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1.
Ann Hematol ; 2024 Jun 06.
Artículo en Inglés | MEDLINE | ID: mdl-38842564

RESUMEN

Acute Myeloid Leukemia (AML) is a life-threatening disease whose induction treatment consists of combination chemotherapy with Idarubicin and Cytarabine for fit patients. Treatment failures are frequent, urging the need for novel treatments for this disease. The DNA Damage Response Mechanism (DDR) comprises numerous molecules and pathways intended to arrest the cell cycle until DNA damage is repaired or else drive the cell to apoptosis. AML-derived cell lines after treatment with Idarubicin and Cytarabine were used for studying the expression profile of 84 DDR genes, through PCR arrays. Utilizing de novo AML patient and control samples we studied the expression of PPP1R15A, CDKN1A, GADD45A, GADD45G, and EXO1. Next, we performed PPP1R15A silencing in AML cell lines in two separate experiments using siRNA and CRISPR-cas9, respectively. Our findings highlight that DDR regulators demonstrate increased expression in patients with high cytogenetic risk possibly reflecting increased genotoxic stress. Especially, PPP1R15A is mainly involved in the recovery of the cells from stress and it was the only DDR gene upregulated in AML patients. The PPP1R15A silencing resulted in decreased viability of Idarubicin and Cytarabine-treated cell lines, in contrast to untreated cells. These findings shed light on new strategies to enhance chemotherapy efficacy and demonstrate that PPP1R15A is an important DDR regulator in AML and its downregulation might be a safe and effective way to increase sensitivity to chemotherapy in this disease.

2.
Funct Integr Genomics ; 23(4): 299, 2023 Sep 14.
Artículo en Inglés | MEDLINE | ID: mdl-37707691

RESUMEN

Triple-negative breast cancer (TNBC) is a subtype of breast cancer characterized by poor prognosis and limited treatment options. Oleuropein and oleocanthal are bioactive chemicals found in extra-virgin olive oil; they have been shown to have anti-cancer potential. In this study, we examined the inhibitory effects of these two natural compounds, on MDA-MB-231 and MDA-MB-468 TNBC cell lines. The human TNBC MDA-MB-231 and MDA-MB-468 cell lines were treated with oleuropein or oleocanthal at ranging concentrations for 48 h. After determining the optimum concentration to reach IC50, using the sulforhodamine B assay, total RNA was extracted after 12, 24, and 48 h from treated and untreated cells. Poly(A)-RNA selection was conducted, followed by library construction and RNA sequencing. Differential gene expression (DEG) analysis was performed to identify DEGs between treated and untreated cells. Pathway analysis was carried out using the KEGG and GO databases. Oleuropein and oleocanthal considerably reduced the proliferation of TNBC cells, with oleocanthal having a slightly stronger effect than oleuropein. Furthermore, multi-time series RNA sequencing showed that the expression profile of TNBC cells was significantly altered after treatment with these compounds, with temporal dynamics and groups of genes consistently affected at all time points. Pathway analysis revealed several significant pathways associated with TNBC, including cell death, apoptotic process, programmed cell death, response to stress, mitotic cell cycle process, cell division, and cancer progression. Our findings suggest that oleuropein and oleocanthal have potential therapeutic benefits for TNBC and can be further investigated as alternative treatment options.


Asunto(s)
Neoplasias de la Mama Triple Negativas , Humanos , Neoplasias de la Mama Triple Negativas/tratamiento farmacológico , Neoplasias de la Mama Triple Negativas/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Expresión Génica , ARN
3.
Funct Integr Genomics ; 23(4): 341, 2023 Nov 21.
Artículo en Inglés | MEDLINE | ID: mdl-37987851

