Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes

Chromosomal rearrangements, including translocations, require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are frequently involved in producing leukemias, lymphomas and sarcomas. Despite the importance of these events, current understanding of their genesis is limited. To examine the origins of chromosomal rearrangements we developed Translocation Capture Sequencing (TC-Seq), a method to document chromosomal rearrangements genome-wide, in primary cells. We examined over 180,000 rearrangements obtained from 400 million B lymphocytes, revealing that proximity between DSBs, transcriptional activity and chromosome territories are key determinants of genome rearrangement. Specifically, rearrangements tend to occur in cis and to transcribed genes. Finally, we find that activation-induced cytidine deaminase (AID) induces the rearrangement of many genes found as translocation partners in mature B cell lymphoma.

Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation

A key finding of the ENCODE project is that the enhancer landscape of mammalian cells undergoes marked alterations during ontogeny. However, the nature and extent of these changes are unclear. As part of the NIH Mouse Regulome Project, we here combined DNaseI hypersensitivity, ChIP-seq, and ChIA-PET technologies to map the promoter-enhancer interactomes of pluripotent ES cells and differentiated B lymphocytes. We confirm that enhancer usage varies widely across tissues. Unexpectedly, we find that this feature extends to broadly transcribed genes, including Myc and Pim1 cell-cycle regulators, which associate with an entirely different set of enhancers in ES and B cells. By means of high-resolution CpG methylomes, genome editing, and digital footprinting, we show that these enhancers recruit lineage-determining factors. Furthermore, we demonstrate that the turning on and off of enhancers during development correlates with promoter activity. We propose that organisms rely on a dynamic enhancer landscape to control basic cellular functions in a tissue-specific manner.

A genome-wide map of CTCF multivalency redefines the CTCF code

The "CTCF code" hypothesis posits that CTCF pleiotropic functions are driven by recognition of diverse sequences through combinatorial use of its 11 zinc fingers (ZFs). This model, however, is supported by in vitro binding studies of a limited number of sequences. To study CTCF multivalency in vivo, we define ZF binding requirements at ∼50,000 genomic sites in primary lymphocytes. We find that CTCF reads sequence diversity through ZF clustering. ZFs 4-7 anchor CTCF to ∼80% of targets containing the core motif. Nonconserved flanking sequences are recognized by ZFs 1-2 and ZFs 8-11 clusters, which also stabilize CTCF broadly. Alternatively, ZFs 9-11 associate with a second phylogenetically conserved upstream motif at ∼15% of its sites. Individually, ZFs increase overall binding and chromatin residence time. Unexpectedly, we also uncovered a conserved downstream DNA motif that destabilizes CTCF occupancy. Thus, CTCF associates with a wide array of DNA modules via combinatorial clustering of its 11 ZFs.

DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes

Recurrent chromosomal translocations underlie both haematopoietic and solid tumours. Their origin has been ascribed to selection of random rearrangements, targeted DNA damage, or frequent nuclear interactions between translocation partners; however, the relative contribution of each of these elements has not been measured directly or on a large scale. Here we examine the role of nuclear architecture and frequency of DNA damage in the genesis of chromosomal translocations by measuring these parameters simultaneously in cultured mouse B lymphocytes. In the absence of recurrent DNA damage, translocations between Igh or Myc and all other genes are directly related to their contact frequency. Conversely, translocations associated with recurrent site-directed DNA damage are proportional to the rate of DNA break formation, as measured by replication protein A accumulation at the site of damage. Thus, non-targeted rearrangements reflect nuclear organization whereas DNA break formation governs the location and frequency of recurrent translocations, including those driving B-cell malignancies.

Global regulation of promoter melting in naive lymphocytes

Lymphocyte activation is initiated by a global increase in messenger RNA synthesis. However, the mechanisms driving transcriptome amplification during the immune response are unknown. By monitoring single-stranded DNA genome wide, we show that the genome of naive cells is poised for rapid activation. In G0, ∼90% of promoters from genes to be expressed in cycling lymphocytes are polymerase loaded but unmelted and support only basal transcription. Furthermore, the transition from abortive to productive elongation is kinetically limiting, causing polymerases to accumulate nearer to transcription start sites. Resting lymphocytes also limit the expression of the transcription factor IIH complex, including XPB and XPD helicases involved in promoter melting and open complex extension. To date, two rate-limiting steps have been shown to control global gene expression in eukaryotes: preinitiation complex assembly and polymerase pausing. Our studies identify promoter melting as a third key regulatory step and propose that this mechanism ensures a prompt lymphocyte response to invading pathogens.

