Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing in Chinese patients / 医学前沿

Primary central nervous system lymphoma (PCNSL) is an uncommon non-Hodgkin's lymphoma with poor prognosis. This study aimed to depict the genetic landscape of Chinese PCNSLs. Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples, whose genomic characteristics and clinicopathologic features were also analyzed. Structural variations were identified in all patients with a mean of 349, which did not significantly influence prognosis. Copy loss occurred in all samples, while gains were detected in 77.9% of the samples. The high level of copy number variations was significantly associated with poor progression-free survival (PFS) and overall survival (OS). A total of 263 genes mutated in coding regions were identified, including 6 newly discovered genes (ROBO2, KMT2C, CXCR4, MYOM2, BCLAF1, and NRXN3) detected in ⩾ 10% of the cases. CD79B mutation was significantly associated with lower PFS, TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS. A prognostic risk scoring system was also established for PCNSL, which included Karnofsky performance status and six mutated genes (BRD4, EBF1, BTG1, CCND3, STAG2, and TMSB4X). Collectively, this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs, thereby enriching the present understanding of the genetic mechanisms of PCNSL.

Multiomics and Multidimensional Testing for Efficacy Monitoring of Patients with Lymphoma / 中国实验血液学杂志

OBJECTIVE@#To explore the role of a new blood-based, multiomics and multidimensional method for evaluating the efficacy of patients with lymphoma.@*METHODS@#10 ml peripheral blood was extracted from each patient, and the genomic copy number aberrations (CNA) and fragment size (FS) were evaluated by low-depth whole genome sequencing of cfDNA, and the level of a group of plasma tumor marker (PTM) were detected at the same time. The cancer efficacy score (CES) was obtained by standardized transformation of the value of above three numerical indexes, and the changes of CES before and after treatment were compared to evaluate the patient's response to the treatment regimen.@*RESULTS@#A total of 35 patients' baseline data were collected, of which 23 cases (65.7%) had elevated CES values. 18 patients underwent the first time test. The results showed that the CES value of 9 patients with positive baseline CES decreased significantly at the first test, and the efficacy evaluation was PR, which was highly consistent with the imaging evaluation results of the same period. At the same time, the CNA variation spectrum of all patients were evaluated and it was found that 23 patients had partial amplification or deletion of chromosome fragments. The most common amplification site was 8q24.21, which contains important oncogenes such as MYC. The most common deletion sites were 1p36.32, 4q21.23, 6q21, 6q27, 14q32.33, and tumor suppressor-related genes such as PRDM1, ATG5, AIM1, FOXO3 and HACE1 were expressed in the above regions, so these deletions may be related to the occurrence and development of lymphoma.@*CONCLUSION@#With the advantages of more convenience, sensitivity and non-invasive, this multiomics and multidimensional efficacy detection method can evaluate the tumor load of patients with lymphoma at the molecular level, and make more accurate efficacy evaluation, which is expected to serve the clinic better.

Gene Polymorphisms of Patients with Lymphoma-Associated Hemophagocytic Syndrome in Longyan area, Fujian Province / 中国实验血液学杂志

OBJECTIVE@#To analyze the gene polymorphisms of patients with lymphoma-associated hemophagocytic syndrome in Longyan area, Fujian province.@*METHODS@#A total of 125 patients with lymphoma-associated hemophagocytic syndrome in Longyan, Fujian province, admitted to Longyan First Hospital from May 2017 to November 2020 were selected. Peripheral venous blood was collected from all the patients, and the genotypes of perforin 1 (PRF1) and interleukin-10 (IL-10) gene loci were detected by PCR-fluorescence probe method, and the correlation between PRF1 and IL-10 gene polymorphisms and lymphoma-associated hemophagocytic syndrome was analyzed.@*RESULTS@#The mutation frequencies of PRF1 gene loci rs885821 (C>T), rs885822 (C>T), rs1889490 (G>A) in patients with lymphoma-associated hemophagocytic syndrome were 10.40%, 78.8% and 64.4%, respectively. The mutation frequencies of rs1800872 (A>C), rs1800871 (C>T) and rs1800896 (G>A) of IL-10 loci were 56.0%, 45.2% and 77.6%, respectively.@*CONCLUSION@#PRF1 and IL-10 gene loci were polymorphic in patients with lymphoma-associated hemophagocytic syndrome in Longyan area, Fujian province. Alleles C and G of PRF1 and IL-10 were risk factors, and alleles T and A were protective factors.

