Joint single cell DNA-seq and RNA-seq of gastric cancer cell lines reveals rules of in vitro evolution

Cancer cell lines are not homogeneous nor are they static in their genetic state and biological properties. Genetic, transcriptional and phenotypic diversity within cell lines contributes to the lack of experimental reproducibility frequently observed in tissue-culture-based studies. While cancer cell line heterogeneity has been generally recognized, there are no studies which quantify the number of clones that coexist within cell lines and their distinguishing characteristics. We used a single-cell DNA sequencing approach to characterize the cellular diversity within nine gastric cancer cell lines and integrated this information with single-cell RNA sequencing. Overall, we sequenced the genomes of 8824 cells, identifying between 2 and 12 clones per cell line. Using the transcriptomes of more than 28 000 single cells from the same cell lines, we independently corroborated 88% of the clonal structure determined from single cell DNA analysis. For one of these cell lines, we identified cell surface markers that distinguished two subpopulations and used flow cytometry to sort these two clones. We identified substantial proportions of replicating cells in each cell line, assigned these cells to subclones detected among the G0/G1 population and used the proportion of replicating cells per subclone as a surrogate of each subclone's growth rate.

P907 Ventriculo-vascular interaction in patients with severe aortic stenosis: a comparison of three different clinical settings

Funding Acknowledgements

This work was supported by CREDO Project - ID: 49182, financed through the SOP IEC -A2-0.2.2.1-2013-1 cofinanced by the ERDF

Ventriculo-arterial coupling (VAC) reflects the interaction between the ventricle and the arterial system and its prognostic role was studied in different clinical settings. VAC can be assessed with echocardiography as the ratio between the arterial elastance (Ea) and the end-systolic left ventricular elastance (EES). Data concerning the role of VAC in severe aortic stenosis (AS) are scarce.

We aimed to determine VAC in patients (pts) with severe AS and assess its relationship with symptoms.

We included 61 consecutive pts with severe AS (vave area < 1 cm2) and we divided them in 3 groups according to their symptoms: group A consisted of 28 pts (81 ± 10 yrs, 14 men) admitted for acute pulmonary edema, group B consisted of 25 pts (76 ± 12 yrs, 13 men) with either angina, syncope or dyspnea class I-III NYHA and group C consisted of 8 asymptomatic patients (71 ± 19 yrs, 3 men). We determined the VAC non-invasively and we compared the results between the 3 groups using one-way analysis of variance and a post-hoc Tukey test.

There were no significant differences in age (p = 0.08) and aortic valve area (p = 0.18) between groups. Variations of Ea and EES between groups were not significant (p = 0.08 and p = 0.94, respectively). However, VAC differed significantly between the 3 groups, being most impaired in group A (1.11 ± 0.69), followed by 0.77 ± 0.23 in group B and 0.73 ± 0.16 in group C (p = 0.03). The left ventricular ejection fraction (EF) also differed significantly between groups: 41 ± 13% in group A, 51 ± 11% in group B and 57 ± 3% in group C (p < 0.001). VAC and the EF had a moderate negative correlation in group A (r=-0.52, p = 0.004) and group B (r=-0.51, p = 0.009), but no correlation in group C (p = 0.37).

VAC is impaired in patients with severe AS and acute heart failure and it differs significantly from VAC in severe AS with chronic, stable symptoms and from VAC in asymptomatic severe AS. This suggests that the progression of symptoms in severe AS might be related to the interactions between the left ventricle and the vascular load, making thus VAC a potential therapeutic target and a parameter to be considered in the thorough evaluation of patients with severe AS.

Group A Group B Group C Ea 2.69 ± 1.31 2.09 ± 0.94 1.95 ± 0.60 p = 0.08 EES 2.93 ± 1.90 2.87 ± 1.33 2.71 ± 0.73 p = 0.94 VAC 1.11 ± 0.69 0.77 ± 0.23* 0.73 ± 0.16* p = 0.03 EF 41 ± 13% 51 ± 11%* 57 ± 3%* p < 0.001 *significant difference with group A

P6470Ventriculo-arterial coupling in severe aortic stenosis: does the flow-gradient pattern play a role?

