Genomic analysis of gene expression in C. elegans.

Until now, genome-wide transcriptional profiling has been limited to single-cell organisms. The nematode Caenorhabditis elegans is a well-characterized metazoan in which the expression of all genes can be monitored by oligonucleotide arrays. We used such arrays to quantitate the expression of C. elegans genes throughout the development of this organism. The results provide an estimate of the number of expressed genes in the nematode, reveal relations between gene function and gene expression that can guide analysis of uncharacterized worm genes, and demonstrate a shift in expression from evolutionarily conserved genes to worm-specific genes over the course of development.

Gene silencing: shrinking the black box of RNAi.

The mysterious mechanism whereby the mere presence of double-stranded RNA can inactivate specific genes is yielding its secrets. Recent results identifying cellular components required for RNAi in Caenorhabditis elegans indicate that the mechanism is conserved, ancient and may provide a defense against selfish DNA.

Genetics: a touch of elegance with RNAi.

RNA-mediated gene interference (RNAi), a rapid, convenient tool for inhibiting gene function in Caenorhabditis elegans, has recently been shown to work in other organisms.

CDC-42 regulates PAR protein localization and function to control cellular and embryonic polarity in C. elegans.

BACKGROUND: The polarization of the anterior-posterior axis (A-P) of the Caenorhabditis elegans zygote depends on the activity of the par genes and the presence of intact microfilaments. Functional links between the PAR proteins and the cytoskeleton, however, have not been fully explored. It has recently been shown that in mammalian cells, some PAR homologs form a complex with activated Cdc42, a Rho GTPase that is implicated in the control of actin organization and cellular polarity. A role for Cdc42 in the establishment of embryonic polarity in C. elegans has not been described. RESULTS: To investigate the function of Cdc42 in the control of cellular and embryonic polarity in C. elegans, we used RNA-mediated interference (RNAi) to inhibit cdc-42 activity in the early embryo. Here, we demonstrate that RNAi of cdc-42 disrupts manifestations of polarity in the early embryo, that these phenotypes depend on par-2 and par-3 gene function, and that cdc-42 is required for the localization of the PAR proteins. CONCLUSIONS: Our genetic analysis of the regulatory relationships between cdc-42 and the par genes demonstrates that Cdc42 organizes embryonic polarity by controlling the localization and activity of the PAR proteins. Combined with the recent biochemical analysis of their mammalian homologs, these results simultaneously identify both a regulator of the PAR proteins, activated Cdc42, and effectors for Cdc42, the PAR complex.

PEP4 gene of Saccharomyces cerevisiae encodes proteinase A, a vacuolar enzyme required for processing of vacuolar precursors.

The proteinase A structural gene of Saccharomyces cerevisiae was cloned by using an immunological screening procedure that allows detection of yeast cells which are aberrantly secreting vacuolar proteins (J. H. Rothman, C. P. Hunter, L. A. Valls, and T. H. Stevens, Proc. Natl. Acad. Sci. USA, 83:3248-3252, 1986). A second cloned gene was obtained on a multicopy plasmid by complementation of a pep4-3 mutation. The nucleotide sequences of these two genes were determined independently and were found to be identical. The predicted amino acid sequence of the cloned gene suggests that proteinase A is synthesized as a 405-amino-acid precursor which is proteolytically converted to the 329-amino-acid mature enzyme. Proteinase A shows substantial homology to mammalian aspartyl proteases, such as pepsin, renin, and cathepsin D. The similarities may reflect not only analogous functions but also similar processing and intracellular targeting mechanisms for the two proteins. The cloned proteinase A structural gene, even when it is carried on a single-copy plasmid, complements the deficiency in several vacuolar hydrolase activities that is observed in a pep4 mutant. A strain carrying a deletion in the genomic copy of the gene fails to complement a pep4 mutant of the opposite mating type. Genetic linkage data demonstrate that integrated copies of the cloned proteinase A structural gene map to the PEP4 locus. Thus, the PEP4 gene encodes a vacuolar aspartyl protease, proteinase A, that is required for the in vivo processing of a number of vacuolar zymogens.

Quantitative analysis of mRNA amplification by in vitro transcription.

Effective transcript profiling in animal systems requires isolation of homogenous tissue or cells followed by faithful mRNA amplification. Linear amplification based on cDNA synthesis and in vitro transcription is reported to maintain representation of mRNA levels, however, quantitative data demonstrating this as well as a description of inherent limitations is lacking. We show that published protocols produce a template-independent product in addition to amplifying real target mRNA thus reducing the specific activity of the final product. We describe a modified amplification protocol that minimizes the generation of template-independent product and can therefore generate the desired microgram quantities of message-derived material from 100 ng of total RNA. Application of a second, nested round of cDNA synthesis and in vitro transcription reduces the required starting material to 2 ng of total RNA. Quantitative analysis of these products on Caenorhabditis elegans Affymetrix GeneChips shows that this amplification does not reduce overall sensitivity and has only minor effects on fidelity.