RESUMEN

tRNA fragments (tRFs) are small non-coding RNAs generated through specific cleavage of tRNAs and involved in various biological processes. Among the different types of tRFs, the 3'-tRFs have attracted scientific interest due to their regulatory role in gene expression. In this study, we investigated the role of 3'-tRF-CysGCA, a tRF deriving from cleavage in the T-loop of tRNACysGCA, in the regulation of gene expression in HEK-293 cells. Previous studies have shown that 3'-tRF-CysGCA is incorporated into the RISC complex and interacts with Argonaute proteins, suggesting its involvement in the regulation of gene expression. However, the general role and effect of the deregulation of 3'-tRF-CysGCA levels in human cells have not been investigated so far. To fill this gap, we stably overexpressed 3'-tRF-CysGCA in HEK-293 cells and performed transcriptomic and proteomic analyses. Moreover, we validated the interaction of this tRF with putative targets, the levels of which were found to be affected by 3'-tRF-CysGCA overexpression. Lastly, we investigated the implication of 3'-tRF-CysGCA in various pathways using extensive bioinformatics analysis. Our results indicate that 3'-tRF-CysGCA overexpression led to changes in the global gene expression profile of HEK-293 cells and that multiple cellular pathways were affected by the deregulation of the levels of this tRF. Additionally, we demonstrated that 3'-tRF-CysGCA directly interacts with thymopoietin (TMPO) transcript variant 1 (also known as LAP2α), leading to modulation of its levels. In conclusion, our findings suggest that 3'-tRF-CysGCA plays a significant role in gene expression regulation and highlight the importance of this tRF in cellular processes.


Asunto(s)
Proteómica , ARN de Transferencia , Humanos , Células HEK293 , ARN de Transferencia/genética , Regulación de la Expresión Génica
4.
Int J Mol Sci ; 25(1)2023 Dec 23.
Artículo en Inglés | MEDLINE | ID: mdl-38203408

RESUMEN

Prostate cancer (PCa) is a global health concern, being a leading cause of cancer-related mortality among males. Early detection and accurate prognosis are crucial for effective management. This study delves into the diagnostic and prognostic potential of 28S rRNA-derived fragments (rRFs) in PCa. Total RNA extracted from 89 PCa and 53 benign prostate hyperplasia (BPH) tissue specimens. After 3'-end polyadenylation, we performed reverse transcription to create first-strand cDNA. Using an in-house quantitative real-time PCR (qPCR) assay, we quantified 28S rRF levels. Post-treatment biochemical relapse served as the clinical endpoint event for survival analysis, which we validated internally through bootstrap analysis. Our results revealed downregulated 28S rRF levels in PCa compared to BPH patients. Additionally, we observed a significant positive correlation between 28S rRF levels and higher Gleason scores and tumor stages. Furthermore, PCa patients with elevated 28S rRF expression had a significantly higher risk of post-treatment disease relapse independently of clinicopathological data. In conclusion, our study demonstrates, for the first time, the prognostic value of 28S rRF in prostate adenocarcinoma. Elevated 28S rRF levels independently predict short-term PCa relapse and enhance risk stratification. This establishes 28S rRF as a potential novel molecular marker for PCa prognosis.


Asunto(s)
Hiperplasia Prostática , Neoplasias de la Próstata , Masculino , Humanos , Hiperplasia Prostática/genética , ARN Ribosómico 28S , Neoplasias de la Próstata/genética , Bioensayo , Enfermedad Crónica
5.
Int J Mol Sci ; 24(22)2023 Nov 18.
Artículo en Inglés | MEDLINE | ID: mdl-38003674

RESUMEN

Hepatocellular carcinoma (HCC) is a highly fatal malignancy with limited therapeutic options and high recurrence rates. Recently, immunotherapeutic agents such as immune checkpoint inhibitors (ICIs) have emerged as a new paradigm shift in oncology. ICIs, such as programmed cell death protein 1 (PD-1) inhibitors, have provided a new source of hope for patients with advanced HCC. Yet, the eligibility criteria of HCC patients for ICIs are still a missing piece in the puzzle. Circular RNAs (circRNAs) have recently emerged as a new class of non-coding RNAs that play a fundamental role in cancer pathogenesis. Structurally, circRNAs are resistant to exonucleolytic degradation and have a longer half-life than their linear counterparts. Functionally, circRNAs possess the capability to influence various facets of the tumor microenvironment, especially at the HCC tumor-immune synapse. Notably, circRNAs have been observed to control the expression of immune checkpoint molecules within tumor cells, potentially impeding the therapeutic effectiveness of ICIs. Therefore, this renders them potential cancer-immune biomarkers for diagnosis, prognosis, and therapeutic regimen determinants. In this review, the authors shed light on the structure and functional roles of circRNAs and, most importantly, highlight the promising roles of circRNAs in HCC immunomodulation and their potential as promising biomarkers and immunotherapeutic regimen determinants.


