C1orf35 contributes to tumorigenesis by activating c-MYC transcription in multiple myeloma

Development of a prognostic model for early-stage gastric cancer-related DNA methylation-driven genes and analysis of immune landscape

Background and Aims

This study aimed to develop a prognostic model based on DNA methylation-driven genes for patients with early-stage gastric cancer and to examine immune infiltration and function across varying risk levels.

Methods

We analyzed data from stage I/II gastric cancer patients in The Cancer Genome Atlas which included clinical details, mRNA expression profiles, and level 3 DNA methylation array data. Using the empirical Bayes method of the limma package, we identified differentially expressed genes (DEGs), and the MethylMix package facilitated the identification of DNA methylation-driven genes (DMGs). Univariate Cox regression and LASSO (least absolute shrinkage and selector operation) analyses were utilized to pinpoint critical genes. A risk score prediction model was formulated using two genes that demonstrated the most significant hazard ratios (HRs). Model performance was evaluated within the initial cohort and verified in the GSE84437 cohort; a nomogram was also constructed based on these genes. We further examined 50 methylation sites associated with three CpG islands in C1orf35 and 14 methylation sites linked to one CpG island in FAAH. The CIBERSORT package was employed to identify immune cell clusters in the prediction model.

Results

A total of 176 DNA methylation-driven genes were refined down to a four-gene signature (ZC3H12A was hypermethylated; GATA3, C1orf35, and FAAH were hypomethylated), which exhibited a significant correlation with overall survival (OS), as evidenced by p-values below 0.05 following univariate Cox regression and LASSO analysis. Specifically, for the risk score prediction model, C1orf35, which had the highest hazard ratio (HR = 2.035, p = 0.028), and FAAH, with the lowest hazard ratio (HR = 0.656, p = 0.012), were selected. The Kaplan-Meier analysis demonstrated distinct survival outcomes between the high-risk and low-risk score groups. The model's predictive accuracy was confirmed with an area under the curve (AUC) of 0.611 for 3-year survival and 0.564 for 5-year survival. Notably, the hypomethylation of the three CpG islands in C1orf35 and the single CpG island in FAAH was significantly different in stage I/II gastric cancer patients compared to normal tissues. Additionally, the high-risk score group showed a notable association with resting CD4 memory T cells.

Conclusion

Promoter hypomethylation of C1orf35 and FAAH in early-stage gastric cancer underscores their potential as biomarkers for accurate diagnosis and treatment. The developed predictive model employing genes affected by DNA methylation serves as a crucial independent prognostic factor in early-stage gastric cancer.

1q21+ is associated with poor prognosis in newly diagnosed multiple myeloma patients with extramedullary disease: a retrospective study

1q21+ is a common cytogenetic abnormality in multiple myeloma (MM) and is considered an independent predictor of poor prognosis; however, its impact on extramedullary disease (EMD) remains unknown. Our study reviewed the clinical relevance and prognostic value of 1q21+ status in 92 patients with NDMM and EMD. 1q21+ was detected in 23.9% (22/92) of patients. Patients with 1q21+ presented with advanced International Staging System stages (P = 0.006), lower level of hemoglobin (P = 0.004), higher percentage of plasma cells in the bone marrow (P < 0.001), higher level of serum β2-microglobulin (7.24 g/L vs. 3.85 g/L, P = 0.003), and higher levels of lactic dehydrogenase (LDH) (206.5 U/L vs. 177 U/L, P = 0.019). The prevalence of soft tissue-related EMD (EMD-S) (54.5% vs. 18.6%, P < 0.001), renal dysfunction (50.5% vs. 17.7%, P = 0.002), and hypercalcemia (27.3% vs. 7.1%, P = 0.011) was also higher. 1q21+ was strongly associated with other high-risk cytogenetic abnormalities, including IgH/FGFR3 (22.7% vs. 4.3%, P = 0.007) and IgH/MAF translocations (22.7% vs. 1.4%, P < 0.001). 1q21+ patients had significantly shorter overall survival (OS) and progression-free survival (PFS) (OS: 24 months vs. 47 months, P = 0.002; PFS: 14 months vs. 38 months, P < 0.001); the poor survival outcomes could not be reversed by autologous hematopoietic stem cell transplantation. Multivariate analysis suggested that 1q21+ , EMD-S, elevated lactate dehydrogenase (LDH) levels, and P53 deletion were independent risk factors for poor prognosis in patients with EMD. In patients with 1q21+ EMD, hypercalcemia, elevated LDH levels, and P53 deletion were independent adverse risk prognostic factors.

