Cancer Genomics & Proteomics最新文献

Background/aim: Neurofibromatosis type 1 (NF1) is a genetic disorder with an incidence of approximately one in 3,000. More than half of the patients have new de novo pathogenic variants of the NF1 gene. In most family cases, all family members share an identical NF1-variant. The aim of the study was to investigate the very rare phenomenon of de novo variants in cases of familial neurofibromatosis type 1 and highlight its implications for genetic testing and counseling.

Patients and methods: Patients underwent clinical examination in our NF outpatient clinic and genetic testing for the NF1-gene was performed by targeted sequencing. All family members were profiled by short-tandem repeat marker analysis. Additionally, a probability calculation was performed for this extremely rare event.

Results: In one NF1 family consisting of mother, father, and two sons, two different pathogenic variants of the NF1 gene were found. The father and one son share one NF1-variant and the other son carries a different de novo NF1-variant. Neither of these two NF1-variants was found in the unaffected mother. Short-tandem repeat analysis confirmed the paternity and revealed that the two sons inherited two different NF1-alleles from their father. The probability of two different NF1-variants occurring in one family is calculated as 1:9,000,000.

Conclusion: Two different NF1-variants in one family is an extremely rare phenomenon: yet its occurrence is not impossible and therefore should be considered in genetic diagnosis and counselling. For an offspring with the indication for neurofibromatosis type 1, but lacking the familial pathogenic variant, a screening of the whole NF1-gene is necessary to detect potential new pathogenic variants and for exact diagnosis.

Background/aim: The disruption of cell-cycle control can lead to an imbalance in cell proliferation, often accompanied by genomic instability, which in turn can facilitate carcinogenesis. This study aimed to examine the impact of CDKN1A rs1801270 and rs1059234 polymorphisms on the risk of childhood acute lymphocytic leukemia (ALL) in Taiwan.

Materials and methods: The genotypes of CDKN1A rs1801270 and rs1059234 in 266 childhood ALL cases and 266 controls were determined using PCR-RFLP techniques.

Results: The genotypic and allelic frequencies for CDKN1A rs1801270 and rs1059234 did not significantly differ between childhood ALL cases and controls (all p>0.05). However, stratified analysis revealed that the CDKN1A rs1801270 AA variant was associated with a reduced risk of childhood ALL in males (OR=0.40, 95%CI=0.20-0.82, p=0.0178). Additionally, the AC and AA genotypes of rs1801270 were linked to a lower risk classification for childhood ALL and longer survival times (OR=0.57 and 0.31, 95%CI=0.33-0.97 and 0.18-0.56, p=0.0538 and 0.0001, respectively). No significant associations were found for rs1059234 in the stratified analyses (p>0.05 for all).

Conclusion: Although CDKN rs1801270 and rs1059234 genotypes were not associated with an overall risk of childhood ALL, CDKN1A rs1801270 polymorphism may serve as a protective predictor in males and as a potential marker for better prognosis of childhood ALL. Validation in larger and more diverse populations is necessary to confirm the feasibility of this predictor.

Background/aim: α1-Acid glycoprotein (AGP), also known as orosomucoid, is an acute-phase protein that has been found increased in plasma of cancer patients. This study investigates the role of AGP expression in clear cell renal cell carcinoma (ccRCC) and its association with clinical outcomes.

Materials and methods: We investigated the correlation between AGP levels and the prognosis of ccRCC through an analysis of The Cancer Genome Atlas (TCGA) database. To examine AGP expression and its clinicopathological associations, immunostaining was performed on paraffin-embedded tissue samples of 92 ccRCC cases.