Asunto(s)
Carcinoma Hepatocelular , Neoplasias Hepáticas , Humanos , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/terapia , ARN Circular/genética , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/terapia , Inmunoterapia , Biomarcadores de Tumor/genética , Microambiente Tumoral/genética
6.
Int J Mol Sci ; 23(17)2022 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-36077156

RESUMEN

Small heat shock proteins (sHSPs) are ubiquitous ATP-independent chaperones that contribute to the maintenance of proteome integrity and functionality. Recent evidence suggests that sHSPs are ubiquitously expressed in numerous types of tumors and have been proposed to be implicated in oncogenesis and malignant progression. Heat shock protein family B member 2 (HSPB2) is a member of the sHSPs, which is found to be expressed, among others, in human breast cancer cell lines and constitutes an inhibitor of apical caspase activation in the extrinsic apoptotic pathway. In this study, we investigated the potential prognostic significance of HSPB2 mRNA expression levels in breast cancer, which represents the most frequent malignancy in females and one of the three most common cancer types worldwide. To this end, malignant breast tumors along with paired non-cancerous breast tissue specimens were used. HSPB2 expression levels were quantified in these two cohorts using a sensitive and accurate SYBR green-based quantitative real-time polymerase chain reaction (q-RT-PCR). Extensive biostatistical analyses were performed including Kaplan-Meier and Cox regression survival analyses for the assessment of the results. The significant downregulation of HSPB2 gene expression was revealed in breast tumors compared to their adjacent non-cancerous breast tissues. Notably, high HSPB2 mRNA expression predicts poor disease-free survival and overall survival of breast cancer patients. Multivariate Cox regression analysis revealed that HSPB2 mRNA overexpression is a significant predictor of poor prognosis in breast cancer, independent of other clinicopathological factors. In conclusion, high HSPB2 mRNA expression levels are associated with breast cancer patients' relapse and poor survival.


Asunto(s)
Neoplasias de la Mama , Proteínas de Choque Térmico Pequeñas , Apoptosis , Biomarcadores de Tumor/genética , Neoplasias de la Mama/patología , Femenino , Proteínas de Choque Térmico HSP27/metabolismo , Humanos , Recurrencia Local de Neoplasia/genética , ARN Mensajero/genética
7.
Pharmacogenomics J ; 21(6): 638-648, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34145402

RESUMEN

Retinoids are widely used in diseases spanning from dermatological lesions to cancer, but exhibit severe adverse effects. A novel all-trans-Retinoic Acid (atRA)-spermine conjugate (termed RASP) has shown previously optimal in vitro and in vivo anti-inflammatory and anticancer efficacy, with undetectable teratogenic and toxic side-effects. To get insights, we treated HaCaT cells which resemble human epidermis with IC50 concentration of RASP and analyzed their miRNA expression profile. Gene ontology analysis of their predicted targets indicated dynamic networks involved in cell proliferation, signal transduction and apoptosis. Furthermore, DNA microarrays analysis verified that RASP affects the expression of the same categories of genes. A protein-protein interaction map produced using the most significant common genes, revealed hub genes of nodal functions. We conclude that RASP is a synthetic retinoid derivative with improved properties, which possess the beneficial effects of retinoids without exhibiting side-effects and with potential beneficial effects against skin diseases including skin cancer.


Asunto(s)
Queratinocitos/efectos de los fármacos , MicroARNs/metabolismo , Espermina/análogos & derivados , Transcriptoma , Tretinoina/análogos & derivados , Apoptosis/efectos de los fármacos , Apoptosis/genética , Proliferación Celular/efectos de los fármacos , Proliferación Celular/genética , Relación Dosis-Respuesta a Droga , Redes Reguladoras de Genes , Células HaCaT , Humanos , Concentración 50 Inhibidora , Queratinocitos/metabolismo , Queratinocitos/patología , MicroARNs/genética , Mapas de Interacción de Proteínas , Transducción de Señal/efectos de los fármacos , Transducción de Señal/genética , Espermina/farmacología , Espermina/toxicidad , Tretinoina/farmacología , Tretinoina/toxicidad
8.
Eur J Haematol ; 106(6): 821-830, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33660275

