Clinicopathological characteristics and genomic profiling in patients with transformed lymphoma: a monocentric retrospective study.

BACKGROUND: Transformed lymphoma occurs when indolent lymphoma transforms into more aggressive lymphoma usually associated with poor prognosis. METHODS: In this study, we analysed the immunophenotypes, prognostic factors and outcomes of 35 patients with transformed lymphoma from among 306 marginal zone lymphoma (MZL), 544 follicular lymphoma (FL) and 871 chronic lymphocytic leukaemia/small lymphocytic lymphoma (CLL/SLL) cases. In addition, we performed whole-exome sequencing study of seven transformed MZL (tMZL) cases. RESULTS: Our results demonstrate that the median time from indolent lymphoma diagnosis to transformed DLBCL was 35 months (range, 14-53 months). The 5-year overall survival (OS) and progression-free survival (PFS) rates after histological transformation (HT) were 50% and 26%, respectively. Kaplan-Meier survival analysis revealed that asynchronous HT and transformed CLL/SLL (tCLL/SLL) were significant adverse prognostic factors for OS after DLBCL HT. We identified mutations involvement in chromatin remodelling (CREBBP and EP300) and regulators of NF-κB signalling (TNFAIP3, BCL10, MYD88, CD79B and CARD11) were affected in tMZL. CONCLUSION: Whole-exome sequencing and copy-number analysis revealed that tMZL derives from the divergent evolution of an ancestral common progenitor clone (CPC). Collectively, this study provides clinicopathological characteristics of three common types of transformed lymphomas and the genetic profile of tMZL with diagnostic and therapeutic implications.

Role of Rituximab in Treatment of Patients With Primary Central Nervous System Lymphoma (PCNSL): A Systematic Review and Meta-Analysis.

Primary central nervous system lymphoma (PCNSL) is a rare form of non-Hodgkin's lymphoma involving the brain, cerebrospinal fluid, spinal cord and eyes. Rituximab has played a prominent role in the treatment of non-Hodgkin's B-cell lymphomas, including aggressive diffuse large B lymphoma. However, as a macromolecular drug, the role of rituximab in the treatment of PCNSL has been controversial. In this systematic review and meta-analysis, we evaluated the role of rituximab in the treatment of PCNSL. We searched articles in the following electronic databases including PubMed, Embase, Cochrane Library, Web of Science, and ClinicalTrials.gov until October 20, 2022.We included 11 studies (3 RCTS and 8 retrospective studies) with a total of 1182 patients. We extracted the baseline characteristics and outcomes of the studies and assessed the risk of bias, then used Review Manager 5.4 for this meta-analysis. The primary outcomes included complete response rate (CR), overall survival (OS), and progression-free survival (PFS). Odds ratios (ORS) and corresponding 95% confidence intervals (CIS) for the primary outcome were analyzed and compared. The results of our statistical analysis show that the use of rituximab was closely correlated with a higher CR(OR 1.70,95%CI 1.17-2.46, P = .005), 3-year OS (OR 2.40, 95%CI 1.53-3.77, P = .0001), 5-year OS (OR 2.75, 95%CI 1.68-4.49, P < .0001), 3-year PFS(OR 4.42, 95%CI 1.15-16.97, P < .0001), 5-year PFS(OR 1.97, 95%CI 1.39-2.78, P = .0001).These results suggest that rituximab may have a positive impact on the prognosis of patients with PCNSL, and may be helpful in the determination of treatment plan for patients with PCNSL.

Tumor-associated M2 macrophages in the immune microenvironment influence the progression of renal clear cell carcinoma by regulating M2 macrophage-associated genes.

