Increased Genetic Instability and Accelerated Progression of Colitis-Associated Colorectal Cancer through Intestinal Epithelium-specific Deletion of Klf4

Integrated whole transcriptome profiling revealed a convoluted circular RNA-based competing endogenous RNAs regulatory network in colorectal cancer

Recently, it has been identified that circRNAs can act as miRNA sponge to regulate gene expression in various types of cancers, associating them with cancer initiation and progression. The present study aims to identify colorectal cancer-related circRNAs and the underpinning mechanisms of circRNA/miRNA/mRNA networks in the development and progress of Colorectal Cancer. Differentially expressed circRNAs, miRNAs, and mRNAs were identified in GEO microarray datasets using the Limma package of R. The analysis of differentially expressed circRNAs resulted in 23 upregulated and 31 downregulated circRNAs. CeRNAs networks were constructed by intersecting the results of predicted and experimentally validated databases, circbank and miRWalk, and by performing DEMs and DEGs analysis using Cytoscape. Next, functional enrichment analysis was performed for DEGs included in ceRNA networks. Followed by survival analysis, expression profile assessment using TCGA and GEO data, and ROC curve analysis we identified a ceRNA sub-networks that revealed the potential regulatory effect of hsa_circ_0001955 and hsa_circ_0071681 on survival-related genes, namely KLF4, MYC, CCNA2, RACGAP1, and CD44. Overall, we constructed a convoluted regulatory network and outlined its likely mechanisms of action in CRC, which may contribute to the development of more effective approaches for early diagnosis, prognosis, and treatment of CRC.

The Roles of Zinc Finger Proteins in Colorectal Cancer

Despite colorectal cancer remaining a leading worldwide cause of cancer-related death, there remains a paucity of effective treatments for advanced disease. The molecular mechanisms underlying the development of colorectal cancer include altered cell signaling and cell cycle regulation that may result from epigenetic modifications of gene expression and function. Acting as important transcriptional regulators of normal biological processes, zinc finger proteins also play key roles in regulating the cellular mechanisms underlying colorectal neoplasia. These actions impact cell differentiation and proliferation, epithelial-mesenchymal transition, apoptosis, homeostasis, senescence, and maintenance of stemness. With the goal of highlighting promising points of therapeutic intervention, we review the oncogenic and tumor suppressor roles of zinc finger proteins with respect to colorectal cancer tumorigenesis and progression.

Krüppel-like Factors 4 and 5 in Colorectal Tumorigenesis

Krüppel-like factors (KLFs) are transcription factors regulating various biological processes such as proliferation, differentiation, migration, invasion, and homeostasis. Importantly, they participate in disease development and progression. KLFs are expressed in multiple tissues, and their role is tissue- and context-dependent. KLF4 and KLF5 are two fascinating members of this family that regulate crucial stages of cellular identity from embryogenesis through differentiation and, finally, during tumorigenesis. They maintain homeostasis of various tissues and regulate inflammation, response to injury, regeneration, and development and progression of multiple cancers such as colorectal, breast, ovarian, pancreatic, lung, and prostate, to name a few. Recent studies broaden our understanding of their function and demonstrate their opposing roles in regulating gene expression, cellular function, and tumorigenesis. This review will focus on the roles KLF4 and KLF5 play in colorectal cancer. Understanding the context-dependent functions of KLF4 and KLF5 and the mechanisms through which they exert their effects will be extremely helpful in developing targeted cancer therapy.

