Directed gap closure in large-scale sequencing projects.

A problem in many sequencing projects is the final closure of gaps left in the clone libraries, which serve as templates for sequencing, because of uncloned or unclonable genomic areas. By use of the Xylella fastidiosa genome as a test system, we present here an approach to generate, in a directed manner, sequence information from those gaps. We suggest using the complete clone library as a competitor against the genomic DNA of interest in a subtractive hybridization procedure similar to representational difference analysis (RDA). The resulting sequence information can be used to screen selectively other clone resources or serve directly for gap closure.

Shotgun sequencing of the human transcriptome with ORF expressed sequence tags.

Theoretical considerations predict that amplification of expressed gene transcripts by reverse transcription-PCR using arbitrarily chosen primers will result in the preferential amplification of the central portion of the transcript. Systematic, high-throughput sequencing of such products would result in an expressed sequence tag (EST) database consisting of central, generally coding regions of expressed genes. Such a database would add significant value to existing public EST databases, which consist mostly of sequences derived from the extremities of cDNAs, and facilitate the construction of contigs of transcript sequences. We tested our predictions, creating a database of 10,000 sequences from human breast tumors. The data confirmed the central distribution of the sequences, the significant normalization of the sequence population, the frequent extension of contigs composed of existing human ESTs, and the identification of a series of potentially important homologues of known genes. This approach should make a significant contribution to the early identification of important human genes, the deciphering of the draft human genome sequence currently being compiled, and the shotgun sequencing of the human transcriptome.

ATP-induced tetramerization and cooperativity in hemoglobin of lower vertebrates.

The importance of intraerythrocytic organic phosphates in the allosteric control of oxygen binding to vertebrate hemoglobin (Hb) is well recognized and is correlated with conformational changes of the tetramer. ATP is a major allosteric effector of snake Hb, since the absence of this nucleotide abolishes the Hb cooperativity. This effect may be related to the molecular weight of about 32,000 for this Hb, which is compatible with the dimeric form. ATP induces a pH-dependent tetramerization of deoxyHb that leads to the recovery of cooperativity. This phenomenon may be partially explained by two amino acid replacements in the beta chains (CD2 Glu-43 --> Thr and G3 Glu-101 --> Val), which result in the loss of two negative charges at the alpha1beta2 interface and favors the dissociation into dimers. The ATP-dependent dimer left arrow over right arrow tetramer may be physiologically important among ancient animal groups that have similar mutations and display variations in blood pH that are governed by these animals' metabolic state. The enormous loss of free energy of association that accompanies Hb oxygenation, and which is also observed at a much lower intensity in higher vertebrate Hbs, must be taken into consideration in allosteric models. We propose that the transition from a myoglobin-like protein to an allosteric one may be of evolutionary significance.

A clinicopathological study of asymptomatic gastric cancer.

The clinicopathological profiles of 419 patients with asymptomatic gastric cancer (AGC) first detected by gastric screening, were reviewed and compared with those of the 1727 patients with symptomatic gastric cancer (SGC). The incidence of AGC increased gradually and has amounted to 30% of the total resected cases in recent years. About 75% of AGC cases were of early cancer and 84% were negative for lymph node metastases. In contrast, only 33% of SGC cases were of early cancer and 57% were node positive. Curative resection was done in 97% of AGC and 75% of SGC. The cumulative 5 and 10 year survival rates of patients with curatively resected AGC were 85.2% and 72.2%, respectively, while those for patients with SGC were 66.8% and 55.4%. These data demonstrated that most patients with asymptomatic gastric cancers could expect a curative resection, i.e. have a better clinical outcome, than those with symptomatic cancer.

[Advanced gastric carcinoma with extensive lymph node metastases successfully treated by sequential methotrexate/5-fluorouracil therapy].

A 62-year-old man having advanced gastric carcinoma with extended lymph node metastases was successfully treated by a palliative gastrectomy and 6 courses of sequential methotrexate/5-fluorouracil therapy. No side effects were observed, and all enlarged abdominal lymph nodes disappeared. The complete response has continued for 11 months after the initial treatment.

Correlation between sialyl Tn antigen and lymphatic metastasis in patients with Borrmann type IV gastric carcinoma.

