KRT15 overexpression predicts poor prognosis in colorectal cancer

High keratin 15 expression reflects favorable prognosis in early cervical cancer patients

OBJECTIVE

Keratin 15 (KRT15) exhibits inconsistent prognostic roles in different cancers, and its prognostic value in early cervical cancer patients who receive tumor resection remains unknown. This study aimed to assess the relationship of KRT15 expression with prognosis in these patients.

METHODS

Totally, 147 early cervical cancer patients who received tumor resection were reviewed in this retrospective study. KRT15 was detected in formalin-fixed paraffin-embedded tumor tissue by immunohistochemistry (IHC). KRT15 IHC scores were computed by multiplying the percentage of positively stained cells (scored as 0-4) and corresponding staining intensity (scored as 0-3), ranging from 0 to 12.

RESULTS

Elevated KRT15 IHC score was linked with moderate to well differentiation (P = 0.005), tumor size ≤ 4 cm (P = 0.017), and International Federation of Gynecology and Obstetrics (FIGO) stage Ia/Ib (P < 0.001). KRT15 IHC score was inversely associated with adjuvant radiotherapy (P = 0.025) and adjuvant chemotherapy (P = 0.016). KRT15 IHC score ≥ 1 was linked with increased disease-free survival (DFS) (P = 0.003) and overall survival (OS) (P = 0.049). Meanwhile, KRT15 IHC score ≥ 1 independently predicted increased DFS (hazard ratio = 0.213, P = 0.017), but not OS (P > 0.05). KRT15 IHC score ≥ 3 and KRT15 IHC score ≥ 6 could not predict DFS or OS (all P > 0.05). By subgroup analyses, KRT15 IHC score ≥ 1 forecasted favorable DFS in patients with age > 45 years, human papillomavirus-positive, squamous carcinoma, and tumor size ≤ 4 cm (all P < 0.05). KRT15 IHC score ≥ 1 and KRT15 IHC score ≥ 3 predicted ascended DFS in patients without adjuvant radiotherapy or adjuvant chemotherapy (all P < 0.05).

CONCLUSION

High KRT15 expression reflects favorable tumor features and longer survival in early cervical cancer patients who receive tumor resection.

EVA1A, a novel and promising prognostic biomarker in colorectal cancer

Purpose

The purpose of this study was to investigate the potential of EVA1A as a prognostic biomarker for Colorectal cancer (CRC).

Methods

The study utilized public databases to analyze the difference in Evala mRNA expression between CRC tumor tissues and adjacent normal tissues. Additionallymunohistochemical staining was performed on 90 paired tissue samples to detect EVA1A expression. The relationship between EVA1A and clinicopathological features was examined, and a Kaplan-Meier survival analysis was conducted. Univariate and multivariate Cox analyses were employed to identify prognostic factors affecting the overall survival (OS) of CRC patients.

Results

The analysis revealed a significant increase in Evala mRNA expression in CRC tumor cells compared to normal controls from public databases (P< 0.05). Immunohistochemical staining further confirmed a significant upregulation of EVA1A expression in CRC tissues (P< 0.05). High EVA1A expression was associated with age, pathological M stage, total tumor stage, and Carbohydrate antigen CA19-9 (CA19-9). Kaplan-Meier analysis demonstrated a significant association between high EVA1A expression and poor OS. Univariate and multivariate analysis identified EVA1A as an independent risk factor for CRC prognosis.

Conclusion

The study suggests that EVA1A is increased in CRC tumor tissues and may serve as a potential biomarker for poor prognosis in CRC.

Tumor keratin 15 expression links with less extent of invasion and better prognosis in papillary thyroid cancer patients receiving tumor resection

OBJECTIVE

Keratin 15 (KRT15) is identified as a useful biomarker in several solid tumors, while its clinical role in papillary thyroid cancer (PTC) remains unknown. Herein, this study is intended to explore the correlation of tumor KRT15 with clinical features and survival in PTC patients who received tumor resection.

METHODS

This study retrospectively screened 350 PTC patients who received tumor resection and 50 thyroid benign lesions (TBL) patients. KRT15 in formalin-fixed paraffin-embedded lesion specimens of all subjects was detected by immunohistochemistry (IHC).