Fecal Microbiota Restoration Modulates the Microbiome in Inflammation-Driven Colorectal Cancer

Chronic inflammation of the colon (colitis) is a known risk factor for inflammatory-driven colorectal cancers (id-CRCs), and intestinal microbiota has been implicated in the etiology of id-CRCs. Manipulation of the microbiome is a clinically viable therapeutic approach to limiting id-CRCs. To understand the microbiome changes that occur over time in id-CRCs, we used a mouse model of id-CRCs with the treatment of azoxymethane (AOM) and dextran sodium sulfate (DSS) and measured the microbiome over time. We included cohorts where the microbiome was restored using cage bedding swapping and where the microbiome was depleted using antibiotics to compare to untreated animals. We identified consistent increases in Akkermansia in mice receiving horizontal microbiome transfer (HMT) via cage bedding swapping, while the control cohort had consistent longitudinal increases in Anaeroplasma and Alistipes. Additionally, fecal lipocalin-2 (Lcn-2), a marker of intestinal inflammation, was elevated in unrestored animals compared to restored and antibiotic-treated counterparts following HMT. These observations suggest a potential role for Akkermansia, Anaeroplasma, and Alistipes in regulating colonic inflammation in id-CRCs.

KLF4 transcription factor in tumorigenesis

Krüppel-like transcriptional factor is important in maintaining cellular functions. Deletion of Krüppel-like transcriptional factor usually causes abnormal embryonic development and even embryonic death. KLF4 is a prominent member of this family, and embryonic deletion of KLF4 leads to alterations in skin permeability and postnatal death. In addition to its important role in embryo development, it also plays a critical role in inflammation and malignancy. It has been investigated that KLF4 has a regulatory role in a variety of cancers, including lung, breast, prostate, colorectal, pancreatic, hepatocellular, ovarian, esophageal, bladder and brain cancer. However, the role of KLF4 in tumorigenesis is complex, which may link to its unique structure with both transcriptional activation and transcriptional repression domains, and to the regulation of its upstream and downstream signaling molecules. In this review, we will summarize the structural and functional aspects of KLF4, with a focus on KLF4 as a clinical biomarker and therapeutic target in different types of tumors.

The complex network of transcription factors, immune checkpoint inhibitors and stemness features in colorectal cancer: A recent update

Cancer immunity is regulated by several mechanisms that include co-stimulatory and/or co-inhibitory molecules known as immune checkpoints expressed by the immune cells. In colorectal cancer (CRC), CTLA-4, LAG3, TIM-3 and PD-1 are the major co-inhibitory checkpoints involved in tumor development and progression. On the other hand, the deregulation of transcription factors and cancer stem cells activity plays a major role in the development of drug resistance and in the spread of metastatic disease in CRC. In this review, we describe how the modulation of such transcription factors affects the response of CRC to therapies. We also focus on the role of cancer stem cells in tumor metastasis and chemoresistance and discuss both preclinical and clinical approaches for targeting stem cells to prevent their tumorigenic effect. Finally, we provide an update on the clinical applications of immune checkpoint inhibitors in CRC and discuss the regulatory effects of transcription factors on the expression of the immune inhibitory checkpoints with specific focus on the PD-1 and PD-L1 molecules.

Stemness potency and structural characteristics of thyroid cancer cell lines

BACKGROUND

Thyroid cancer is the most frequent type of endocrine malignancy. Thyroid carcinomas are derived from the follicular epithelium and classified as papillary (PTC) (85%), follicular (FTC) (12%), and anaplastic (ATC) (<3%). Thyroid cancer could arise from thyroid cancer stem-like cells (CSCs). CSCs are cancer cells that feature stem-like properties. Kruppel-like factor (KLF4) and Stage-spesific embryonic antigen 1 (SSEA-1) are types of stem cell markers. Filamentous actin (F-actin) is an essential part of the cellular cytoskeleton. The purpose of this study was to evaluate the stem cell potency and the spatial distribution of the cytoskeletal element F-actin in PTC, FTC, and ATC cell lines.

MATERIALS AND METHODS

Normal thyroid cell line (NTC) Nthy-ori-3-1, PTC cell line BCPAP, FTC cell line FTC-133 and ATC cell line 8505c were stained with SSEA-1 and KLF4 for stem cell potency and F-actin for cytoskeleton. The morphological properties of cells were assessed by a scanning electron microscope (SEM) and elemental ratios were compared with EDS.

