d-3p for follow-up research, identified the interaction site in RSK4 by comparing the sequence, and mutated it. Thereafter, we used the dual-luciferase reporter system, real-time PCR (RT-PCR), and Western blotting to assess the effect of miR-548d-3p on RSK4. The proliferation, apoptosis, migration, and invasion of gastric cancer cells were evaluated using MTT assay, propidium iodide (PI), EdU, annexin V-FITC/PI apoptosis detection kit, wound healing assay, and transwell assay after overexpression of miR-548d-3p and RSK4. Finally, a nude mouse tumorigenesis experiment was conducted to explore the role of RSK4-targeting miR-548d-3p in tumorigenesis.

Results

miR-548d-3p negatively regulated the expression of RSK4, resulting in suppressed apoptosis, enhanced proliferation, migration, and invasion of gastric cancer cells, and accelerated tumor growth. In addition, an increase in miR-548d-3p expression enhanced the mRNA levels of CDK2, cyclin A1, cyclin D1, Bax, Bcl-2, N-cadherin, and Vimentin, and decreased E-cadherin mRNA levels by targeting RSK4.

Conclusion

miR-548d-3p promotes gastric cancer by lowering the expression of RSK4.

Effect of RSK4 on Biological Characteristics of Gastric Cancer

Purpose

Gastric cancer is one of the most common cancers with high mortality. Emerging evidences show that ribosomal s6 kinase4 (RSK4) may be an anti-oncogene in several types of cancers, while its function in GC is still unclear. In the present study, we investigated the role of RSK4 in GC progression using MGC-803 and HGC-27 cell lines in vitro and in vivo.

Methods

The expression of RSK4 in gastric cancer cells was evaluated using RT-qPCR and Western blot analysis. We transfected cells with RSK4 siRNA to reduce the expression of RSK4 and then evaluated the effect of RSK4 on cellular function. MTT and cell cycle assays were used to study its effect on cell growth. Flow cytometry was used to evaluate cell apoptosis. Wound healing and Transwell assays were performed to investigate metastasis. Stable cell lines with or without RSK4 knockdown were constructed with lentivirus and tumor-bearing mice were used to investigate the effect of RSK4 on cancer progression.

Results

The results revealed that reduction of RSK4 expression inhibited cell apoptosis and promoted cell proliferation, migration, and invasion. Additionally, RSK4 knockdown promoted tumorigenesis in vivo.

Conclusion

Our study demonstrated that RSK4 serves as a tumor suppressor in GC.

Estradiol promotes the progression of ER+ breast cancer through methylation-mediated RSK4 inactivation

Background: It’s well documented that estrogen plays a vital role in breast cancer progression, but the molecular mechanisms underlying it still remains incompletely clear. This study aimed to explore whether ribosomal protein S6 kinase 4 (RSK4) was involved in estrogen-induced breast cancer development and its underlying mechanism.

Methods: The expressions of estrogen receptor (ER) and RSK4 were assessed by immunohistochemistry, RT-PCR and Western blotting. The methylation of RSK4 promoter was evaluated by bisulfite genomic sequencing. MTT, clone formation, flow cytometry and Transwell chamber assays were performed to detect cell proliferation, clone formation, apoptosis and invasion abilities. Luciferase gene reporter assay was used to detect the transcriptional activity of RSK4. The expressions of methyltransferases, such as DNMT1, DNMT3A and DNMT3B were tested by Western blotting.

Results: ER expression and RSK4 methylation were significantly elevated in ER positive (ER+) breast cancer tissues and MCF-7 cells, whereas RSK4 expression was reduced. 17β-estradiol (E2) treatment obviously decreased RSK4 expression and transcriptional activity, as well as promoted cell proliferation, clone formation and invasion and reduced cell apoptosis in ER+ MCF-7 cells. Furthermore, E2 reduced RSK4 expression through promoting DNMT3B-induced RSK4 methylation.

Conclusion:  In summary, the present study reveals that estrogen promotes the progression of breast cancer through methylation-mediated RSK4 inactivation in ER+ breast cancer. Our study might provide a novel target for the treatment of ER+ breast cancer.

Effect of RSK4 on biological characteristics of colorectal cancer

Background

This study aimed to investigate the expression of P90 Ribosomal Protein S6 kinase 4 (RSK4) in colorectal cancer cells and its biological function.

