Development of an assay to predict oxaliplatin sensitivity from formalin-fixed, paraffin-embedded (FFPE) colorectal cancer tissues

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Background: Genomic profiling has improved our understanding of the underlying biology of tumors, accuracy of diagnosing disease, predictions of the courses of disease, and ability to determine the therapeutic agents that will be most effective in the treatment of particular tumors. However, in order for assays involving microarray data to be useful in the clinical setting, the ability to generate reliable and consistent data from FFPE tissues is essential.

Methods: Cancer cell lines from the NCI-60 collection exhibiting greatest sensitivity or resistance to oxaliplatin were identified. These cells were grown in culture, fixed for 24 hours in formalin, and paraffin-embedded. RNA from the FFPE cells was isolated, amplified, and hybridized to Affymetrix arrays. A Bayesian binary regression analysis was used to generate a predictor of oxaliplatin sensitivity from the gene expression data. Metastatic derived xenografts (MDXs) from resected colorectal tumors were established and treated with oxaliplatin. Samples from tumors prior to treatment were paraffin-embedded and used for RNA extraction, amplification, and hybridization to Affymetrix arrays. The gene expression signature predicting sensitivity to oxaliplatin was then validated with response data from MDXs treated with oxaliplatin.

Results: A predictor consisting of 300 genes that could predict sensitivity to oxaliplatin was generated using FFPE samples. Significant correlation was observed between the predicted probability of oxaliplatin sensitivity and the tumor growth inhibition measurement for a given MDX (p=0.0012).

Conclusions: Reliable and consistent predictions of oxaliplatin sensitivity can be obtained from gene expression data from FFPE tissues. This method has potential utility in the clinical setting. The ability to predict response to a therapeutic in a FFPE sample has the potential to guide the choice of therapeutics, resulting in an option that could be most effective in treating an individual with metastatic colorectal cancer.

No significant financial relationships to disclose.

An ethnographic, controlled study of the use of a computer-based histology atlas during a laboratory course

OBJECTIVE

To evaluate the use and effect of a computer-based histology atlas during required laboratory sessions in a medical school histology course.

DESIGN

Ethnographic observation of students' interactions in a factorial, controlled setting.

MEASUREMENTS

Ethnographer's observations; student and instructor self-report survey after each laboratory session with items rated from 1 (least) to 7 (best); microscope practicum scores at the end of the course.

RESULTS

Between groups assigned the atlas and those not, the ethnographer found qualitative differences in the semantic categories used by students in communicating with each other and with the faculty. Differences were also found in the quality of the interactions and in the learning styles used with and without the computer present in the laboratory. The most interactive learning style was achieved when a pair of students shared a computer and a microscope. Practicum grades did not change with respect to historical controls. Students assigned the atlas, compared with those not assigned, reported higher overall satisfaction (a difference in score of 0.1, P = 0.003) and perceived their fellow students to be more helpful (a difference of 0.11, P = 0.035). They rated the usefulness of the microscope lower (a difference of 0.23, P<0.001).

CONCLUSION

A computer-based histology atlas induces qualitative changes in the histology laboratory environment. Most students and faculty reacted positively. The authors did not measure the impact on learning, but they found that there are aspects of using the atlas that instructors must manipulate to make learning optimal. Ethnographic techniques can be helpful in delineating the context and defining what the interventions might be.

Risk factors for nonelective hospital readmissions

We previously reported a predictive model that identified potentially modifiable risk factors for nonelective readmission to a county hospital. The objectives of this study were to determine if those risk factors were generalizable to a different population. We found that the previously reported risk factors were generalizable, and other potentially modifiable risk factors were identified in this population of veterans. However, further research is needed to establish whether or not the risk factors can be modified and whether or not modification improves outcomes.

Polychaetoid is required to restrict segregation of sensory organ precursors from proneural clusters in Drosophila

Reduction of wild-type activity of the polychaetoid (pyd) gene results in formation of extra mechanosensory bristles on the head and notum of adult Drosophila. Loss of pyd function results in decreased ability to restrict sensory organ precursor (SOP) formation to a single cell per proneural cluster. Although the initial proneural cluster pattern of achaete expression is not altered in pyd mutants, extra cells within proneural clusters express the high levels of achaete characteristic of SOPs. This observation suggests that pyd+ functions as a negative regulator of achaete-scute complex expression within the proneural cluster. Synergistic interactions between pyd and Notch, Delta and extramacrochaetae mutations support this model. We also demonstrate that pyd is required for normal eye development.

An intervention on discharge polypharmacy

OBJECTIVE

To determine if providing a way to cancel pre-admission prescriptions would reduce the number of active drug prescriptions (RXs) at discharge.