RESULTS

PTCs had greater percentages of SSEA-1 and KLF4 protein intensity (0.32% and 0.49%, respectively) than NTCs. ATCs had a greater proportion of KLF4 expression (0.8%) than NTCs. NTCs and FTCs had increased F-actin intensity across the cell, but PTCs had the lowest among these four cell lines. NTCs and PTCs, as well as NTCs and FTCs, have statistically identical aspect ratios and round values. These values, however, were statistically different in ATCs.

CONCLUSION

The study of stem cell markers and the cytoskeletal element F-actin in cancer and normal thyroid cell lines may assist in the identification of new therapeutic targets and contribute in the understanding of treatment resistance mechanisms.

Identification of hub genes and pathways in colitis-associated colon cancer by integrated bioinformatic analysis

Background

Colitis-associated colon cancer (CAC) patients have a younger age of onset, more multiple lesions and invasive tumors than sporadic colon cancer patients. Early detection of CAC using endoscopy is challenging, and the incidence of septal colon cancer remains high. Therefore, identifying biomarkers that can predict the tumorigenesis of CAC is in urgent need.

Results

A total of 275 DEGs were identified in CAC. IGF1, BMP4, SPP1, APOB, CCND1, CD44, PTGS2, CFTR, BMP2, KLF4, and TLR2 were identified as hub DEGs, which were significantly enriched in the PI3K-Akt pathway, stem cell pluripotency regulation, focal adhesion, Hippo signaling, and AMPK signaling pathways. Sankey diagram showed that the genes of both the PI3K-AKT signaling and focal adhesion pathways were upregulated (e.g., SPP1, CD44, TLR2, CCND1, and IGF1), and upregulated genes were predicted to be regulated by the crucial miRNAs: hsa-mir-16-5p, hsa-mir-1-3p, et al. Hub gene-TFs network revealed FOXC1 as a core transcription factor. In ulcerative colitis (UC) patients, KLF4, CFTR, BMP2, TLR2 showed significantly lower expression in UC-associated cancer. BMP4 and IGF1 showed higher expression in UC-Ca compared to nonneoplastic mucosa. Survival analysis showed that the differential expression of SPP1, CFRT, and KLF4 were associated with poor prognosis in colon cancer.

Conclusion

Our study provides novel insights into the mechanism underlying the development of CAC. The hub genes and signaling pathways may contribute to the prevention, diagnosis and treatment of CAC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-022-01065-7.

KLF16 enhances stress tolerance of colorectal carcinomas by modulating nucleolar homeostasis and translational reprogramming

Translational reprogramming is part of the unfolded protein response (UPR) during endoplasmic reticulum (ER) stress, which acts to the advantage of cancer growth and development in different stress conditions. But the mechanism of ER stress-related translational reprogramming in colorectal carcinoma (CRC) progression remains unclear. Here, we identified that Krüppel-Like Factor 16 (KLF16) can promote CRC progression and stress tolerance through translational reprogramming. The expression of KLF16 was upregulated in CRC tissues and associated with poor prognosis for CRC patients. We found that ER stress inducers can recruit KLF16 to the nucleolus and increase its interaction with two essential proteins for nucleolar homeostasis, nucleophosmin1 (NPM1) and fibrillarin (FBL). Moreover, knockdown of KLF16 can dysregulate nucleolar homeostasis in CRC cells. Translation-reporter system and polysome profiling assays further showed that KLF16 can effectively promote cap-independent translation of ATF4, which can enhance ER-phagy and proliferation of CRC cells. Overall, our study unveils a previously unrecognized role for KLF16 as an ER stress regulator through mediating translational reprogramming to enhance stress tolerance of CRC cells and provides a potential therapeutic vulnerability.