RESULTS

KRT15 was reduced in PTC patients compared to TBL patients (P < 0.001). Furthermore, KRT15 was negatively associated with tumor size (P = 0.017), extrathyroidal invasion (P = 0.007), pathological tumor (pT) stage (P < 0.001), and postoperative radioiodine application (P = 0.008) in PTC patients. Regarding prognostic value, high KRT15 (cut-off by an IHC value of 3) is linked with prolonged accumulating disease-free survival (DFS) (P = 0.008) and overall survival (OS) (P = 0.008) in PTC patients. Also, the multivariate Cox regression model showed that high KRT15 (vs. low) was an independent factor for longer DFS (hazard ratio = 0.433, P = 0.049), but not for OS (P > 0.050) in PTC patients. Subgroup analyses revealed that KRT15 possessed a better prognostic value in PTC patients with age ≥ 55 years, tumor size > 4 cm, pathological node stage 1, or pathological tumor-node-metastasis stage ≤ 2 (all P < 0.050).

CONCLUSION

Increased tumor KRT15 associates with a lower invasive degree, prolonged DFS, and OS, revealing its prognostic utility in PTC patients undergoing tumor resection.

Silencing of keratin 15 impairs viability and mobility while facilitating the doxorubicin chemosensitivity by inactivating the β‑catenin pathway in liver cancer

Keratin 15 (KRT15) regulates the invasion as well as the stemness and is associated with tumor size and metastasis of several gastrointestinal cancers apart from liver cancer. The present study aimed to explore the effect of KRT15 knockdown on liver cancer malignant behaviors and its interaction with the β-catenin pathway. Small interfering (si)-KRT15 and si-negative control (NC) were transfected into liver cancer cell lines, followed by the addition or not of CHIR-99021 (a β-catenin agonist). Cell viability, invasion, apoptosis, and the half maximal inhibitory concentration (IC50) value of doxorubicin (Dox) were then assessed. The present study illustrated that KRT15 gene and protein expression levels were upregulated in most liver cancer cell lines (Huh7, PLC, Hep3B and HepG2) compared to the normal liver cell line THLE-2. si-KRT15 reduced cell viability and invasive cell count while promoting the apoptosis rate in Huh7 and HepG2 cells. In addition, si-KRT15 also reduced the IC50 value of Dox. Furthermore, si-KRT15 inactivated the β-catenin pathway as reflected by β-catenin, cyclin D1 and c-Myc expression levels in Huh7 and HepG2 cells. Subsequently, CHIR-99021 treatment increased the cell viability and invasive cell count while reducing the apoptosis rate in Huh7 and HepG2 cells. Concurrently, the IC50 value of Dox was also increased. Notably, CHIR-99021 treatment attenuated the effect of si-KRT15 on mediating the aforementioned Huh7 and HepG2 cell malignant behaviors and Dox chemosensitivity. In conclusion, KRT15 knockdown suppressed viability and mobility but facilitated Dox chemosensitivity via inactivating the β-catenin pathway in liver cancer, suggesting its potential as a target for liver cancer treatment.

KRT15 in early breast cancer screening and correlation with HER2 positivity, pathological grade and N stage

Objective: This study was designed to explore KRT15 dysregulation and its correlation with clinical characteristics among ductal carcinoma in situ (DCIS), DCIS with microinvasion (DCIS-MI) and invasive breast cancer (IBC) patients. Methods: KRT15 from lesion samples of 50 DCIS patients, 48 DCIS-MI patients and 50 IBC patients was detected by immunohistochemistry. Results: KRT15 discriminated IBC patients from DCIS patients (area under the curve [AUC] = 0.895; 95% CI = 0.836-0.954) and DCIS-MI patients (AUC = 0.707; 95% CI = 0.606-0.808). In DCIS patients, KRT15 was negatively correlated with pathological grade (p = 0.015). In DCIS-MI patients, KRT15 was positively related to estrogen receptor positivity but negatively associated with Ki-67 (both p < 0.05). In IBC patients, KRT15 was negatively linked to HER2 positivity, histological grade, N stage and tumor node metastasis stage (all p < 0.05). Conclusion: KRT15 assessment may help with early breast cancer screening.