Methods

We selected early SW480 and HCT116 colorectal cancer cell lines, using Lipofectamine™ 2000 transfection reagent carrying RSK4 gene transfected into cells to establish the colorectal cancer cell lines with high expression of RSK4. RT-PCR and western blot (WB) analysis confirmed RSK4 expression in SW480 and HCT116 cancer cell lines. We used methylthiazoltetrazolium (MTT) assay and flow cytometry to detect the proliferation of colorectal cancer cells. After transfection of RSK4, the effect of RSK4 on the RNA levels associated with epithelial–mesenchymal transition (EMT) of colorectal cancer cells was analyzed by real-time fluorescence quantitative PCR and the expression of EMT-related protein was detected by WB analysis.

Results

After transfection of RSK4 overexpression, the MTT assay detected that RSK4 could significantly inhibit the growth of colorectal cancer cells in vitro; flow cytometry detected that S-phase cells decreased significantly, and G0/1 cells increased significantly (P < 0.05). The invasion ability of SW480 and HCT116 cells transfected with RSK4 was markedly lower than that in the control group, and the difference was statistically significant (P < 0.05). Fluorescent quantitative PCR and WB analysis showed that the expression of EMT-associated molecular E-cadherin was remarkably increased and the expression of Snail was significantly decreased (P < 0.01).

Conclusion

RSK4 gene in colorectal cancer cell lines with low expression of RSK4 after transfection can inhibit the growth and invasion of tumor cells. RSK4 gene may inhibit EMT and inhibit metastasis of colorectal cancer cells, may be a potential tumor suppressor gene and inhibit tumor distant metastasis, and may provide the biological basis for new therapeutic targets.

Clinicopathological significance of ribosomal protein S6 kinase A6 in lung squamous cell carcinoma: an immunohistochemical and RNA-seq study

Ribosomal protein S6 kinase A6 (RPS6KA6) is a downstream factor of the ERK-MAPK pathway and has been extensively studied in various types of cancer. However, the role of RPS6KA6 in lung squamous cell carcinoma (LUSC) remains unclear. This study investigated expression of the RPS6KA6 and its clinicopathological correlation with LUSC and explored genetic alterations in the ribosomal protein S6 kinase (RSK) family in LUSC and their impact on the survival of patients. Expression of the RPS6KA6 protein in 175 LUSC samples and 30 normal lung tissues samples was determined by immunohistochemistry (IHC). RPS6KA6 protein expression in the LUSC tissues was significantly higher compared with that in the normal lung tissues (P=0.017). Overexpression of RPS6KA6 protein correlated with tumor size (r=0.260, P=0.001), lymph node metastasis (r=0.683, P<0.001), and TNM stage (r=0.378, P<0.001). RPS6KA6 RNA-seq data were obtained from the Cancer Genome Atlas (TCGA) and ONCOMINE database. RPS6KA6 mRNA expression in the LUSC tissues was significantly higher than that in paired noncancerous samples (TCGA: P=0.005; ONCOMINE: P=0.018). According to the cBioPortal online software, three detecting methods, including Seqv2, Array and U133, identified that the frequency of the genetic alterations in the RSKs in LUSC were 77%, 44%, and 42%, respectively. However, survival analysis of LUSC patients with or without RSKs genetic alterations reached no statistical significance. This study suggests that RPS6KA6 may be an oncogene in LUSC, and that expression of the RPS6KA6 protein is associated with the progression of LUSC. The RSK genes are frequently altered in LUSC, but the alterations have no significant effect on the survival of patients.

While it is not deliberate, much of today's biomedical research contains logical and technical flaws, showing a need for corrective action

Biomedical research has advanced swiftly in recent decades, largely due to progress in biotechnology. However, this rapid spread of new, and not always-fully understood, technology has also created a lot of false or irreproducible data and artifacts, which sometimes have led to erroneous conclusions. When describing various scientific issues, scientists have developed a habit of saying "on one hand… but on the other hand…", because discrepant data and conclusions have become omnipresent. One reason for this problematic situation is that we are not always thoughtful enough in study design, and sometimes lack enough philosophical contemplation. Another major reason is that we are too rushed in introducing new technology into our research without assimilating technical details. In this essay, we provide examples in different research realms to justify our points. To help readers test their own weaknesses, we raise questions on technical details of RNA reverse transcription, polymerase chain reactions, western blotting and immunohistochemical staining, as these methods are basic and are the base for other modern biotechnologies. Hopefully, after contemplation and reflection on these questions, readers will agree that we indeed know too little about these basic techniques, especially about the artifacts they may create, and thus many conclusions drawn from the studies using those ever-more-sophisticated techniques may be even more problematic.

