A Core Genome Multilocus Sequence Typing Scheme for Proteus mirabilis / 生物医学与环境科学（英文）

OBJECTIVE@#A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in Proteus mirabilis.@*METHODS@#In this work, we propose a publicly available cgMLST scheme for P. mirabilis using chewBBACA. In total 72 complete P. mirabilis genomes, representing the diversity of this species, were used to set up a cgMLST scheme targeting 1,842 genes, 635 unfinished (contig, chromosome, and scaffold) genomes were used for its validation.@*RESULTS@#We identified a total of 205 CGs from 695 P. mirabilis strains with regional distribution characteristics. Of these, 159 unique CGs were distributed in 16 countries. CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes. Nine virulence genes ( papC, papD, papE, papF, papG, papH, papI, papJ, and papK) related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20. These CGs require attention due to potential risks.@*CONCLUSION@#This research innovatively performs high-resolution molecular typing of P. mirabilis using whole-genome sequencing technology combined with a bioinformatics pipeline (chewBBACA). We found that the CGs of P. mirabilis showed regional distribution differences. We expect that our research will contribute to the establishment of cgMLST for P. mirabilis.

Screening for myeloid mutations in patients with myelodysplastic syndromes and AML with myelodysplasia-related changes

ABSTRACT Introduction: One of the most critical complications in myelodysplastic syndromes (MDS) is the progression to acute myeloid leukemia (AML). The dynamics of clonal evolution in MDS and how acquired mutations can be used as biomarkers to track disease progression remains under investigation. Objective and method: Herein, we investigated the frequency of common myeloid clonal mutations (FLT3, NPM1, JAK2, IDH1 and IDH2) in 88 patients with MDS and 35 AML patients with myelodysplasia-related changes, followed at a single reference center in northeastern Brazil. Results: Overall, 9/88 (10%) ofthe MDSpatients and 9/35 (26%) of the secondary AML patients had at least one mutation. While the JAK2 V617F mutation was the most frequent in the MDS patients, the FLT3, NPM1, IDH1 and IDH2 mutations were more frequently found in the secondary AML group. Furthermore, there was a higher frequency of FLT3, NPM1, IDH1 and IDH2 mutations in MDS patients classified as high-risk subtypes than in those of lower risk. Conclusion: Despite the limited sample size, our data suggest that mutations in FLT3, NPM1, IDH1 and IDH2 genes could be potential biomarkers to detect early disease progression in MDS.

Significance of paroxysmal nocturnal hemoglobinuria clone in immunosuppressive therapy for children with severe aplastic anemia / 中国当代儿科杂志

OBJECTIVES@#To study the association between paroxysmal nocturnal hemoglobinuria (PNH) clone and immunosuppressive therapy (IST) in children with severe aplastic anemia (SAA).@*METHODS@#A retrospective analysis was performed on the medical data of 151 children with SAA who were admitted and received IST from January 2012 to May 2020. According to the status of PNH clone, these children were divided into a negative PNH clone group (n=135) and a positive PNH clone group (n=16). Propensity score matching was used to balance the confounding factors, and the impact of PNH clone on the therapeutic effect of IST was analyzed.@*RESULTS@#The children with positive PNH clone accounted for 10.6% (16/151), and the median granulocyte clone size was 1.8%. The children with positive PNH clone had an older age and a higher reticulocyte count at diagnosis (P<0.05). After propensity score matching, there were no significant differences in baseline features between the negative PNH clone and positive PNH clone groups (P>0.05). The positive PNH clone group had a significantly lower overall response rate than the negative PNH clone group at 6, 12, and 24 months after IST (P<0.05). The evolution of PNH clone was heterogeneous after IST, and the children with PNH clone showed an increase in the 3-year cumulative incidence rate of aplastic anemia-PNH syndrome (P<0.05).@*CONCLUSIONS@#SAA children with positive PNH clone at diagnosis tend to have poor response to IST and are more likely to develop aplastic anemia-PNH syndrome.