Genome instability and lymphoma / 中南大学学报(医学版)

Lymphoma is one of the most common malignant tumor of the hematologic system. The genome instability is not only an important molecular basis for the development of lymphoma, but also has important value in the diagnosis and prognosis of lymphoma. There are 2 types of genome instability: Microsatellite instability (MSI/MIN) at gene level and chromosomal instability at chromosome level. Through the study on genes associated with lymphoma, the unstable genes associated with lymphoma could be found, meanwhile the mechanism of its occurrence and development of lymphoma could be explored, and the important basis of molecular biology could also be provided in the field of current hot lymphoma precision medical research.

analysis of gene expression variations in lymphoma, using a fuzzy classification model

Introduction: Cancer is a major cause of mortality in the modern world, and one of the most important health problems in societies. During recent years, research on cancer as a system biology disease is focused on molecular differences between cancer cells and healthy cells. Most of the proposed methods for classifying cancer using gene expression data act as black boxes and lack biological interpretability. The goal of this study is to design an interpretable fuzzy model for classifying gene expression data of Lymphoma cancer

Method: In this research, the investigated microarray contained 45 samples of lymphoma. Total number of genes was 4026 samples. At first, we offer a hybrid approach to reduce the data dimension for detecting genes involved in lymphoma cancer. In lymphoma microarray, six out of 4029 genes were selected. Then, a fuzzy interpretable classifier was presented for classification of data. Fuzzy inference was performed using two rules which had the highest scores. Weka3.6.9 software was used to reduce the features and the fuzzy classifier model was implemented in MATLAB R2010a. Results of this study were assessed by two measures of accuracy and precision

Results: In pre-processing stage, in order to classify gene expression data of Lymphoma, six out of 4026 genes were identified as cancer-causing genes, and then the fuzzy classifier model was applied on the obtained data. The accuracy of the results of classification was 96 percent using 10 rules with the highest scores and that using 2 rules with the highest scores was about 98 percent

Conclusion: In the proposed approach, for the first time, a fully fuzzy method named a minimal rule fuzzy classification [MRFC] was introduced for extracting fuzzy rules with biological interpretability and meaning extraction from gene expression data. Among the most outstanding features of this method is the ability of extracting a small set of rules to interpret effective gene expression in cancer patients. Another result of this approach is successfully addressing the problem of disproportion between the number of samples and genes in microarrays with the proposed Filter-Wrapper Feature Selection method [FWFS]

Association of oxidative stress and DNA damage with grafting time in patients with multiple myeloma and lymphoma submitted to autologous hematopoietic stem cell transplantation / Associação do estresse oxidativo e dano ao DNA com o tempo de enxertia em pacientes com mieloma múltiplo e linfomas submetidos a transplante autólogo de células-tronco hematopoéticas

ABSTRACT The aim of the study was to investigate the association between oxidative stress and DNA damage with grafting time in patients submitted to autologous hematopoietic stem-cell transplantation (HSCT). The study included 37 patients submitted to autologous HSCT diagnosed with Multiple Myeloma (MM) and lymphoma (Hodgkin’s and non-Hodgkin’s). Biomarkers of oxidative stress and DNA damage index (DI) were performed at baseline (pre-CR) of the disease and during the conditioning regimen (CR), one day after the HSCT, ten days after HSCT and twenty days after HSCT, as well as in the control group consisting of 30 healthy individuals. The outcomes showed that both groups of patients had an hyperoxidative state with high DI when compared to baseline and to the control group and that the CR exacerbated this condition. However, after the follow-up period of the study, this picture was re-established to the baseline levels of each pathology. The study patients with MM showed a mean grafting time of 10.75 days (8 to 13 days), with 10.15 days (8 to 15 days) for the lymphoma patients. In patients with MM, there was a negative correlation between the grafting time and the basal levels of GPx (r = -0.54; p = 0.034), indicating that lower levels of this important enzyme are associated with a longer grafting time. For the DI, the correlation was a positive one (r = 0.529; p = 0.030). In the group with lymphoma, it was observed that the basal levels of NOx were positively correlated with grafting time (r = 0.4664, p = 0.032). The data indicate the potential of these biomarkers as predictors of toxicity and grafting time in patients with MM and Lymphomas submitted to autologous HSCT.