Background: Renal clear cell carcinoma (RCC) has negative prognosis and high mortality due to its early diagnosis difficulty and early metastasis. Although previous studies have confirmed the negative progression of RCC is closely related to M2 macrophages in tumor-associated macrophages (TAMs), the specific mechanism is still unknown. Methods: We used immunofluorescence labeling and flow cytometry to detect the proportion of M2 macrophages in RCC tissues. And bioinformatics technique was used to obtain 9 M2 macrophage-related model genes, including SLC40A1, VSIG4, FUCA1, LIPA, BCAT1, CRYBB1, F13A, TMEM144, COLEC12. Using these genes, model formulas are constructed to devide samples into high and low risk groups, and then the overall survival (OS), progression-free survival (PFS) and Gene set enrichment analysis (GSEA) of the high and low risk groups were analyzed. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to measure the expression of model genes between normal kidney tissue and RCC tissue, as well as between HK-2 cell and 786-O cell. Besides, we induced the M2 differentiation of THP-1 cell, and then co-cultured with the RCC cell 786-O in transwell to observe what effect M2 macrophages will cause on the invasion, migration and the expression of model genes of RCC. Results: Our study demonstrated M2 macrophages in RCC was about 2 folds that of normal renal tissue (P<0.0001) and M2 macrophages affected the prognosis of patients with RCC by affecting the co-expressed genes, which were mainly enriched in immune-related pathways. The results of in vitro experiments showed that in RCC tissues and 786-O cells, the model gene FUCA1 was down-regulated, and SLC40A1, VSIG4, CRYBB1 and LIPA were up-regulated. Besides, the results of co-culture showed that after 786-O co-culture with M2 macrophages, the ability of migration and invasion was promoted and the expressions of FUCA1, SLC40A1, VSIG4, CRYBB1, LIPA and TMEM144 were all up-regulated. Conclusion: The proportion of tumor-associated M2 macrophages in RCC tissues is upregulated, and M2 macrophages promote the progression of RCC by regulating the expression of SLC40A1, VSIG4, FUCA1, LIPA, BCAT1, CRYBB1, F13A, TMEM144, COLEC12 genes, thereby affecting the prognosis of patients with RCC.

Whole-exome sequencing of a patient with primary central nervous system T-cell lymphoma: Clinicopathological features and genomic profiling.

Primary central nervous system T-cell lymphoma (T-PCNSL) is a rare neoplasm, and its underlying genetic features are poorly understood. Herein, we present the case of a 64-year-old man with T-PCNSL who presented with left-side limb weakness. Brain magnetic resonance imaging revealed a right parietal space-occupying lesion. Immunohistochemically, the tumor was positive for CD3, CD4, CD5, CD8, and CD56, and the Ki-67 labeling index was approximately 20%. These pathological features are consistent with those of T-cell lymphoma. Whole exome sequencing was performed, and we found a variant in the ACSS3 gene that could be related to disease pathogenesis. Our findings may help advance our understanding of the molecular pathogenesis of T-PCNSL. Further molecular analysis of such cases could help to improve adjuvant molecular diagnostic methods and targeted therapies for T-PCNSL.

Cinnamaldehyde causes developmental neurotoxicity in zebrafish via the oxidative stress pathway that is rescued by astaxanthin.

Toxicology studies provide a reliable dose range for the use of compounds. Zebrafish show unique advantages in toxicology research. Cinnamaldehyde (Cin) is one of the main active compounds isolated from Cinnamon trees and other species of the genus Cinnamomum. In this study, we investigated the developmental neurotoxicity of cinnamaldehyde in zebrafish and preliminarily explored its underlying mechanism. Cinnamaldehyde causes developmental neurotoxicity in zebrafish, as evidenced by the damage to ventricular structures, eye malformations, shortened body length, trunk curvature, decreased neuronal fluorescence, and pericardial oedema. Moreover, it can induce abnormal behaviour and gene expression in zebrafish. After treatment with the oxidative stress inhibitor astaxanthin, the behaviour and abnormal gene expression were reversed. All of these data demonstrated that the developmental neurotoxicity of cinnamaldehyde might be attributed to oxidative stress. In addition, this study also confirmed that zebrafish is a reliable model for toxicity studies.

Association analysis of risk genes identified by SCHEMA with schizophrenia in the Chinese Han population.

