Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms

We developed mobility shift analysis of single-stranded DNAs on neutral polyacrylamide gel electrophoresis to detect DNA polymorphisms. This method follows digestion of genomic DNA with restriction endonucleases, denaturation in alkaline solution, and electrophoresis on a neutral polyacrylamide gel. After transfer to a nylon membrane, the mobility shift due to a nucleotide substitution of a single-stranded DNA fragment could be detected by hybridization with a nick-translated DNA fragment or more clearly with RNA copies synthesized on each strand of the DNA fragment as probes. As the mobility shift caused by nucleotide substitutions might be due to a conformational change of single-stranded DNAs, we designate the features of single-stranded DNAs as single-strand conformation polymorphisms (SSCPs). Like restriction fragment length polymorphisms (RFLPs), SSCPs were found to be allelic variants of true Mendelian traits, and therefore they should be useful genetic markers. Moreover, SSCP analysis has the advantage over RFLP analysis that it can detect DNA polymorphisms and point mutations at a variety of positions in DNA fragments. Since DNA polymorphisms have been estimated to occur every few hundred nucleotides in the human genome, SSCPs may provide many genetic markers.

Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction

We report a rapid and sensitive method for the detection of base changes in given sequences of genomic DNA. This technique is based on the facts that specific regions of genomic sequences can be efficently labeled and amplified simultaneously by using labeled substrates in the polymerase chain reaction and that in nondenaturing polyacrylamide gels, the electrophoretic mobility of single-stranded nucleic acid depends not only on its size but also on its sequence. The process does not involve restriction enzyme digestion, blotting, or hybridization to probes. We found that most single base changes in up to 200-base fragments could be detected as mobility shifts. RAS oncogene activation was detected by this technique. We also show that the interspersed repetitive sequences of human, Alu repeats are highly polymorphic.

ERCC1 mRNA levels complement thymidylate synthase mRNA levels in predicting response and survival for gastric cancer patients receiving combination cisplatin and fluorouracil chemotherapy

PURPOSE

We have previously shown that relative thymidylate synthase (TS) mRNA levels in primary gastric adenocarcinomas treated with fluorouracil (5-FU) and cisplatin are inversely associated with response and survival. This is a presumed function of TS as a target for 5-FU activity. We now test the hypotheses that the relative mRNA level of the excision repair cross-complementing (ERCC1) gene is inversely associated with response and survival as an independent function of cisplatin efficacy.

PATIENTS AND METHODS

Patients had intact, untreated, primary gastric adenocarcinoma cancer and were evaluated for eligibility on a preoperative cisplatin infusion-5-FU protocol. cDNA, derived from primary gastric tumors before chemotherapy, was used to determine ERCC1 mRNA levels, expressed as the ratio of polymerase chain reaction (PCR) product of the ERCC1 gene and the beta-actin gene.

RESULTS

The median ERCC1 mRNA level from 38 primary gastric cancers (33 assessable for response) was 5.8 x 10(-3) (range, 1.8 x 10(-3) to 19.5 x 10(-3)). Of 17 responding patients, 13 (76%) were less than or equal to 5.8 x 10(-3) and four were greater than 5.8 x 10(-3) (P = .003). The median survival for patients with ERCC1 mRNA levels less than or equal to 5.8 x 10(-3) has not been reached, whereas for those greater than 5.8 x 10(-3) it was 5.4 months (P = .034). The median TS mRNA level, 3.7 x 10(-3) (range, 0.9 to 18.9) also segregated responsive versus resistant tumors (P = .024). With both ERCC1 and TS mRNA levels below their medians, 11 of 13 patients (85%) responded; with both ERCC1 and TS mRNA levels above their medians, two of 10 patients (20%) responded (P = .003).

CONCLUSION

Considered separately, either ERCC1 or TS mRNA levels in a primary gastric adenocarcinoma has a statistically significant relationship to response. ERCC1 mRNA levels have a statistically significant association with survival; in this cohort TS mRNA levels did not reach statistically significant association with survival as in our previous publication. Whether these molecular parameters are independent of each other as predictors of outcome remains to be determined.

Brachial–ankle pulse wave velocity: an index of central arterial stiffness?