A Kaleidoscope of Keratin Gene Expression and the Mosaic of Its Regulatory Mechanisms

Keratins are a family of intermediate filament-forming proteins highly specific to epithelial cells. A combination of expressed keratin genes is a defining property of the epithelium belonging to a certain type, organ/tissue, cell differentiation potential, and at normal or pathological conditions. In a variety of processes such as differentiation and maturation, as well as during acute or chronic injury and malignant transformation, keratin expression undergoes switching: an initial keratin profile changes accordingly to changed cell functions and location within a tissue as well as other parameters of cellular phenotype and physiology. Tight control of keratin expression implies the presence of complex regulatory landscapes within the keratin gene loci. Here, we highlight patterns of keratin expression in different biological conditions and summarize disparate data on mechanisms controlling keratin expression at the level of genomic regulatory elements, transcription factors (TFs), and chromatin spatial structure.

Single-cell RNA sequencing reveals intratumoral heterogeneity and potential mechanisms of malignant progression in prostate cancer with perineural invasion

Background: Prostate cancer (PCa) is the second most common cancer among men worldwide. Perineural invasion (PNI) was a prominent characteristic of PCa, which was recognized as a key factor in promoting PCa progression. As a complex and heterogeneous disease, its true condition is difficult to explain thoroughly with conventional bulk RNA sequencing. Thus, an improved understanding of PNI-PCa progression at the single-cell level is needed. Methods: In this study, we performed scRNAseq on tumor tissues of three PNI-PCa patients. Principal component analysis (PCA) and Uniform manifold approximation and projection (UMAP) were used to reduce dimensionality and visualize the cellular composition of tumor tissues. The differently expressed genes among each cluster were identified by EdgeR. GO enrichment analysis was used to understand the roles of genes within the clusters. Pseudotime cell trajectory was used to reveal the molecular pathways underlying cell fate decisions and identify genes whose expression changed as the cells underwent transition. We applied CellPhoneDB to identify cell-cell interactions among the epithelial and neural cells in PNI-PCa. Results: Analysis of the ∼17,000 single-cell transcriptomes in three PNI prostate cancer tissues, we identified 12 major cell clusters, including neural cells and two epithelial subtypes with different expression profiles. We found that basal/intermediate epithelial cell subtypes highly expressed PCa progression-related genes, including PIGR, MMP7, and AGR2. Pseudotime trajectory analysis showed that luminal epithelial cells could be the initiating cells and transition to based/intermediate cells. Gene ontology (GO) enrichment analysis showed that pathways related to cancer progressions, such as lipid catabolic and fatty acid metabolic processes, were significantly enriched in basal/intermediate cells. Our analysis also suggested that basal/intermediate cells communicate closely with neural cells played a potential role in PNI-PCa progression. Conclusion: These results provide our understanding of PNI-PCa cellular heterogeneity and characterize the potential role of basal/intermediate cells in the PNI-PCa progression.

Non-steroidal anti-inflammatory drugs and biomarkers: A new paradigm in colorectal cancer

Colorectal cancer is a sporadic, hereditary, or familial based disease in its origin, caused due to diverse set of mutations in large intestinal epithelial cells. Colorectal cancer (CRC) is a common and deadly disease that accounts for the 4^th worldwide highly variable malignancy. For the early detection of CRC, the most common predictive biomarker found endogenously are KRAS and ctDNA/cfDNA along with SEPT9 methylated DNA. Early detection and screening for CRC are necessary and multiple methods can be employed to screen and perform early diagnosis of CRC. Colonoscopy, an invasive method is most prevalent for diagnosing CRC or confirming the positive result as compared to other screening methods whereas several non-invasive techniques such as molecular analysis of breath, urine, blood, and stool can also be performed for early detection. Interestingly, widely used medicines known as non-steroidal anti-inflammatory drugs (NSAIDs) to reduce pain and inflammation have reported chemopreventive impact on gastrointestinal malignancies, especially CRC in several epidemiological and preclinical types of research. NSAID acts by inhibiting two cyclooxygenase enzymes, thereby preventing the synthesis of prostaglandins (PGs) and causing NSAID-induced apoptosis and growth inhibition in CRC cells. This review paper majorly focuses on the diversity of natural and synthetic biomarkers and various techniques for the early detection of CRC. An approach toward current advancement in CRC detection techniques and the role of NSAIDs in CRC chemoprevention has been explored systematically. Several prominent governing mechanisms of the anti-cancer effects of NSAIDs and their synergistic effect with statins for an effective chemopreventive measure have also been discussed in this review paper.