A Patient with Sequential Diseases of Langerhans Cell Sarcoma, Langerhans Cell Histiocytosis, and Acute Lymphoblastic Leukemia / 罕见病研究

Langerhans cell histiocytosis(LCH)and Langerhans cell sarcoma(LCS)are characterized by clone proliferation of Langerhans-type cells, which may occur concurrently or sequentially with T-cell acute lymphoblastic leukemia (T-ALL) and other Lymphoid neoplasms. A 15-year old female patient diagnosed with T-ALL developed LCH involving multiple systems during maintenance chemotherapy of T-AL. After treated with chemotherapy with improved result, the patient showed progression of the illness and refractory to the second-line treatment. We found c.G35A (p.G12D)mutation in the KRAS gene and used the targeted drug Trametinib for treatment. The treatment proved effective, leading to partial remission within a week. Three months after Trametinib treatment, the patient developed new lymphadenopathy. Biopsy revealed the existence of LCS. The disease progressed quickly, and the patient died 7 days after diagnosis of LCS. The case of patients with T-ALL then developing LCH and LCS sequentially is extraordinarily rare. The causes of the case is unclear and may be related to cell transdifferentiation, clonal evolution, and chemotherapy. Targeted drugs can contain this disease for a short time.

Clonal evolution and clinical significance of trisomy 8 in acquired bone marrow failure / 中华血液学杂志

Objective@#To analyze clonal evolution and clinical significance of trisomy 8 in patients with acquired bone marrow failure.@*Methods@#The clinical data of 63 patients with acquired bone marrow failure accompanied with isolated trisomy 8 (+8) from June 2011 to September 2018 were analyzed retrospectively, the clonal evolution patterns and relationship with immmunosuppressive therapy were summarized.@*Results@#Totally 24 male and 39 female patients were enrolled, including 39 patients with aplastic anemia (AA) and 24 patients with relatively low-risk myelodysplastic syndrome (MDS) . Mean size of+8 clone in MDS patients[65% (15%-100%) ]was higher than that of AA patients[25% (4.8%-100%) , z=3.48, P=0.001]. The patients were was divided into three groups (<30%, 30%-<50%,and ≥50%) according to the proportion of+8 clone. There was significant difference among the three groups between AA[<30%:55.6% (20/36) ; 30-50%: 22.2% (8/36) ; ≥50%22.2% (8/36) ]and MDS patients[<30%:19.0% (4/21) ; 30%-<50%:19.0% (4/21) ; ≥50%61.9% (13/21) ] (P=0.007) . The proportion of AA patients with+8 clone <30% was significantly higher than that of MDS patients (P=0.002) ; and the proportion of AA patients with+8 clone ≥50%was significantly lower than that of MDS patients (P=0.002) . The median age of AA and MDS patients was respectively 28 (7-61) years old and 48.5 (16-72) years old. Moreover, there was no correlation between age and+8 clone size in AA or MDS (rs=0.109, P=0.125; rs=-0.022, P=0.924, respectively) . There was statistical difference in total iron binding capacity, transferrin and erythropoietin between high and low clone group of AA patients (P=0.016, P=0.046, P=0.012, respectively) , but no significant difference in MDS patients. The immunosuppressive therapy (IST) efficacy of AA and MDS patients was respectively 66.7% and 43.8% (P=0.125) . Comparing with initial clone size (27.3%) , the +8 clone size (45%) of AA patients was increased 1-2 year after IST, but no statistical difference (z=0.83, P=0.272) . Consistently, there was no significant change between initial clone size (72.5%) and 1-2 year clone size (70.5%) after IST in MDS patients. There was no significant difference in IST efficient rate between +8 clone size expansion and decline group of in AA patients at 0.5-<1, 1-2 and>2 years after IST. We found four dynamic evolution patterns of +8 clone, which were clone persistence (45%) , clone disappearance (30%) , clone emergence (10%) and clone recurrence (15%) .@*Conclusions@#AA patients had a low clone burden, while MDS patients had a high burden of +8 clone. The +8 clone of AA patients didn’t significantly expanded after IST, and the changes of +8 clone also had no effect on IST response.