Brachial-ankle pulse wave velocity (baPWV) is a promising technique to assess arterial stiffness conveniently. However, it is not known whether baPWV is associated with well-established indices of central arterial stiffness. We determined the relation of baPWV with aortic (carotid-femoral) PWV, leg (femoral-ankle) PWV, and carotid augmentation index (AI) by using both cross-sectional and interventional approaches. First, we studied 409 healthy adults aged 18-76 years. baPWV correlated significantly with aortic PWV (r = 0.76), leg PWV (r = 0.76), and carotid AI (r = 0.52). A stepwise regression analysis revealed that aortic PWV was the primary independent correlate of baPWV, explaining 58% of the total variance in baPWV. Additional 23% of the variance was explained by leg PWV. Second, 13 sedentary healthy men were studied before and after a 16-week moderate aerobic exercise intervention (brisk walking to jogging; 30-45 min/day; 4-5 days/week). Reductions in aortic PWV observed with the exercise intervention were significantly and positively associated with the corresponding changes in baPWV (r = 0.74). A stepwise regression analysis revealed that changes in aortic PWV were the only independent correlate of changes in baPWV (beta = 0.74), explaining 55% of the total variance. These results suggest that baPWV may provide qualitatively similar information to those derived from central arterial stiffness although some portions of baPWV may be determined by peripheral arterial stiffness.

How sensitive is PCR-SSCP?

Single-strand conformation polymorphism analysis (SSCP) is a rapid method for detection of minor sequence changes in polymerase chain reaction-amplified DNA. Since the first reported use of SSCP in 1989 (Orita et al., 1989), this technique has been used widely to detect mutations in oncogenes, tumor suppressor genes, and genes responsible for genetic diseases. Published mutations that have been detected using this technique include base substitutions, small insertions and deletions, and rearrangements. This technique has also been applied for the detection of DNA polymorphisms at various loci of the human genome (reviewed by Hayashi, 1991; Hayashi, 1993). However, many factors can influence the sensitivity of SSCP, and its optimization is highly empirical. In this review, we estimate the percentage of mutations that can be detected by this technique under various controlled conditions, and describe some critical elements affecting sensitivity.

Scratching behavior induced by pruritogenic but not algesiogenic agents in mice

We compared the behavioral effects of treatment with pruritogenic and algesiogenic agents in mice. The animals were given subcutaneous injections of pruritogenic agents, compound 48/80 (3-100 micrograms), substance P (10-300 micrograms) and histamine (3-300 micrograms), and algesiogenic agents, capsaicin (30 and 100 micrograms) and dilute formalin (5 mg of formaldehyde), into the rostral back, and scratching of the injected site by the hind paws was counted. Compound 48/80 and substance P dose dependently elicited the scratching behavior, but histamine, capsaicin and dilute formalin were without significant effects at the doses examined. These results suggest that compound 48/80- and substance P-induced scratching of the injected site is due to itch, but not to pain. The data did not provide support for the idea that histamine produces itch in the mouse.

C-myc transcript is induced in rat liver at a very early stage of regeneration or by cycloheximide treatment

In rats, partial hepatectomy induces reasonably synchronized DNA replication in the remaining liver after approximately 20 h. Events occurring during the earlier stages of liver regeneration are of interest because they may tell us how cells in vivo respond when they move from a differentiated resting state (G0 phase) to a proliferative state. We report here that the expression of the c-myc oncogene is increased up to 10-15-fold of the normal level within 1-3 h after partial hepatectomy. This expression begins to decrease rapidly after 4 h and has returned to less than double the normal level after 8 h, at which time replicative DNA synthesis has still not begun. A still larger increase in c-myc transcription (approximately 600-fold) is observed in the liver when protein synthesis is inhibited by an injection of cycloheximide. These findings suggest the existence of a short-lived protein that is synthesized soon after partial hepatectomy, and which suppresses the expression of c-myc.

Risk factors for corneal endothelial injury during phacoemulsification

PURPOSE

To determine the principal risk factors for corneal endothelial injury during phacoemulsification.

SETTING

Hayashi Eye Hospital, Fukuoka, Japan.

METHODS

We prospectively investigated 859 consecutive eyes of 800 patients who had had phacoemulsification surgery. The percentage of corneal endothelial cell loss at 3 months after surgery was quantitated using specular microscopy. The firmness of the nucleus was graded by Emery's classification prior to surgery. We selected nine variables that could be associated with endothelial injury. The univariate associations between the endothelial cell loss and these variables were evaluated using simple correlation coefficients. A multiple linear regression analysis was performed to identify independent predictors of endothelial cell loss.