Probably less than one-tenth of the genes produce only the wild type protein without at least one additional protein isoform in some human cancer cell lines

To estimate how many genes produce multiple protein isoforms, we electrophoresed proteins from MCF7 and MDA-MB231 (MB231) human breast cancer cells in SDS-PAGE and excised narrow stripes of the gel at the 48kD, 55kD and 72kD. Proteins in these stripes were identified using liquid chromatography and tandem mass spectrometry. A total of 765, 750 and 679 proteins from MB231 cells, as well as 470, 390 and 490 proteins from MCF7 cells, were identified from the 48kD, 55kD and 72kD stripes, respectively. We arbitrarily allowed a 10% technical variation from the proteins' theoretical molecular mass (TMM) and considered those proteins with their TMMs within the 43-53 kD, 49-61 kD and 65-79 kD ranges as the wild type (WT) expected from the corresponding stripe, whereas those with a TMM above or below this range as a smaller- or larger-group, respectively. Only 263 (34.4%), 269 (35.9%) and 151 (22.2%) proteins from MB231 cells and 117 (24.9%), 135 (34.6%) and 130 (26.5%) proteins from MCF7 cells from the 48kD, 55kD and 72kD stripes, respectively, belonged to the WT, while the remaining majority belonged to the smaller- or larger-groups. Only about 3-16%, on average about 10% regardless of the stripe and cell line, of the proteins appeared in only one stripe and within the WT range, while the remaining preponderance appeared also in additional stripe(s) or had a larger or smaller TMM. We conclude that few (fewer than 10%) of the human genes produce only the WT protein without additional isoform(s).

Restoration of Arpin suppresses aggressive phenotype of breast cancer cells

Arpin, a negative regulator of the actin-related protein-2/3 (Arp2/3) complex, is downregulated and predicts poor prognosis in breast cancer patients. However, its biological relevance in breast cancer is still unclear. This study was conducted to investigate the roles of Arpin in breast cancer growth and invasion. We overexpressed Arpin expression in MCF-7 and MDA-MB-231 breast cancer cells and examined the effects of restoration of Arpin on cell proliferation, colony formation, cell cycle distribution, invasion in vitro and tumorigenesis in vivo. The related molecular mechanism(s) was determined. It was found that ectopic expression of Arpin significantly decreased cell proliferation, colony formation, and tumorigenicity. Flow cytometric analysis showed that overexpression of Arpin significantly increased the percentage of G0/G1-phase cells and decreased the percentage of S-phase cells. Moreover, restoration of Arpin impaired the invasiveness of breast cancer cells, as determined by Transwell invasion assays. Mechanistically, overexpression of Arpin inhibited the phosphorylation of Akt in breast cancer cells. Co-expression of a constitutively active form of Akt blunted the suppression of cell proliferation and invasion by Arpin. Taken together, we provide evidence that Arpin acts as a tumor suppressor in breast cancer, which is associated with inhibition of Akt signaling. Restoration of Arpin may represent a promising therapeutic strategy against breast cancer progression.

It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research

There have been tens of thousands of RNAs deposited in different databases that contain sequences of two genes and are coined chimeric RNAs, or chimeras. However, "chimeric RNA" has never been lucidly defined, partly because "gene" itself is still ill-defined and because the means of production for many RNAs is unclear. Since the number of putative chimeras is soaring, it is imperative to establish a pellucid definition for it, in order to differentiate chimeras from regular RNAs. Otherwise, not only will chimeric RNA studies be misled but also characterization of fusion genes and unannotated genes will be hindered. We propose that only those RNAs that are formed by joining two RNA transcripts together without a fusion gene as a genomic basis should be regarded as authentic chimeras, whereas those RNAs transcribed as, and cis-spliced from, single transcripts should not be deemed as chimeras. Many RNAs containing sequences of two neighboring genes may be transcribed via a readthrough mechanism, and thus are actually RNAs of unannotated genes or RNA variants of known genes, but not chimeras. In today's chimeric RNA research, there are still several key flaws, technical constraints and understudied tasks, which are also described in this perspective essay.