Results: AGP expression was found to be higher in RCC cell lines compared to normal renal epithelial cells. Analysis of the TCGA dataset showed that patients with AGP gene expression had significantly worse overall survival. However, AGP expression was not correlated with age, sex, or cancer stage. A mouse monoclonal antibody against AGP was generated. This antibody reacted with human and mouse hepatocytes, but not in AGP-deficient mice. From 92 examined ccRCC cases, AGP protein expression was detected in 89 cases, with only 3 being negative. AGP expression levels did not correlate with clinicopathological factors, such as age, tumor size, or nuclear grade. CD14, a receptor of AGP, was found to be expressed in Iba1-positive monocytes and tumor-associated macrophages (TAMs) but not in other cell types like lymphocytes or cancer cells. No significant correlation was found between AGP expression and the number of Iba1-positive cells in ccRCC tissues. Iba1-positive cells were correlated with Fuhrman grade, and patients with ≥30% Iba1-positive cells were, on average, significantly younger and had more aggressive tumor.

Conclusion: AGP expression is linked to poorer survival in ccRCC, but its association with immune cell infiltration (via Iba1-positive cells) is unclear.

Background/aim: Myelodysplastic syndromes (MDSs) are clonal bone marrow disorders characterized by ineffective hematopoiesis. They are classified based on morphology and genetic alterations, with SF3B1 variants linked to favorable prognosis and MECOM rearrangements associated with poor outcomes. The combined effects of these alterations remain unclear. We report an MDS patient carrying both SF3B1 and MECOM alterations who developed transient eosinophilia accompanied by a TNIP1::PDGFRB chimera in a subset of MECOM-affected cells.

Case report: A 73-year-old woman was diagnosed with myeloid neoplasia with excess blasts and multilineage dysplasia (MDS-EB1). Six months later, SF3B1 mutations were identified, leading to a diagnosis of MDS-SF3B1. Despite azacitidine treatment, her condition worsened, showing hypercellular bone marrow and eosinophilia. Genetic analysis revealed a t(2;3)(p15~23;q26)/MECOM rearrangement and TNIP1::PDGFRB chimera. Imatinib eradicated eosinophilia and reduced TNIP1::PDGFRB-positive cells, but the MECOM-clone persisted. Subsequent treatments, including hydroxyurea, mercaptopurine, and low-dose cytarabine, were ineffective. FLT3 mutations and high EVI1 transcript levels were later detected. The patient succumbed to progressive disease.

Conclusion: This case highlights the complexity of MDS and the importance of genetic abnormalities in treatment planning. Persistent MECOM rearrangement and the TNIP1::PDGFRB chimera emphasize the need for further research into resistance mechanisms.

Background/aim: Cholangiocarcinoma (CCA) is an aggressive hepatobiliary malignancy characterized by genomic heterogeneity. KRAS mutations play a significant role in influencing patient prognosis and guiding therapeutic decision-making. This study aimed to determine the prevalence and prognostic significance of KRAS mutations in CCA, asses the detection of KRAS G12/G13 mutations in plasma cell-free DNA (cfDNA), and evaluate the prognostic value of KRAS G12/G13 mutant allele frequency (MAF) in cfDNA in relation to clinicopathological data and patient survival.

Materials and methods: A retrospective analysis of 937 CCA patients was performed using data from cBioPortal to examine KRAS mutation profiles and their association with survival. Plasma from 101 CCA patients was analyzed for KRAS G12/G13 mutations in the cfDNA using droplet digital PCR, and the results were compared with tissue-based sequencing from 78 matched samples.

Results: KRAS driver mutations were found in 15.6% of patients, with common variants being G12D (37.0%), G12V (24.0%) and Q61H (8.2%). Patients harboring KRAS mutations exhibited decreased overall and recurrence-free survival. KRAS G12/G13 mutations were detected in 14.9% of cfDNA samples, showing moderate concordance with tissue sequencing, and achieving 80% sensitivity and 93% specificity. Elevated KRAS G12/G13 MAF in cfDNA, combined with high CA19-9 levels, correlated with poorer survival outcomes.

Conclusion: The presence of KRAS mutations was associated with poor survival in CCA, underscoring the importance of KRAS mutations as prognostic markers. The detection of KRAS mutations in cfDNA demonstrated potential as a promising non-invasive alternative for mutation detection and, when combined with CA19-9 levels, may improve prognostic efficacy in CCA.