RESULTS

In the simple regression analysis, older age, small pupil diameter, high nucleus grade, large nucleus, greater infusion volume, type of IOL implanted, and a greater amount of total emitted ultrasound energy were univariately associated with endothelial cell loss. In the multiple linear regression analysis, the best final model (R2 = 0.42) identified high nucleus grade, greater infusion volume, type of IOL implanted, and large nucleus as independent predictors of endothelial cell loss.

CONCLUSION

Both univariate and multivariate analyses identified the firmness of the nucleus as the most significant risk factor for endothelial cell loss. Therefore, mechanical contact with nuclear fragments is considered the principal cause of endothelial injury.

Cyclin-dependent kinase 2 (Cdk2) is required for centrosome duplication in mammalian cells

Centrosome duplication is indispensable for the formation of the bipolar mitotic spindle. Surprisingly, even if DNA replication or mitosis is inhibited, centrosome duplication can still occur [1] [2] [3] [4] [5]. Thus, it remains unknown how centrosome duplication is coordinated with the cell cycle. Here, we show that centrosome duplication requires cyclin-dependent kinase 2 (Cdk2) in mammalian cells. We have found that in Chinese hamster ovary (CHO) cells, whereas centrosome duplication is not inhibited by hydroxyurea (HU) treatment, which arrests the cells in S phase, it is inhibited by mimosine treatment, which arrests the cells in late G1 phase. Cdk2 activity was higher in HU-treated cells than in mimosine-treated cells. Remarkably, inhibition of the Cdk2 activity in HU-treated cells with butyrolactone I or roscovitine [6], or by expression of the Cdk inhibitor p21(Waf1/Cip1), blocked the continued centrosome duplication. Moreover, overexpression of Cdk2 reversed the inhibition of centrosome duplication by mimosine treatment. These results indicate a requirement of Cdk2 activity for centrosome duplication and therefore suggest an underlying mechanism for the coordination of centrosome duplication with the cell cycle.

Prospective cohort study of the risk of prostate cancer among rotating-shift workers: findings from the Japan collaborative cohort study

Shift workers have been reported to have an increased risk of some cancers. However, the risk of prostate cancer in shift workers is not known to have been examined previously. This study prospectively examined the association between shift work and risk of prostate cancer incidence among 14,052 working men in Japan enrolled in a large-scale prospective cohort. A baseline survey was conducted between 1988 and 1990. Subjects were asked to indicate the most regular work schedule they had undertaken previously: day work, rotating-shift work, or fixed-night work. During 111,974 person-years, 31 cases of prostate cancer were recorded. The Cox proportional hazards model was used to estimate the risk, with adjustments for age, family history of prostate cancer, study area surveyed, body mass index, smoking, alcohol drinking, job type, physical activity at work, workplace, perceived stress, educational level, and marriage status. Compared with day workers, rotating-shift workers were significantly at risk for prostate cancer (relative risk = 3.0, 95% confidence interval: 1.2, 7.7), whereas fixed-night work was associated with a small and nonsignificant increase in risk. This report is the first known to reveal a significant relation between rotating-shift work and prostate cancer.

Epithelial collagens and glycosaminoglycans in the embryonic cornea. Macromolecular order and morphogenesis in the basement membrane

The embryonic corneal epithelium synthesizes both collagen and chondroitin sulfate and excretes them across the basement membrane into the subepithelial space where they assemble into a spiraling orthogonal matrix of fibrils. The assembly of collagen into fibrils is first apparent at the outer face of the basement membrane in a region of ordered chondroitin sulfate molecules. Hyaluronate, another morphogenetically important corneal macromolecule, is produced at these early stages only by the inner endothelium. These correlated biosynthetic and ultrastructural data demonstrate discrete macromolecular products of the two corneal epithelia with differing morphogenetic properties and functions.

Low tibial osteotomy for varus-type osteoarthritis of the ankle

In this retrospective study we have assessed the results of low tibial valgus osteotomy for varus-type osteoarthritis of the ankle and its indications. We performed an opening wedge osteotomy in 25 women (26 ankles). The mean follow-up was for eight years and three months (2 years 3 months to 17 years 11 months). Of the 26 ankles, 19 showed excellent or good clinical results. Their mean scores for pain, walking, and activities of daily living were significantly improved but there was no change in the range of movement. In the ankles which were classified radiologically as stage 2 according to our own grading system, with narrowing of the medial joint space, and in 11 as stage 3a, with obliteration of the joint space at the medial malleolus only, the joint space recovered. In contrast, such recovery was seen in only two of 12 ankles classified as stage 3b, with obliteration of the joint space advancing to the upper surface of the dome of the talus. Low tibial osteotomy is indicated for varus-type osteoarthritis of stage 2 or stage 3a.