Application of single cell sequencing in breast cancer research / 中华内分泌外科杂志

Single cell sequencing developed in recent years,which studies genome and transcriptome at single cell level,is more suitable for solving problems on minor special sample studies,heterogenous population analysis and finding concurrent or mutually exclusive genomic events,compared to bulk sequencing.For breast cancer,which is highly heterogeneous,bulk sequencing data is not enough for solving many clinical problems,and single cell sequencing precisely plays an important role in it.This review,focusing on a minor special cell population in breast cancer (such as cancer stem cells,circulating tumor cells,et al),tumor heterogeneity and clonal evolution,and chemotherapy resistance,summarized application of single cell sequencing in breast cancer research in recent years,and discussed the future research directions.

Molecular origins of cancer and future cancer therapy / 中华肿瘤杂志

The accumulation of genomic and epigenetic changes gives rise to the tumorigenesis and progression. Currently, clonal evolution model and cancer stem cell model, two leading theories of caner origin, are becoming complementary to one another to explain the nature of tumor heterogeneity. Precision medicine that is based on the next generation sequencing and big data describes the phenomena of tumor heterogeneity more precisely. The future cancer therapy may need more comprehensive and dynamical understandings of the distinct subclones of tumor and follow the trends of cancer evolution.

Improving the understanding of pediatric myelodysplastic syndrome / 中华实用儿科临床杂志

Myelodysplastic syndromes(MDS)represent a heterogeneous group of myeloid neoplasms initiated from stem cells and/or progenitor cells,which is primarily a disease of elderly.In childhood,MDS is uncommon.As for its mechanism,there has been a considerable improvement,involving cytogenetics,molecular biology.Besides,the rela-tionship between hematological clonal evolution and initiation,development and prognosis of MDS,has also been repor-ted systemically.These mechanisms are summarized and some characteristics of pediatric cases are reviewed.

Gene mutation and clonal evolution in patients with myelodysplastic syndromes after treatment of azacitidine / 白血病·淋巴瘤

At the 58th American Society of Hematology Annual Meeting,there were many reports on clonal evolution related with blood disease.Gene mutation and clonal evolution after treatment of azacitidine (AZA) in myelodysplastic syndromes (MDS) were summarized to explore the relationship between clonal evolution and treatment response and clinical process in MDS,and to provide reference for clinical treatment decision.

Research and application progression of gene mutations in leukemia: reports from the 56th American Society of Hematology annual meeting / 白血病·淋巴瘤

The study of gene mutations in leukemia has made great progress during the past decade,which brought innovative changes in understanding of the biological nature and development law of various leukemia.It improves not only the diagnosis,classification and prognosis of leukemia,but also the development of targeted drugs and therapy,which has greatly improved treatment of various types of leukemia.Research on gene mutations is still a hot topic in the 56th American Society of Hematology (ASH) annual meeting in 2014.Research progress in this area and related reports in the 56th ASH meeting will be introduced together with the authors' work experience in this article.

Abnormal clones and clonal evolution of bcr-abl-negative myeloproliferative neoplasms / 白血病·淋巴瘤

In recent years,studies committed to the myeloproliferative neoplasms (MPN) pathogenesis suggest that potential somatic genetic alterations,and epigenetic events might contribute to MPN development,influence the MPN disease phenotype,progression,and promote transformation.The most relevant mutations identified so far can be broadly classified into two main groups.Mutations associated with dysregulated JAK-STATsignal transduction pathway,including mutations in JAK2,CALR,MPL,CBL,LNK,SOCS.Mutations in several epigenetic modifiers,including mutations in TET2,ASXL1,IDH1/2,DNMT3A,EZH2 and so on.In this paper,the abnormal clones and clonal evolution of MPN were reviewed.