RESUMEN

OBJECTIVE: 3' tRNA-derived fragments (3' tRFs) are important epigenetic regulators in normal and pathological conditions. In this study, we aimed to explore the potential value of a 3' tRF as a prognostic and/or screening biomarker for B-cell chronic lymphocytic leukemia (B-CLL). METHODS: Publicly available next-generation sequencing data from 20 B-CLL cases were analyzed, followed by prediction of targets of the most abundantly and ubiquitously expressed 3' tRFs, leading to selection of tRF-LeuAAG/TAG . PBMCs were isolated from blood samples of 91 B-CLL patients and 43 non-leukemic donors, followed by total RNA extraction, in-vitro polyadenylation, and first-strand cDNA synthesis. Next, a real-time quantitative PCR (qPCR) assay was developed for the accurate quantification of tRF-LeuAAG/TAG and applied in all samples, prior to biostatistical analysis. RESULTS: High tRF-LeuAAG/TAG levels are associated with inferior overall survival (OS) of B-CLL patients. The unfavorable significance of tRF-LeuAAG/TAG was independent of established prognostic factors in B-CLL. Stratified Kaplan-Meier OS analysis uncovered the unfavorable prognostic role of high tRF-LeuAAG/TAG levels for patients in Binet A or Rai I stage, negative CD38 expression, mutated, or unmutated IGHV genomic locus. CONCLUSION: Our approach revealed the independent prognostic value of a particular 3' tRF, derived from tRNALeuAAG and tRNALeuTAG (tRF-LeuAAG/TAG ) in B-CLL.


Asunto(s)
Biomarcadores de Tumor , Leucemia Linfocítica Crónica de Células B , ARN Neoplásico , ARN de Transferencia de Leucina , Anciano , Anciano de 80 o más Años , Biomarcadores de Tumor/sangre , Biomarcadores de Tumor/genética , Supervivencia sin Enfermedad , Femenino , Humanos , Leucemia Linfocítica Crónica de Células B/sangre , Leucemia Linfocítica Crónica de Células B/genética , Leucemia Linfocítica Crónica de Células B/mortalidad , Masculino , Persona de Mediana Edad , ARN Neoplásico/sangre , ARN Neoplásico/genética , ARN de Transferencia de Leucina/sangre , ARN de Transferencia de Leucina/genética , Tasa de Supervivencia
9.
Genomics ; 112(6): 4268-4276, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-32659328

RESUMEN

Alternative splicing is commonly involved in carcinogenesis, being highly implicated in differential expression of cancer-related genes. Recent studies have shown that the human CEACAM19 gene is overexpressed in malignant breast and ovarian tumors, possessing significant biomarker attributes. In the present study, 3' rapid amplification of cDNA ends (3' RACE) and next-generation sequencing (NGS) were used for the detection and identification of novel CEACAM19 transcripts. Bioinformatical analysis of our NGS data revealed novel splice junctions between previously annotated exons and ultimately new exons. Next, fifteen novel CEACAM19 transcripts were identified with Sanger sequencing. Additionally, their expression profile was investigated in a wide panel of human cell lines, using nested PCR with variant-specific primers. The broad expression pattern of the CEACAM19 gene, along with the fact that its overexpression has previously been associated with ovarian and breast cancer progression, indicate the potential of novel CEACAM19 transcripts as putative diagnostic and/or prognostic biomarkers.