PRMT3-mediated arginine methylation of IGF2BP1 promotes oxaliplatin resistance in liver cancer

Although oxaliplatin-based chemotherapy has been effective in the treatment of hepatocellular carcinoma (HCC), primary or acquired resistance to oxaliplatin remains a major challenge in the clinic. Through functional screening using CRISPR/Cas9 activation library, transcriptomic profiling of clinical samples, and functional validation in vitro and in vivo, we identify PRMT3 as a key driver of oxaliplatin resistance. Mechanistically, PRMT3-mediated oxaliplatin-resistance is in part dependent on the methylation of IGF2BP1 at R452, which is critical for the function of IGF2BP1 in stabilizing the mRNA of HEG1, an effector of PRMT3-IGF2BP1 axis. Also, PRMT3 overexpression may serve as a biomarker for oxaliplatin resistance in HCC patients. Collectively, our study defines the PRTM3-IGF2BP1-HEG1 axis as important regulators and therapeutic targets in oxaliplatin-resistance and suggests the potential to use PRMT3 expression level in pretreatment biopsy as a biomarker for oxaliplatin-resistance in HCC patients.

Prognostic value of 18F-fluorodeoxyglucose positron emission tomography/computed tomography at diagnosis in untreated multiple myeloma patients: a systematic review and meta-analysis

Multiple myeloma is a clonal B-lymphocyte tumor of terminally differentiated plasma cells. ¹⁸F-FDG PET/CT can provide valuable data for the diagnosis, restaging, and evaluate prognosis of multiple myeloma (MM). This meta-analysis aimed to evaluate the prognostic value of pre-treatment ¹⁸F-FDG PET/CT at diagnosis in MM patients. Related researches came from Embase, PubMed, and Cochrane Library databases through a systematic search, and the last one was updated on April 26, 2021. Cochran Q test and I-squared statistics were used to test for heterogeneity among the studies analyzed. The fixed model and random model were used to combine results when appropriate. Stata 12.0 was used to perform statistical analysis, and p < 0.05 was considered statistically significant. A total of 16 articles with 2589 patients were included in this study. Our results indicated PET/CT has an excellent prognostic role in MM, that higher SUV_max, more FL and EMD were associated with poor OS and PFS. SUVmax: OS (HR 1.89, 95% CI 1.47-2.44), PFS (HR 1.34, 95% CI 1.18-1.51); Fl: OS (HR 2.65, 95% CI 1.83-3.79), PFS (HR 1.61, 95% CI 1.40-1.86); EMD: OS (HR 2.11, 95% CI 1.41-3.16), PFS (HR 2.18, 95% CI 1.69-2.81). Furthermore, similar results were observed in most subgroup analyzes. Conclusion Pre-treatment ¹⁸F-FDG PET/CT examination has prognostic value for myeloma patients and has guiding significance for clinical treatment.

miR-106b-5p Intensifies the Proliferative Potential of Spermatogonial Stem Cells as a Prerequisite for Male Infertility Treatment

Although numerous studies have investigated the molecular basis of male infertility, various aspects of this area have remained uncovered. Over the past years, researchers have reported the significant potential of miRNAs in posttranscriptional regulatory roles. By targeting mRNAs, these notable molecules can modulate the processes related to male infertility. On the other side, the outstanding potential of male germline stem cells, SSCs, includes their application in infertility treatment. SSCs retain normal spermatogenesis and fertility by adjusting both SSC self-renewal and differentiation. Therefore, for the characterization and manipulation of SSCs, effective and efficient in vitro culture methods are essential in supporting their maintenance and development. In this regard, the present investigation was undertaken to evaluate the impact of one of the recently conspicuous miRNAs, miR-106b, in SSCs enrichment. As a result, we first found that the SSCs induced with miR-106b-5p highly express TGF-β1, which is known as a regulator of epigenetic modifiers and downstream genes. We next sought to show that self-renewal markers, including c-Myc, Oct-4, and Sox2, are increased in the induced SSC group. The intended miRNA also induced the inhibitor of differentiation 4 (ID4) and aided to remain unmethylated in SSCs. Additionally, for the tumorigenicity possibility of the manipulation, we indicated that PTEN, a tumor-suppressor gene, expressed remarkably in the induced SSCs. In conclusion, our findings showed that miR-106b-5p enhances the proliferative potential of SSCs, making it a substantial factor for therapeutic strategies of male infertility.