RPA accumulation during class switch recombination represents 5'-3' DNA-end resection during the S-G2/M phase of the cell cycle

Activation-induced cytidine deaminase (AID) promotes chromosomal translocations by inducing DNA double-strand breaks (DSBs) at immunoglobulin (Ig) genes and oncogenes in the G1 phase. RPA is a single-stranded DNA (ssDNA)-binding protein that associates with resected DSBs in the S phase and facilitates the assembly of factors involved in homologous repair (HR), such as Rad51. Notably, RPA deposition also marks sites of AID-mediated damage, but its role in Ig gene recombination remains unclear. Here, we demonstrate that RPA associates asymmetrically with resected ssDNA in response to lesions created by AID, recombination-activating genes (RAG), or other nucleases. Small amounts of RPA are deposited at AID targets in G1 in an ATM-dependent manner. In contrast, recruitment in the S-G2/M phase is extensive, ATM independent, and associated with Rad51 accumulation. In the S-G2/M phase, RPA increases in nonhomologous-end-joining-deficient lymphocytes, where there is more extensive DNA-end resection. Thus, most RPA recruitment during class switch recombination represents salvage of unrepaired breaks by homology-based pathways during the S-G2/M phase of the cell cycle.

Postoperative hemodynamic and metabolic changes in patients with subarachnoid hemorrhage

Positron emission tomography was performed using an oxygen-15 gas inhalation technique to measure regional cerebral blood flow, metabolic rate for oxygen, oxygen extraction fraction, and cerebral blood volume in 13 patients with subarachnoid hemorrhage during the period of delayed vasospasm after surgery as well as in 10 volunteers as controls. Compared with the controls, the patients showed decreased hemoglobin concentration and decreased total arterial oxygen content due to postoperative hemodilution. Global reductions in the metabolic rate for oxygen and in the tissue oxygen supply were noted even in the apparently normal cortex of the patients in spite of adequate blood flow and adequate oxygen extraction fraction. In addition, regional reductions in blood flow and in perfusion reserve were seen in the cortical territory corresponding to cerebral vasospasm. Our results indicate that two processes are involved in the pathophysiology of cerebral vasospasm: 1) generalized impairment of oxygen metabolism with a reduced tissue oxygen supply, even in the apparently normal cortex, and 2) additional impairment of regional perfusion in the territory of vasospasm.

Isolation and characterization of an endogenous drug-binding inhibitor present in uremic serum

Isolation of an endogenous ligand solute from uremic serum was performed by high-performance liquid chromatography. This ligand solute inhibited the binding of diphenylhydantoin and tryptophan to plasma protein, and was considered to be one of the endogenous drug-binding inhibitors present in uremic serum. The gas chromatographic-mass spectrometric analysis revealed that this inhibitor is 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid, which is known to be a constituent of urine.

Underestimation of serum albumin by the bromcresol purple method and a major endogenous ligand in uremia

In hemodialyzed patients, the serum albumin concentration determined by the bromcresol purple (BCP) method was lower than that determined by an immunological method. The degree of underestimation appeared to be well correlated to the serum concentration of 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF), a major endogenous ligand substance present in uremic serum. CMPF inhibited in vitro the binding of BCP to serum protein and human serum albumin. Our results suggest that CMPF is a major interferent in the underestimation of the serum albumin concentration by the BCP method in uremia.

A major inhibitor of phenytoin binding to serum protein in uremia

A major endogenous ligand substance, 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF), accumulated in the sera of uremic patients, inhibited phenytoin binding to pooled serum obtained from healthy subjects and to human serum albumin in a concentration usually observed in the sera of patients with uremia. This suggests that CMPF is a major drug-binding inhibitor present in uremic serum and may be one of the so-called 'uremic toxins'.

