Distinguishing between cancer cell differentiation and resistance induced by all-trans retinoic acid using transcriptional profiles and functional pathway analysis

Plant-derived extracts and metabolic modulation in leukemia: a promising approach to overcome treatment resistance

Leukemic cells acquire complex and often multifactorial mechanisms of resistance to treatment, including various metabolic alterations. Although the use of metabolic modulators has been proposed for several decades, their use in clinical practice has not been established. Natural products, the so-called botanical drugs, are capable of regulating tumor metabolism, particularly in hematopoietic tumors, which could partly explain the biological activity attributed to them for a long time. This review addresses the most recent findings relating to metabolic reprogramming-Mainly in the glycolytic pathway and mitochondrial activity-Of leukemic cells and its role in the generation of resistance to conventional treatments, the modulation of the tumor microenvironment, and the evasion of immune response. In turn, it describes how the modulation of metabolism by plant-derived extracts can counteract resistance to chemotherapy in this tumor model and contribute to the activation of the antitumor immune system.

LncRNA-PAX8-AS1 Silencing Decreases Cell Viability, Enhances Apoptosis, and Suppresses Doxorubicin Resistance in Myeloid Leukemia via the miR-378g/ERBB2 Axis

Objective

Considering the role of lncRNAs reported as regulators in acute myeloid leukemia (AML) progression, the current research aims to investigate the role of PAX8-AS1 in chemo-resistant AML.

Methods

Human AML cells HL60 and human doxorubicin (ADM)-resistant AML cells (HL60/ADM cells) were used to establish in vitro models of chemo-sensitive AML and refractory/recurrent AML, respectively. CCK-8 assay and flow cytometry were used to determine cell resistance to ADM, viability, and apoptosis. PAX8-AS1, miR-378g, and ERBB2 expressions in the models and/or AML patients were quantified via qRT-PCR or Western blot. The miRNA/mRNA axis targeted by PAX8-AS1 was analyzed using Starbase, TargetScan, or GEO and validated through a dual-luciferase reporter assay. The expressions of Bcl-2, Bax, and C Caspase-3 in cells were quantitated by Western blot.

Results

The highly expressed PAX8-AS1 was observed in AML patients and HL60 cells, which was more evident in refractory/recurrent AML patients and HL60/ADM cells. Compared with that in ADM-treated parental HL60 cells, the viability of ADM-treated HL60/ADM cells remained strong. PAX8-AS1 overexpression increased viability and Bcl-2 expression, while diminishing apoptosis, Bax, and C Caspase-3 expressions in HL60 cells. However, the abovementioned aspects were oppositely impacted by PAX8-AS1 silencing in HL60/ADM cells. PAX8-AS1 directly targeted miR-378g, whose expression pattern is opposite to that of PAX8-AS1 in AML. MiR-378g upregulation abrogated the effects of PAX8-AS1 overexpression on HL60 cells. MiR-378g downregulation offset PAX8-AS1 silencing-induced effects on HL60/ADM cells. Moreover, ERBB2 was recognized as the target of miR-378g, with a higher expression in HL60/ADM cells than in HL60 cells.

Conclusion

PAX8-AS1 silencing decreases cell viability, enhances apoptosis, and suppresses ADM resistance in AML via regulating the miR-378g/ERBB2 axis.

Integrative analysis of expression, prognostic significance and immune infiltration of RFC family genes in human sarcoma

Objective: To reveal the expression and prognostic value of replication factor C family genes (RFCs) in patients with sarcoma.

Results: The results showed that the mRNA expression levels of RFC2, RFC3, RFC4, and RFC5 were increased in sarcoma tissues. In addition, Cancer Cell Line Encyclopedia (CCLE) dataset analysis indicated that RFC1, RFC2, RFC3, RFC4, and RFC5 were elevated expressed in sarcoma cell lines. Moreover, Gene Expression Profiling Interactive Analysis (GEPIA) and Kaplan-Meier Plotter showed that highly expressed RFC2-5 were associated with poor overall survival (OS) or relapse-free survival (RFS) in sarcoma patients. The results of the Tumor Immune Estimation Resource (TIMER) database indicated that the expression of RFCs was negatively correlated with the infiltration of CD4+ T cells and macrophages.