Background

Ventriculo-arterial coupling (VAC) assesses the interplay between ventricular contractility and afterload and it is calculated as the ratio between arterial elastance (Ea) and end-systolic left ventricular elastance (EES). Severe aortic stenosis (AS) carries different configurations according to transvalvular flow rates and pressure gradients and each of these entities has its particularities in terms of physiology and clinical outcome. Little has been studied so far regarding the changes of VAC in severe AS.

Purpose

We sought to assess the VAC non-invasively in patients (pts) with severe AS and to characterize it according to the flow-gradient pattern.

Methods

We included 61 consecutive pts with severe AS (78±13 years, 30 men, indexed aortic valve area <0.6 cm2/m2), for whom we performed a comprehensive echocardiography. VAC was determined as the ratio between Ea and EES. Patients were divided in 4 groups, depending on stroke volume index (low-flow [LF] vs. normal-flow [NF]: 35 ml/m2) and mean transaortic pressure gradient (low-gradient [LG] vs. normal gradient [NG]: 40 mm Hg). This resulted in the following flow-gradient patterns: LFLG, LFNG, NFLG, NFNG. Data were compared between groups with one-way analysis of variance and then with a Tukey test.

Results

There were 11 pts (18%) in the LFLG group, 20 pts (32.8%) in the LFNG group, 8 pts (13.2%) in the NFLG group and 22 pts (36%) in the NGNG group. The arterial elastance was highest in the LFLG group: 3.37±1.49 vs. 2.79±0.92 in the LFNG, 2.05±0.57 in the NFLG and 1.54±0.49 in the NFNG group (p<0.001). The ventricular elastance was also highest in the LFLG group (4.03±2.46) vs. 3.16±1.33 in the LFNG, 2.21±1.22 in the NFLG and 2.29±0.78 in the NFNG group (p=0.007). VAC was most impaired in the NFLG group (1.35±1.08), followed by LFNG group (1.00±0.47), LFLG group (0.93±0.27) and NFNG group (0.70±0.14) (p=0.01). Valvulo-arterial impedance (ZVA) was highest in the LFNG group: 7.78±2.15, followed by 7.38±2.17 in the LFLG group, 4.93±1.17 in the NFLG group and 4.33±1.23 in the NFNG group (p<0.001). VAC and ZVA showed no significant correlation (p=0.27), with VAC being significantly more impaired in patients with abnormal ZVA (>4.5 mm Hg/ml/m2): 0.99±0.60 vs. 0.73±0.20 (p=0.02).

Conclusion

The ventriculo-vascular interaction in severe AS varies noticeably according to the flow-gradient pattern. Low-gradient states, particularly NFLG, have the most impaired VAC. This study supports the idea that these 4 configurations are different clinical entities and it highlights the importance of integrating the flow-gradient pattern for a comprehensive evaluation of AS severity.

Acknowledgement/Funding

This work was supported by CREDO Project - ID: 49182, financed through the SOP IEC -A2-0.2.2.1-2013-1 cofinanced by the ERDF

P744Ventriculo-arterial interplay in acute pulmonary edema: relationship with the ejection fraction and the clinical outcome

Acknowledgement/Funding

This work was supported by CREDO Project - ID: 49182, financed through the SOP IEC-A2-0.2.2.1-2013-1 cofinanced by the ERDF

Perinatal distress in 1p36 deletion syndrome can mimic hypoxic ischemic encephalopathy

1p36 deletion syndrome is a well-described condition with a recognizable phenotype, including cognitive impairment, seizures, and structural brain anomalies such as periventricular leukomalacia (PVL). In a large series of these individuals by Battaglia et al., "birth history was notable in 50% of the cases for varying degrees of perinatal distress." Given the potential for perinatal distress, seizures and PVL, we questioned if this disorder has clinical overlap with hypoxic ischemic encephalopathy (HIE). We reviewed the medical records of 69 individuals with 1p36 deletion to clarify the perinatal phenotype of this disorder and determine if there is evidence of perinatal distress and/or hypoxic injury. Our data provides evidence that these babies have signs of perinatal distress. The majority (59% term; 75% preterm) needed resuscitation and approximately 18% had cardiac arrest. Most had abnormal brain imaging (84% term; 73% preterm) with abnormal white matter findings in over half of patients. PVL or suggestion of "hypoxic insult" was present in 18% of term and 45% of preterm patients. In conclusion, individuals with 1p36 deletion have evidence of perinatal distress, white matter changes, and seizures, which can mimic HIE but are likely related to their underlying chromosome disorder.