BACKGROUND: Schizophrenia is a chronic brain disorder. Previously, the Schizophrenia Exome Sequencing Meta-analysis consortium identified 10 highest risk genes related to schizophrenia. This study aimed to analyze the relationship between the 10 highest risk genes identified by the SCHEMA and schizophrenia in a Chinese population. METHODS: A total of 225 variants in 10 genes were screened in a Chinese population of 6836 using a customized array. All variants were annotated through the Variant Effect Predictor tool, and the functional impacts of missense variants were assessed based on sorting intolerant from tolerant and PolyPhen-2 scores. The SHEsisPlus tool was used to analyze the association between risk genes and schizophrenia at the locus and gene levels. RESULTS: At the locus level, no missense variants significantly related to schizophrenia were found, but we detected three missense variants that appeared only in cases, including TRIO p. Arg1185Gln, RB1CC1 p. Arg1514Cys, and HERC1 p. Val4517Leu. At the gene level, five genes (TRIO, RB1CC1, HERC1, GRIN2A, and CACAN1G) with more than one variant analyzed were kept for the gene-level association analysis. Only the association between RB1CC1 and schizophrenia reached a significant level (OR = 1.634; 95% CI, 1.062-2.516; P = 0.025). CONCLUSION: In this study, we determined that RB1CC1 might be a risk gene for schizophrenia in the Chinese population. Our results provide new evidence for recognizing the correlation of these risk genes with the Chinese schizophrenia population.

Expression and Clinical Significance of Th1/Th2/Th17 Cytokines and Lymphocyte Subsets in PCNSL.

Purpose: Primary central nervous system lymphoma (PCNSL) responds favorably to radiation, chemotherapy and targeted drug therapy. However survival is usually worse, the treatment-related drug resistance and recurrence are still clinical problems to be solved urgently. Studies have shown that cytokines are expressed in varying degrees in patients with lymphoma, which is significantly related to the progression, poor prognosis and drug resistance of lymphoma. We explore the expression and clinical significance of Th1/Th2/Th17 cytokines and lymphocyte subsets in patients with PCNSL to provide a more sufficient theoretical basis for its diagnosis and treatment. Patients and Methods: We measured and analysed the levels of Th1/Th2/Th17 cytokines and the distribution of lymphocyte subsets (including Treg cells, CD3+, CD4+, CD8+, CD19+, and CD4+/CD8+) in 39 patients with PCNSL and 96 patients with diffuse large B-cell lymphoma (DLBCL) without central nervous system involvement. The cytokines of 13 healthy people and the lymphocyte subsets of 27 healthy people were measured as the control group. Results: We found a significant difference in the level of Th1/Th2/Th17 cytokines and lymphocyte subsets between PCNSL and healthy controls, especially IL-2, after treatment, which was significantly higher than before treatment (p<0.01). However, the level of CD19+ and CD4+/CD8+ decreased while CD8+ and CD3+ increased after treatment (regardless of whether the treatment was effective), and the difference was statistically significant. In addition, our analysis of different prognostic factors found that HD-MTX-based chemotherapy appears to have a longer progression-free survival and overall survival than osimertinib-based chemotherapy. Conclusion: There are significant differences in Th1/Th2/Th17 cytokines and lymphocyte subsets among PCNSL, DLBCL, and healthy controls, and their detection is helpful for the diagnosis, treatment, and prognosis of PCNSL. HD-MTX-based chemotherapy may still be the first choice for PCNSL.

Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes.

BACKGROUND: Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species. RESULTS: Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63-69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24-27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42-44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7-10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407 to 6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value. CONCLUSIONS: We sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.

Genetic risk of clozapine-induced leukopenia and neutropenia: a genome-wide association study.