Protein multiplicity can lead to misconduct in western blotting and misinterpretation of immunohistochemical staining results, creating much conflicting data

Western blotting (WB) and immunohistochemical staining (IHC) are common techniques for determining tissue protein expression. Both techniques require a primary antibody specific for the protein in question. WB data is band(s) on a membrane while IHC result is a staining on a tissue section. Most human genes are known to produce multiple protein isoforms; in agreement with that, multiple bands are often found on the WB membrane. However, a common but unspoken practice in WB is to cut away the extra band(s) and present for publication only the band of interest, which implies to the readers that only one form of protein is expressed and thus the data interpretation is straightforward. Similarly, few IHC studies discuss whether the antibody used is isoform-specific and whether the positive staining is derived from only one isoform. Currently, there is no reliable technique to determine the isoform-specificity of an antibody, especially for IHC. Therefore, cutting away extra band(s) on the membrane usually is a form of misconduct in WB, and a positive staining in IHC only indicates the presence of protein product(s) of the to-be-interrogated gene, and not necessarily the presence of the isoform of interest. We suggest that data of WB and IHC involving only one antibody should not be published and that relevant reports should discuss whether there may be protein multiplicity and whether the antibody used is isoform-specific. Hopefully, techniques will soon emerge that allow determination of not only the presence of protein products of genes but also the isoforms expressed.

Two RNAs or DNAs May Artificially Fuse Together at a Short Homologous Sequence (SHS) during Reverse Transcription or Polymerase Chain Reactions, and Thus Reporting an SHS-Containing Chimeric RNA Requires Extra Caution

Tens of thousands of chimeric RNAs have been reported. Most of them contain a short homologous sequence (SHS) at the joining site of the two partner genes but are not associated with a fusion gene. We hypothesize that many of these chimeras may be technical artifacts derived from SHS-caused mis-priming in reverse transcription (RT) or polymerase chain reactions (PCR). We cloned six chimeric complementary DNAs (cDNAs) formed by human mitochondrial (mt) 16S rRNA sequences at an SHS, which were similar to several expression sequence tags (ESTs).These chimeras, which could not be detected with cDNA protection assay, were likely formed because some regions of the 16S rRNA are reversely complementary to another region to form an SHS, which allows the downstream sequence to loop back and anneal at the SHS to prime the synthesis of its complementary strand, yielding a palindromic sequence that can form a hairpin-like structure.We identified a 16S rRNA that ended at the 4th nucleotide(nt) of the mt-tRNA-leu was dominant and thus should be the wild type. We also cloned a mouse Bcl2-Nek9 chimeric cDNA that contained a 5-nt unmatchable sequence between the two partners, contained two copies of the reverse primer in the same direction but did not contain the forward primer, making it unclear how this Bcl2-Nek9 was formed and amplified. Moreover, a cDNA was amplified because one primer has 4 nts matched to the template, suggesting that there may be many more artificial cDNAs than we have realized, because the nuclear and mt genomes have many more 4-nt than 5-nt or longer homologues. Altogether, the chimeric cDNAs we cloned are good examples suggesting that many cDNAs may be artifacts due to SHS-caused mis-priming and thus greater caution should be taken when new sequence is obtained from a technique involving DNA polymerization.

To Know How a Gene Works, We Need to Redefine It First but then, More Importantly, to Let the Cell Itself Decide How to Transcribe and Process Its RNAs

Recent genomic and ribonomic research reveals that our genome produces a stupendous amount of non-coding RNAs (ncRNAs), including antisense RNAs, and that many genes contain other gene(s) in their introns. Since ncRNAs either regulate the transcription, translation or stability of mRNAs or directly exert cellular functions, they should be regarded as the fourth category of RNAs, after ribosomal, messenger and transfer RNAs. These and other research advances challenge the current concept of gene and raise a question as to how we should redefine gene. We can either consider each tiny part of the classically-defined gene, such as each mRNA variant, as a “gene”, or, alternatively and oppositely, regard a whole genomic locus as a “gene” that may contain intron-embedded genes and produce different types of RNAs and proteins. Each of the two ways to redefine gene not only has its strengths and weaknesses but also has its particular concern on the methodology for the determination of the gene's function: Ectopic expression of complementary DNA (cDNA) in cells has in the past decades provided us with great deal of detail about the functions of individual mRNA variants, and will make the data less conflicting with each other if just a small part of a classically-defined gene is considered as a “gene”. On the other hand, genomic DNA (gDNA) will better help us in understanding the collective function of a genomic locus. In our opinion, we need to be more cautious in the use of cDNA and in the explanation of data resulting from cDNA, and, instead, should make delivery of gDNA into cells routine in determination of genes' functions, although this demands some technology renovation.