Background/aim: G protein-coupled estrogen receptor 1 (GPER1) appears to play a tumor-suppressive role in cervical squamous cell carcinoma (CSCC)GPER1 suppression leads to significantly increased expression of serpin family E member 1 (SERPINE1)/protein plasminogen activator inhibitor type 1 (PAI-1). The question arises, what role does SERPINE1/PAI-1 play in GPER1-dependent tumorigenic potential of CSCC.

Materials and methods: SiHa and C33A CSCC cells were treated with GPER1 agonist G1 or antagonist G36. SERPINE1/PAI-1 expression was suppressed by RNAi and success was confirmed by RT-qPCR. Protein expression of PAI-1 was quantified by Western blot. Viability was analyzed using resazurin assay, while migration was investigated using gap closure. Colony and tumor sphere formation were used to test clonogenicity.

Results: After G1 treatment, viability of SiHa and C33A cells remained unchanged. Cell migration was dose-dependently reduced. SiHa and C33A cells formed significantly fewer and smaller colonies as well as spheroids. Furthermore, treatment with G1 led to decreased expression of SERPINE1/PAI-1, while blockade of GPER1 with G36 resulted in significantly increased SERPINE1/PAI-1 expression. After suppression of SERPINE1/PAI-1 in SiHa cells using RNAi, cell viability remained unaffected; however, significantly smaller colonies were formed, and fewer and smaller spheroids were developed. Cell migration remained unaffected.

Conclusion: Activation of GPER1 reduces clonogenicity and migration of CSCC cells and suppresses expression of SERPINE1/PAI-1. Suppression of SERPINE1/PAI-1 in CSCC cells reduces tumorigenic potential. GPER1 may be a suitable target for suppression of SERPINE1/PAI-1 in CSCC. However, SERPINE1/PAI-1 does not appear to be the decisive factor for GPER1-regulated cell migration.

Background/aim: The Kaplan-Meier curves for patients treated with immune checkpoint inhibitors (ICIs) display a small group of potentially-cured patients with long-term survival, creating a 'kangaroo-tail' shape of the survival curve. However, the mechanistic basis of this phenomenon and what occurs in patients whose cancer is resistant to ICIs remain unclear. The present study aimed to answer these questions.

Materials and methods: We analyzed mutations in mouse 4T1 mammary-gland-derived cancer cells expressing the hemagglutinin antigen (4T1-HA), which were grown in either wild-type mice or cytotoxic T-lymphocyte (CTL)-loaded immunocompromised mice (RAG-/- + ACT) under immune stress. These mutations were compared to those in 4T1-HA cells grown in RAG-/- mice without immune stress as a control.

Results: The number of gene mutations, the tumor mutation burden (TMB) and microsatellite instability (MSI) scores were increased in the cancer cells under immune stress. The mutations in the antigen protein were such that the protein retained its immunogenicity and could still function as a neoantigen. Repeated immune recognition of additional neoantigens may lead to the kangaroo-tail survival phenomenon. The common genetic mutations of the analyzed 4T1-HA cells under immune stress included genes related to immune response. Analysis of alternative splicing of genes showed that are accumulated gene alterations under immune stress related to cancer-cell proliferation. Copy-number variation (CNV) analysis indicated that normal-antigen presentation and immune responses may be impaired under immune stress.

Conclusion: Cancer cells, under immune stress, may acquire both immune escape capabilities and increased immunogenicity. This dual effect could lead to either resistance or response to ICIs, respectively.

Background/aim: Bile tract cancer (BTC) is a malignant tumor with a poor prognosis. Recent studies have reported the heterogeneity of the genomic background and gene alterations in BTC, but its genetic heterogeneity and molecular profiles remain poorly understood. Whole-genome sequencing may enable the identification of novel actionable gene mutations involved in BTC carcinogenesis, malignant progression, and treatment resistance.

Patients and methods: We performed whole-genome sequencing of six BTC samples to elucidate its genetic heterogeneity and identify novel actionable gene mutations. Somatic mutations, structural variations, copy number alterations, and their associations with clinical factors were analyzed.