DESIGN

A randomized non-blinded clinical trial.

SETTING

Inpatient acute medical service of a university affiliated Veterans Administration medical center.

PARTICIPANTS

Twelve medicine ward teams were randomized to control and intervention groups. Patients controlled had been discharged from these teams during 12 weeks and were receiving outpatient medications from this facility at hospital admission; control = 180, intervention = 168.

INTERVENTION

At discharge, intervention teams used a computer-generated drug list to cancel or renew previous outpatient RXs or to prescribe new medications. Control teams could not cancel outpatient drugs and wrote all medications on individual prescriptions.

MEASUREMENTS

The difference between admission and discharge RXs.

RESULTS

There were no significant differences in patients' age, sex, race, Charlson Index (CI), or LOS between patient groups at discharge. The intervention group had fewer RXs on admission (5.4 vs 6.2, P < .05) and at discharge was not significantly different (2.9 vs 2.9, P = .87) from the control group.

CONCLUSIONS

Providing a method for canceling pre-admission medications did not reduce the number of RXs at discharge. Further research is needed to evaluate the appropriateness of the large increase in RXs from admission to discharge for patients in acute hospital settings.

Some techniques for the analysis of work sampling data

Work sampling is an observational technique that produces counts representing the number of times that an individual has been observed performing each of several tasks. These data are collected using either systematic or random times of observation, and typically exhibit correlation between repeated observations on the same individual, with the degree of correlation being a function of the amount of time elapsed between measurements. Using several recently developed statistical techniques, we illustrate how it is possible to carry out analyses of these nominal outcomes that account for the correlation between repeated outcomes. We use description of a work sampling study to motivate the techniques and we compare empirically results from analyses based on several different underlying assumptions.

Screening for social and environmental problems in a VA primary care setting

Social workers are in an ideal position to identify and treat social and environmental problems early in the continuum of care. Information on these problems will facilitate informed decision making on the development and reallocation of resources to better meet patients needs. This study assessed the social and environmental problems of 132 patients seen in a primary care clinic at a university-affiliated Veterans Affairs (VA) medical center. The most prevalent social problems were financial difficulties, personal stress, family problems, legal concerns, and employment concerns. When asked, nearly one-third of all respondents requested social work services or information about services related to their problems. The findings suggest a clear need for social work interventions in VA primary care clinics that focus on both psychosocial problems.

Collaborative QI in community-based long term care

BACKGROUND

In a statewide demonstration project funded by The Robert Wood Johnson Foundation, the state of Indiana, vendors, clients and Indiana University researchers began working together in 1992 to use quality improvement (QI) techniques to improve the delivery of community-based long term care services. QI STRATEGIES: These collaborators, working with state Area Agencies on Aging (AAAs) case managers, are implementing two strategies--Normative Treatment Planning (NTP), which standardizes the clinical assessment of client needs and the prescription of services by case managers, and the Client Feedback System (CFS), a systematic method for obtaining feedback from long term care clients on the quality of in-home services.

CURRENT STATUS

This community-based long term care project has been implemented in AAAs throughout the state of Indiana. In January 1995 the state's 16 AAAs were randomly assigned to four experimental or control groups to assess the project's effectiveness. In the interim, clients are surveyed by telephone every six months to evaluate their satisfaction with services and clinical needs.

LESSONS LEARNED

The experience suggests several lessons: (1) build on existing and successful activities; (2) involve a wide range of participants, not just innovators; (3) obtain buy-in from trade and professional associations that represent program participants; (4) turn national attention given to the program into an asset; (5) conduct separate data collection to evaluate an intervention's success; (6) visit the field often; (7) pay as much attention to program implementation as to development; and (8) provide ongoing, informal educational opportunities for the field.

SUMMARY AND CONCLUSIONS

This project has resulted in significant movement toward a shared quality improvement vocabulary, information system, and a shared vision of high-quality home care.

Primary care physician productivity: the physician factor

OBJECTIVES

To model physician productivity as a function of clinic (support system) characteristics and physician characteristics and to model the time a physician spends with the patient as a function of patient characteristics.

DESIGN

Observational study.

SETTING

A general medicine clinic of a university-affiliated Veterans Affairs medical center.

PATIENTS

A cohort of 2,520 patients having 2,721 consecutive outpatient visits to 56 physicians.

MAIN OUTCOME MEASURES

Physician productivity defined as patients seen/physician/hour and time (minutes) spent with the patient.