Origin of tumor stem cells / 白血病·淋巴瘤

Cancer stem cells (CSCs) are units in cancer evolution.The elucidation the origin of CSCs has great significance on prevention and treatment of cancers.This paper discusses possible origins,genetic pathways and mechanisms of CSC on the basis of the literature and authors' research.Normal stem cells could be malignantly transformed to CSC through long term accumulation of gene mutations.Induction to pluripotent stem cells by reprogramming is a possible pathway for somatic cells to become CSCs.Dedifferentiation of cancer cells to CSCs is another pathway.Epithelial-mesenchymal transition (EMT),which is an important mechanism for cellular plasticity,plays important roles in cancer metastasis and stemness of cancer cells.Cell-fusion inducing EMT could be a mechanism for the genesis of CSCs.Infection of some virus is also related to the genesis of CSCs.The complexity of cancer biology was also discussed.

Clinical Relevance of High-Resolution Single Nucleotide Polymorphism Array in Patients with Relapsed Acute Lymphoblastic Leukemia with Normal Karyotype: A Report of Three Cases

We report three patients with normal karyotype (NK) ALL, who showed genetic aberrations as determined by high-resolution single nucleotide polymorphism array (SNP-A) analysis at both diagnosis and relapse. We evaluated the clinical relevance of the SNP-A assay for the detection of subtle changes in the size of affected genetic lesions at relapse as well as the prognostic value of the assay. In our patients, application of the SNP-A assay enabled sensitive detection of cryptic changes affecting clinically important genes in NK ALL. Therefore, this assay seems to be more advantageous compared to other conventional methods such as FISH assay, HemaVision (DNA Technology, Denmark), and conventional karyotyping for the detection of an "unstable genotype" at relapse, which may be associated with microscopic clonal evolution and poor prognosis. Further comprehensive studies are required to confirm the issues presented by our case patients in this report.

Outcome of children with severe acquired aplastic anemia treated with rabbit antithymocyte globulin and cyclosporine A, / Resultado de crianças com anemia aplástica grave adquirida tratadas com globulina antitimocítica de coelho e ciclosporina A,

Objective: To evaluate the outcome of children with severe acquired aplastic anemia treated with rabbit antithymocyte globulin and cyclosporine as first-line treatment at this institution. Methods: Retrospective analysis of 26 pediatric patients with aplastic anemia, treated between 1996 and 2011 with rabbit antithymocyte globulin plus cyclosporine. Results: The overall response rate at six months was 34.6% (9/26), and the cumulative incidence of relapse was 26.5% (95% confidence interval [CI]: 1.4%-66%) at 5 years. The cumulative incidence of clonal evolution after immunosuppressive therapy was 8.3% (95% CI: 0.001%-53.7%) at five years with both clonal evolutions in non-responders who acquired monosomy 7 karyotype. The overall survival at five years was 73.6% (95% CI: 49.2%-87.5%). Conclusions: The present results confirm the poor response rate with rabbit antithymocyte globulin as first therapy in pediatrics patients, similar to what has been reported for patients of all ages. This confirmation is problematic in Brazil, given the lack of horse antithymocyte globulin in many markets outside the United States. .