B7-H4 is a potential diagnostic and prognostic biomarker in colorectal cancer and correlates with the epithelial-mesenchymal transition

Background

As a negative co-stimulatory molecule of the B7 family, B7-H4 has recently attracted increased attention. However, the clinical value of B7-H4 in colorectal cancer (CRC) remains controversial and requires further investigation. This study aimed to investigate the role of B7-H4 in the clinical diagnosis and survival prognosis of CRC.

Methods

The relationships between B7-H4 expression, immune cell infiltration, epithelial-mesenchymal transition (EMT), clinicopathological features, and survival prognosis were determined through the TCGA database and verified in a large CRC cohort (n = 1118).

Results

The results showed the level of B7-H4 mRNA expression was significantly increased in the CRC tumor tissues compared with normal tissues (P <  0.001). Immunohistochemistry showed that B7-H4 protein expression was also up-regulated in CRC. The positive rate of B7-H4 in CRC tumor tissues was 76.38%, which was significantly higher than that in non-tumor tissues (P <  0.001). Overexpression of B7-H4 was positively correlated with lymph node metastasis, advanced TNM stage, and poor tumor differentiation (P = 0.012; 0.009; 0.014). Prognostic analysis showed high B7-H4 expression was associated with significantly shorter OS. Multivariate analysis demonstrated the risk of death in CRC patients with high B7-H4 expression is 1.487 times that of low B7-H4 expression. In addition, B7-H4 expression was negatively correlated with the epithelial marker E-cadherin (P <  0.001) and positively correlated with the mesenchymal marker vimentin (P <  0.001) in CRC tissues. However, B7-H4 expression was not associated with the immunosuppressive microenvironment in CRC.

Conclusion

B7-H4 may represent a potential biomarker for the diagnosis and prognosis of CRC and enhance CRC invasion by promoting EMT.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-022-10159-5.

Upregulated keratin 15 links to the occurrence of lymphovascular invasion, stromal cervical invasion as well as unfavorable survival profile in endometrial cancer patients

Keratin 15 (KRT15) overexpression links with tumor initiation, metastasis, and poor survival in several solid carcinomas. While its clinical relevance is scarcely reported in endometrial cancer (EC). Therefore, the current study aimed to investigate the abnormal expression of KRT15 and its correlation with clinical characteristics, survival in EC patients. Totally, 135 surgical EC patients were enrolled. KRT15 protein expression in formalin-fixed and paraffin-embedded tumor and adjuvant tissues was detected by immunohistochemical staining; meanwhile, KRT15 mRNA expression in fresh-frozen tumor and adjacent tissues was detected by reverse transcription-quantitative polymerase chain reaction. KRT15 protein and mRNA expressions were higher in tumor tissue compared with adjacent tissue (both P < .001). Elevated KRT15 protein expression was correlated with the occurrence of lymphovascular invasion (P = .010) and more advanced International Federation of Gynecology and Obstetrics stage (P = .018); meanwhile, elevated KRT15 mRNA expression was linked with more advanced International Federation of Gynecology and Obstetrics stage (P = .038) and marginally associated with the occurrence of stromal cervical invasion (P = .052). Besides, KRT15 protein and mRNA expressions were not correlated with other clinical features (all P > .05). KRT15 protein high was marginally correlated with poor accumulating disease-free survival (DFS) (P = .091) and overall survival (OS) (P = .059); meanwhile, the correlation of KRT15 mRNA expression with accumulating DFS (P = .212) and OS (P = .092) was even weaker. However, multivariate Cox's regressions showed that tumor KRT15 protein (high vs low) was independently correlated with poor DFS (P = .045) and OS (P = .043). KRT15 is abnormally increased in EC tissue, meanwhile, its upregulation links to the occurrence of lymphovascular invasion, stromal cervical invasion, and poor prognosis in EC patients.