RESULTS

Physicians saw a mean (+/- SD) of 1.62 +/- 0.68 patients/hour. Clinic characteristics explained 8.2% of the variability of session-specific physician productivity. Controlling for clinic characteristics, a factor representing the physician explained an additional 55.4%. A model for overall physician productivity, using physician characteristics, explained 84.9% of the variance, and time spent with the patient was an important predictor. Modeling physician time with patients, patient characteristics accounted for only 7% of the variability. Controlling for patient characteristics, the individual physician again provided the greatest explanatory power, an additional 22.8% of the variability.

CONCLUSIONS

Physicians' practice patterns, rather than clinic or patient characteristics, may account for most of the variation in physician productivity. Given the magnitude of the influence of individual practice patterns, interventions to increase productivity need to consider methods to affect physician behavior.

A case manager intervention to reduce readmissions

BACKGROUND

Acute hospitalizations represent substantial financial liability to closed health care systems. Among hospitalized patients, those with repeated admissions are high-cost users. Most managed care plans employ case management to control hospital use. This technique attempts to detect and fulfill unmet medical and social needs, intensify postdischarge care, identify and mobilize effective community services, and enhance primary care access. Despite the popularity of case management to control hospital use, few trials have examined its efficacy.

METHODS

We conducted a randomized controlled trial of an intervention of case managers at a university-affiliated Veterans Affairs medical center. Six hundred sixty-eight patients aged 45 years or older who were discharged from the general medicine inpatient service, who had access to a telephone, and who received primary care at the hospital's clinics were randomized to the intervention (N = 333) and control (N = 335) groups. Within 24 hours of discharge, case managers mailed educational materials and access information to intervention patients, and within 5 days they called to review and resolve unmet needs, early warning signs, barriers to keeping appointments, and any readmissions. Case managers contacted intervention patients if they made no visits for 30 days. This resulted in a total of 6260 patient-case manager contacts. Control and intervention patients were followed up for 12 months.

RESULTS

Intervention patients had more frequent visits per patient per month to the general medicine clinic (0.30 +/- 0.23 vs 0.26 +/- 0.22, P = .008), but we detected no significant differences between groups in nonelective readmissions, readmission days, or total readmissions.

CONCLUSIONS

Frequent contacts for education, care, and accessibility by case managers using protocols were ineffective in reducing nonelective readmissions.

The effect of antibodies to subunit V of cytochrome oxidase on cyanide inhibition of electron transfer

Binding of antibodies raised against subunit V of mammalian cytochrome oxidase to the intact membranous enzyme is redox-sensitive, suggesting the existence of 'open' and 'closed' protein conformers (Freedman, J.A., Cooper, C.E., Leece, B., Nicholls, P. and Chan, S.H.P. (1988) Biochem. Cell Biol. 66, 1210-1217). Similar open and closed states for the oxygen-reacting site have been proposed to explain cyanide binding kinetics (Jensen, P., Wilson, M.T., Aasa, R. and Malmström, B.G. (1984) Biochem. J. 224, 829-837). We therefore examined cyanide inhibition of oxidase activity polarographically and spectrophotometrically using soluble oxidase preincubated with and without anti-subunit V or non-immune rabbit gamma-globulin. The subunit-specific antibody decreased the cyanide 'on' rate and essentially eliminated the rapid phase of cyanide binding. We conclude that (i), bound antibody blocks HCN binding; (ii), antibody and HCN probably bind to the same conformation of the oxidase and (iii), the 'open'-'closed' conformation change that modulates binding of HCN may be similar to that which modulates antibody binding. The results are consistent with some reciprocating models of electron transfer and energy transduction by the oxidase (cf., Wikström, M.K.F., Krab, K. and Saraste, M. (1981) Cytochrome Oxidase: A Synthesis).

Replication of the multidimensionality of activities of daily living

We attempted to replicate the three-dimensional factor structure of a previously proposed ADL scale and demonstrate an association between the advanced ADL dimension and cognitive function. Data used in these analyses were baseline assessments of health and functional status of hospitalized patients enrolled in a randomized controlled trial of case managers as a means of reducing health care utilization. We submitted 14 items from the OARS to a two-stage process of principal components factor analysis. Four significant dimensions emerged that were remarkably similar to the advanced, basic, and household ADL dimensions reported by Wolinsky and Johnson (1991). In this sample of hospitalized patients, however, incontinence emerged as a weak fourth dimension. Multiple regression of SPMSQ mental status examination scores on these ADL dimensions demonstrates the association between cognitive function and the advanced ADL dimension. These data confirm that the underlying structure of ADLs consists of at least three separate dimensions, one of which is aligned with cognitive capacity.