An analysis of blastic plasmacytoid dendritic cell neoplasm with translocations involving the MYC locus identifies t(6;8)(p21;q24) as a recurrent cytogenetic abnormality

AIMS

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive neoplasm with leukaemic features and frequent skin involvement. Translocations involving the MYC locus have been recently identified as recurrent cytogenetic abnormalities in this entity. The aim of this study was to assess the clinicopathological, immunophenotypic and genetic features in MYC-rearranged BPDCN cases.

METHODS AND RESULTS

Pathology archives from six major institutes were queried for cases of BPDCN with 8q24 MYC translocations, and two cases were identified. A literature review identified 14 cases. Clinicopathological features, immunophenotype and cytogenetic and molecular data were reviewed. In these 16 MYC-rearranged cases, the median age at diagnosis was 70.5 years, and there was a male predominance. Whereas all cases showed marrow involvement, skin lesions (62.5%) and lymphadenopathy (50%) were variably seen. The median survival was 11 months. The median percentage of blasts in peripheral blood was 9%. All cases showed expression of CD4, with 10 of 16 being positive for CD56. HLA-DR, CD123, TCL1 and CD303 were positive in all cases tested. Cytogenetic analysis revealed a single recurrent translocation partner of MYC at 6p21 in 11 cases (69%), whereas four cases showed different MYC translocation partners (2p12, Xq24, 3p25, and 14q32). Interestingly, the group of patients with t(6;8)(p21;q24) showed an older median age at diagnosis (74 years) and a remarkably shorter median survival (3 months).

CONCLUSIONS

Translocations involving the 8q24 MYC locus more frequently manifest as t(6;8)(p21;q24), and, given its association with specific clinicopathological features suggesting even more aggressive behaviour, t(6;8)(p21;q24) indicate a genetically defined subgroup within BPDCN.

Isolated Follicles Enriched for Centroblasts and Lacking t(14;18)/BCL2 in Lymphoid Tissue: Diagnostic and Clinical Implications

We sought to address the significance of isolated follicles that exhibit atypical morphologic features that may be mistaken for lymphoma in a background of reactive lymphoid tissue. Seven cases that demonstrated centroblast-predominant isolated follicles and absent BCL2 staining in otherwise-normal lymph nodes were studied. Four of seven cases showed clonal B-cell proliferations amid a polyclonal B cell background; all cases lacked the IGH-BCL2 translocation and BCL2 protein expression. Although three patients had invasive breast carcinoma at other sites, none were associated with systemic lymphoma up to 44 months after diagnosis. The immunoarchitectural features of these highly unusual cases raise the question of whether a predominance of centroblasts and/or absence of BCL2 expression could represent a precursor lesion or atypical reactive phenomenon. Differentiating such cases from follicular lymphoma or another mimic is critical, lest patients with indolent proliferations be exposed to unnecessarily aggressive treatment.

An analysis of MYC and EBV in diffuse large B-cell lymphomas associated with angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma not otherwise specified

Composite diffuse large B-cell lymphomas (DLBCLs) with peripheral T-cell lymphomas (PTCLs) are rare co-occurrences with poorly understood pathologic features. Herein, we describe 15 distinct cases of DLBCL occurring in association with PTCL, including angioimmunoblastic T-cell lymphoma (AITL; n = 12) and PTCL, not otherwise specified (n = 3). Sheets of large B cells were seen in all cases, with Hodgkin/Reed-Sternberg-like (HRS-L) cells present in 6 cases. When compared to cases of AITL without DLBCL, HRS-L cells were more frequently seen in cases of AITL with DLBCL (P = .02). Epstein-Barr virus (EBV) expression was seen in 10 of 15 cases, and in those with HRS-L cells, EBV expression was detected invariably in at least a subset of the HRS-L cells. MYC gene rearrangements were consistently absent, although 6 of the 10 cases showed MYC overexpression by immunohistochemistry in the neoplastic B cells; a frequency significantly increased compared to other cases of DLBCL not associated with a T-cell lymphoma: 29 of 166 (P = .005). In addition, when MYC was overexpressed in DLBCL, it was also weakly present in the HRS-L cells. The increased and frequent morphologic presence of HRS-L cells in association with this composite lymphoma raises a possible link between their occurrence and DLBCLs in PTCLs; furthermore, the frequent detection of MYC protein expression and EBV infection in these cases suggests a possible role of these pathways in B-cell lymphomagenesis.