RESUMO O objetivo do estudo foi investigar a associação entre estresse oxidativo e dano ao DNA com o tempo de enxertia em pacientes submetidos ao transplante de células-tronco hematopoéticas autólogo (TCTH). Participaram do estudo 37 pacientes submetidos ao TCTH autólogo com diagnóstico de mieloma múltiplo (MM) e Linfomas (Hodgkin e não Hodgkin). Biomarcadores de estresse oxidativo e índice de dano ao DNA (ID) foram determinados no estado basal (Pré-RC) das doenças e durante o regime de condicionamento (RC), um dia após o TCTH, dez dias após o TCTH e vinte dias após o TCTH e no grupo controle composto por 30 individuos saudáveis. Os resultados demonstraram que os dois grupos de pacientes apresentaram um estado hiperoxidativo com elevado ID quando comparados ao estado basal e ao grupo controle e que o RC exacerbou essa condição. No entanto, após o tempo de acompanhamento do estudo, esse quadro foi reestabelecido ao estado basal de cada patologia. Os pacientes do estudo com MM apresentaram uma média do tempo de enxertia de 10,75 dias (8 a 13 dias), e de 10,15 dias (8 a 15 dias) para o grupo Linfoma. Nos pacientes com MM houve uma correlação negativa entre o tempo de enxertia e os níveis basais de GPx (r=-0,54; p=0,034), indicando que níveis mais baixos de GPx estão relacionados a um maior tempo de enxertia, e para o ID, a correlação foi positiva (r=0,529; p=0,030). No grupo com Linfoma, observou-se que os níveis basais de NOx correlacionaram-se positivamente com o tempo de enxertia (r= 0,4664; p=0,032). Os dados apontam para o potencial desses biomarcadores como preditores da toxicidade e do tempo de enxertia em pacientes com MM e Linfomas submetidos ao TCTH autólogo

Relevance of prognostic factors in the decision-making of stem cell transplantation in Myelodysplastic Syndromes / Relevância dos fatores prognósticos na decisão do transplante de células-tronco na Síndrome Mielodisplásica

ABSTRACT The hematopoietic stem cell transplantation (HSCT) is the only curative alternative for Myelodysplastic Syndrome (MDS), but many patients are not eligible for this treatment, as there are several limiting factors, especially in the case of patients with low-risk MDS. The aim of this study is to discuss the factors that can guide the decision-making on referring or not a patient to HSCT. Three cases of MDS, two of which were submitted to HSCT are presented. We intend to report the difficulties in referring patients with MDS to transplant and the prognostic factors that contribute to define eligibility.

RESUMO O transplante de células-tronco hematopoéticas (TCTH) é a única alternativa curativa para Síndrome Mielodisplásica (SMD), porém muitos pacientes não são elegíveis para esta opção, pois existem diversos fatores limitantes, principalmente no caso de pacientes com SMD de baixo risco. O objetivo do estudo é discutir os fatores que podem orientar a decisão no encaminhamento ou não para o TCTH. São apresentados três casos de SMD, dos quais dois foram submetidos ao TCTH. Nos propomos a relatar as dificuldades no encaminhamento dos pacientes com SMD ao transplante e os fatores prognósticos que contribuem para definir a elegibilidade.

Seroprevalence and seroincidence of Leptospira infection in dogs during a one-year period in an endemic urban area in Southern Brazil

INTRODUCTION: Leptospirosis is a zoonosis that affects both humans and animals. Dogs may serve as sentinels and indicators of environmental contamination as well as potential carriers for Leptospira. This study aimed to evaluate the seroprevalence and seroincidence of leptospirosis infection in dogs in an urban low-income community in southern Brazil where human leptospirosis is endemic. METHODS: A prospective cohort study was designed that consisted of sampling at recruitment and four consecutive trimestral follow-up sampling trials. All households in the area were visited, and those that owned dogs were invited to participate in the study. The seroprevalence (MAT titers ≥100) of Leptospira infection in dogs was calculated for each visit, the seroincidence (seroconversion or four-fold increase in serogroup-specific MAT titer) density rate was calculated for each follow-up, and a global seroincidence density rate was calculated for the overall period. RESULTS: A total of 378 dogs and 902.7 dog-trimesters were recruited and followed, respectively. The seroprevalence of infection ranged from 9.3% (95% CI; 6.7 - 12.6) to 19% (14.1 - 25.2), the seroincidence density rate of infection ranged from 6% (3.3 - 10.6) to 15.3% (10.8 - 21.2), and the global seroincidence density rate of infection was 11% (9.1 - 13.2) per dog-trimester. Canicola and Icterohaemorraghiae were the most frequent incident serogroups observed in all follow-ups. CONCLUSIONS: Follow-ups with mean trimester intervals were incapable of detecting any increase in seroprevalence due to seroincident cases of canine leptospirosis, suggesting that antibody titers may fall within three months. Further studies on incident infections, disease burden or risk factors for incident Leptospira cases should take into account the detectable lifespan of the antibody. .