Synthesis and secretion of nerve growth factor by mouse astroglial cells in culture

Astroglial cells cultured from the mouse brain have been found to synthesize and secrete a material(s) with nerve growth factor-like immunoreactivity (NGF-LI) into their culture medium. A material(s) with NGF-LI showed identical properties to those of beta NGF purified from the mouse submaxillary gland in immunoreactivity, molecular weight, isoelectric point, and neurite outgrowth stimulatory activity. These results indicate that astroglial cells cultured from mouse brain are able to synthesize and secrete beta NGF in culture.

Tumor immune microenvironment and nivolumab efficacy in EGFR mutation-positive non-small-cell lung cancer based on T790M status after disease progression during EGFR-TKI treatment

Background

The efficacy of programmed death-1 blockade in epidermal growth factor receptor gene (EGFR) mutation-positive non-small-cell lung cancer (NSCLC) patients with different mechanisms of acquired resistance to EGFR tyrosine kinase inhibitors (TKIs) is unknown. We retrospectively evaluated nivolumab efficacy and immune-related factors in such patients according to their status for the T790M resistance mutation of EGFR.

Patients and methods

We identified 25 patients with EGFR mutation-positive NSCLC who were treated with nivolumab after disease progression during EGFR-TKI treatment (cohort A). Programmed death-ligand 1 (PD-L1) expression and tumor-infiltrating lymphocyte (TIL) density in tumor specimens obtained after acquisition of EGFR-TKI resistance were determined by immunohistochemistry. Whole-exome sequencing of tumor DNA was carried out to identify gene alterations. The relation of T790M status to PD-L1 expression or TIL density was also examined in an independent cohort of 60 patients (cohort B).

Results

In cohort A, median progression-free survival (PFS) was 2.1 and 1.3 months for T790M-negative and T790M-positive patients, respectively (P = 0.099; hazard ratio of 0.48 with a 95% confidence interval of 0.20-1.24). Median PFS was 2.1 and 1.3 months for patients with a PD-L1 expression level of ≥1% or <1%, respectively (P = 0.084; hazard ratio of 0.37, 95% confidence interval of 0.10-1.21). PFS tended to increase as the PD-L1 expression level increased with cutoff values of ≥10% and ≥50%. The proportion of tumors with a PD-L1 level of ≥10% or ≥50% was higher among T790M-negative patients than among T790M-positive patients of both cohorts A and B. Nivolumab responders had a significantly higher CD8+ TIL density and nonsynonymous mutation burden.

Conclusion

T790M-negative patients with EGFR mutation-positive NSCLC are more likely to benefit from nivolumab after EGFR-TKI treatment, possibly as a result of a higher PD-L1 expression level, than are T790M-positive patients.

Effect of cataract surgery on intraocular pressure control in glaucoma patients

PURPOSE

To examine the effect of cataract surgery on intraocular pressure (IOP) control in eyes with angle-closure glaucoma (ACG) and open-angle glaucoma (OAG).

SETTING

Hayashi Eye Hospital, Fukuoka, Japan.

METHODS

This study included 74 eyes with ACG and 68 eyes with OAG having cataract surgery. The IOP was measured and the number of glaucoma medications recorded preoperatively, 1 month postoperatively, and then every 3 months. The IOP control in the 2 groups was compared using survival analysis, with failure criteria being an IOP greater than 21 mm Hg, addition of medications, or the need for additional glaucoma surgery.

RESULTS

The mean IOP and number of medications decreased significantly after surgery in both groups (P <.0001). However, the mean decrease in IOP and percentage of IOP reduction in the ACG group were greater than in the OAG group, and fewer medications were required in the ACG group. The cumulative survival probability of IOP control at 24 months was 91.9% in the ACG group and 72.1% in the OAG group. The survival curve in the ACG group was significantly better than in the OAG group (P =.0012). The IOP was controlled without medication in 30 eyes (40.5%) in the ACG group and 13 (19.1%) in the OAG group; the difference between groups was significant (P =.0055).

CONCLUSIONS

Cataract surgery substantially reduced IOP and the number of medications required for IOP control in glaucomatous eyes. Specifically, cataract extraction normalized the IOP in most eyes with ACG.