The expression of sialyl Tn (STn) antigen in 180 patients with Borrmann type IV gastric carcinomas was examined immunohistochemically. The rate of positive STn staining was 32% (57/180) for the primary tumours, and this positive staining correlated well with tumour extension, lymph node metastasis (P < 0.05) and peritoneal dissemination (P < 0.01). One-third (5/15) of patients with positive STn-staining cancer cells had a high level of serum STn. Lesions with positive STn staining were related to a lower survival rate for the patients (P < 0.05). Proliferative activity of the tumour, as measured by proliferating nuclear antigen (PCNA) labelling percentage and argyrophilic nucleolar organiser region (AgNOR) count, was significantly higher (41.5 +/- 13.0%, 3.78 +/- 0.98) in the STn-positive group than in the STn-negative group (34.2 +/- 13.2%, 3.48 +/- 0.85) (P < 0.01, P < 0.05 respectively). Estimating STn antigen may be useful for predicting the likelihood of lymph node metastasis or peritoneal dissemination and the clinical prognosis for patients with Borrmann type IV gastric carcinoma.

S100 protein positive human breast carcinomas: an immunohistochemical study.

An immunohistochemical study for S100 protein was performed on 95 human breast carcinomas. S100 protein positive carcinoma cells were recognized in 54 cases (57%). The S100 protein positive and negative carcinomas were then compared in terms of stage, histologic type, nuclear grade, appearance of minute calcification, immunoreactivity for estrogen receptor (ER), tumor recurrent pattern, and prognosis. The S100 protein positive cases had a tendency to show a low nuclear grade (P < 0.01). They were also more often seen in the ER positive group. For further analysis of the nature of S100 protein positive carcinoma cells, immunoreactivity for neuron-specific enolase (NSE) and actin was investigated. The positive staining for NSE and actin was seen in 46 cases (48%) and 3 cases (3%), respectively. There was, however, no specific correlation among the S100 protein. NSE, or actin staining. The nature of S100 protein positive carcinoma cells still remains unclear. The S100 protein positive carcinomas, however, exhibit relatively better characteristics.

[Effect of adjuvant chemotherapy for patients with early gastric cancer].

Effects of adjuvant chemotherapy following curative resection were evaluated in patients with early gastric cancer. According to postoperative chemotherapy, seven hundred and thirty-one patients were divided into four groups as follows. MMC+FT group: those who received mitomycin C and tegafur; MMC group: those receiving MMC; FT group: those given tegafur or 5-FU; NC group: those who never received chemotherapy. Postoperative recurrence was observed in 25(3.4%) of the 731 patients. Relationships between rates of recurrence or survival with clinicopathological findings were assessed among the four groups. In cases with cancer cell invasion of the intralesional veins, recurrence tended to occur less in the groups given postoperative chemotherapy, compared to the NC group. When a positive venous invasion was determined, rates of recurrence in the MMC+FT, MMC, FT and NC groups, were 7.4, 0, 0 and 35.7%, respectively. On the other hand, in relation to other clinicopathological findings, no differences were observed in rates of recurrence among those groups. As for the survival rate, no differences were observed in the clinicopathological findings among the four groups. These findings indicate that adjuvant chemotherapy may contribute to prevention of postoperative recurrence in patients with early gastric cancer, especially in cases with positive venous invasion.

[Pharmacodynamic study on the effectiveness of UFT against cancer of gastro-intestinal (GI) tract].

Preoperative oral administration of either 5-FU 200 mg/day (15 patients) or UFT (tegafur plus uracil at a 1:4 molar ratio) 400 mg/day (22 patients) were carried out was carried out against the patients cancer of GI-tract 3 consecutive days till the morning of the operation. Serial blood samples of peripheral and portal veins were obtained for the measurement of concentration of 5-FU. The Concentration of 5-FU in normal and tumor tissues was measured in 13 patients given UFT pre-operatively. Thymidylate synthase inhibition rate were also measured in 5 of them. Furthermore, AgNOR count of tumor tissue before and after administration of UFT were examined in 11 patients. Following conclusions were obtained. (1) The Concentration of 5-FU in peripheral venous blood of UFT group was significantly higher than that of 5-FU group during 1-5 hrs after the last dose (p < 0.05). (2) The concentration of 5-FU in portal venous blood of 5-FU group was higher than that of UFT group during initial 2 hrs after the last dose. However, during 3 to 7 hrs after the last dose, UFT group showed a higher concentration. (3) In UFT group, the concentration of 5-FU in tumor tissue was significantly higher than that in normal tissue (p < 0.01). Consequently, preoperative administration of UFT can be effective for prevention of intraoperative prevention of hematogenous metastasis via portal system in cancer of gastrointestinal tract.