Inhibition of hepatic glutathione S-transferases by a major endogenous ligand substance present in uremic serum

A major endogenous ligand substance present in uremic serum, 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid, inhibited the in vitro activity of bovine and rat liver glutathione S-transferases. Our results suggested that endogenous ligand substances retained in uremic serum have some toxic activities other than the inhibition of drug binding to serum protein observed in uremia.

Results of surgical treatment of patients with T3 non-small cell lung cancer

Sixty-one patients with T3 non-small cell lung cancer were surgically treated in our department from February, 1974, through April, 1986. The overall 5-year survival, excluding patients with pleurisy, was 23%, and the 5-year survival for patients undergoing complete resection and incomplete resection was 42% and 10%, respectively (p less than 0.01). Survival in patients with T3 N0 and T3 N1 or N2 disease was 33% and 0 at 5 years, respectively. The prognosis for patients with pleurisy was poor, and all died within 3 years. Therefore, complete lung resection should be done in patients with T3 N0 non-small cell lung cancer if complete resection is expected. Long-term survival is less likely for patients with lymph node metastases if complete resection cannot be performed.

Circulating plasmacytoid dendritic cells in patients with primary and Helicobacter pylori-associated immune thrombocytopenia

OBJECTIVES

Immune thrombocytopenia (ITP) is an autoimmune disorder characterized by the production of autoreactive antibodies against platelet antigens. Although dysfunction of multiple aspects of cellular immunity is considered to be important in the pathogenesis of ITP, it has not been clarified which cell types play a principal role.

METHODS

We enrolled 46 untreated patients with chronic ITP and 47 healthy adult volunteers, and investigated by flow cytometry the percentage and absolute number of cells in their peripheral blood that participate in the regulation of cellular immunity. These included plasmacytoid dendritic cells (pDCs), myeloid dendritic cells (mDCs), natural killer (NK) cells, natural killer T (NKT) cells, regulatory T (Treg) cells, and Th17 cells.

RESULTS

We found a significant reduction in the absolute number of pDCs, but not of mDCs, in patients with ITP when compared with healthy controls (P < 0.001). Reduced numbers of circulating pDCs were observed in both Helicobacter pylori (H. pylori)-positive and Helicobacter pylori (H. pylori)-negative patients with ITP. In contrast, there were no significant differences in the numbers of circulating Treg cells, Th17 cells, NK cells, or NKT cells. Interestingly, we observed increases in the number of pDCs after H. pylori eradication by antibiotics in responders but not in non-responders, while pDCs and mDCs decreased markedly after prednisolone therapy in both responders and non-responders. In patients without treatment, low pDC numbers persisted during the observational period.

CONCLUSIONS

We demonstrated that the number of circulating pDCs is low in patients with primary and H. pylori-associated ITP and that it changes depending on treatment modality. Further investigation is warranted with regard to the role of pDCs in the immunopathogenesis of ITP.

Profiling of endogenous ligand solutes that bind to serum proteins in sera of patients with uremia

The profiling of endogenous ligand solutes in sera of patients with uremia was performed by using an ultrafiltration device and high-performance liquid chromatography. Seventeen endogenous ligand solutes, which are ultraviolet-absorbing substances, were detected in a sample volume of 40 microliters, and four ligand solutes were tentatively identified as indoxylsulfate, hippuric acid, 2-hydroxybenzoylglycine, and 3-indoleacetic acid. One of these ligand solutes designated as peak P was thought to be a candidate for a major drug-binding inhibitor in uremia.

Difference in regional hepatic blood flow in liver segments--non-invasive measurement of regional hepatic arterial and portal blood flow in human by positron emission tomography with H2(15)O

Organ blood flow can be quantitatively measured by positron emission tomography (PET). As the liver has dual blood supplies, arterial and portal, regional hepatic blood flow had not been measured quantitatively. However, we succeeded in simultaneously measuring both regional hepatic arterial and portal blood flow by PET in non-stressed patients. Mean regional portal hepatic blood flow in patients with normal liver and cirrhotic liver was 57.5 and 36.7 ml/minutes/100 g, respectively. Mean regional arterial blood flow was 42.5 and 30.7 ml/minutes/100 g, respectively. A significant difference between regional portal hepatic blood flows in normal and cirrhotic patients was noted. Mean regional portal hepatic blood flow in the lateral, medial, anterior, and posterior segments of the liver was 29.8, 43.4, 50.0, and 40.9 ml/minutes/100 g, respectively. Mean regional arterial blood flow in each liver segment was 37.6, 30.0, 28.2, and 31.6 ml/minutes/100 g, respectively. A significant difference between regional portal hepatic blood flows in lateral and anterior segment was noted. The p value was less than 0.025 and the 95% confidence interval of the difference between means was from -20.2 to -2.7 ml/minutes/100 g by ANOVA. These results showed that regional hepatic blood flow is not the same in all the liver segments.