Culture at a Higher Temperature Mildly Inhibits Cancer Cell Growth but Enhances Chemotherapeutic Effects by Inhibiting Cell-Cell Collaboration

Acute febrile infections have historically been used to treat cancer. To explore the underlying mechanism, we studied chronic effects of fever on cancer cell growth and chemotherapeutic efficacy in cell culture. We found that culturing cancer cells at 39°C mildly inhibited cell growth by arresting the cells at the G1 phase of the cell cycle. When cells were seeded in culture dishes at a lower density, e.g. about 1000–2000 cells per 35-mm dish, the growth inhibition was much greater, manifested as many fewer cell colonies in the 39°C dishes, compared with the results at a higher density seeding, e.g. 20,000 cells per dish, suggesting that cell-cell collaboration as the Allee effect in cell culture is inhibited at 39°C. Withdrawal of cells from serum enhanced the G1 arrest at 39°C and, for some cell lines such as A549 lung cancer cells, serum replenishment failed to quickly drive the cells from the G1 into the S and G2-M phases. Therapeutic effects of several chemotherapeutic agents, including clove bud extracts, on several cancer cell lines were more potent at 39°C than at 37°C, especially when the cells were seeded at a low density. For some cell lines and some agents, this enhancement is long-lasting, i.e. continuing after the cessation of the treatment. Collectively these results suggest that hyperthermia may inhibit cancer cell growth by G1 arrest and by inhibition of cell-cell collaboration, and may enhance the efficacy of several chemotherapeutic agents, an effect which may persist beyond the termination of chemotherapy.

Epigenetic analysis of sporadic and Lynch-associated ovarian cancers reveals histology-specific patterns of DNA methylation

Diagnosis and treatment of epithelial ovarian cancer is challenging due to the poor understanding of the pathogenesis of the disease. Our aim was to investigate epigenetic mechanisms in ovarian tumorigenesis and, especially, whether tumors with different histological subtypes or hereditary background (Lynch syndrome) exhibit differential susceptibility to epigenetic inactivation of growth regulatory genes. Gene candidates for epigenetic regulation were identified from the literature and by expression profiling of ovarian and endometrial cancer cell lines treated with demethylating agents. Thirteen genes were chosen for methylation-specific multiplex ligation-dependent probe amplification assays on 104 (85 sporadic and 19 Lynch syndrome-associated) ovarian carcinomas. Increased methylation (i.e., hypermethylation) of variable degree was characteristic of ovarian carcinomas relative to the corresponding normal tissues, and hypermethylation was consistently more prominent in non-serous than serous tumors for individual genes and gene sets investigated. Lynch syndrome-associated clear cell carcinomas showed the highest frequencies of hypermethylation. Among endometrioid ovarian carcinomas, lower levels of promoter methylation of RSK4, SPARC, and HOXA9 were significantly associated with higher tumor grade; thus, the methylation patterns showed a shift to the direction of high-grade serous tumors. In conclusion, we provide evidence of a frequent epigenetic inactivation of RSK4, SPARC, PROM1, HOXA10, HOXA9, WT1-AS, SFRP2, SFRP5, OPCML, and MIR34B in the development of non-serous ovarian carcinomas of Lynch and sporadic origin, as compared to serous tumors. Our findings shed light on the role of epigenetic mechanisms in ovarian tumorigenesis and identify potential targets for translational applications.

Isoforms of wild type proteins often appear as low molecular weight bands on SDS-PAGE

Immunoblotting, after polyacrylamide gel electrophoresis with sodium dodecyl sulfate (SDS-PAGE), is a technique commonly used to detect specific proteins. SDS-PAGE often results in the visualization of protein band(s) in addition to the one expected based on the theoretical molecular mass (TMM) of the protein of interest. To determine the likelihood of additional band(s) being nonspecific, we used liquid chromatography - mass spectrometry to identify proteins that were extracted from bands with the apparent molecular mass (MM) of 40 and 26 kD, originating from protein extracts derived from non-malignant HEK293 and cancerous MDA-MB231 (MB231) cells separated using SDS-PAGE. In total, approximately 57% and 21% of the MS/MS spectra were annotated as peptides in the two cell samples, respectively. Moreover, approximately 24% and 36.2% of the identified proteins from HEK293 and MB231 cells matched their TMMs. Of the identified proteins, 8% from HEK293 and 26% from MB231 had apparent MMs that were larger than predicted, and 67% from HEK293 and 37% from MB231 exhibited smaller MM values than predicted. These revelations suggest that interpretation of the positive bands of immunoblots should be conducted with caution. This study also shows that protein identification performed by mass spectrometry on bands excised from SDS-PAGE gels could make valuable contributions to the identification of cancer biomarkers, and to cancer-therapy studies.