Conclusions: There were significant differences in the expression of RFCs between normal tissue and sarcoma tissue, and RFC2, RFC3, RFC4, and RFC5 might be promising prognostic biomarkers for sarcoma.

Methods: The expression of RFCs was analyzed using the ONCOMINE dataset and GEPIA dataset. CCLE dataset was used to assess the expression of RFCs in the cancer cell line. The prognostic value of RFCs was evaluated by GEPIA and Kaplan-Meier analysis. Furthermore, the association between RFCs and their co-expressed genes were explored via ONCOMINE and GEPIA datasets. We used the TIMER dataset to analyze the immune cell infiltration of RFCs in sarcoma.

Mechanical phenotyping reveals unique biomechanical responses in retinoic acid-resistant acute promyelocytic leukemia

All-trans retinoic acid (ATRA) is an essential therapy in the treatment of acute promyelocytic leukemia (APL), but nearly 20% of patients with APL are resistant to ATRA. As there are no biomarkers for ATRA resistance that yet exist, we investigated whether cell mechanics could be associated with this pathological phenotype. Using mechano-node-pore sensing, a single-cell mechanical phenotyping platform, and patient-derived APL cell lines, we discovered that ATRA-resistant APL cells are less mechanically pliable. By investigating how different subcellular components of APL cells contribute to whole-cell mechanical phenotype, we determined that nuclear mechanics strongly influence an APL cell's mechanical response. Moreover, decondensing chromatin with trichostatin A is especially effective in softening ATRA-resistant APL cells. RNA-seq allowed us to compare the transcriptomic differences between ATRA-resistant and ATRA-responsive APL cells and highlighted gene expression changes that could be associated with mechanical changes. Overall, we have demonstrated the potential of "physical" biomarkers in identifying APL resistance.

Screening of cervical cancer-related hub genes based on comprehensive bioinformatics analysis

BACKGROUND

Since the molecular mechanisms of cervical cancer (CC) have not been completely discovered, it is of great significance to identify the hub genes and pathways of this disease to reveal the molecular mechanisms of cervical cancer.

OBJECTIVE

The study aimed to identify the biological functions and prognostic value of hub genes in cervical cancer.

METHODS

The gene expression data of CC patients were downloaded from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. The core genes were screened out by differential gene expression analysis and weighted gene co-expression network analysis (WGCNA). R software, the STRING online tool and Cytoscape software were used to screen out the hub genes. The GEPIA public database was used to further verify the expression levels of the hub genes in normal tissues and tumour tissues and determine the disease-free survival (DFS) rates of the hub genes. The protein expression of the survival-related hub genes was identified with the Human Protein Atlas (HPA) database.

RESULTS

A total of 64 core genes were screened, and 10 genes, including RFC5, POLE3, RAD51, RMI1, PALB2, HDAC1, MCM4, ESR1, FOS and E2F1, were identified as hub genes. Compared with that in normal tissues, RFC5, POLE3, RAD51,RMI1, PALB2, MCM4 and E2F1 were all significantly upregulated in cervical cancer, ESR1 was significantly downregulated in cervical cancer, and RFC5 expression in CC patients was significantly related to OS. In the DFS analysis, no significant difference was observed in the expression level of RFC5 in cervical cancer patients. Finally, RFC5 protein levels verified by the HPA database were consistently upregulated with mRNA levels in CC samples.

CONCLUSIONS

RFC5 may play important roles in the occurrence and prognosis of CC. It could be further explored and validated as a potential predictor and therapeutic target for CC.