Objetivo: Avaliar o resultado de crianças com anemia aplástica grave adquirida tratadas com globulina antitimocítica de coelho e ciclosporina como tratamento inicial em nosso instituto. Métodos: Análise retrospectiva de 26 pacientes pediátricos com anemia aplástica tratados entre 1996 e 2011 com globulina antitimocítica de coelho e ciclosporina. Resultados: A taxa de resposta geral em seis meses foi de 34,6% (9/26), e a incidência acumulada de recorrência foi de 26,5% (intervalo de confiança [IC] de 95%,1,4%-66%) em cinco anos. A incidência acumulada de evolução clonal após a terapia imunossupressora foi de 8,3% (IC 95%, 0,001%-53,7%) em cinco anos, com ambas as evoluções clonais em pacientes sem resposta que adquiriram o cariótipo com monossomia 7. A sobrevida geral em cinco anos foi de 73,6% (IC 95%, 49,2%-87,5%). Conclusões: Nossos resultados confirmam a baixa taxa de resposta com globulina antitimocítica de coelho como terapia inicial em pacientes pediátricos, da mesma forma como relatado para pacientes de todas as idades. Essa confirmação é problemática em nosso país devido à falta de globulina antitimocítica de cavalo em muitos mercados fora dos Estados Unidos, incluindo o Brasil. .

Cancer stem cell: A rogue responsible for tumor development and metastasis.

Cancer stem cells are a small population of cells in a tumor. They have the ability to self-renew and maintain the tumor. The most apt and accepted hypothesis for tumor development is Cancer Stem Cells. This review focuses on this concept of cancer stem cells, serving their purpose and leading to the development of tumor. There are many cell biomarkers which have been described for the identification and characterization of cancer stem cells. The most prominent of the cellular markers for the detection of cancer stem cells; CD133, CD44, ALDH-1 along with some others have been discussed in detail in this review.

Cancer stem cells - the current status of an old concept: literature review and clinical approaches

As regards their morphology and biology, tumours consist of heterogeneous cell populations. The cancer stem cell (CSC) hypothesis assumes that a tumour is hierarchically organized and not all of the cells are equally capable of generating descendants, similarly to normal tissue. The only cells being able to self-renew and produce a heterogeneous tumour cell population are cancer stem cells. CSCs probably derive from normal stem cells, although progenitor cells may be taken into consideration as the source of cancer stem cells. CSCs reside in the niche defined as the microenvironment formed by stromal cells, vasculature and extracellular matrix. The CSC assays include FACS sorting, xenotransplantation to immunodeficient mice (SCID), incubation with Hoechst 33342 dye, cell culture in non-adherent conditions, cell culture with bromodeoxyuridine. CSCs have certain properties that make them resistant to anticancer therapy, which suggests they may be the target for potential therapeutic strategies.

Evolución clonal en la leucemia mieloide crónica / Clonal evolution in chronic myeloid leukemia

Evolución clonal en la leucemia mieloide crónica se denomina a la presencia de alteraciones cromosómicas adicionales al cromosoma Filadelfia. Ocurre aproximadamente en el 30 por ciento de los pacientes en fase acelerada y en el 80 por ciento de los pacientes en crisis blástica. Es considerada un criterio de la fase acelerada de la enfermedad. Aunque se plantea que su presencia implica peor pronóstico, su significado es controversial y está en dependencia de la alteración citogenética específica, su frecuencia en el cariotipo, la asociación con otras alteraciones citogenéticas y clínicas de progresión, relación con el tiempo en que aparece en la evolución de la enfermedad y los tratamientos empleados

Clonal evolution in chronic myeloid leukemia is defined as the presence of a variety of additional, nonrandom chromosomal abnormalities besides the Philadelfia chromosome. It occurs in approximately 30 percent of patients in accelerated phase and 80 percent of patients in blastic phase. It is considered a criterion for accelerated phase. Although it is associated with a poor prognosis, its significance is controversial. It depends on the specific cytogenetic abnormality, its frequency in karyotype study, the association with other progression clinical and cytogenetic alterations, its relationship with the time of appearance during the course of the disease and the therapy used

Coexisting with Clonal Evolution and BCR-ABL Mutant in CML Patients Treated with Second-generation Tyrosine Kinase Inhibitors Predict the Discrepancy of in vitro Drug Sensitivity / Journal of the Korean Cancer Association, 대한암학회지