BACKGROUND: Clozapine is considered to be the most effective antipsychotic medication for schizophrenia. However, it is associated with several adverse effects such as leukopenia, and the underlying mechanism has not yet been fully elucidated. The authors performed a genome-wide association study (GWAS) in a Chinese population to identify genetic markers for clozapine-induced leukopenia (CIL) and clozapine-induced neutropenia (CIN). METHODS: A total of 1879 patients (225 CIL cases, including 43 CIN cases, and 1,654 controls) of Chinese descent were included. Data from common and rare single nucleotide polymorphisms (SNPs) were tested for association. The authors also performed a trans-ancestry meta-analysis with GWAS results of European individuals from the Clozapine-Induced Agranulocytosis Consortium (CIAC). RESULTS: The authors identified several novel loci reaching the threshold of genome-wide significance level (P < 5 × 10-8). Three novel loci were associated with CIL while six were associated with CIN, and two T cell related genes (TRAC and TRAT1) were implicated. The authors also observed that one locus with evidence close to genome-wide significance (P = 5.08 × 10-8) was near the HLA-B gene in the major histocompatibility complex region in the trans-ancestry meta-analysis. CONCLUSIONS: The associations provide novel and valuable understanding of the genetic and immune causes of CIL and CIN, which is useful for improving clinical management of clozapine related treatment for schizophrenia. Causal variants and related underlying molecular mechanisms need to be understood in future developments.

Trans-Ancestry Mutation Landscape of Hepatoblastoma Genomes in Children.

Hepatoblastoma (HB) is the most common malignant tumor in the liver of infants and young children. The incidence rate varies among different populations. However, genetic differences in HB patients with different epidemiological and ancestral backgrounds have not been found. In this study, we aim to analyze data from 16 patients treated at our center and collected published data from whole-exome sequencing studies on HB, and to explore the genetic differences between races. Data from a total of 75 HB patients of three races (24 Asian, 37 Caucasian and 14 Hispanic) were analyzed. We identified 16 genes with recurrent somatic mutations and 7 core pathway modules. Among them, the Wnt/ß-catenin pathway had the highest mutation rate, and the mutation frequency in Caucasians and Hispanics was approximately twice as high as that in Asians. In addition, this study compared the characteristics of gene mutations between patients who underwent preoperative chemotherapy and those who did not and found that there was no significant difference in gene mutations between the two groups. We also preliminarily verified the function of cancer-associated candidate genes (CTNNB1 and KMT2D). In conclusion, we found ethnic differences in HB biology at the genomic level, which expands our understanding of the genetics of HB in children.

Cigarette smoking and schizophrenia: Mendelian randomisation study.

BACKGROUND: The link between schizophrenia and cigarette smoking has been well established through observational studies. However, the cause-effect relationship remains unclear. AIMS: We conducted Mendelian randomisation analyses to assess any causal relationship between genetic variants related to four smoking-related traits and the risk of schizophrenia. METHOD: We performed a two-sample Mendelian randomisation using summary statistics from genome-wide association studies (GWAS) of smoking-related traits and schizophrenia (7711 cases, 18 327 controls) in East Asian populations. Single nucleotide polymorphisms (SNPs) correlated with smoking behaviours (smoking initiation, smoking cessation, age at smoking initiation and quantity of smoking) were investigated in relation to schizophrenia using the inverse-variance weighted (IVW) method. Further sensitivity analyses, including Mendelian randomisation-Egger (MR-Egger), weighted median estimates and leave-one-out analysis, were used to test the consistency of the results. RESULTS: The associated SNPs for the four smoking behaviours were not significantly associated with schizophrenia status. Pleiotropy did not inappropriately affect the results. CONCLUSIONS: Cigarette smoking is a complex behaviour in people with schizophrenia. Understanding factors underlying the observed association remains important; however, our findings do not support a causal role of smoking in influencing risk of schizophrenia.

Copy Number Analysis Reveal Genetic Risks of Penile Cancer.