Immunologic abnormalities in patients with malignant lymphoproliferative diseases.

The B- and T-lymphocyte distribution was studied in 45 patients with malignant lymphoproliferative diseases. Eight patients with untreated Hodgkin's disease had normal mean percentages of complement receptor lymphocyte (CRL) cells and T-cells; however, the mean absolute number of T-cells was decreased. T-lymphocytes were also decreased in 3 patients with Hodgkin's disease treated 7-24 months previously. The number of T-lymphocytes increased markedly in all patients after treatment. Lymphocyte surface markers in non-Hodgkin's lymphoma showed distinctive patterns. Patients with leukemic reticuloendotheliosis or "hairy cell leukemia" characteristically had low percentages of CRL but normal or increased percentages of surface immunoglobulin-positive lymphocytes. The mean percentage and number of T-lymphocytes in this group were normal. Eight patients with nodular lymphocytic lymphoma and 2 patients with nodular lymphocytic-histiocytic lymphoma had normal mean numbers of CRL but decreased numbers of T-lymphocytes. Of 6 patients with diffuse lymphocytic lymphoma, 4 had elevated percentages and numbers of CRL. Despite low percentages, normal numbers of T-lymphocytes were found in 3 of these patients.

Differences between black and white women with breast cancer in time from symptom recognition to medical consultation. Black/White Cancer Survival Study Group.

BACKGROUND: Studies in the United States have reported that Black women have higher fatality rates than White women following a diagnosis of breast cancer and are more likely to be diagnosed with late-stage cancers. PURPOSE: To evaluate reasons for these racial differences, we explored the difference between Black and White women in the length of time from symptom recognition to initial medical consultation. We also evaluated the extent to which other factors related to the length of this interval might contribute to any observed racial difference. METHODS: As part of a collaborative study of differences in the survival rates of Black patients and White patients with cancer, we interviewed a sample of 410 Black women and 325 White women from Atlanta, New Orleans, and San Francisco/Oakland who were newly diagnosed in 1985 or 1986 with invasive breast cancer. Retrospective data were collected on symptoms, dates of symptom recognition and initial medical consultation, and several other factors which may affect the interval between symptom recognition and medical consultation. Data were analyzed as if from a follow-up study, using product limit procedures and proportional hazards regression. RESULTS: At diagnosis, Black women with breast cancer were two times more likely to have stage IV breast cancer and one and one-half times more likely to have stage III breast cancer than White women with breast cancer and were only approximately one-half as likely to have stage I breast cancer. Similarly, Black women were almost twice as likely as White women to have tumors that were larger than 5 cm or tumors that had extensions to the chest wall or skin at presentation. However, the average rate at which Black women with breast cancer obtained an initial medical consultation lagged behind that for White women by only a slight but statistically significant difference (15%). The median time between symptom recognition and medical consultation was slightly longer for Black women (16 days) than for White women (14 days) (P = .06). Adjustment for other characteristics predictive of the length of this interval had little effect on racial differences. The racial differences tended to vary somewhat by age and metropolitan area, suggesting that the results may not apply equally to all demographic subgroups and regions in the United States. CONCLUSION: This small difference in the time from symptom recognition to medical consultation is unlikely to account for the large racial differences in survival rates and in stage of disease at the time of diagnosis.

Breast cancer: factors associated with stage at diagnosis in black and white women. Black/White Cancer Survival Study Group.