Class Ib MHC-Mediated Immune Interactions Play a Critical Role in Maintaining Mucosal Homeostasis in the Mammalian Large Intestine

Lymphocytes within the intestinal epithelial layer (IEL) in mammals have unique composition compared with their counterparts in the lamina propria. Little is known about the role of some of the key colonic IEL subsets, such as TCRαβ⁺CD8⁺ T cells, in inflammation. We have recently described liver-enriched innate-like TCRαβ⁺CD8αα regulatory T cells, partly controlled by the non-classical MHC molecule, Qa-1^b, that upon adoptive transfer protect from T cell-induced colitis. In this study, we found that TCRαβ⁺CD8αα T cells are reduced among the colonic IEL during inflammation, and that their activation with an agonistic peptide leads to significant Qa-1^b-dependent protection in an acute model of colitis. Cellular expression of Qa-1^b during inflammation and corresponding dependency in peptide-mediated protection suggest that Batf3-dependent CD103⁺CD11b^- type 1 conventional dendritic cells control the protective function of TCRαβ⁺CD8αα T cells in the colonic epithelium. In the colitis model, expression of the potential barrier-protective gene, Muc2, is enhanced upon administration of a Qa-1b agonistic peptide. Notably, in steady state, the mucin metabolizing Akkermansia muciniphila was found in significantly lower abundance amid a dramatic change in overall microbiome and metabolome, increased IL-6 in explant culture, and enhanced sensitivity to dextran sulfate sodium in Qa-1b deficiency. Finally, in patients with inflammatory bowel disease, we found upregulation of HLA-E, a Qa-1^b analog with inflammation and biologic non-response, in silico, suggesting the importance of this regulatory mechanism across species.

A Crosstalk between Diet, Microbiome and microRNA in Epigenetic Regulation of Colorectal Cancer

A still growing interest between human nutrition in relation to health and disease states can be observed. Dietary components shape the composition of microbiota colonizing our gastrointestinal tract which play a vital role in maintaining human health. There is a strong evidence that diet, gut microbiota and their metabolites significantly influence our epigenome, particularly through the modulation of microRNAs. These group of small non-coding RNAs maintain cellular homeostasis, however any changes leading to impaired expression of miRNAs contribute to the development of different pathologies, including neoplastic diseases. Imbalance of intestinal microbiota due to diet is primary associated with the development of colorectal cancer as well as other types of cancers. In the present work we summarize current knowledge with particular emphasis on diet-microbiota-miRNAs axis and its relation to the development of colorectal cancer.

Loss of Mucosal p32/gC1qR/HABP1 Triggers Energy Deficiency and Impairs Goblet Cell Differentiation in Ulcerative Colitis

BACKGROUND & AIMS

Cell differentiation in the colonic crypt is driven by a metabolic switch from glycolysis to mitochondrial oxidation. Mitochondrial and goblet cell dysfunction have been attributed to the pathology of ulcerative colitis (UC). We hypothesized that p32/gC1qR/HABP1, which critically maintains oxidative phosphorylation, is involved in goblet cell differentiation and hence in the pathogenesis of UC.

METHODS

Ex vivo, goblet cell differentiation in relation to p32 expression and mitochondrial function was studied in tissue biopsies from UC patients versus controls. Functional studies were performed in goblet cell-like HT29-MTX cells in vitro. Mitochondrial respiratory chain complex V-deficient, ATP8 mutant mice were utilized as a confirmatory model. Nutritional intervention studies were performed in C57BL/6 mice.

RESULTS

In UC patients in remission, colonic goblet cell differentiation was significantly decreased compared to controls in a p32-dependent manner. Plasma/serum L-lactate and colonic pAMPK level were increased, pointing at high glycolytic activity and energy deficiency. Consistently, p32 silencing in mucus-secreting HT29-MTX cells abolished butyrate-induced differentiation and induced a shift towards glycolysis. In ATP8 mutant mice, colonic p32 expression correlated with loss of differentiated goblet cells, resulting in a thinner mucus layer. Conversely, feeding mice an isocaloric glucose-free, high-protein diet increased mucosal energy supply that promoted colonic p32 level, goblet cell differentiation and mucus production.