KRT15 promotes colorectal cancer cell migration and invasion through β-catenin/MMP-7 signaling pathway

KRT15 has been reported to act as an oncogene in colorectal cancer. However, whether KRT15 promotes colorectal cancer migration and invasion remain unclear. In this study, western blot and qRT-PCR assay were used to determine the expression of KRT15 in colorectal cancer cells. Wound-healing and transwell migration assay were performed to assess the migration of colorectal cancer cells. Matrigel transwell invasion assay was employed to examine the invasion of colorectal cancer cells. We found that KRT15 was highly expressed in colorectal cancer cells. Ectopic expression of KRT15 dramatically promoted colorectal cancer cell migration and invasion. Conversely, silencing KRT15 remarkably suppressed the migration and invasion of colorectal cancer cells. Importantly, we found that MMP-7 was crucial for KRT15-induced migration and invasion of colorectal cancer cells. Knockdown of MMP-7 significantly diminished the migration and invasion induced by KRT15; overexpression of MMP-7 almost completely rescued the inhibitory effects of KRT15 shRNAs on colorectal cancer cell migration and invasion. In addition, by gain- and loss-of function, we confirmed that β-catenin was responsible for the increased expression of MMP-7 induced by KRT15 colorectal cancer cell lines. In conclusion, KRT15 promotes migration and invasion of colorectal cancer cell at least partly through β-catenin/MMP7 signaling pathway, suggesting KRT15 is a potential therapeutic target for patients with metastatic colorectal cancer.

A pan-cancer analysis of the oncogenic role of Keratin 17 (KRT17) in human tumors

Background

Although new evidence from cells or animals suggests a relationship between Keratin 17 (KRT17) and cancer, no pan-cancer analysis is currently available.

Methods

The expression level of KRT17 in generalized carcinoma was detected by the Tumor Immune Estimation Resource, version 2 (TIMER2) database, and then verified the protein expression of KRT17 in different cancer species in UALCAN database, and analyzed the relationship between the expression level of KRT17 and the clinical stage and survival of different cancers. We further explored the genetic variation of KRT17 in different tumor types included in The Cancer Genome Atlas (TCGA) and the specific mutations in each domain. The changes of KRT17 protein phosphorylation levels and protein expression levels at different phosphorylation sites in different tumors were explored. TIMER2 database was used to explore the potential relationship between the infiltration level of different immune cells and KRT17 gene expression in different TCGA cancer types. Finally, the protein binding to KRT17 and genes related to KRT17 expression were explored by STRING database and TCGA database.

Results

KRT17 is overexpressed in most malignancies, and we observed a distinct relationship between KRT17 expression and tumor patient prognosis. Enhanced phosphorylation levels of S13, S24, S32, and S39 were observed in several tumors, such as lung adenocarcinoma (LUAD), colon and ovarian cancers, and uterine corpus endometrial carcinoma (UCEC). Intermediate filament cytoskeleton and keratinization may be simultaneously acting with KRT17 on tumor pathogenesis.

Conclusions

Our pan-cancer analysis provides relatively complete information on the oncogenic functions of KRT17 in various cancers.

Novel Diagnostic Biomarkers in Colorectal Cancer

Colorectal cancer (CRC) is still a leading cause of cancer death worldwide. Less than half of cases are diagnosed when the cancer is locally advanced. CRC is a heterogenous disease associated with a number of genetic or somatic mutations. Diagnostic markers are used for risk stratification and early detection, which might prolong overall survival. Nowadays, the widespread use of semi-invasive endoscopic methods and feacal blood tests characterised by suboptimal accuracy of diagnostic results has led to the detection of cases at later stages. New molecular noninvasive tests based on the detection of CRC alterations seem to be more sensitive and specific then the current methods. Therefore, research aiming at identifying molecular markers, such as DNA, RNA and proteins, would improve survival rates and contribute to the development of personalized medicine. The identification of “ideal” diagnostic biomarkers, having high sensitivity and specificity, being safe, cheap and easy to measure, remains a challenge. The purpose of this review is to discuss recent advances in novel diagnostic biomarkers for tumor tissue, blood and stool samples in CRC patients.