Acute myeloid leukemia with monosomal karyotype: morphologic, immunophenotypic, and molecular findings

OBJECTIVES

Acute myeloid leukemia (AML) with monosomal karyotype (MK) recently has been reported to be associated with worse outcome than the traditional complex karyotype.

METHODS

In this retrospective study of 111 patients with AML, we identified 14 patients with MK (13% of all patients with AML) using the definition proposed by Breems et al.

RESULTS

Five (36%) of these 14 patients had a loss of a single chromosome in the presence of other structural abnormalities, and nine (64%) had a loss of two or more autosomal chromosomes. Patients with AML-MK presented at an older age, with lower bone marrow blasts, and their blasts less frequently expressed CD34. Most patients with AML-MK had morphologic multilineage dysplasia and were predominantly subclassified as having AML with myelodysplasia-related changes (AML-MRC). Molecular analysis showed a significant absence of NPM1 and FLT3 in patients with AML-MK.

CONCLUSIONS

Outcome data showed that patients with AML-MK had significantly worse overall survival, disease-free survival, and complete response compared with the rest of the patients with AML as well as within the AML-MRC group.

Activating HRAS mutation in agminated Spitz nevi arising in a nevus spilus

IMPORTANCE

Spitz nevi are benign melanocytic proliferations that can sometimes be clinically and histopathologically difficult to distinguish from melanoma. Agminated Spitz nevi have been reported to arise spontaneously, in association with an underlying nevus spilus, or after radiation or chemotherapy. However, to our knowledge, the genetic mechanism for this eruption has not been described.

OBSERVATIONS

We report a case of agminated Spitz nevi arising in a nevus spilus and use exome sequencing to identify a clonal activating point mutation in HRAS (GenBank 3265) (c.37G→C) in the Spitz nevi and underlying nevus spilus. We also identify a secondary copy number increase involving HRAS on chromosome 11p, which occurs during the development of the Spitz nevi.

CONCLUSIONS AND RELEVANCE

Our results reveal an activating HRAS mutation in a nevus spilus that predisposes to the formation of Spitz nevi. In addition, we demonstrate a copy number increase in HRAS as a "second hit" during the formation of agminated Spitz nevi, which suggests that both multiple Spitz nevi and solitary Spitz nevi may arise through similar molecular pathways. In addition, we describe a unique investigative approach for the discovery of genetic alterations in Spitz nevi.

Pediatric acute myeloid leukemia as classified using 2008 WHO criteria: a single-center experience

The classification of acute myeloid leukemia (AML) has evolved to the most recent World Health Organization (WHO) schema, which integrates genetic, morphologic, and prognostic data into a single system. However, this system was devised using adult data and how this system applies to a pediatric cohort is unknown. Performing a retrospective chart review, we examined our single-center experience with AML in 115 children and classified their leukemia using the WHO 2008 schema. We examined patient samples for mutations of FLT3, NPM1, and CEBPA. Overall survival was calculated within categories. In our pediatric population, most cases of AML had recurrent genetic abnormalities of favorable prognosis. More than 10% of patients in our series were categorized as AML, with myelodysplasia-related changes, an entity not well-described in pediatric patients. In addition, a large proportion of patients were categorized with secondary, therapy-related AML. To our knowledge, this is the first application of the WHO 2008 classification to a pediatric cohort. In comparison to adult studies, AML in the pediatric population shows a distinct distribution within the WHO 2008 classification.

Prognostic relevance of integrated genetic profiling in acute myeloid leukemia

BACKGROUND

Acute myeloid leukemia (AML) is a heterogeneous disease with respect to presentation and clinical outcome. The prognostic value of recently identified somatic mutations has not been systematically evaluated in a phase 3 trial of treatment for AML.