Omics Technologies to Decipher Regulatory Networks in Granulocytic Cell Differentiation

Induced granulocytic differentiation of human leukemic cells under all-trans-retinoid acid (ATRA) treatment underlies differentiation therapy of acute myeloid leukemia. Knowing the regulation of this process it is possible to identify potential targets for antileukemic drugs and develop novel approaches to differentiation therapy. In this study, we have performed transcriptomic and proteomic profiling to reveal up- and down-regulated transcripts and proteins during time-course experiments. Using data on differentially expressed transcripts and proteins we have applied upstream regulator search and obtained transcriptome- and proteome-based regulatory networks of induced granulocytic differentiation that cover both up-regulated (HIC1, NFKBIA, and CASP9) and down-regulated (PARP1, VDR, and RXRA) elements. To verify the designed network we measured HIC1 and PARP1 protein abundance during granulocytic differentiation by selected reaction monitoring (SRM) using stable isotopically labeled peptide standards. We also revealed that transcription factor CEBPB and LYN kinase were involved in differentiation onset, and evaluated their protein levels by SRM technique. Obtained results indicate that the omics data reflect involvement of the DNA repair system and the MAPK kinase cascade as well as show the balance between the processes of the cell survival and apoptosis in a p53-independent manner. The differentially expressed transcripts and proteins, predicted transcriptional factors, and key molecules such as HIC1, CEBPB, LYN, and PARP1 may be considered as potential targets for differentiation therapy of acute myeloid leukemia.

Transcriptome Analysis Reveals Possible Immunomodulatory Activity Mechanism of Chlorella sp. Exopolysaccharides on RAW264.7 Macrophages

In this study, the exopolysaccharides of Chlorella sp. (CEP) were isolated to obtain the purified fraction CEP4. Characterization results showed that CEP4 was a sulfated heteropolysaccharide. The main monosaccharide components of CEP4 are glucosamine hydrochloride (40.8%) and glucuronic acid (21.0%). The impact of CEP4 on the immune activity of RAW264.7 macrophage cytokines was detected, and the results showed that CEP4 induced the production of nitric oxide (NO), TNF-α, and IL-6 in a dose-dependent pattern within a range of 6 μg/mL. A total of 4824 differentially expressed genes (DEGs) were obtained from the results of RNA-seq. Gene enrichment analysis showed that immune-related genes such as NFKB1, IL-6, and IL-1β were significantly upregulated, while the genes RIPK1 and TLR4 were significantly downregulated. KEGG pathway enrichment analysis showed that DEGs were significantly enriched in immune-related biological processes, including toll-like receptor (TLR) signaling pathway, cytosolic DNA-sensing pathway, and C-type lectin receptor signaling pathway. Protein–protein interaction (PPI) network analysis showed that HSP90AB1, Rbx1, ISG15, Psmb6, Psmb3, Psmb8, PSMA7, Polr2f, Rpsa, and NEDD8 were the hub genes with an essential role in the immune activity of CEP4. The preliminary results of the present study revealed the potential mechanism of CEP4 in the immune regulation of RAW264.7 macrophages, suggesting that CEP4 is a promising immunoregulatory agent.

DNA repair gene expression is associated with differential prognosis between HPV16 and HPV18 positive cervical cancer patients following radiation therapy

Cervical cancers are almost always induced by HPV infections, of which HPV16 and HPV18 are predominant. Cancers associated with these strains are induced through DNA repair factors and have a differential response to radiation therapy. Hence this study focuses on finding DNA repair gene expression differences in HPV16 and HPV18 positive cervical cancers after radiation therapy. A higher number of somatic mutations were observed in HPV16 positive cervical tumours for patients that were disease free when compared to those who recurred/progressed. Moreover, hierarchal clustering of RNAseq data from The Cancer Genome Atlas was conducted to identify groups of DNA repair genes associated with a differential prognosis for cervical cancer following postoperative radiation therapy. TP53BP1, MCM9 (at higher than mean levels), POLR2F and SIRT6 (at lower than mean levels), were associated with an increase in patients experiencing cervical cancer recurrence/progression following postoperative radiation therapy when HPV18 positive, but not HPV16 positive. The expression patterns of these genes provide an explanation for the higher rate of postoperative radiation therapy resistance associated with HPV18 positive cervical cancer patients. Therefore, HPV18 positive cervical tumours may be more likely retain a greater non-homologous end joining and homologous recombination pathway activity, which could dampen the effect of postoperative radiation therapy. Moreover, greater susceptibility to postoperative radiation therapy could be caused by the reliance of cervical cancer cells upon the single-strand annealing and nucleotide excision pathways for repair of DNA damage.