Pathology and prognosis of gastric carcinoma. Findings in 10,000 patients who underwent primary gastrectomy.

BACKGROUND: Despite recent advances in diagnosis and treatment, gastric carcinoma remains a major cause of death in the world. METHODS: The clinicopathologic profile of 10,000 consecutive patients who underwent primary gastrectomy during 1962-1989 were reviewed and prognostic factors influencing survival in those with gastric carcinoma were analyzed in 7031 patients. RESULTS: Incidence of gastrectomy for carcinoma has increased steadily and the rate of early carcinoma exceeded that of advanced carcinoma in the recent period of 1985-1989. Five-year and 10-year survival rates were 46.1% and 35.2% in 3868 patients with advanced carcinoma, and 88.8% and 77.3% in 3163 patients with early carcinoma, respectively. In patients with advanced carcinoma, significantly poorer survival rates were noticed for patients older than 70 years of age, those who underwent total gastrectomy, tumors involving the entire stomach or greater than 10 cm in diameter, a macroscopic diffusely infiltrative pattern, adenosquamous histologic type, positive surgical resection margins, or lymph node metastasis. None of the above poor prognostic features were identified in patients with early gastric carcinoma group except for those older than 70 years of age. Although lymph node metastases were present in 10% of early gastric carcinomas, this feature did not impart a poor prognosis. Patients with advanced carcinoma grossly resembling an early carcinoma had an intermediate prognosis, suggesting the existence of a developmentally midstage lesion between early and advanced carcinoma. CONCLUSIONS: The study illustrates that the most important role for clinicians treating with gastric carcinoma should be early detection and aggressive surgery for resectable tumors, followed by detailed pathologic examination.

Invasive ductal carcinoma of the breast with a predominant intraductal component: cooperative clinicopathologic study in seven Japanese centers.

A nationwide multicenter joint study was undertaken to investigate the clinicopathologic characteristics of invasive ductal carcinoma of the breast with a predominant intraductal component, a diagnostic entity proposed in the histologic typing of breast tumors by the World Health Organization in 1981. A total of 368 tumors, of which 218 were studied pathologically between 1983 and 1987 and 150 between 1971 and 1977, were accumulated for the present study from seven medical institutes in Japan. The incidence of such types of tumor was higher in the latter period than in the former, as was that of pure intraductal carcinomas. Seventy of the 368 tumors displayed metastatic nodal involvement and nine tumor deaths were observed from 150 tumors followed up for over 10 years following radical mastectomy, the overall quantity of the extraductal stromal invasion clearly acting on lymph node metastases and patients' outcome. We consider a total stromal invasion of greater than 5 mm to be critical in the prognosis of patients with tumor of this type.

Renal failure due to cholesterol embolization following percutaneous transluminal renal angioplasty.

Percutaneous transluminal renal angioplasty was performed in a 63-year-old diabetic woman who had renovascular hypertension with solitary functioning kidney and diffuse atherosclerosis. Angioplasty was technically successful, while thereafter, fever and myalgia of legs occurred with gradual increases in blood urea nitrogen and creatinine. The patient became uremic over a month after angioplasty and was placed on dialysis. She died six months after angioplasty. Autopsy revealed cholesterol embolization in bilateral kidney, pancreas and spleen, causing subacute renal failure. It is suggested that careful assessment of the patient should be made when determining the need for renal angioplasty for renovascular hypertension with a solitary functioning kidney.

Ductal carcinoma of the breast. An analysis of proportions of intraductal and invasive components.