METHODS

We performed a mutational analysis of 18 genes in 398 patients younger than 60 years of age who had AML and who were randomly assigned to receive induction therapy with high-dose or standard-dose daunorubicin. We validated our prognostic findings in an independent set of 104 patients.

RESULTS

We identified at least one somatic alteration in 97.3% of the patients. We found that internal tandem duplication in FLT3 (FLT3-ITD), partial tandem duplication in MLL (MLL-PTD), and mutations in ASXL1 and PHF6 were associated with reduced overall survival (P=0.001 for FLT3-ITD, P=0.009 for MLL-PTD, P=0.05 for ASXL1, and P=0.006 for PHF6); CEBPA and IDH2 mutations were associated with improved overall survival (P=0.05 for CEBPA and P=0.01 for IDH2). The favorable effect of NPM1 mutations was restricted to patients with co-occurring NPM1 and IDH1 or IDH2 mutations. We identified genetic predictors of outcome that improved risk stratification among patients with AML, independently of age, white-cell count, induction dose, and post-remission therapy, and validated the significance of these predictors in an independent cohort. High-dose daunorubicin, as compared with standard-dose daunorubicin, improved the rate of survival among patients with DNMT3A or NPM1 mutations or MLL translocations (P=0.001) but not among patients with wild-type DNMT3A, NPM1, and MLL (P=0.67).

CONCLUSIONS

We found that DNMT3A and NPM1 mutations and MLL translocations predicted an improved outcome with high-dose induction chemotherapy in patients with AML. These findings suggest that mutational profiling could potentially be used for risk stratification and to inform prognostic and therapeutic decisions regarding patients with AML. (Funded by the National Cancer Institute and others.).

Effects of long-term culture on human embryonic stem cell aging

In recent years, human embryonic stem (hES) cells have become a promising cell source for regenerative medicine. Although hES cells have the ability for unlimited self-renewal, potential adverse effects of long-term cell culture upon hES cells must be investigated before therapeutic applications of hES cells can be realized. Here we investigated changes in molecular profiles associated with young (<60 passages) and old (>120 passages) cells of the H9 hES cell line as well as young (<85 passages) and old (>120 passages) cells of the PKU1 hES cell line. Our results show that morphology, stem cell markers, and telomerase activity do not differ significantly between young and old passage cells. Cells from both age groups were also shown to differentiate into derivatives of all 3 germ layers upon spontaneous differentiation in vitro. Interestingly, mitochondrial dysfunction was found to occur with prolonged culture. Old passage cells of both the H9 and PKU1 lines were characterized by higher mitochondrial membrane potential, larger mitochondrial morphology, and higher reactive oxygen species content than their younger counterparts. Teratomas derived from higher passage cells were also found to have an uneven preference for differentiation compared with tumors derived from younger cells. These findings suggest that prolonged culture of hES cells may negatively impact mitochondrial function and possibly affect long-term pluripotency.

Occult cancer of the fallopian tube in a BRCA2 germline mutation carrier at prophylactic salpingo-oophorectomy

BACKGROUND

Women with a germline BRCA1 or BRCA2 mutation have a significantly increased risk of developing ovarian cancer compared with women in the general population and may consider bilateral prophylactic oophorectomy as a risk-reducing option.

CASE

We report a case of occult fallopian tube cancer diagnosed at prophylactic surgery in a patient with a BRCA2 mutation.

CONCLUSIONS

This report acts as a reminder of the importance of removing as much of the fallopian tube as possible during prophylactic surgery in BRCA1 and BRCA2 carriers and of the need for careful pathological examination of surgical specimens after surgery.

Defective double-strand DNA break repair and chromosomal translocations by MYC overexpression

DNA repair mechanisms are essential for the maintenance of genomic integrity. Disruption of gene products responsible for DNA repair can result in chromosomal damage. Improperly repaired chromosomal damage can result in the loss of chromosomes or the generation of chromosomal deletions or translocations, which can lead to tumorigenesis. The MYC protooncogene is a transcription factor whose overexpression is frequently associated with human neoplasia. MYC has not been previously implicated in a role in DNA repair. Here we report that the overexpression of MYC disrupts the repair of double-strand DNA breaks, resulting in a several-magnitude increase in chromosomal breaks and translocations. We found that MYC inhibited the repair of gamma irradiation DNA breaks in normal human cells and blocked the repair of a single double-strand break engineered to occur in an immortal cell line. By spectral karyotypic analysis, we found that MYC even within one cell division cycle resulted in a several-magnitude increase in the frequency of chromosomal breaks and translocations in normal human cells. Hence, MYC overexpression may be a previously undescribed example of a dominant mutator that may fuel tumorigenesis by inducing chromosomal damage.