Changes in anterior chamber angle width and depth after intraocular lens implantation in eyes with glaucoma

OBJECTIVE

To examine the changes in anterior chamber angle width and depth induced by intraocular lens (IOL) implantation in eyes with angle-closure glaucoma (ACG), in eyes with open-angle glaucoma (OAG), and in eyes with no evidence of glaucoma or ocular hypertension.

DESIGN

A comparative, nonrandomized, interventional study.

PARTICIPANTS

Seventy-seven eyes with ACG, 73 eyes with OAG, and 74 control eyes undergoing cataract extraction and IOL implantation.

INTERVENTION

All eyes underwent phacoemulsification and soft acrylic IOL implantation.

MAIN OUTCOME MEASURES

The angle width and depth of the anterior chamber were measured using a Scheimpflug videophotography system before surgery, and at 1 week and at 1, 3, 6, 9, and 12 months after surgery.

RESULTS

Before surgery, the mean anterior chamber angle width and depth in the ACG group was less than that in either the OAG or control groups by approximately 10 degrees in angle width and 1.0 mm in depth (P < 0.0001). After cataract extraction and IOL implantation, the angle width and depth increased significantly in all three groups (P < 0.0001). Although the width and depth in the ACG group were still smaller than that in the other groups, the differences decreased to 2 degrees for angle width and 0.3 mm for depth. In addition, no significant differences were found in these values between the OAG and control groups before or after surgery. Furthermore, no significant changes were observed in the angle width or depth in any of the three groups throughout the postoperative observation period. As expected, the mean preoperative intraocular pressure (IOP) in the ACG and OAG groups was higher than that in the control group. After cataract surgery, however, the mean IOP decreased significantly and was almost the same in all three groups at 1, 6, and 12 months after surgery.

CONCLUSIONS

The width and depth of the anterior chamber angle in eyes with ACG increased significantly after cataract extraction and IOL implantation and became similar to that in eyes with OAG and that in normal eyes, which may lead to the decrease in IOP seen in the postoperative period. No significant changes were observed in angle width and depth in any of the three groups after surgery.

Calcium spirulan, an inhibitor of enveloped virus replication, from a blue-green alga Spirulina platensis

Bioactivity-directed fractionation of a hot H2O extract from a blue-green alga Spirulina platensis led to the isolation of a novel sulfated polysaccharide named calcium spirulan (Ca-SP) as an antiviral principle. This polysaccharide was composed of rhamnose, ribose, mannose, fructose, galactose, xylose, glucose, glucuronic acid, galacturonic acid, sulfate, and calcium. Ca-SP was found to inhibit the replication of several enveloped viruses, including Herpes simplex virus type 1, human cytomegalovirus, measles virus, mumps virus, influenza A virus, and HIV-1. It was revealed that Ca-SP selectively inhibited the penetration of virus into host cells. Retention of molecular conformation by chelation of calcium ion with sulfate groups was suggested to be indispensable to its antiviral effect.

Penetrating atherosclerotic ulcer of the aorta: imaging features and disease concept

Penetrating atherosclerotic ulcer is an ulcerating atherosclerotic lesion that penetrates the elastic lamina and is associated with hematoma formation within the media of the aortic wall. This pathologic condition is distinct from classic aortic dissection and aortic rupture; however, care should be taken in making the diagnosis, particularly if the disease is discovered incidentally. At computed tomography (CT), penetrating atherosclerotic ulcer manifests as focal involvement with adjacent subintimal hematoma and is often associated with aortic wall thickening or enhancement. Magnetic resonance imaging is superior to conventional CT in differentiating acute intramural hematoma from atherosclerotic plaque and chronic intraluminal thrombus and allows unenhanced multiplanar imaging. Spiral CT involves shorter examination times and allows high-quality two- and three-dimensional image reconstruction. CT angiography can demonstrate complex spatial relationships, mural abnormalities, and extraluminal pathologic conditions. Transesophageal echocardiography has been reported to be highly sensitive and specific in the differentiation of aortic disease, and intravascular ultrasonography may also be useful in this setting. Although rupture or other life-threatening complications are rare, patients with penetrating atherosclerotic ulcer must be followed up, particularly during the 1st month after onset. Surgical treatment may become necessary in cases involving evidence of intramural hematoma expansion, signs of impending rupture, inability to control pain, or blood pressure changes.