BACKGROUND: Numerous studies have reported differences in cancer staging at diagnosis and in survival between Black and White patients with breast cancer. Utilizing data obtained from the National Cancer Institute's (NCI's) Black/White Cancer Survival Study for the period 1985-1986, a new study is presented here that systematically examines multiple explanatory factors (e.g., lack of mammograms) associated with these cancer-staging differences. PURPOSE: We evaluated within a single study the relationship of selected demographic, lifestyle, antecedent medical experiences, and health care access factors to cancer staging at diagnosis in Black and White breast cancer patients. METHODS: Data utilized in this population-based cohort study of 1222 eligible women (649 Black and 573 White) newly diagnosed for the period 1985-1986 with histologically confirmed primary breast cancer were obtained from the NCI's Black/White Cancer Survival Study. Sources of data included abstracts of hospital medical records, central review of histology slides by a study consultant pathologist, and patient interviews obtained from three metropolitan areas: Atlanta, New Orleans, and San Francisco-Oakland. Within each area, 70% of all Black incident cases were randomly selected, and a sample of White cases, frequency matched by age groups (20-49 years, 50-64 years, and 65-79 years), was selected for comparison. Stage of breast cancer at diagnosis was classified according to the international tumor-lymph node-metastases (TNM) system. Statistical models utilized in this study included the log-linear and polychotomous logistic regression with multiple predictor variables. RESULTS: Factors associated with cancer staging were differentially expressed in Blacks and Whites. Indicators of access to health care, a lack of mammograms, and an increased body mass index significantly (P < .02) contributed to stage differences in Blacks, whereas income was marginally associated (P = .06) with stage for Whites only. Nuclear grade, having a breast examination by a physician, and a history of patient delay explained approximately 50% of the excess risk for stage III-IV cancer versus stage I-IIN0 cancer among Blacks compared with Whites (odds ratio reduction from 2.19 to 1.68). CONCLUSION: These findings suggest that no single factor or group of factors can explain more than half of the race-stage differences noted in this study with respect to Black and White breast cancer patients.

Determinants of black/white differences in colon cancer survival.

BACKGROUND: Blacks have lower survival rates for colon cancer than whites, possibly related to more advanced stages of disease at diagnosis and to socioeconomic differences between blacks and whites. While the black/white difference in colon cancer survival is well documented, the few studies that have investigated this difference have been limited by the modest number and type of explanatory factors that were considered. PURPOSE: We analyzed data from the National Cancer Institute Black/White Cancer Survival Study to determine 1) what characteristics might contribute to the racial difference in colon cancer survival and 2) if a survival disparity remained between black and white patients after adjustment was made for these characteristics. METHODS: This prospective study included 454 blacks and a stratified random sample of 521 whites, aged 20-79 years, with cancer of the colon diagnosed from January 1, 1985, through December 31, 1986, and who were residents of the metropolitan areas of Atlanta, New Orleans, and San Francisco/Oakland. Follow-up was truncated on December 31, 1990. Cox proportional hazards regression was used to estimate the death rate among blacks relative to that among whites after adjustment for potential explanatory factors, including sociodemographic factors, concurrent (comorbid) medical conditions, stage at diagnosis, tumor characteristics, and treatment. All P values were calculated from two-tailed tests of statistical significance. RESULTS: After adjustment for age, sex, and geographic area, the black-to-white mortality hazard ratio (HR) was 1.5 (95% confidence interval [CI] = 1.2-1.9), indicating that the risk of death among black patients was 50% higher than that among white patients. Further adjustment for stage reduced the excess cancer mortality to 20% (HR = 1.2; 95% CI = 1.0-1.5), decreasing the overall racial difference in excess mortality from 50% to 20% or to a 60% reduction in excess mortality. Although adjustment for poverty reduced the excess mortality by 20%, adjusting for both stage and poverty did not further reduce the racial difference. Among patients with stages II and III disease, blacks had lower survival rates than whites (HR = 1.8; 95% CI = 1.0-3.1 and HR - 1.5; 95% CI = 1.0-2.3, respectively). Among those patients with metastatic disease (stage IV), survival was similar for whites and blacks. CONCLUSIONS: Stage at diagnosis accounted for more than half of the excess colon cancer mortality observed among blacks. Poverty and other socioeconomic conditions, general health status, tumor characteristics, and general patterns of treatment did not further explain the remaining survival disadvantage among blacks. IMPLICATIONS: Because the racial disparity was confined to earlier stages, future studies should investigate whether blacks have more advanced disease at diagnosis and whether less aggressive treatment is provided because of understanding.

Effects of patient management guidelines on physician practice patterns: the Community Hospital Oncology Program experience.

The Community Hospital Oncology Program (CHOP), funded under contracts by the National Cancer Institute (NCI) from 1981 to 1984, was designed to be a model for delivery of the most up-to-date cancer care in the community setting. Site specific patient management guidelines (PMGs) were developed by physicians who saw a majority of cancer patients in each community and represent a consensus of the most current information on pretreatment evaluation and management for each cancer site. There was the potential for PMGs to have a strong effect on physician practice patterns. A patterns of care study (POC) was conducted in the 17 CHOPs to determine the influence of guidelines on practice patterns. The practice elements examined in this report are clinical staging for breast and small-cell lung cancer, medical oncology consultation for breast cancer patients with positive lymph nodes, and radiation therapy consultation for rectal and small-cell lung cancer. These elements were in all CHOP guidelines. Except for physicians most active in the CHOP, the data provide no evidence of diffusion of guideline principles to the majority of practicing physicians. Although all guidelines contained discussion of the importance of staging before definitive treatment for breast cancer, only 33% of the 1,922 charts examined had a stage recorded. In small-cell lung cancer, 67% of the 388 charts examined had stage recorded. The years in practice of the primary physician had an inverse relationship to practice patterns as defined by the guidelines. Physician specialty was also a determinant of practice patterns for small-cell lung cancer. However, participation in guideline development and their dissemination did not significantly influence the patterns of care elements examined in this study.