Expression pattern of microRNAs related with response to trastuzumab in breast cancer

BACKGROUND

Although an immense effort has been made to develop a novel biomarker for response to trastuzumab, no reliable biomarkers are available to guide management, expect for HER2. The aim of this study was to examine the relationship between microRNA (miRNA) expression and resistance to trastuzumab.

METHODS

Differentially expressed miRNAs between trastuzumab-resistant and trastuzumab-sensitive cell lines were analyzed using microarrays. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to determine the functions of differentially expressed miRNA and their targeted genes. Furthermore, the protein-protein interactions (PPI) network was analyzed. Serum samples were collected from patients with HER2-positive breast cancer who were treated with trastuzumab. We validated the miRNAs expression levels by quantitative reverse-transcription polymerase chain reaction (qRT-PCR) in these serums. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the predictive performance of the miRNA.

RESULTS

Using miRNA microarrays, 151 miRNAs that significant differentially expressed between the trastuzumab-resistant and sensitive cells were identified, including 46 upregulated and 105 downregulated miRNAs. Results of real-time PCR confirmed seven miRNAs in cell lines. PI3K-Akt signaling pathway was involved in regulating biological function according to KEGG analysis. Compared with the serums of trastuzumab-sensitive patients, three miRNAs, namely miR-200b, miR-135b, and miR-29a, were identified to be upregulated, and miR-224 was downregulated in the trastuzumab-resistant serums. ROC analysis showed that four miRNAs were correlated with trastuzumab resistance. Furthermore, three subnetwork modules of PPI network were obtained.

CONCLUSION

The results indicated that miRNAs were reliable predictive biomarkers for response to trastuzumab.

Proteomic Profiling of Acute Promyelocytic Leukemia Identifies Two Protein Signatures Associated with Relapse

PURPOSE

Acute promyelocytic leukemia (APL) is the most prognostically favorable subtype of Acute myeloid leukemia (AML). Defining the features that allow identification of APL patients likely to relapse after therapy remains challenging.

EXPERIMENTAL DESIGN

Proteomic profiling is performed on 20 newly diagnosed APL, 205 non-APL AML, and 10 normal CD34+ samples using Reverse Phase Protein Arrays probed with 230 antibodies.

RESULTS

Comparison between APL and non-APL AML samples identifies 8.3% of the proteins to be differentially expressed. Proteins higher expressed in APL are involved in the pro-apoptotic pathways or are linked to higher proliferation. The "MetaGalaxy" approach that considers proteins in relation to other assayed proteins stratifies the APL patients into two protein signatures. All of the relapse patients (n = 4/4) are in protein signature 2 (S2). Comparison of proteins between the signatures shows significant differences in relative expression for 38 proteins. Protein expression summary plots suggest less translational activity in combination with a less proliferative character for S2 compared to signature 1.

CONCLUSIONS AND CLINICAL RELEVANCE

This study provides a potential proteomic-based classification of APL patients that may be useful for risk stratification and therapeutic guidance. Validation in a larger independent cohort is required.

Single-Cell Analysis Reveals Regional Reprogramming During Adaptation to Massive Small Bowel Resection in Mice

BACKGROUND & AIMS

The small intestine (SI) displays regionality in nutrient and immunological function. Following SI tissue loss (as occurs in short gut syndrome, or SGS), remaining SI must compensate, or "adapt"; the capacity of SI epithelium to reprogram its regional identity has not been described. Here, we apply single-cell resolution analyses to characterize molecular changes underpinning adaptation to SGS.

METHODS

Single-cell RNA sequencing was performed on epithelial cells isolated from distal SI of mice following 50% proximal small bowel resection (SBR) vs sham surgery. Single-cell profiles were clustered based on transcriptional similarity, reconstructing differentiation events from intestinal stem cells (ISCs) through to mature enterocytes. An unsupervised computational approach to score cell identity was used to quantify changes in regional (proximal vs distal) SI identity, validated using immunofluorescence, immunohistochemistry, qPCR, western blotting, and RNA-FISH.