PURPOSE: Second-generation tyrosine kinase inhibitors (second TKIs) such as nilotinib and dasatinib control the activity of most ABL kinase domain mutations observed in patients with imatinib resistance. Although in vitro data show that both agents can inhibit all mutations except T315I, some discrepancies have been observed in a small subset of mutation clones. Cytogenetic clonal evolution is the important resistance mechanism of chronic myeloid leukemia (CML). Accordingly, we observed the clinical significance of coexisting with clonal evolution and BCR-ABL mutant in CML patients treated with second TKIs. MATERIALS AND METHODS: We monitored BCR-ABL transcript kinetics, interrelationship of clones expressing non-mutated and mutant transcripts and clonal aberrations within Philadelphia (Ph) positive and negative clones, respectively, in eight patients with CML receiving dasatinib or nilotinib for 3~41 months. RESULTS: Clinical responses were correlated with in vitro sensitivity of the BCR-ABL mutants to the second TKIs in four patients. Four patients showed resistance to the second TKIs as compared to in vitro observations; three of them developed chromosomal abnormalities in the Ph chromosome positive or negative metaphases. Another patient lost the original mutation but acquired a more resistant new mutation and became resistant to the second TKI. CONCLUSION: Cytogenetic clonal evolution is an independent poor prognostic factor in CML, which could explain the onset of mechanisms for second TKIs resistance to ABL kinase domain mutations. The results indicate that an additional evaluation of chromosomal abnormalities is warranted when BCR-ABL mutants are more resistant than indicated by in vitro data.

Detection of Clonal T Cell Receptor ? Gene Rearrangement in Children with Acute Lymphoblastic Leukemia and Its Clinical Significance / 实用儿科临床杂志

Objective To investigate the clonal rearrangement of T cell receptor (TCR) ? gene which was of monoclonality,oligoclona-lity or clonal evolution /subclonality during the course of disease in patients with acute lymphoblastic leukemia (ALL) and its significance.Methods Between Sep. 2004 and Sep. 2007,70 patients with ALL were diagnosed in Department of Pediatrics of the First Affiliated Hospital of Guangxi Medical University,among which 51 cases were boys and 19 cases were girls.Their ages ranged from 2 years to 14 years (average age was 8.5 years).DNA samples were extracted from bone marrow cells or venous blood cells by phenol/phenol-isoamyl alcohol-chloroform/isoamyl alcohol law.DNA was amplified by polymerase chain reaction (PCR).Single strand conformation polymorphism analysis (SSCP) of silver stained technique was employed to detect PCR products.Results The amplification products of 23 cases of the 70 ALL patients were positive,in which 10 cases still had positive results in period of complete remission and had poor sensitivity to chemotherapeutic drugs,4 cases were of oligoclonality/ subclonality,and 2 cases were of clonal evolution with poor prognosis.Conclusions Detecting TCR ? gene rearrangement reflects clonal evolution of leukemia cells.The oligoclonality clonal evolution continues to exist,whose multiplication is the main reason of recurrent ALL.Detecting TCR? gene rearrangement,evaluating ALL of the patient's prognosis,the judgment of recurrence and the development of individualized treatment programs have great guiding significance,which can maximize the possibility of the sick children to make long-term disease-free survival and reduce the side effects of chemotherapy on the long-term basis.

A Case of Chronic Myelogenous Leukemia with ider(22)(q10)t(9;22)(q34;q11.2) as Clonal Evolution / 대한진단검사의학회지

The ider(22)(q10)t(9;22)(q34;q11.2) is a rare secondary karyotypic aberration of Philadelphia chromosome positive chronic myelogenous leukemia (Ph+ CML) and was associated with disease progression and poor clinical outcomes in most of the previously reported cases. We experienced a case of Ph+ CML with the occurrence of ider(22)(q10)t(9;22)(q34;q11.2) as clonal evolution preceding an hematologic feature of accelerated phase for 3 years. So this chromosomal abnormality was not always correlated with poor prognosis. Relevant literature was reviewed.