Asunto(s)
Empalme Alternativo , Antígenos de Neoplasias/genética , Moléculas de Adhesión Celular/genética , Antígenos de Neoplasias/metabolismo , Moléculas de Adhesión Celular/metabolismo , Línea Celular Tumoral , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Neoplasias/genética , Neoplasias/metabolismo , Isoformas de ARN/metabolismo
10.
Genomics ; 112(1): 943-951, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31200028

RESUMEN

The human RNASEK gene encodes Ribonuclease κ, an endoribonuclease that belongs to a highly conserved protein family of metazoans. Recent evidence suggests that the mRNA levels of the RNASEK gene possess biomarker attributes in patients with prostate cancer. In the present study, we used 3' RACE and next-generation sequencing (NGS) to detect and identify novel RNASEK transcripts. Computational analysis of the NGS data revealed new alternative splicing events that support the existence of novel RNASEK alternative transcripts. As a result, eight RNASEK splice variants were discovered and their expression profile was analyzed with the use of nested PCR in a wide panel of human cell lines, originating from several cancerous and/or normal human tissues. Based on in silico analysis, six of the eight novel RNASEK transcripts are predicted to encode new protein isoforms, while the remaining two splice variants could be considered as nonsense-mediated mRNA decay (NMD) candidates.


Asunto(s)
Empalme Alternativo , Endorribonucleasas/genética , Línea Celular , Línea Celular Tumoral , Endorribonucleasas/química , Endorribonucleasas/metabolismo , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Isoenzimas/química , Isoenzimas/genética , Isoenzimas/metabolismo , Neoplasias/enzimología , Neoplasias/genética , Isoformas de ARN/metabolismo , Análisis de Secuencia de ARN
12.
Int J Mol Sci ; 22(5)2021 Feb 27.
Artículo en Inglés | MEDLINE | ID: mdl-33673480

RESUMEN

Multiple myeloma (MM) is a common hematological malignancy arising from terminally differentiated plasma cells. In the majority of cases, symptomatic disease is characterized by the presence of bone disease. Multiple myeloma bone disease (MMBD) is a result of an imbalance in the bone-remodeling process that leads to increased osteoclast activity and decreased osteoblast activity. The molecular background of MMBD appears intriguingly complex, as several signaling pathways and cell-to-cell interactions are implicated in the pathophysiology of MMBD. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate the expression of their target mRNAs. Numerous miRNAs have been witnessed to be involved in cancer and hematological malignancies and their role has been characterized either as oncogenic or oncosuppressive. Recently, scientific research turned towards miRNAs as regulators of MMBD. Scientific data support that miRNAs finely regulate the majority of the signaling pathways implicated in MMBD. In this review, we provide concise information regarding the molecular pathways with a significant role in MMBD and the miRNAs implicated in their regulation. Moreover, we discuss their utility as molecular biomarkers and highlight the putative usage of miRNAs as novel molecular targets for targeted therapy in MMBD.


Asunto(s)
MicroARNs/metabolismo , Mieloma Múltiple/metabolismo , Transducción de Señal , Animales , Enfermedades Óseas , Remodelación Ósea , Vesículas Extracelulares , Regulación Neoplásica de la Expresión Génica , Genes Relacionados con las Neoplasias , Humanos , Mieloma Múltiple/genética
13.
Int J Mol Sci ; 22(23)2021 Dec 05.
Artículo en Inglés | MEDLINE | ID: mdl-34884950

RESUMEN

Multiple myeloma (MM) is the second most common hematological malignancy, arising from terminally differentiated B cells, namely plasma cells. miRNAs are small non-coding RNAs that participate in the post-transcriptional regulation of gene expression. In this study, we investigated the role of nine miRNAs in MM. CD138+ plasma cells were selected from bone marrow aspirates from MM and smoldering MM (sMM) patients. Total RNA was extracted and in vitro polyadenylated. Next, first-strand cDNA synthesis was performed using an oligo-dT-adapter primer. For the relative quantification of the investigated miRNAs, an in-house real-time quantitative PCR (qPCR) assay was developed. A functional in silico analysis of the miRNAs was also performed. miR-16-5p and miR-155-5p expression was significantly lower in the CD138+ plasma cells of MM patients than in those of sMM patients. Furthermore, lower levels of miR-15a-5p, miR-16-5p, and miR-222-3p were observed in the CD138+ plasma cells of MM patients with osteolytic bone lesions, compared to those without. miR-125b-5p was also overexpressed in the CD138+ plasma cells of MM patients with bone disease that presented with skeletal-related events (SREs). Furthermore, lower levels of miR-223-3p were associated with significantly worse overall survival in MM patients. In conclusion, we propose a miRNA signature with putative clinical utility in MM.