CONCLUSION

We here describe a new molecular mechanism linking mucosal energy deficiency in UC to impaired, p32-dependent goblet cell differentiation that may be therapeutically prevented by nutritional intervention.

Transcription factors in colorectal cancer: molecular mechanism and therapeutic implications

Colorectal cancer (CRC) is a major cause of cancer mortality worldwide, however, the molecular mechanisms underlying the pathogenesis of CRC remain largely unclear. Recent studies have revealed crucial roles of transcription factors in CRC development. Transcription factors essential for the regulation of gene expression by interacting with transcription corepressor/enhancer complexes and they orchestrate downstream signal transduction. Deregulation of transcription factors is a frequent occurrence in CRC, and the accompanying drastic changes in gene expression profiles play fundamental roles in multistep process of tumorigenesis, from cellular transformation, disease progression to metastatic disease. Herein, we summarized current and emerging key transcription factors that participate in CRC tumorigenesis, and highlighted their oncogenic or tumor suppressive functions. Moreover, we presented critical transcription factors of CRC, emphasized the major molecular mechanisms underlying their effect on signal cascades associated with tumorigenesis, and summarized of their potential as molecular biomarkers for CRC prognosis therapeutic response, as well as drug targets for CRC treatment. A better understanding of transcription factors involved in the development of CRC will provide new insights into the pathological mechanisms and reveal novel prognostic biomarkers and therapeutic strategies for CRC.

Recent Discoveries on the Involvement of Krüppel-Like Factor 4 in the Most Common Cancer Types

Krüppel-like factor 4 (KLF4) is a transcription factor highly conserved in evolution. It is particularly well known for its role in inducing pluripotent stem cells. In addition, KLF4 plays many roles in cancer. The results of most studies suggest that KLF4 is a tumor suppressor. However, the functioning of KLF4 is regulated at many levels. These include regulation of transcription, alternative splicing, miRNA, post-translational modifications, subcellular localization, protein stability and interactions with other molecules. Simple experiments aimed at assaying transcript levels or protein levels fail to address this complexity and thus may deliver misleading results. Tumor subtypes are also important; for example, in prostate cancer KLF4 is highly expressed in indolent tumors where it impedes tumor progression, while it is absent from aggressive prostate tumors. KLF4 is important in regulating response to many known drugs, and it also plays a role in tumor microenvironment. More and more information is available about upstream regulators, downstream targets and signaling pathways associated with the involvement of KLF4 in cancer. Furthermore, KLF4 performs critical function in the overall regulation of tissue homeostasis, cellular integrity, and progression towards malignancy. Here we summarize and analyze the latest findings concerning this fascinating transcription factor.

The membrane-bound and soluble form of melanotransferrin function independently in the diagnosis and targeted therapy of lung cancer

Melanotransferrin (MFI2) is a newly identified tumor-associated protein, which consists of two forms of proteins, membrane-bound (mMFI2) and secretory (sMFI2). However, little is known about the expression pattern and their relevance in lung cancer. Here, we found that both two forms of MFI2 are highly expressed in lung cancer. The expression of MFI2 in lung cancer was detected by using the public database and qRT-PCR. Overexpression and knockdown cell lines and recombinant sMFI2 protein were used to study the function of mMFI2 and sMFI2. RNA-seq, protein chip, ChIP assay, Immunoprecipitation, ELISA, and immunofluorescence were used to study the molecular biological mechanism of mMFI2 and sMFI2. We found that mMFI2 promoted the expression of EMT’s common marker N-cadherin by downregulating the transcription factor KLI4, which in turn promoted tumor metastasis; sMFI2 could promote the metastasis of autologous tumor cells in an autocrine manner but the mechanism is different from that of mMFI2. In addition, sMFI2 was proved could inhibit the migration of vascular endothelial cells and subsequently enhance angiogenic responses in a paracrine manner. We propose that the expressions and functions of the two forms of MFI2 in lung cancer are relatively independent. Specifically, mMFI2 was a potential lung cancer therapeutic target, while sMFI2 was highly enriched in advanced lung cancer, and could be used as a tumor staging index.