RESULTS

Uniform Manifold Approximation and Projection-based clustering and visualization revealed differentiation trajectories from ISCs to mature enterocytes in sham and SBR. Cell identity scoring demonstrated segregation of enterocytes by regional SI identity: SBR enterocytes assumed more mature proximal identities. This was associated with significant upregulation of lipid metabolism and oxidative stress gene expression, which was validated via orthogonal analyses. Observed upstream transcriptional changes suggest retinoid metabolism and proximal transcription factor Creb3l3 drive proximalization of cell identity in response to SBR.

CONCLUSIONS

Adaptation to proximal SBR involves regional reprogramming of ileal enterocytes toward a proximal identity. Interventions bolstering the endogenous reprogramming capacity of SI enterocytes-conceivably by engaging the retinoid metabolism pathway-merit further investigation, as they may increase enteral feeding tolerance, and obviate intestinal failure, in SGS.

The reproductive life cycle of cancer: Hypotheses of cell of origin, TP53 drivers and stem cell conversions in the light of the atavistic cancer cell theory

Polyploid giant cancer cells (PGCCs) found in different solid cancers are reproductive cyst-like structures surrounded by an actin envelop. They give rise by hyper-polyploidisation to numerous progeny (microcells, neotic cells) that start a primitive multi-lined lineage and generate subsequent PGCCs by asymmetric cell division and cyclic differentiation. This cancer cell life cycle has multiple similarities with the life cycle of lower eukaryotes (protists) substantiating the atavistic theory of cancer. The primitive cancer life cycle contains several cell types including primary cancer stem cells, somatic cells, as well as reproductive cells, that differentiate new atavistic cyst like structures (aCLSs, PGCCs). Accordingly, cancer stem cells are not transformed normal stem cells (hSCs). Similarities between CSCs and normal hSCs arise from the evolutionary common origin of primitive eukaryotes and more highly evolved eukaryotic cells (stemness evolution). The cell of origin of cancer, as postulated here is a deregulated human cell that has lost, not only relevant control mechanisms and mitotic capacity, but also its normal human p53 network becoming useless for the atavistic life cycle. We believe that this protoprecursor of cancer reactivates an ancient primitive TP53 network originating from the common eukaryotic ancestor. This atavistic p53 helpes to repair genotoxic DNA damages of reproductive cancer cells including CSCs but not DNA damages of somatic cancer cells exposed to genotoxic stress.

Impact of viral presence in tumor on gene expression in non-small cell lung cancer

Background

In our recent study, most non-small-lung cancer (NSCLC) tumor specimens harbored viral DNA but it was absent in non-neoplastic lung. However, their targets and roles in the tumor cells remain poorly understood. We analyzed gene expression microarrays to identify genes and pathways differentially altered between virus-infected and uninfected NSCLC tumors.

Methods

Gene expression microarrays of 30 primary and 9 metastatic NSCLC patients were preprocessed through a series of quality control analyses. Linear Models for Microarray Analysis and Gene Set Enrichment Analysis were used to assess differential expression.

Results

Various genes and gene sets had significantly altered expressions between virus-infected and uninfected NSCLC tumors. Notably, 22 genes on the viral carcinogenesis pathway were significantly overexpressed in virus-infected primary tumors, along with three oncogenic gene sets. A total of 12 genes, as well as seven oncogenic and 133 immunologic gene sets, were differentially altered in squamous cell carcinomas, depending on the virus. In adenocarcinoma, 14 differentially expressed genes (DEGs) were identified, but no oncogenic and immunogenic gene sets were significantly altered. In bronchioloalveolar carcinoma, several genes were highly overexpressed in virus-infected specimens, but not statistically significant. Only five of 69 DEGs (7.2%) from metastatic tumor analysis overlapped with 1527 DEGs from the primary tumor analysis, indicating differences in host cellular targets and the viral impact between primary and metastatic NSCLC.

Conclusions

The differentially expressed genes and gene sets were distinctive among infected viral types, histological subtypes, and metastatic disease status of NSCLC. These results support the hypothesis that tumor viruses play a role in NSCLC by regulating host genes in tumor cells during NSCLC differentiation and progression.

Electronic supplementary material

The online version of this article (10.1186/s12885-018-4748-0) contains supplementary material, which is available to authorized users.