Asunto(s)
Biomarcadores de Tumor/genética , Perfilación de la Expresión Génica/métodos , MicroARNs/genética , Mieloma Múltiple/genética , Adulto , Anciano , Femenino , Regulación Neoplásica de la Expresión Génica , Humanos , Masculino , Persona de Mediana Edad , Mieloma Múltiple/inmunología , Análisis de Supervivencia , Sindecano-1/metabolismo
14.
Mol Carcinog ; 59(1): 116-125, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31709619

RESUMEN

Small heat shock proteins (sHSPs) participate in numerous cellular functions including cell signaling, differentiation, and apoptosis. Deregulation of the physiological expression level of sHSPs has been associated with several malignancies. Heat shock protein beta 3 (HSPB3) is the third member of the sHSP family in human and is mainly expressed in skeletal and smooth muscles. In this study, we investigated the potential prognostic significance of HSPB3 expression in colorectal adenocarcinoma, the most frequent type of colorectal cancer. For this purpose, we isolated total RNA from 188 colorectal adenocarcinoma specimens and 68 paired noncancerous ones. After reverse transcription of 2 µg total RNA, we quantified HSPB3 levels by using an in-house-developed real-time quantitative polymerase chain reaction method, based on the SYBR Green chemistry. Comparison of HSPB3 levels among 68 pairs of colorectal tumors and their adjacent noncancerous mucosae uncovered the downregulation of HSPB3 expression in the majority of malignant colorectal tumors. More importantly, high HSPB3 expression is associated with poor relapse-free survival (RFS) and overall survival (OS) of patients with colorectal adenocarcinoma. Multivariable Cox regression analysis revealed that HSPB3 overexpression could serve as an adverse prognostic biomarker in colorectal adenocarcinoma, independent of tumor location, histological grade, and TNM stage. Patients' stratification according to tumor location, histological grade, and TNM stage revealed that high HSPB3 messenger RNA expression retains its unfavorable prognostic potential regarding OS, in particular groups of patients with substantially different prognosis. In conclusion, high HSPB3 expression is associated with poor RFS and OS of patients with colorectal adenocarcioma, independently of clinicopathological prognosticators.


Asunto(s)
Adenocarcinoma/genética , Neoplasias Colorrectales/genética , Regulación Neoplásica de la Expresión Génica , Proteínas de Choque Térmico/genética , Adenocarcinoma/diagnóstico , Adulto , Anciano , Anciano de 80 o más Años , Biomarcadores de Tumor/genética , Neoplasias Colorrectales/diagnóstico , Femenino , Humanos , Masculino , Persona de Mediana Edad , Pronóstico , ARN Mensajero/genética , Análisis de Supervivencia
15.
Genomics ; 111(4): 642-652, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-29614347

RESUMEN

Tissue kallikrein, kallikrein-related peptidases (KLKs), and plasma kallikrein form the largest group of serine proteases in the human genome, sharing many structural and functional properties. Several KLK transcripts have been found aberrantly expressed in numerous human malignancies, confirming their prognostic or/and diagnostic values. However, the process of alternative splicing can now be studied in-depth due to the development of Next-Generation Sequencing (NGS). In the present study, we used NGS to discover novel transcripts of the KLK1 and KLK2 genes, after nested touchdown PCR. Bioinformatics analysis and PCR experiments revealed a total of eleven novel KLK transcripts (two KLK1 and nine KLK2 transcripts). In addition, the expression profiles of each novel transcript were investigated with nested PCR experiments using variant-specific primers. Since KLKs are implicated in human malignancies, qualifying as potential biomarkers, the quantification of the presented novel transcripts in human samples may have clinical applications in different types of cancer.