Development of thymic lymphomas in mice disrupted of Brca2 allele in the thymus

Germ-line mutations in BRCA2 predispose to early-onset cancer. Homozygous mutant mouse, which has Brca2 truncated in exon 11 exhibit paradoxic occurrence of growth retardation and development of thymic lymphomas. However, due to its large embryonic lethality, cohort studies on the thymic lymphomas were not feasible. With the aid of Cre-loxP system, we demonstrate here that thymus-specific disruption of Brca2 allele without crossing it to p53-mutant background leads to the development of thymic lymphomas. Varying from 16 weeks to 66 weeks after birth, 25% of mice disrupted of Brca2 in the thymus died of thymic lymphomas, whereas previous report did not observe lymphomagenesis using similar Cre-loxP system. Future analysis of thymic lymphomas from these mice presented here will provide information on the cooperative mutations that are required for the BRCA2-associated pathogenesis of cancer.

Imunofenotipagem e rearranjo gênico em doenças pulmonares linfocíticas e linfoproliferativas / Immunophenotyping and gene rearrangement analysis in lymphoid/lymphoproliferative disorders of the lungs

OBJETIVO: Determinar a utilidade, na prática rotineira, da análise da clonalidade dos linfócitos T e B nos tecidos pulmonares por reação em cadeia da polimerase no diagnóstico das doenças linfoproliferativas pulmonares. MÉTODOS: Avaliaram-se, mediante análise imunohistoquímica e rearranjo molecular dos genes, 8 casos de pneumonia intersticial linfocítica (PIL) e 7 casos de doenças linfoproliferativas pulmonares. RESULTADOS: Todos os 8 casos de PIL expressaram imunocoloração moderada a forte para CD3, em contraste com apenas 2 casos de linfoma e 1 caso de pseudolinfoma. Rearranjo gênico foi detectado em 4 de 8 casos de PIL, o que mudou o diagnóstico de PIL para linfoma, indicando, assim, a importância da detecção de rearranjo gênico em casos de PIL. Nesta situação, rearranjo gênico usando-se os pares de primers VH/JH e Vgama11/Jgama12 foi detectado em 3 e 1 casos de PIL, respectivamente, e não foram detectadas anormalidades gênicas usando-se as pares Dbeta1/Jbeta2 e Vgama101/Jgama12. Uma associação positiva foi detectada entre a intensidade de imunoexpressão CD20 e CD68 e rearranjo gênico usando-se o par de primers VH/JH. Antes do rearranjo gênico, 4 pacientes com PIL morreram rapidamente, enquanto que, após o rearranjo gênico, apenas 1 paciente com PIL morreu. CONCLUSÕES: A detecção de células B e T monoclonais por imunofenotipagem e reação em cadeia da polimerase mostrou impacto no diagnóstico de linfomas pulmonares em pacientes previamente diagnosticados com PIL. Portanto, imunofenotipagem e reação em cadeia da polimerase devem ser incluídas como métodos de 'padrão ouro' na rotina diagnóstica.

OBJECTIVE: To determine the usefulness, in routine practice, of using polymerase chain reaction to analyze B and T lymphocyte clonality in pulmonary tissue as a tool for the diagnosis of pulmonary lymphoproliferative disorders. METHODS: Immunohistochemistry and molecular gene rearrangement analysis were performed in order to assess 8 cases of lymphoid interstitial pneumonia (LIP) and 7 cases of pulmonary lymphoproliferative disorders. RESULTS: All 8 cases of LIP presented moderate to strong immunostaining for CD3, compared with only 2 cases of lymphoma and 1 case of pseudolymphoma (p = 0.02). Gene rearrangement was detected in 4 of the 8 cases, which changed the diagnosis from LIP to lymphoma, showing the importance of gene rearrangement detection in cases of LIP. In this situation, gene rearrangement using the VH/JH and Vgamma11/Jgamma12 primer pairs was detected in 3 cases and 1 case, respectively, and no gene abnormalities were found using the Dbeta1/Jbeta2 and Vgamma101/Jgamma12 primer pairs in any of the cases. A significant positive association was found between the intensity of CD20 and CD68 expression and gene rearrangement using the VH/JH primer pair. Prior to the gene rearrangement, 4 patients with LIP died quickly, whereas only one patient with LIP died after the gene rearrangement. CONCLUSIONS: Detection of monoclonal B and T cells by immunophenotyping and polymerase chain reaction had an impact on the diagnosis of pulmonary lymphomas in patients previously diagnosed with LIP. Therefore, immunophenotyping and polymerase chain reaction should be used as 'gold standard' techniques in routine practice.