Displacement by anionic drugs of endogenous ligands bound to albumin in uremic serum

Impaired binding of anionic drugs to serum albumin in patients with uremia is thought to be due to the accumulation of endogenous substances that bind to albumin. In this study the displacement by the anionic drugs diazepam, warfarin, and salicylic acid, which are known to be representative drugs for the binding sites on the albumin molecule, of several endogenous ligands that bind to albumin in uremic serum was examined. The free fractions of the ligands bound to albumin were separated by ultrafiltration in the presence and the absence of test drugs and assayed by high-performance liquid chromatography. Diazepam displaced indoxyl sulfate (IS), hippuric acid (HA), and indole-3-acetic acid (IAA), and warfarin displaced IS, HA, ISAA, and 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid from serum albumin. However, salicylic acid did not displace the substance examined. The methods reported here are useful for determining the binding sites of the endogenous ligands on albumin and to clarify the drug-ligand interaction on albumin molecule in uremic serum.

Systematic separation of medium-sized biologically active peptides by high-performance liquid chromatography

The systematic separation of medium-sized biologically active peptides by high-performance liquid chromatography (HPLC) is described. Three steps are involved: first, high-performance sodium dodecyl sulphate (SDS) gel chromatography on a newly developed column. TSK-GEL 2000SW; secondly, ion-pair reversed-phase HPLC using stepwise elution mobile phases containing SDS and tetrabutylammonium phosphate; thirdly, high-performance cation-exchange chromatography on a Partisil SCX column for purification, using stepwise gradient elution with volatile buffers. Removal of SDS was possible in the final step. This systematic method is fast, reproducible and gives excellent separations and recoveries.

Quantification of human splenic blood flow (quantitative measurement of splenic blood flow with H2(15)O and a dynamic state method: 1)

Positron emission tomography (PET) by means of a dynamic state method and H2(15)O was performed to quantify splenic blood flow in 20 patients who had no hepatic functional disorders. Non-linear regression analysis was applied to determine splenic blood flow. In calculating arterial input function for the spleen, our original exponential method was used to facilitate computerization. Mean splenic blood flow per 100 g of spleen (SBF) was 168.0 ml/min/100 g with a standard error (SE) of 12.4 ml/min. The mean spleen-blood partition coefficient for water (rho) was 0.767 with a SE of 0.020. Significant correlations were noted between the values for SBF obtained by the exponential method and linear method in which individual increasing values for arterial 15O concentration were used rectilinearly (r = 0.96, p < 0.005) and also between the values for rho obtained by the two methods (r = 0.95, p < 0.005). In order to validate the application of a one compartment model to an organ with a large blood volume such as the spleen, a further experiment was performed with a water flow model simulating splenic circulation. We succeeded in quantifying regional splenic blood flow by PET. It was thought that the quantification of splenic blood flow by our method would be beneficial in the study of splenic circulation, which is expected to be altered under conditions of portal hypertension, liver dysfunction and shock, etc.

Widespread crystalline inclusions affecting podocytes, tubular cells and interstitial histiocytes in the myeloma kidney

Numerous crystalline inclusions were observed in glomerular and tubular epithelial cells in a 46-year-old female patient with multiple myeloma and renal dysfunction. On light microscopy, epithelial cells were filled with homogenous materials and were remarkably swollen. Infiltrations of histiocytes with expanded cytoplasm were also seen in the interstitium of the kidney and bone marrow. On electron microscopy, cytoplasmic inclusions had crystalline structure showing rhomboid and oval shapes. Immunofluorescence study revealed that these cells were positive for IgG-kappa. The combination chemotherapy followed by autologous stem cell transplantation led to a partial resolution of her renal dysfunction, continued by a slight reduction in the number of crystalline-containing podocytes at the second renal biopsy. Crystal inclusions in the kidney are rarely found and cause renal impairment in multiple myeloma.