Results: The average number of somatic mutations detected in each case was 53,705, with SNVs accounting for most of these mutations (85.02%). None of the 331 mutations related to BTC in The Cancer Genome Atlas (TCGA) database were found in the mutations identified in our study. A higher prevalence of gene mutations was observed in samples without vascular invasion than in those with vascular invasion. Several genes with differences in mutation accumulation between groups were identified, including ADAMTS7, AHNAK2, and CAPN10.

Conclusion: Our study provides novel insights into the genomic landscape of BTC and highlights the potential of whole-genome sequencing analysis to identify actionable gene mutations and understand the molecular mechanisms underlying this malignancy. The high mutational burden, structural variations, and copy number alterations observed in BTC samples in this study underscore the genetic complexity and heterogeneity of this disease.

Background/aim: Glioma, the most common type of primary brain tumor, is characterized by high malignancy, recurrence, and mortality. Long non-coding RNA (lncRNA) H19 is a potential biomarker for glioma diagnosis and treatment due to its overexpression in human glioma tissues and its involvement in cell division and metastasis regulation. This study aimed to identify potential therapeutic targets involved in glioma development by analyzing gene expression profiles regulated by H19.

Materials and methods: To elucidate the role of H19 in A172 and U87MG glioma cell lines, cell counting, colony formation, and wound healing assays were conducted. RNA-seq data analysis and bioinformatics analyses were performed to reveal the molecular interactions of H19.

Results: Cell-based experiments showed that elevated H19 levels were related to cancer cell survival, proliferation, and migration. Bioinformatics analyses identified 2,084 differentially expressed genes (DEGs) influenced by H19 which are involved in cancer progression. Specifically, ANXA5, CLEC18B, RAB42, CXCL8, OASL, USP18, and CDCP1 were positively correlated with H19 expression, while CSDC2 and FOXO4 were negatively correlated. These DEGs were predicted to function as oncogenes or tumor suppressors in gliomas, in association with H19.

Conclusion: These findings highlight H19 and its associated genes as potential diagnostic and therapeutic targets for gliomas, emphasizing their clinical significance in patient survival.

Background/aim: Methionine restriction selectively arrests cancer cells during the S-phase of the cell cycle. We hypothesized that DNA damage may occur in S-phase in cancer cells during methionine restriction. To determine if this occurs, we used MiaPaCa-2^Tet-On 53BP1-green fluorescent protein (GFP) pancreatic cancer cells, which report GFP fluorescence in real time after DNA-damage response (DDR) in these cells. We also determined whether a chemotherapy drug in combination with methionine restriction increases the rate of DNA damage.

Materials and methods: MiaPaCa-2^Tet-On 53BP1-GFP cells were used for in vitro experiments. The 25% and 50% inhibitory concentrations (IC₂₅ and IC₅₀, respectively) of recombinant methioninase (rMETase) and paclitaxel on MiaPaCa-2^Tet-On 53BP1-GFP pancreatic cancer cells were determined. Cell viability and DDR with rMETase alone, paclitaxel alone, and their combination were measured in MiaPaCa-2^Tet-On 53BP1-GFP cells.

Results: The IC₂₅ of rMETase on MiaPaCa-2^Tet-On 53BP1-GFP cells was 1.66 U/ml. The IC₂₅ for paclitaxel on MiaPaCa-2^Tet-On 53BP1-GFP cells was 3.31 nM. The combination of rMETase and paclitaxel synergistically reduced the viability of MiaPaCa-2^Tet-On 53BP1-GFP cells. The IC₅₀ of paclitacel on MiaPaCa-2^Tet-On 53BP1-GFP cells was 5.1 nM. The IC₅₀ of rMETase on MiaPaCa-2^Tet-On 53BP1-GFP cells was 2.3 U/ml. The combination of rMETase (IC₅₀) plus paclitaxel (IC₅₀) on MiaPaCa-2^Tet-On 53BP1-GFP cells also caused more DNA damage than either agent alone.

Conclusion: The present study suggests the synergy of methionine restriction and chemotherapy is due, at least in part, to DNA damage of cancer cells.