Lack of DNA damage induced by fluoride on mouse lymphoma and human fibroblast cells by single cell gel (comet) assay

O flúor tem sido amplamente usado na Odontologia, pois é um agente profilático efetivo e específico contra a cárie dentária. Entretanto, o flúor em excesso pode representar perigos à saúde humana, especialmente por causar agressão ao material genético. Testes de genotoxicidade constituem uma parte importante da pesquisa do câncer para a avaliação de risco de possíveis carcinógenos. Neste estudo, danos ao DNA associados à exposição ao flúor foram avaliados pelo teste de células individualizadas em gel de agarose (teste do cometa) in vitro. Células de linfoma murino e fibroblastos humanos foram expostas ao fluoreto de sódio (NaF) nas concentrações finais de 7 a 100 µg/mL durante 3 h a 37ºC. Os resultados mostraram que o NaF não contribuiu para os danos ao DNA em ambos os tipos celulares estudados e em todas as concentrações testadas, conforme demonstrado pelas médias do momento da cauda e intensidade da cauda dos cometas. Estes achados são clinicamente importantes, uma vez que representam uma importante contribuição para a avaliação do risco potencial à saúde associada à exposição a agentes geralmente empregados na prática odontológica.

The Role of Microsatellite Instability in Development of Gastric Lymphoma / 대한소화기학회지

No abstract availble.

Support vector machines for novel class detection in Bioinformatics

Novelty detection techniques might be a promising way of dealing with high-dimensional classification problems in Bioinformatics. We present preliminary results of the use of a one-class support vector machine approach to detect novel classes in two Bioinformatics databases. The results are compatible with theory and inspire further investigation.

Immunoglobulin and T-cell receptor gene rearrangement analysis in malignant lymphoid neoplasms

Gene rearrangement analysis using Southern-blot hybridization technique is a standard method for evaluating clonal receptor gene rearrangement. Both clonality and lineage can be identified in lymphoid neoplasms by the demonstration of one or more rearranged antigen receptor genes of the immunoglobulin supergene family-immunoglobulin and T-cell receptor genes. To evaluate the diagnostic applicability of antigen receptor gene rearrangements in the diagnosis of malignant lymphomas and leukemias, the authors performed a gene rearrangement analysis of 54 cases by southern blot hybridization technique. One or two clonally rearranged bands were detected in the malignant lymphomas and in the lymphoblastic leukemias with a false-negative rate of 13.8%. No clonal, rearranged band was detected in benign reactive hyperplasias, carcinomas or non-lymphocytic leukemias. Rearrangement analysis could resolve the lineage, clonality and stage of differentiation of malignant lymphoid neoplasms.

Estudo cromossômico em leucemia, linfoma e câncer de pulmäo / Leukemias, lymphomas and lung cancer: chromosomic studies

Os autores descrevem os resultados da análise citogenética realizada em 16 pacientes portadores de leucemia, linfoma e câncer de pulmäo. Neste grupo forma observadas alteraçöes cromossômicas constitucionais, como duplicaçäo e translocaçäo, quebras cromossômicas preferenciais e variantes de heterocromatina constitutiva. Embora näo tenha sido possível detectar uma associaçäo direta destas características com a condiçäo neoplásica, taus achados em cerca de 37 porcento da amostra sugerem que algumas tenham desempenhado um papel no desenvolvimento maligno de seus portadores.

Influencia del genotipo del huesped en la formacion de las metastasis de un linfoma transplantable de rata / Influence of host genotype in the development of metastasis in a transplantable lymphoma in rats

Se estudió el comportamiento de un linfoma transplantable de rata (L-TACB) en tres líneas m, e R y e S con diferente susceptibilidad al tumor y a la frecuencia de metástasis, y en los híbridos mx eR, mx eS y eRx eS. Los tumores de la línea m tuvieron mayor tamño (p < 0,01) que los de eR. Sin embargo, el porcentaje de regresión fue menor (p < 0.001) en eR, evidenciando que la tasa de crecimiento del L-TACB fue independiente de la capacidad de rechazo del tumor. En la línea m y en el híbrido mx eS, apesar de desarrollar tumores muy grandes, sólo un animal de cada grupo tuvo metástasis; en cambio, en la sublínea eR en el híbrido mx eR con tumores de tamaños similares o menortes, la frecuencia de metástasis fue mucho mayor (p < 0,01). La aparición de metástasis estuvo parcialmente asociada al tamaño tumral. Estos resultado sugieren que el crescimiento del L-TACB, la capacidad de rechazo y la formación de metástasis estarían regidos por genes independientes con cierto grado de asociación