Chromosome 1 instability in multiple myeloma: Aberrant gene expression, pathogenesis, and potential therapeutic target

Multiple myeloma (MM), the terminally differentiated B cells malignancy, is widely considered to be incurable since many patients have either developed drug resistance or experienced an eventual relapse. To develop precise and efficient therapeutic strategies, we must understand the pathogenesis of MM. Thus, unveiling the driver events of MM and its further clonal evolution will help us understand this complicated disease. Chromosome 1 instabilities are the most common genomic alterations that participate in MM pathogenesis, and these aberrations of chromosome 1 mainly include copy number variations and structural changes. The chromosome 1q gains/amplifications and 1p deletions are the most frequent structural changes of chromosomes in MM. In this review, we intend to focus on the genes that are affected by chromosome 1 instability: some tumor suppressors were lost or down regulated in 1p deletions, and others that contributed to tumorigenesis were upregulated in 1q gains/amplifications. We have summarized their biological function as well as their roles in the MM pathogenesis, hoping to uncover potential novel therapeutical targets and promote the development of future therapeutic approaches.

FABP5, a Novel Immune-Related mRNA Prognostic Marker and a Target of Immunotherapy for Multiple Myeloma

Objective: Multiple myeloma is an incurable hematological malignancy. It is imperative to identify immune markers for early diagnosis and therapy. Here, this study analyzed immune-related mRNAs and assessed their prognostic value and therapeutic potential.

Methods: Abnormally expressed immune-related mRNAs were screened between multiple myeloma and normal bone marrow specimens in the GSE47552 and GSE6477 datasets. Their biological functions were then explored. Survival analysis was presented for assessing prognosis-related mRNAs. CIBERSORT was utilized for identifying 22 immune cell compositions of each bone marrow specimen. Correlation between FABP5 mRNA and immune cells was then analyzed in multiple myeloma.

Results: Thirty-one immune-related mRNAs were abnormally expressed in multiple myeloma, which were primarily enriched in B cells-related biological processes and pathways. Following validation, FABP5 mRNA was a key risk factor of multiple myeloma. Patients with its up-regulation usually experienced unfavorable outcomes. There were distinct differences in the infiltration levels of B cells naïve, B cells memory, plasma cells, T cells CD4 naïve, resting memory CD4 T cells, activated memory CD4 T cells, Tregs, resting NK cells, M0 macrophages, M1 macrophages, M2 macrophages, and neutrophils between multiple myeloma and normal samples. FABP5 mRNA had correlations to B cells memory, B cells naïve, dendritic cells activated, macrophages M0, macrophages M1, macrophages M2, neutrophils, activated NK cells, resting memory CD4 T cells, CD8 T cells and Tregs.

Conclusion: Collectively, our data showed that FABP5 mRNA was related to immune microenvironment, which could be a target of immunotherapy and prognostic marker for multiple myeloma.

Heat stress and immune response phenotype affect DNA methylation in blood mononuclear cells from Holstein dairy cows

Heat stress negatively affects health and production in cows. Examining the cellular response to heat stress could reveal underlying protective molecular mechanisms associated with superior resilience and ultimately enable selection for more resilient cattle. This type of investigation is increasingly important as future predictions for the patterns of heat waves point to increases in frequency, severity, and duration. Cows identified as high immune responders based on High Immune Response technology (HIR) have lower disease occurrence compared to their average and low immune responder herd-mates. In this study, our goal was to identify epigenetic differences between high and low immune responder cows in response to heat stress. We examined genome-wide DNA methylation of blood mononuclear cells (BMCs) isolated from high and low cows, before and after in vitro heat stress. We identified differential methylation of promoter regions associated with a variety of biological processes including immune function, stress response, apoptosis, and cell signalling. The specific differentially methylated promoter regions differed between samples from high and low cows, and results revealed pathways associated with cellular protection during heat stress.

Gene networks and transcriptional regulators associated with liver cancer development and progression

BACKGROUND

Treatment options for hepatocellular carcinoma (HCC) are limited, and overall survival is poor. Despite the high frequency of this malignoma, its basic disease mechanisms are poorly understood. Therefore, the aim of this study was to use different methodological approaches and combine the results to improve our knowledge on the development and progression of HCC.

METHODS

Twenty-three HCC samples were characterized by histological, morphometric and cytogenetic analyses, as well as comparative genomic hybridization (aCGH) and genome-wide gene expression followed by a bioinformatic search for potential transcriptional regulators and master regulatory molecules of gene networks.