Upregulated Expression of Actin-Like 6A is a Risk Factor Affecting the Prognosis of Pancreatic Cancer

Purpose

Actin-like 6A (ACTL6A), a regulatory subunit of the ATP-dependent chromatin-remodeling complex SWI/SNF, acts as an oncogenic factor. This study is aimed at evaluating the correlation between ACTL6A expression and clinicopathological parameters in pancreatic cancer (PC) patients.

Methods

The differences of Actl6a mRNA expression between PC tissues and normal pancreatic tissues were analyzed in public databases, and ACTL6A expression was then determined and confirmed in 60 paired tissue specimens using immunohistochemistry staining. The association analysis between ACTL6A expression and the clinicopathological characteristics was analyzed, as well as Kaplan–Meier survival analysis. Univariate and multivariate Cox analyses were performed to identify the prognostic factors in the overall survival (OS) of patients with PC.

Results

The mRNA expression of Actl6a showed significantly higher in PC compared to normal controls (p < 0.05) from public databases. The score of immunohistochemistry staining further confirmed that ACTL6A expression was significantly upregulated in PC tissues (p < 0.001) through immunohistochemistry staining. High ACTL6A expression was associated with lymphovascular space invasion of PC. Kaplan–Meier analysis revealed that the high expression of ACTL6A was markedly associated with poor OS. Moreover, univariate and multivariate analysis demonstrated that ACTL6A acted as an independent risk factor for PC prognosis.

Conclusion

ACTL6A is upregulated in PC and acts as a risk factor for poor prognosis in patients with PC, and therefore clinicians could around it design preventive measures and individualized treatment to improve mortality in patients with PC.

Identification of Six Prognostic Genes in EGFR-Mutant Lung Adenocarcinoma Using Structure Network Algorithms

This study aims to determine hub genes related to the incidence and prognosis of EGFR-mutant (MT) lung adenocarcinoma (LUAD) with weighted gene coexpression network analysis (WGCNA). From The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we used 253 EGFR-MT LUAD samples and 38 normal lung tissue samples. At the same time, GSE19188 was additionally included to verify the accuracy of the predicted gene. To discover differentially expressed genes (DEGs), the R package “limma” was used. The R packages “WGCNA” and “survival” were used to perform WGCNA and survival analyses, respectively. The functional analysis was carried out with the R package “clusterProfiler.” In total, 1450 EGFR-MT–specific DEGs were found, and 7 tumor-related modules were marked with WGCNA. We found 6 hub genes in DEGs that overlapped with the tumor-related modules, and the overexpression level of B3GNT3 was significantly associated with the worse OS (overall survival) of the EGFR-MT LUAD patients (p < 0.05). Functional analysis of the hub genes showed the metabolism and protein synthesis–related terms added value. In conclusion, we used WGCNA to identify hub genes in the development of EGFR-MT LUAD. The established prognostic factors could be used as clinical biomarkers. To confirm the mechanism of those genes in EGFR-MT LUAD, further molecular research is required.

Cytokeratin 5 and cytokeratin 6 expressions are unconnected in normal and cancerous tissues and have separate diagnostic implications