Histological characteristics of breast carcinoma in blacks and whites.

Tumor characteristics of 963 newly diagnosed invasive breast cancer cases from the population-based Black/White Cancer Survival Study were evaluated. Representative slides of the tumors were requested from all participating hospitals of three metropolitan areas and reviewed by one expert pathologist, blinded in regard to the age and race of patients. Nine tumor characteristics were evaluated for black and white patients. After adjusting for age, stage, and metropolitan area, blacks were significantly more likely to have high grade nuclear atypia [odds ratio (OR) = 1.97, 95% confidence interval (CI) = 1.27-3.04]; high mitotic activity (OR = 2.05, 95% CI = 1.34-3.14), grade 3 tumors (OR = 1.58, 95% CI = 1.02-2.45), and more necrosis (OR = 1.51, 95% CI = 1.16-1.98); and less likely to have well defined tubular formation (OR = 0.57, 95% CI = 0.42-0.77), marked fibrosis (OR = 0.65, 95% CI = 0.45-0.94), and positive estrogen receptor status (OR = 0.78, 95% CI = 0.58-1.05). These black/white differences remained after controlling for socioeconomic status (SES), body mass index, use of alcohol and tobacco, reproductive experience, and health care access and utilization. No significant racial differences were found for blood vessel invasion and lymphatic invasion. Although white women of high SES had more favorable tumors than those of low SES, the same pattern was not observed for blacks. High SES black women had statistically nonsignificant elevated ORs of a high mitotic index and tumor grade. These racial differences in tumor biology may have etiological and clinical implications.

Systemic RNAi in Caenorhabditis elegans.

RNA interference (RNAi) in Caenorhabditis elegans induced by ingestion or injection of double-stranded RNA (dsRNA) spreads throughout the organism and is even transmitted to the progeny. We have identified two proteins required for spreading of RNAi, SID-1 and SID-2, whose structure, subcellular localization, and expression pattern have been informative for how dsRNA can be transported into and between cells. SID-1 is a transmembrane protein that functions as a pore or channel that transports dsRNA into and out of cells. Proteins homologous to SID-1 are present in a wide range of invertebrate and vertebrate animals but are absent from plants. SID-2 is a small transmembrane protein that is expressed in the gut and localizes strongly to the luminal membrane where it appears to act as a receptor for uptake of dsRNA from the environment. Characterization of SID-2 activity in a variety of Caenorhabditis nematodes indicates that C. elegans SID-2 may have a novel activity.

Epidemiology, stage at diagnosis, and tumor biology of breast carcinoma in multiracial and multiethnic populations.

All women, regardless of their racial or ethnic origin or heritage, are at risk of developing breast cancer. Variations in breast carcinoma incidence rates among multicultural populations suggest that etiologic factors differ in their biologic expression and impact on disease outcome. Key among those factors that affect breast carcinoma development are the roles of genetics and the environment, the reproductive experience and the effects of endogenous and exogenous hormones in women, the change in immune status and host vulnerability, and the biologic determinants of breast carcinoma. Cultural dynamics, sociodemographic differences, and behavioral characteristics across population subgroups modulate how biologic disease is expressed among different races and ethnic groups. These interactions contribute to the observed variations in breast carcinoma incidence, mortality, and survival. Stage, a measure of disease status, is used to assess prognosis, plan treatment, and evaluate outcome. Numerous studies have reported a more advanced stage of breast carcinoma at diagnosis in racial/ethnic subgroups, especially among women from African American, Hispanic, American Indian, and native Hawaiian cultures. Factors associated with advanced stage at diagnosis in multicultural populations range from changes in the basic biological characteristics at the molecular and cellular level, to more complex behavioral attributes unique to a particular multicultural population, to societal issues-such as access to care and socioeconomic conditions-all of which impact on the health measure called "stage at diagnosis." Rapid advancements in knowledge of cancer biology and of genetic markers and tumor products are providing new mechanisms for identifying etiologic pathways that can be utilized for better screening, detection, treatment and monitoring of disease. Further studies are needed that evaluate the biologic and molecular alterations in tumor development, progression, and response to therapy. Public health attention needs to be directed toward the societal influences that impact breast carcinoma development, as well as augmenting recognition of the need for culturally appropriate, broad-based behavioral changes at the community level. In addition, continued efforts are needed to ensure the inclusion of multicultural population subgroups and minority investigators in all aspects of research-basic, clinical and applied.