Modified cyclophosphamide, hydroxydaunorubicin, vincristine, and prednisone therapy for posttransplantation lymphoproliferative disease in pediatric patients undergoing solid organ transplantation

PURPOSE

The authors report the use of a cyclophosphamide, hydroxydaunorubicin, vincristine, and prednisone (CHOP)-based chemotherapy regimen in treating six children with posttransplantation lymphoproliferative disorder (PTLD) that developed after solid organ transplantation.

MATERIALS AND METHODS

The chemotherapy regimen consisted of a 29-day induction with CHOP and then as many as 15 cycles of maintenance therapy using methotrexate and cytarabine alternating with vincristine, adriamycin, mercaptopurine, and prednisone.

RESULTS

All patients attained remission. One patient died of sepsis while in remission. Four of the five remaining patients have been followed-up in remission for as long as 8 years without losing the graft. One of the patients experienced relapse after completing therapy and subsequently died with disease.

CONCLUSIONS

The authors conclude that pediatric patients with PTLD after solid organ transplantation that fails conservative management can be treated successfully with CHOP-based chemotherapy.

The in vivo production of Spodoptera littoralis nuclear polyhedrosis virus

The in vivo production of the nucleopolyhedrovirus (NPV) of the Egyptian cotton leafworm Spodoptera littoralis was studied experimentally. Larvae (7 days old) of 30-50 mg were experimentally infected with a range of NPV doses then harvested alive at various times after dosing to determine the effect of dose and incubation time on NPV productivity. Maximum NPV production achieved after 7 days incubation was 1.86 x 10(9) polyhedral inclusion bodies (PIBs) per larvae using an inoculum of 1 x 10(4) PIBs. Adjusting the inoculum dose had limited impact on NPV productivity but the correct selection of harvesting time was crucial in maximising the yield, both to achieve peak NPV production in individual larvae and to avoid losses from the death and disintegration of larvae if harvesting was delayed too long.

Cytochrome P-450 in culture forms of Trypanosoma cruzi

Trypanosoma cruzi epimastigote and trypomastigote forms contain microsomal peptides in the 40-60,000 mol. wt region, some of which are heme-staining-positive and are induced by phenobarbital, as indicated by SDS-gel electrophoresis and by double-labeling experiments. Epimastigotes show induced peptides of mol. wt 56,000, 52,000, 49,000, 44,000, 42,000 and 40,500 whereas only one peptide (52,500 mol. wt) is increased in trypomastigotes. Fractionation of microsomes derived from epimastigotes by octylamine Sepharose-4B column chromatography reveals the presence of two heme peptides with mol. wt of 55,800 and 56,600. The pooled fraction has a typical cytochrome P-450 CO-difference spectrum and appears to correspond to a high spin form. The demonstration of the existence of this family of hemoproteins in T. cruzi further supports the idea that resistance to chemotherapeutic agents is due to active metabolism. The active metabolism, however, may not be similar in the various developmental forms of this organism since differences exist in the patterns of induction of heme-positive microsomal peptides.

Further studies of the antigenic properties of H3N2 strains of influenza A isolated from swine in South East Asia

H3N2 strains of influenza A isolated from swine in Hong Kong were compared with human strains of H3N2 influenza A variants in reciprocal HI tests using ferret sera. One isolate from swine was indistinguishable from A/Hong Kong/68, one set of viruses isolated in 1976 and 1977 was most related to A/Hong Kong/68 but was not identical to it, two isolates from 1976 were 'bridging strains' that cross-reacted equally with the contemporary variants A/Victoria/3/75 and A/Texas/1/77, similarly to a small number of recent human isolates, and two isolates from 1977 were similar to A/Victoria/3/75. These general relationships were supported by neuraminidase inhibition tests. The findings confirm and extend previous results indicating that swine may be a reservoir of old and novel variants of influenza A H3N2 strains related to those that infect man.