Cytokeratins (CKs) 5 and 6 are functionally unrelated but often analyzed together using bispecific antibodies in diagnostic immunohistochemistry. To better understand the diagnostic utility of CK5 or CK6 alone, tissue microarrays with > 15,000 samples from 120 different tumor types as well as 608 samples of 76 different normal tissues were analyzed by immunohistochemistry. In normal tissues, both CKs occurred in the squamous epithelium; CK5 dominated in basal and CK6 in suprabasal layers. CK5 (not CK6) stained basal cells in various other organs. Within tumors, both CK5 and CK6 were seen in > 95% of squamous cell carcinomas, but other tumor entities showed different results: CK5 predominated in urothelial carcinoma and mesothelioma, but CK6 in adenocarcinomas. Joint analysis of both CK5 and CK6 obscured the discrimination of epithelioid mesothelioma (100% positive for CK5 alone and for CK5/6) from adenocarcinoma of the lung (12.8% positive for CK5 alone; 23.7% positive for CK5/6). CK5 and CK6 expressions were both linked to high grade, estrogen receptor, and progesterone receptor negativity in breast cancer (p < 0.0001 each), grade/stage progression in urothelial cancer (p < 0.0001), and RAS mutations in colorectal cancer (p < 0.01). Useful diagnostic properties which are commonly attributed to CK5/6 antibodies such as basal cell staining in the prostate, distinction of adenocarcinoma of the lung from squamous cell carcinoma and epithelioid mesothelioma, and identification of basal-type features in urothelial cancer are solely driven by CK5. At least for the purpose of distinguishing thoracic tumors, monospecific CK5 antibodies may be better suited than bispecific CK5/6 antibodies.

Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor

It is well known that cervical cancer poses the fourth most malignancy threat to women worldwide among all cancer types. There is a tremendous improvement in realizing the underlying molecular associations in cervical cancer. Several studies reported pieces of evidence for the involvement of various genes in the disease progression. However, with the ever-evolving bioinformatics tools, there has been an upsurge in predicting numerous genes responsible for cervical cancer progression and making it highly complex to target the genes for further evaluation. In this article, we prioritized the candidate genes based on the sequence similarity analysis with known cancer genes. For this purpose, we used the concept of the moment of inertia tensor, which reveals the similarities between the protein sequences more efficiently. Tensor for moment of inertia explores the similarity of the protein sequences based on the physicochemical properties of amino acids. From our analysis, we obtained 14 candidate cervical cancer genes, which are highly similar to known cervical cancer genes. Further, we analyzed the GO terms and prioritized these genes based on the number of hits with biological process, molecular functions, and their involvement in KEGG pathways. We also discussed the evidence-based involvement of the prioritized genes in other cancers and listed the available drugs for those genes.

Pan-cancer characterization of long non-coding RNA and DNA methylation mediated transcriptional dysregulation

BACKGROUND

Disruption of DNA methylation (DNAm) is one of the key signatures of cancer, however, detailed mechanisms that alter the DNA methylome in cancer remain to be elucidated.

METHODS

Here we present a novel integrative analysis framework, called MeLncTRN (Methylation mediated LncRNA Transcriptional Regulatory Network), that integrates genome-wide transcriptome, DNA methylome and copy number variation profiles, to systematically identify the epigenetically-driven lncRNA-gene regulation circuits across 18 cancer types.

FINDING

We show that a significant fraction of the aberrant DNAm and gene expression landscape in cancer is associated with long noncoding RNAs (lncRNAs). We reveal distinct types of regulation between lncRNA modulators and target genes that are operative in either only specific cancers or across cancers. Functional studies identified a common theme of cancer hallmarks that lncRNA modulators may participate in. The coupled lncRNA gene interactions via DNAm also serve as markers for classifications of cancer subtypes with different prognoses.

INTERPRETATION

Our study reveals a vital layer of DNAm and associated expression regulation for many cancer-related genes and we also provide a valuable database resource for interrogating epigenetically mediated lncRNA-gene interactions in cancer.

FUNDING

National Natural Science Foundation of China [91959106, 31871255].

Low KRT15 expression is associated with poor prognosis in patients with breast invasive carcinoma