Asunto(s)
Empalme Alternativo , Calicreínas/genética , Neoplasias/genética , Línea Celular Tumoral , Humanos , Isoenzimas/genética , Isoenzimas/metabolismo , Calicreínas/metabolismo , Neoplasias/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo
16.
Genomics ; 2019 May 22.
Artículo en Inglés | MEDLINE | ID: mdl-31128263

RESUMEN

Τhe carnitine palmitoyltransferase (CPT) system is responsible for transporting long-chain acyl-CoAs from cytoplasm into the mitochondria. This system consists of two l-carnitine acyltransferases (CPT1 and CPT2) and the carnitine acylcarnitine translocase. In mammals, two CPT1 homologs (CPT1A and CPT1B) were previously described. By using positional cloning gene approaches, RT-PCR, and next-generation sequencing (NGS), we sought to identify novel human genes that might be involved in fatty acid metabolism. Thus, we discovered a third CPT1 homolog (CATL1/CPT1C), transcribed into two major protein-coding transcripts. This gene on chromosome 19q13.33 encodes a protein participating in the control of whole-body glucose homeostasis and is predominantly expressed in the central nervous system. Steroid hormones affect CPT1C mRNA expression in human prostate and breast cancer cell lines. Although the major involvement of CPT1C in fatty acid catabolism makes it a crucial gene for cellular homeostasis, its precise role in oxidative stress needs further investigation. Sequence data from this article have been deposited to the GenBank Data Library under Accession No. AF331918.1.

17.
Int J Mol Sci ; 21(22)2020 Nov 23.
Artículo en Inglés | MEDLINE | ID: mdl-33238574

RESUMEN

The utility of circular RNAs (circRNAs) as molecular biomarkers has recently emerged. However, only a handful of them have already been studied in colorectal cancer (CRC). The purpose of this study was to identify new circRNAs deriving from BCL2L12, a member of the BCL2 apoptosis-related family, and investigate their potential as biomarkers in CRC. Total RNA extracts from CRC cell lines and tissue samples were reversely transcribed. By combining PCR with divergent primers and nested PCR followed by Sanger sequencing, we were able to discover two BCL2L12 circRNAs. Subsequently, bioinformatical tools were used to predict the interactions of these circRNAs with microRNAs (miRNAs) and RNA-binding proteins (RBPs). Following a PCR-based pre-amplification, real-time qPCR was carried out for the quantification of each circRNA in CRC samples and cell lines. Biostatistical analysis was used to assess their potential prognostic value in CRC. Both novel BCL2L12 circRNAs likely interact with particular miRNAs and RBPs. Interestingly, circ-BCL2L12-2 expression is inversely associated with TNM stage, while circ-BCL2L12-1 overexpression is associated with shorter overall survival in CRC, particularly among TNM stage II patients. Overall, we identified two novel BCL2L12 circRNAs, one of which can further stratify TNM stage II patients into two subgroups with substantially distinct prognosis.


Asunto(s)
Biomarcadores de Tumor/sangre , Neoplasias Colorrectales/genética , Proteínas Musculares/genética , Proteínas Proto-Oncogénicas c-bcl-2/genética , ARN Circular/genética , Adulto , Anciano , Anciano de 80 o más Años , Neoplasias Colorrectales/sangre , Neoplasias Colorrectales/patología , Biología Computacional , Femenino , Regulación Neoplásica de la Expresión Génica/genética , Humanos , Masculino , MicroARNs/sangre , Persona de Mediana Edad , Proteínas Musculares/sangre , Proteínas Proto-Oncogénicas c-bcl-2/sangre , ARN Circular/sangre , Proteínas de Unión al ARN/sangre , Proteínas de Unión al ARN/genética
18.
Int J Mol Sci ; 21(22)2020 Nov 13.
Artículo en Inglés | MEDLINE | ID: mdl-33202911

RESUMEN

Colorectal cancer (CRC) is a highly heterogenous malignancy with an increased mortality rate. Aberrant splicing is a typical characteristic of CRC, and several studies support the prognostic value of particular transcripts in this malignancy. l-DOPA decarboxylase (DDC) and its derivative neurotransmitters play a multifaceted role in physiological and pathological states. Our recent data support the existence of 6 DDC novel exons. In this study, we investigated the existence of additional DDC novel exons and transcripts, and their potential value as biomarkers in CRC. Next-generation sequencing (NGS) in 55 human cell lines coupled with Sanger sequencing uncovered 3 additional DDC novel exons and 20 splice variants, 7 of which likely encode new protein isoforms. Eight of these transcripts were detected in CRC. An in-house qPCR assay was developed and performed in TNM II and III CRC samples for the quantification of transcripts bearing novel exons. Extensive biostatistical analysis uncovered the prognostic value of specific DDC novel exons for patients' disease-free and overall survival. The revised DDC exon structure, the putative protein isoforms with distinct functions, and the prognostic value of novel exons highlight the pivotal role of DDC in CRC progression, indicating its potential utility as a molecular biomarker in CRC.