The effect of anther orientation on the production of microspore-derived embryoids and plants of Hordeum vulgare cv. Sabarlis.

The orientation of barley anthers on culture medium had a marked effect on their response. Embryoids developed only in the upper lobes of anthers cultured on edge, i.e. with a single lobe in contact with the culture medium. Anthers cultured flat, i.e. with both lobes in contact with the medium, did not respond. Careful orientation of anthers at the start of incubation resulted in a mean yield of 20 green plants per 100 anthers cultured.

Specification of anteroposterior cell fates in Caenorhabditis elegans by Drosophila Hox proteins.

Antennapedia class homeobox (Hox) genes specify cell fates in successive anteroposterior body domains in vertebrates, insects and nematodes. The DNA-binding homeodomain sequences are very similar between vertebrate and Drosophila Hox proteins, and this similarity allows vertebrate Hox proteins to function in Drosophila. In contrast, the Caenorhabditis elegans homeodomains are substantially divergent. Further, C. elegans differs from both insects and vertebrates in having a non-segmented body as well as a distinctive mode of development that involves asymmetric early cleavages and invariant cell lineages. Here we report that, despite these differences, Drosophila Hox proteins expressed in C. elegans can substitute for C. elegans Hox proteins in the control of three different cell-fate decisions: the regulation of cell migration, the specification of serotonergic neurons, and the specification of a sensory structure. We also show that the specificity of one C. elegans Hox protein is partly determined by two amino acids that have been implicated in sequence-specific DNA binding. Together these findings suggest that factors important for target recognition by specific Hox proteins have been conserved throughout much of the animal kingdom.

Evidence from mosaic analysis of the masculinizing gene her-1 for cell interactions in C. elegans sex determination.

Sex in Caenorhabditis elegans is determined by a regulatory cascade of seven interacting autosomal genes controlled by three X-linked genes in response to the X chromosome-to-autosome (X/A) ratio. XX animals (high X/A) develop as self-fertile hermaphrodites, and XO animals (low X/A) develop as males. The activity of the first gene in the sex-determining cascade, her-1, is required for male sexual development. XO her-1 loss-of-function mutants develop as self-fertile hermaphrodites, whereas XX her-1 gain-of-function mutants develop as masculinized intersexes. By genetic mosaic analysis using a fused free duplication linking her-1 to a cell-autonomous marker gene, we show here that her-1 expression in a sexually dimorphic cell is neither necessary nor sufficient for that cell to adopt a male fate. Our results suggest that her-1 is expressed in many, possibly all, cells and that its gene product can function non-autonomously through cell interactions to determine male sexual development.

Spatial and temporal controls target pal-1 blastomere-specification activity to a single blastomere lineage in C. elegans embryos.

The early asymmetric cleavages of Caenorhabditis elegans embryos produce blastomeres with distinct developmental potentials. Here, we show that the caudal-like homeodomain protein PAL-1 is required to specify the somatic identity of one posterior blastomere in the 4 cell embryo. We find that pal-1 activity is sequentially restricted to this blastomere. First, at the 4 cell stage, it is translated only in the two posterior blastomeres. Then, its function is restricted to one of these blastomeres. This second targeting step is dependent on the activities of the posteriorly localized SKN-1 and asymmetrically segregated PIE-1 proteins. We propose that the segregation of PIE-1, combined with the temporal decay of SKN-1, targets pal-1 activity to this posterior lineage, thus coupling the regulation of this conserved posterior patterning gene to asymmetric cell cleavages.

The tra-1 gene determines sexual phenotype cell-autonomously in C. elegans.

The tra-1 gene plays a central role in C. elegans sex determination. XX animals develop as hermaphrodites when tra-1 is active and as males when it is not. By analyzing a large number of tra-1 genetic mosaics we have shown that, with the expected exception of vulval induction by the hermaphrodite gonad, tra-1 functions cell-autonomously, consistent with a role as an intracellular component of a signaling pathway. Moreover, all the sexual differentiation genes under tra-1 control must also function cell-autonomously. Our results have additional implications for several aspects of postembryonic development, including mechanisms of sex-specific directed cell migrations and the question of an organizer in the male tail.