OBJECTIVES: To evaluate copy number alterations (CNAs) in genes associated with penile cancer (PeC) and determine their correlation and prognostic ability with PeC. METHODS: Whole-exome sequencing was performed for tumor tissue and matched normal DNA of 35 patients diagnosed with penile squamous cell carcinoma from 2011 to 2016. Somatic CNAs were detected using the Genome Analysis Toolkit (GATK). Retrospective clinical data were collected and analyzed. All the data were statistically analyzed using SPSS 16.0 software. The cancer-specific survival rates were estimated by Kaplan-Meier curves and compared with the log-rank test. RESULTS: CNAs in the MYCN gene was detected in 19 (amplification: 54.29%) patients. Other CNAs gene targets were FAK (amplification: 45.72%, deletion: 8.57%), TP53 (amplification: 2.86%, deletion: 51.43%), TRKA (amplification: 34.29%, deletion: 2.86%), p75NTR (amplification: 5.71%, deletion: 42.86%), Miz-1 (amplification: 14.29%, deletion: 20.00%), Max (amplification: 17.14%, deletion: 2.86%), Bmi1 (amplification:14.29%, deletion: 48.57%), and MDM2 (amplification: 5.71%, deletion: 45.72%). The CNAs in MYCN and FAK correlated significantly with patient prognosis (P<0.05). The 3-year Recurrence-free survival rate was 87.10% among patients followed up. The 5-year survival rate of patients with MYCN amplification was 69.2%, compared to 94.4% in the non-amplification group. The 5-year survival rate of patients with FAK amplification was 65.6%, compared to 94.7% in the non-amplification group. The PPI network showed that TP53 and MYCN might play meaningful functional roles in PeC. CONCLUSION: MYCN and FAK amplification and TP53 deletion were apparent in PeC. MYCN and TP53 were hub genes in PeC. MYCN and FAK amplification was also detected and analyzed, and the findings indicated that these two genes are predictors of poor prognosis in PeC.

Body Mass Index and Polycystic Ovary Syndrome: A 2-Sample Bidirectional Mendelian Randomization Study.

BACKGROUND: Observational studies have shown a link between elevated body mass index (BMI) and the risk of polycystic ovary syndrome (PCOS). While Mendelian randomization (MR) studies in Europeans have suggested a causal role of increased BMI in PCOS, whether the same role is suggested in Asians has yet to be investigated. We used MR studies to infer causal effects using genetic data from East Asian populations. METHODS AND FINDINGS: We performed a 2-sample bidirectional MR analysis using summary statistics from genome-wide association studies (GWAS) of BMI (with up to 173 430 individuals) and PCOS (4386 cases and 8017 controls) in East Asian populations. Seventy-eight single nucleotide polymorphisms (SNPs) correlated with BMI were selected as genetic instrumental variables to estimate the causal effect of BMI on PCOS using the inverse-variance weighted (IVW) method. To test the reliability of the results, further sensitivity analyses included MR-Egger regression, weighted median estimates, and leave-one-out analysis. The IVW analysis indicated a significant association between high BMI and the risk of PCOS (odds ratio per standard deviation higher BMI, 2.208; 95% confidence interval 1.537 to 3.168, P = 1.77 × 10-5). In contrast, the genetic risk of PCOS had no significant effect on BMI. CONCLUSIONS: The results of our bidirectional MR study showed that an increase in BMI causes PCOS, while PCOS does not cause an increased BMI. This study provides further genetic support for a link between BMI and PCOS. Further research is needed to interpret the potential mechanisms of this association.

Mutational landscape of penile squamous cell carcinoma in a Chinese population.

Penile squamous cell carcinoma (PSCC) is a malignancy that affects the skin and tissues of the penis, but the knowledge of pathogenesis and carcinogenesis is limited. Here, we characterize the PSCC genomic landscape using whole-exome sequencing. Of the 30 paired blood and tumor samples, we identified recurrent mutations in 11 genes; confirmed previous findings for FAT1 (4/30), HRAS (4/30), NOTCH1 (4/30), TP53 (3/30) and PIK3CA (3/30); and revealed novel candidate driver genes [CASP8 (4/30), SLITRK2 (3/30), FLG (3/30) and TRRAP (3/30)]. Our in vitro experiments suggested CASP8 was involved in mediating TRAIL-induced apoptosis of penile cancer cell lines. We also observed the frequently altered pathways for potential therapeutic implications: alterations in the Notch (30% of sample altered), RTK-RAS (26.7% altered) and Hippo (23.3% altered) pathways accounted for over 50% of tumors. The frequently altered genes (>10%) in these pathways were proved to be expressed in penile tumors by immunohistochemistry assay. These findings provide new insight into the mutational and pathway landscapes of PSCC and suggest potential novel therapeutic opportunities for this malignancy.