Although keratin 15 (KRT15) has been indicated to be overexpressed in several types of tumor, its role in breast invasive carcinoma (BRCA) has so far remained elusive. The aim of the present study was to explore KRT15 expression in BRCA based on data obtained from The Cancer Genome Atlas and The Genotype-Tissue Expression. KRT15 expression was compared using a Wilcoxon rank-sum test. Functional enrichment analysis was performed to reveal the biological roles and pathways of KRT15. The association between KRT15 expression and immune-cell infiltration was evaluated via single-sample gene set enrichment analysis (ssGSEA). To investigate the relationship between clinicopathological features and KRT15 expression, the prognostic value of KRT15 and other clinical factors was evaluated using Cox regression analysis and Kaplan-Meier (KM) plots. Subgroup prognostic analysis was also performed using forest plots and KM curves. Finally, a tissue microarray was used to assess KRT15 expression in BRCA tissues. KRT15 expression was significantly lower in BRCA tissues compared with that in normal tissues. Functional enrichment analysis suggested that KRT15-related genes were primarily enriched in the transmembrane transporter complex, cornification and ligand-receptor interactions. Increased KRT15 was associated with several tumor-suppressive pathways. ssGSEA revealed that high KRT15 expression was significantly associated with natural killer-cell, B-cell and mast-cell infiltration. Significant associations were observed between low KRT15 expression and advanced stage clinicopathological factors, as well as unfavorable overall survival (OS) and disease-specific survival. Multivariate Cox regression analysis suggested that KRT15 was an independent prognostic factor for OS (P=0.039; hazard ratio, 0.590; 95% CI, 0.358-0.974). Subgroup prognostic analysis demonstrated that low KRT15 was a reliable predictor of poor OS. Immunohistochemistry of a tissue microarray indicated that positive KRT15 expression rates were significantly higher in normal tissues compared with those in the BRCA tissues. In conclusion, low KRT15 expression was significantly associated with poor prognosis in patients with BRCA. Thus, KRT15 may serve an important role in BRCA progression and may be used as a promising prognostic marker for diagnostic and prognostic analyses in patients with BRCA.

Critical roles of the lncRNA CASC11 in tumor progression and cancer metastasis: The biomarker and therapeutic target potential

The frequency of human suffering from cancer is increasing annually across the globe. This has fueled numerous investigations aimed at the prevention and cure of various cancers. Long non-coding RNA (lncRNA) are known to play a crucial role in cancer. For instance, cancer susceptibility candidate 11 (CASC11), as one of the long non-coding RNAs, has been reported to be overexpressed in various tumors. This review elucidates the mechanism by which lncRNA CASC11 regulates tumors' biological processes and affirms its value as a therapeutic target for tumors. Through systematic analysis and review of relevant articles in PubMed, we revealed the pathophysiological mechanism of CASC11 on the tumor by regulating the biological processes of tumor such as proliferation, autophagy, apoptosis, thereby promoting tumor metastasis. We also revealed the regulatory pathways of CASC11 in different tumors, for instance by acting on a variety of microRNAs, oncogenic proteins, carcinogens, and transcription factors. Consequently, CASC11 regulates cancer proliferation, apoptosis, and invasion by altering the WNT/β-catenin signaling pathway and epithelial–mesenchymal transition (EMT). Furthermore, CASC11 expression has a high pertinence with clinical prognosis, suggesting that it is a potential marker for malignant tumors or a clinical adjuvant therapy in the future.

Placental transcriptome profile of women with sickle cell disease reveals differentially expressed genes involved in migration, trophoblast differentiation and inflammation

Sickle cell disease (SCD) is a group of disorders whose common characteristic is the presence of hemoglobin (Hb) S in erythrocytes. The main consequence of this abnormality is vaso-occlusion, which can affect almost all organs including the placenta. This study aimed to evaluate the gene expression profile in placentas of women with SCD by means of total RNA sequencing. For this, we proposed a case-control study, with three groups of pregnant women: HbSS (n = 10), HbSC (n = 14) and HbAA (n = 21). The results showed differences in expression in a number of genes such as NOS2 (fold change, FC = 4.52), HLAG (FC = 5.56), ASCL2 (FC = 3.61), CXCL10 (FC = -3.66) and IL1R2 (FC = 3.92) for the HbSC group and S100A8 (FC = -3.82), CPXM2 (FC = 4.57), CXCL10 (FC = -4.59), CXCL11 (FC = -3.72) and CAMP (FC = -4.55) for the HbSS group. Differentially expressed genes are mainly associated with migration, trophoblast differentiation and inflammation. The causes leading to altered gene expression in placentas of sickle cell patients are not fully understood, but the presence of intravascular hemolysis and vaso-occlusion, with cycles of ischemia and reperfusion, may contribute to the emergence of an environment which can be very harmful for placental physiology, altering the nutrient supply and metabolic exchange for fetal growth.