RESULTS

Histological evaluation revealed low, intermediate and high-grade HCCs, and gene expression analysis split them into two main sets: GE1-HCC and GE2-HCC, with a low and high proliferation gene expression signature, respectively. Array-based comparative genomic hybridization demonstrated a high level of chromosomal instability, with recurrent chromosomal gains of 1q, 6p, 7q, 8q, 11q, 17q, 19p/q and 20q in both HCC groups and losses of 1p, 4q, 6q, 13q and 18q characteristic for GE2-HCC. Gene expression and bioinformatics analyses revealed that different genes and gene regulatory networks underlie the distinct biological features observed in GE1-HCC and GE2-HCC. Besides previously reported dysregulated genes, the current study identified new candidate genes with a putative role in liver cancer, e.g. C1orf35, PAFAH1B3, ZNF219 and others.

CONCLUSION

Analysis of our findings, in accordance with the available published data, argues in favour of the notion that the activated E2F1 signalling pathway, which can be responsible for both inappropriate cell proliferation and initial chromosomal instability, plays a pivotal role in HCC development and progression. A dedifferentiation switch that manifests in exaggerated gene expression changes might be due to turning on transcriptional co-regulators with broad impact on gene expression, e.g. POU2F1 (OCT1) and NFY, as a response to accumulating cell stress during malignant development. Our findings point towards the necessity of different approaches for the treatment of HCC forms with low and high proliferation signatures and provide new candidates for developing appropriate HCC therapies.

Gain/Amplification of Chromosome Arm 1q21 in Multiple Myeloma

Simple Summary

Multiple myeloma (MM), a plasma cell neoplasm, is an incurable hematological malignancy. Gain/amplification of chromosome arm 1q21 (1q21+) is the most common adverse genomic abnormality associated with disease progression and drug resistance. While possible mechanisms of 1q21+ occurrence and candidate genes in the 1q21 amplicon have been suggested, the precise pathogenesis of MM with 1q21+ is unknown. Herein, we review the current knowledge about the clinicopathological features of 1q21+ MM, which can assist in effective therapeutic approaches for MM patients with 1q21+.

Abstract

Multiple myeloma (MM), a plasma cell neoplasm, is an incurable hematological malignancy characterized by complex genetic and prognostic heterogeneity. Gain or amplification of chromosome arm 1q21 (1q21+) is the most frequent adverse chromosomal aberration in MM, occurring in 40% of patients at diagnosis. It occurs in a subclone of the tumor as a secondary genomic event and is more amplified as the tumor progresses and a risk factor for the progression from smoldering multiple myeloma to MM. It can be divided into either 1q21 gain (3 copies) or 1q21 amplification (≥4 copies), and it has been suggested that the prognosis is worse in cases of amplification than gain. Trisomy of chromosome 1, jumping whole-arm translocations of chromosome1q, and tandem duplications lead to 1q21+ suggesting that its occurrence is not consistent at the genomic level. Many studies have reported that genes associated with the malignant phenotype of MM are situated on the 1q21 amplicon, including CKS1B, PSMD4, MCL1, ANP32E, and others. In this paper, we review the current knowledge regarding the clinical features, prognostic implications, and the speculated pathology of 1q21+ in MM, which can provide clues for an effective treatment approach to MM patients with 1q21+.

MicroRNAs in cancer therapy: Their involvement in oxaliplatin sensitivity/resistance of cancer cells with a focus on colorectal cancer

The resistance of cancer cells into chemotherapy has restricted the efficiency of anti-tumor drugs. Oxaliplatin (OX) being an anti-tumor agent/drug is extensively used in the treatment of various cancer diseases. However, its frequent application has led to chemoresistance. As a consequence, studies have focused in finding underlying molecular pathways involved in OX resistance. MicroRNAs (miRs) are short endogenous non-coding RNAs that are able to regulate vital biological mechanisms such as cell proliferation and cell growth. The abnormal expression of miRs occurs in pathological events, particularly cancer. In the present review, we describe the involvement of miRs in OX resistance and sensitivity. The miRs are able to induce the oncogene factors and mechanisms, resulting in stimulation OX chemoresistance. Also, onco-suppressor miRs can enhance the sensitivity of cancer cells into OX chemotherapy and trigger apoptosis and cell cycle arrest, leading to reduced viability and progression of cancer cells. MiRs can also enhance the efficacy of OX chemotherapy. It is worth mentioning that miRs affect various down-stream targets in OX resistance/sensitivity such as STAT3, TGF-β, ATG4B, FOXO1, LATS2, NF-κB and so on. By identification of these miRs and their upstream and down-stream mediators, further studies can focus on targeting them to sensitize cancer cells into OX chemotherapy and induce apoptotic cell death.