Multifaceted regulation and functions of replication factor C family in human cancers

Replication factor C (RFC) family is a complex comprised of the RFC1, RFC2, RFC3, RFC4, and RFC5 subunits, which acts as a primer recognition factor for DNA polymerase. It is reported that RFC, biologically active in various malignant tumors, may play an important role in the proliferation, progression, invasion, and metastasis of cancer cells. It could act as an oncogene or tumor suppressor gene based on the cellular and histological characteristics of the tumor. In this review, we summarized the updated researches on the structure, physiological function, and expression pattern of RFC in a variety of tumors, the underlying mechanisms on carcinogenesis, and the potentials of RFC family members in the diagnosis and prognosis prediction.

Identification of RFC5 as a novel potential prognostic biomarker in lung cancer through bioinformatics analysis

Lung cancer is the leading cause of mortalities among all types of cancer. Therefore, the screening of biomarkers that are related with the progression of lung cancer is crucial for early diagnosis and efficient therapy of lung cancer. In the present study, bioinformatic analysis identified replication factor C 5 (RFC5) as a potential novel oncogene in lung cancer. RFC5 functions as a clamp loader and is involved in DNA replication and repair. Analysis of public databases and reverse transcription-quantitative polymerase chain reaction indicated that RFC5 was significantly increased in tumor tissues compared with adjacent normal tissues. A high RFC5 expression was observed to be associated with more aggressive malignant clinicopathological features, including higher T stage, more advanced regional lymph node metastasis and a higher probability of relapse. Notably, there were notable differences in overall survival (OS), first progression and post-progression survival between the high RFC5 expression group and low RFC5 expression group. Univariate and multivariate Cox regression analyses indicated that RFC5 was an independent risk factor that was associated with poorer OS and disease-free survival. According to GSEA, several gene sets that are associated with cell cycle and DNA damage were enriched in the RFC5 overexpression group, which indicated that RFC5 might promote the proliferation of lung cancer cells. Our finding indicated that RFC5 might be a novel prognostic biomarker of lung cancer, and it might be serve as a potential diagnosis and therapy target for lung cancer in the future.

ATRA increases iodine uptake and inhibits the proliferation and invasiveness of human anaplastic thyroid carcinoma SW1736 cells: Involvement of β-catenin phosphorylation inhibition

All-trans-retinoic acid (ATRA) can enhance iodine uptake capability of thyroid tumors, but the mechanisms remain poorly understood. The aim of the present study was to investigate the effects of ATRA on isotope susceptibility, proliferation and invasion of anaplastic thyroid carcinoma (ATC) and potential mechanisms. SW1736 cells were treated with 1 µmol/l ATRA or 1% ethanol for 5 days. A cell line stably expressing β-catenin-shRNA was established. An iodine uptake assay was performed using ¹²⁵I. Proliferation and invasiveness were tested using MTT and Transwell assays, respectively. Western blotting was used to assess the expression of β-catenin, glycogen synthase kinase-3β (GSK-3β), sodium/iodine symporter (NIS) and proteins involved in epithelial-mesenchymal transition. Cells pretreated with ATRA were injected subcutaneously into SCID mice. Mice were intraperitoneally injected with ¹³¹I once on the first day of treatment, and tumor growth was then assessed. After 35 days of ¹³¹I treatment, ATRA-pretreated tumor volume and weight were decreased compared with the ¹³¹I alone group (163.32±19.57 vs. 332.06±21.37 mm³; 0.35±0.14 vs. 0.67±0.23 g, both P<0.05). Similar results were observed in the β-catenin shRNA-pretreated tumors. ATRA also increased the uptake of iodine by SW1736 cells (P<0.01), and similar results were observed in β-catenin shRNA cells. ATRA treatment decreased the cell proliferation and invasion compared with control cells (all P<0.05), similar to β-catenin shRNA. ATRA treatment decreased the expression of phosphorylated (p-)β-catenin, p-GSK-3β, vimentin, and fibronectin, and increased the expression of NIS and E-cadherin, compared with the control. ATRA increased the iodine uptake and inhibited the proliferation and invasion of SW1736 cells, involving β-catenin phosphorylation. In conclusion, ATRA could be used to improve the isotope sensitivity of ATC.