One hundred and ninety patients with mammary ductal carcinoma were studied to evaluate the correlation of proportions of intraductal and invasive tumor growth to histologic and immunohistochemical features. Initially, attempts were made to divide the cases into 6 groups according to the proportion of extraductal invasive areas within the whole tumor. It has been found that ductal carcinoma could be divided, on this criterion, into 2 groups. One comprised tumors in which invasive areas made up less than 20% of the tumor, the other included those with invasive areas exceeding 20%. In the former, intraductal and invasive components exhibited a lower grade of nuclear and tumor component and a higher incidence of cells with CEA immune positivity. The latter manifested higher grades in both intraductal and invasive components and a lower incidence of CEA positive cells. Many of the latter tumors had a solid or comedo-like growing pattern of the intraductal component. There was a significant difference in the prognosis between the two categories. We conclude that like intraductal carcinomas, invasive ductal carcinomas with a predominant intraductal component should be considered a lower grade malignancy.

Extramammary Paget's disease: comparative histopathologic studies of intraductal carcinoma of the breast and apocrine adenocarcinoma.

We examined 32 cases (38 lesions) of extramammary Paget's disease (EMPD) in relation to comparative studies on intraductal carcinoma of the breast (ductal carcinoma in situ, DCIS) and apocrine adenocarcinoma (AAC). Lesions included scrotum (18 lesions), vulva (8), axilla (6), groin (3), penis (2) and chest wall (1), and the distribution was compatible with that of apocrine or supernumerary mammary glands. Histologically, extra-mammary Paget's and DCIS cells exhibited a large amount of a pale-stained cytoplasm. The cytoplasm of AAC cells frequently contained granules, was eosinophilic and differed from that of Paget's or DCIS cells. Immunohistochemical studies revealed positive reactions for polyclonal and monoclonal antibodies to carcinoembryonic antigen in all EMPD and most DCIS, but not in AAC. Recent studies have shown that extramammary Paget's cells exhibit characteristics of glandular epithelial cells and that most cases of EMPD are not accompanied by an underlying carcinoma. The results obtained in this study, coupled with data on the frequency of the supernumerary breasts, lead to the speculation that extramammary Paget's cells originate from ectopic mammary glands or from pluripotential germinative cells in the epidermis, capable of differentiating toward the mammary glands.

Sulphomucin-secreting intestinal metaplasia in the human gastric mucosa. An association with intestinal-type gastric carcinoma.

Sixty-three gastrectomy specimens (21 with early intestinal type carcinoma, 21 with early diffuse carcinoma, and 21 with benign nonneoplastic lesions) were examined histochemically to determine the distribution of intestinal metaplasia (IM), particularly the sulphomucin-secreting type (Type IIB IM). The frequency and distribution of Type IIB IM were similar, irrespective of the disease, when age of the patient was matched and if the extension of the IM was similar. Type IIB IM was usually observed in the mucosa along the lesser curvature of the lower portion of the stomach, particularly in elderly patients and was mainly located in the deeper foveolae and intermingled with or transient to those in other types of IM. These findings suggest that a casual relationship between Type IIB IM and intestinal type carcinoma is dubious.

Small cell carcinoma of the esophagus.

Ten cases of small cell carcinoma of the esophagus were studied clinicopathologically and immunohistochemically. Seven of the ten were also examined by electron microscopy. Histologically, six were oat cell type, four the intermediate cell type, and multiple histologic sections revealed squamous and glandular differentiations in small or minute areas of seven and two tumors, respectively. In four of the six polypoid tumors, the epithelium covering the tumor showed a malignant conversion accompanied by a proliferation of small anaplastic cells. Another one showed a cribriform pattern in a small area of the tumor. Argyrophilic tumor cells were seen in six cases and tumor cells immunohistochemically positive for ACTH and calcitonin were seen in six, and three cases, respectively. Neurosecretory granules were evident in three of the seven cases examined by electron microscopy. These findings suggest that a small cell carcinoma of the esophagus differentiates toward a squamous, glandular, or neurosecretory lesion, thereby supporting the idea of a totipotential stem cell origin of this tumor. The prognosis of patients with this tumor was poor, in accord with the evidence of aggressive lymphatic and blood vessel permeation.