Possible formation of mitochondrial-RNA containing chimeric or trimeric RNA implies a post-transcriptional and post-splicing mechanism for RNA fusion

Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine.

Cyclin-dependent kinase 4 may be expressed as multiple proteins and have functions that are independent of binding to CCND and RB and occur at the S and G 2/M phases of the cell cycle

Cyclin-dependent kinase 4 (CDK4) is known to be a 33 kD protein that drives G 1 phase progression of the cell cycle by binding to a CCND protein to phosphorylate RB proteins. Using different CDK4 antibodies in western blot, we detected 2 groups of proteins around 40 and 33 kD, respectively, in human and mouse cells; each group often appeared as a duplet or triplet of bands. Some CDK4 shRNAs could decrease the 33 kD wild-type (wt) CDK4 but increase some 40 kD proteins, whereas some other shRNAs had the opposite effects. Liquid chromatography-mass spectrometry/mass spectrometry analysis confirmed the existence of CDK4 isoforms smaller than 33 kD but failed to identify CDK4 at 40 kD. We cloned one CDK4 mRNA variant that lacks exon 2 and encodes a 26 kD protein without the first 74 amino acids of the wt CDK4, thus lacking the ATP binding sequence and the PISTVRE domain required for binding to CCND. Co-IP assay confirmed that this ΔE2 protein lost CCND1- and RB1-binding ability. Moreover, we found, surprisingly, that the wt CDK4 and the ΔE2 could inhibit G 1-S progression, accelerate S-G 2/M progression, and enhance or delay apoptosis in a cell line-specific manner in a situation where the cells were treated with a CDK4 inhibitor or the cells were serum-starved and then replenished. Hence, CDK4 seems to be expressed as multiple proteins that react differently to different CDK4 antibodies, respond differently to different shRNAs, and, in some situations, have previously unrecognized functions at the S-G 2/M phases of the cell cycle via mechanisms independent of binding to CCND and RB.

The p90 RSK family members: common functions and isoform specificity

The p90 ribosomal S6 kinases (RSK) are implicated in various cellular processes, including cell proliferation, survival, migration, and invasion. In cancer, RSKs modulate cell transformation, tumorigenesis, and metastasis. Indeed, changes in the expression of RSK isoforms have been reported in several malignancies, including breast, prostate, and lung cancers. Four RSK isoforms have been identified in humans on the basis of their high degree of sequence homology. Although this similarity suggests some functional redundancy between these proteins, an increasing body of evidence supports the existence of isoform-based specificity among RSKs in mediating particular cellular processes. This review briefly presents the similarities between RSK family members before focusing on the specific function of each of the isoforms and their involvement in cancer progression.

Ribosomal s6 protein kinase 4: a prognostic factor for renal cell carcinoma

Background:

The expression and function of ribosomal s6 protein kinase 4 (RSK4) in renal cell carcinoma (RCC) are unknown.

Methods:

Immunohistochemistry was used to detect the expression of RSK4 in RCC, and the relationship between RSK4 expression and clinicopathological features as well as prognosis of RCC patients was statistically analysed. Ectopic RSK4 expression in RCC cell lines was performed to determine its effect on cell cycle regulation, tumour invasiveness, and metastatic capability.

Results:

RSK4 was overexpressed in RCCs (P=0.003), compared with normal tissues, and the expression varied in different RCC subtypes (P=0.021), especially in two subtypes of papillary RCCs (P=0.001). RSK4 expression was positively correlated with high pT stage (P<0.001), high Fuhrman grade (P<0.001), lymph node involvement (P<0.001), and presence of distant metastasis (P=0.039), and could predict poor outcome in RCC patients. Molecular studies showed that overexpression of RSK4 could promote cell cycle progression and enhance the invasive and metastatic capability of RCC cell lines and vice versa.

Conclusion:

The expression pattern and molecular mechanisms of RSK4 in RCCs indicate that it could be a potential independent prognostic factor and serve as a new potential therapeutic target for RCC patients.