Loss of the Krüppel-like factor 4 tumor suppressor is associated with epithelial-mesenchymal transition in colorectal cancer

Aim:

Colorectal cancer (CRC) is the third leading cancer-related cause of death due to its propensity to metastasize. Epithelial-mesenchymal transition (EMT) is a multistep process important for invasion and metastasis of CRC. Krüppel-like factor 4 (KLF4) is a zinc finger transcription factor highly expressed in differentiated cells of the intestinal epithelium. KLF4 has been shown to play a tumor suppressor role during CRC tumorigenesis - its loss accelerates development and progression of cancer. The present study examined the relationship between KLF4 and markers of EMT in CRC.

Methods:

Immunofluorescence staining for KLF4 and EMT markers was performed on archived patient samples after colorectal cancer resection and on colonic tissues of mice with colitis-associated cancer.

Results:

We found that KLF4 expression is lost in tumor sections obtained from CRC patients and in those of mouse colon following azoxymethane and dextran sodium sulfate (AOM/DSS) treatment when compared to their respective normal appearing mucosa. Importantly, in CRC patient tumor sections, we observed a negative correlation between KLF4 levels and mesenchymal markers including TWIST, β-catenin, claudin-1, N-cadherin, and vimentin. Similarly, in tumor tissues from AOM/DSS-treated mice, KLF4 levels were negatively correlated with mesenchymal markers including SNAI2, β-catenin, and vimentin and positively correlated with the epithelial marker E-cadherin.

Conclusion:

These findings suggest that the loss of KLF4 expression is a potentially significant indicator of EMT in CRC.

KLF4 overexpression decreases the viability, invasion and migration of papillary thyroid cancer cells

Kruppel-like factor 4 (KLF4) has been implicated in a number of different types of cancer; however, the role of KLF4 in papillary thyroid cancer remains elusive. The present study aimed to investigate the role of KLF4 in papillary thyroid cancer and its potential underlying molecular mechanisms. The expression of KLF4 in thyroid tumor tissue and adjacent non-cancerous tissues were detected via immunohistochemistry and western blotting. The papillary thyroid cancer cell line, KTC1, was transfected with viruses carrying KLF4 overexpression vectors. The relative expression of KLF4, E-cadherin, N-cadherin, Vimentin, matrix metalloproteinase (MMP)2, MMP9 and collagen was detected via quantitative-PCR. The viability of KTC1 cells was detected using a cell counting kit-8 assay at 24, 48 and 72 h. Cell invasion was examined via a transwell invasion assay. Cell migration was examined via a scratch migration assay at 0 and 24 h. Compared with adjacent non-cancerous tissues, the expression of KLF4 was significantly lower in thyroid tumor tissues. The expression of KLF4 in KTC1 cells were significantly increased compared with the blank or negative control groups. The expression of N-cadherin, MMP2, MMP9 and collagen was significantly decreased in the KLF4 overexpression group. The viability of KTC1 cells was markedly decreased in KLF4 overexpression group at 24, 48 and 72 h when compared with the blank or negative control groups. The invasion of KTC1 cells in the KLF4 overexpression group was markedly decreased. Compared with the negative control group, the KTC1 cell migration in the KLF4 overexpression group was markedly decreased at 24 h. The expression of KLF4 was also significantly lower in thyroid tumor tissues. The cell viability, tumor invasion and migration ability and expression levels of N-cadherin, MMP2, MMP9 and collagen in papillary thyroid cancer cells were markedly decreased with KLF4 overexpression.