Asunto(s)
Empalme Alternativo , Descarboxilasas de Aminoácido-L-Aromático , Neoplasias Colorrectales , Exones , Regulación Enzimológica de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Proteínas de Neoplasias , Descarboxilasas de Aminoácido-L-Aromático/biosíntesis , Descarboxilasas de Aminoácido-L-Aromático/genética , Línea Celular Tumoral , Neoplasias Colorrectales/enzimología , Neoplasias Colorrectales/genética , Progresión de la Enfermedad , Células HEK293 , Humanos , Isoenzimas/biosíntesis , Isoenzimas/genética , Proteínas de Neoplasias/biosíntesis , Proteínas de Neoplasias/genética , Transcripción Genética
19.
Biol Chem ; 399(9): 1065-1071, 2018 09 25.
Artículo en Inglés | MEDLINE | ID: mdl-29874189

RESUMEN

Tissue kallikrein, kallikrein-related peptidases (KLKs), and plasma kallikrein form the largest group of serine proteases in the human genome, sharing many structural and functional characteristics. In this study, we describe the molecular cloning of four novel splice variants of the human KLK11 and KLK12 genes, discovered by combining 3' rapid amplification of cDNA ends (3' RACE), next-generation sequencing (NGS) technology, advanced bioinformatic analysis and Sanger sequencing. Expression analysis of these new transcripts in cell lines originating from 17 cancerous and two normal tissues revealed the expression pattern of each transcript. These novel KLK11 and KLK12 splice variants represent new potential cancer biomarkers.


Asunto(s)
Empalme Alternativo/genética , Calicreínas/genética , Serina Endopeptidasas/genética , Secuencia de Aminoácidos , Clonación Molecular , Biología Computacional , Humanos , Calicreínas/metabolismo , Análisis de Secuencia de ADN , Serina Endopeptidasas/metabolismo
20.
Hematol Oncol ; 36(4): 693-700, 2018 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-30129144

RESUMEN

The demethylating factor 5-azacytidine (5-AZA) improves survival in intermediate-2 and high-risk myelodysplastic syndrome (MDS) patients [according to the International Prognostic Score System (IPSS)] responding to treatment. However, the outcome of patients achieving stable disease (SD) is unclear. This retrospective study of the Hellenic MDS Study Group included 353 intermediate-2 or high IPSS risk patients treated with 5-AZA. Forty-four out of 86 (51.6%) patients achieving SD and continuing treatment with 5-AZA showed a lower risk of transformation of MDS to acute myeloid leukemia (AML) and increased overall survival (OS), compared to SD patients who discontinued the treatment (estimated median AML-free survival = 38 months, 95% CI = 10.7-65.3 vs 15 months, 95% CI = 10.4-19.6, P < .001; estimated median OS = 20 months, 95% CI = 5.5-34.5 vs 11 months, 95% CI = 5.8-16.2, P < .001). Moreover, SD patients continuing treatment with 5-AZA had no differences in AML-free survival compared to patients showing response to 5-AZA (estimated median AML-free survival = 38 months, 95% CI = 10.7-65.3 vs 31 months, 95% CI = 23.6-38.4, P = .45; estimated median OS 20 months, 95% CI = 5.5-34.5 vs 25 months, 95% CI = 21.3-28.7, P = .50). In conclusion, MDS patients achieving SD in the first 6 months of treatment with 5-AZA as best response should continue receiving 5-AZA as they may benefit from prolonged treatment.


Asunto(s)
Antimetabolitos Antineoplásicos/uso terapéutico , Azacitidina/uso terapéutico , Síndromes Mielodisplásicos/tratamiento farmacológico , Adulto , Anciano , Anciano de 80 o más Años , Femenino , Humanos , Masculino , Persona de Mediana Edad , Pronóstico , Estudios Retrospectivos , Factores de Riesgo , Tasa de Supervivencia , Resultado del Tratamiento
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