Undifferentiated carcinoma of the lung with osteoclast-like giant cells

We treated a patient with undifferentiated carcinoma of the lung, with osteoclast-like giant cells resembling those of the giant cell tumor of bone. The clinical and morphologic characteristics of this case are documented, and the literature concerning this type of tumor is reviewed. The tumor differed histologically from the pleomorphic carcinoma, which occurs most commonly in the lung, and showed diverse pleomorphic manifestation with benign looking osteoclast-like multinucleated cells and bizarre giant cells. In addition, and undifferentiated carcinoma with a sarcoma-like appearance containing small areas of papillary adenocarcinoma was evident in the tumor.

Duodenal metastasis from large cell carcinoma of the lung: report of a case

Duodenal metastasis from primary lung cancer is extremely rare. It rarely shows any symptoms, and the prognosis for this condition is poor. We herein describe the case of a 46-year-old woman with primary lung cancer who underwent a left upper lobectomy. Severe anemia was observed about 20 days after lobectomy. Gastroduodenoscopy showed duodenal metastasis. Simultaneously, brain metastasis was also detected using magnetic resonance imaging. The patient underwent a local resection of the duodenum and a tumor resection of the brain. Postoperative irradiation of the brain metastases and systemic chemotherapy of the lung metastases were performed, and complete remission occurred. However, abdominal lymph node metastasis recurred, and the patient died 1 year after the lobectomy.

Role of tumor-infiltrating lymphocytes in the host defense mechanism against lung cancer

Tumor-infiltrating lymphocytes (TIL) and tumor-associated macrophages (TAM) were recovered from 22 patients with primary lung cancer. The TIL did not exhibit any cytolytic activity against various target cells. The average percentage of TIL recovered was 6.7 +/- 1.3% in patients without recurrence, as compared to 3.6 +/- 0.6% in those with recurrence within 2 years after complete resection of lung cancer (P less than 0.05). The average cytostatic activity of TAM was 38.5 +/- 6.8% in patients without recurrence, although it was 25.2 +/- 4.6% in those with recurrence within 2 years after complete resection (P less than 0.1). The activity of macrophage activating factor (MAF) induced by TIL was also higher in patients showing no recurrence. A significant positive correlation was observed between MAF activity induced by TIL and the cytostatic activity of individual TAM. These results suggest that antitumor activity of TAM may be controlled by specifically sensitized TIL through lymphokines.

Metastatic tumor extending through the inferior vena cava into the right atrium: a case report of carcinoma of the uterine cervix with para-aortic lymph node metastases

Carcinoma of the uterine cervix with cardiac metastasis is not uncommon in autopsy cases. However, an intraatrial tumor extending through the inferior vena cava (IVC) from the site of para-aortic lymph node metastasis has never been reported. A 57-year-old Japanese woman was admitted to an emergency care unit complaining of mild chest pain and shortness of breath. She had progressive multiple lymphatic metastases of stage IIIB squamous cell carcinoma of the uterine cervix that had initially been treated with concurrent chemoradiation. Echocardiogram showed pedunculated tumor in the right atrium (RA), and computed tomography demonstrated multiple pulmonary tumor embolism. Surgical specimen from the RA showed squamous cell carcinoma resembling the primary cervical tumor, and the peduncle appeared to originate from within the IVC. Postoperative ultrasonography showed severe stenosis of the abdominal IVC due to the invasive growth of para-aortic lymph node metastases. The stalk of the tumor originated from this lesion. We present an extremely unusual case of intraatrial metastatic tumor originating from the para-aortic lymph nodes of cervical cancer.

Quantitative measurement of renal function using Ga-68-EDTA

We studied renal function using a positron emission tomography with C15O gas and 68Ga-EDTA in 6 normal subjects (male, 21-77 years old). The blood volume (ml/100 g (kidney] was 19.2 +/- 1.8 for the one 21 years old subject and 11.8 +/- 2.0 for the rest (65-77 years old). The glomerular filtration rate (ml/min/100 g (kidney] was 57.8 +/- 1.1 for the 21 years old subject and 30.4 +/- 2.8 for the rest.