Cytochrome c oxidase: structure, function, and membrane topology of the polypeptide subunits

Mitochondrial cytochrome c oxidase and its bacterial homologs catalyze electron transfer and proton translocation reactions across membranes. The eukaryotic enzyme complex consists of a large number of polypeptide subunits. Three of the subunits (I, II, and III) are mitochondrially encoded while the remaining 6 (yeast) to 10 (bovine) are nuclear encoded. Antibody and chemical-labelling experiments suggest that subunits I-III and most (but not all) of the nuclear-encoded subunits span the inner mitochondrial membrane. Subunits I and II are the catalytic core of the enzyme. Subunit I contains haem a, haem a3 and CuB, while subunit II contains CuA and the cytochrome c binding site. Subunit III and most of the nuclear subunits are essential for the assembly of a functional catalytic enzyme. Some nuclear subunits are present as isozymes, although little functional difference has yet been detected between enzyme complexes composed of different isozymes. Therefore, any additional role attributed to the nuclear-encoded subunits beyond that of enzyme assembly must be tentative. We suggest that enough evidence exists to support the idea that modification of the larger nuclear subunits (IV, V, and possibly VI) can effect enzyme turnover in vitro. Whether this is a physiological control mechanism remains to be seen.

Effects of subunit V antibodies on the topology of the subunit and the activity of beef heart cytochrome-c oxidase

Redox-sensitive epitopes on subunit V of beef heart cytochrome-c oxidase were demonstrated previously using polyclonal subunit-specific antibodies raised in rabbits. The antibodies only slightly inhibited electron transfer, and the accessibility of their epitopes depended on the presence of a membrane and on the redox state of the oxidase. The present paper describes additional preparations of antibodies raised against subunit V. These antibodies have an even higher subunit specificity, they are more than three times as inhibitory against electron transfer, and their binding does not require a membrane. Moreover, the redox-sensitive nature of their binding to detergent-dispersed oxidase is sensitive to the method of its isolation. We discuss inferences that can be drawn from a detailed quantitative comparison of the interactions of the two antibody preparations with the antigen in different environments. The techniques used in the comparison can be used to examine other perturbants of the oxidase as to their effects on specific segments of the enzyme.

Effects of antibodies to intact cytochrome-c oxidase and its subunit V on the enzymatic activity

Antibodies have been raised in rabbits against whole beef heart cytochrome-c oxidase and purified subunit V. Antioxidase recognizes nearly all the enzyme subunits but reacts very strongly with subunits II and IV. Antisubunit V is quite specific against subunit V. Inhibition of enzyme activity by antioxidase is typically biphasic in time, indicating populations of both rapidly and slowly reacting molecules. Variation of cytochrome c concentration shows partially competitive kinetics, but the antibody also affects "internal" enzymatic events, including the catalytic turnover induced by N,N,N',N'-tetramethyl-p-phenylenediamine alone and the spin-state change in cytochrome a3 that follows reduction of cytochrome a. No spectral effects can be seen however. Antioxidase also inhibits proteoliposomal respiration with external cytochrome c, but not that with internally trapped cytochrome c. No functionally significant epitopes are detectable on the N side of the membrane in proteoliposomes, although some small effects can be seen with submitochondrial particles. Antisubunit V inhibits the isolated enzyme by at least 60%. The inhibition at high ionic strength induces a biphasic pattern with respect to cytochrome c concentration. Antisubunit V may thus slow the dissociation of cytochrome c from its complex with the enzyme. Antisubunit V has only small effects on the activities of proteoliposomal and submitochondrial particle oxidase in either orientation. On subunit V, some sites, the binding of which can give rise to inhibition, are thus not accessible to antisubunit V when the enzyme is embedded in a functional membrane system.

Two monoclonal antibody lines directed against subunit IV of cytochrome oxidase: a study of opposite effects

Two monoclonal lines of antibodies were isolated with specificities against the amino half of Subunit IV of beef heart cytochrome oxidase. The lines had nonoverlapping epitopes. Both bound to the matrix face of membranous oxidase, neither bound to the cytoplasmic face. One line (QA4/C4) stimulated electron transfer in soluble or membranous oxidase, while the other (QA4) inhibited that activity by both oxidase preparations. These effects on electron transfer activity were not altered by the inclusion or omission of detergent. ATP depressed the binding of either antibody to either soluble or membranous oxidase. In the absence of ATP, QA4/C4 stimulated electron transfer only in the high affinity phase of cytochrome c oxidation (with decreased KM and increased Vmax), causing slight inhibition in the low affinity phase (with decreased KM). In the presence of ATP, QA4/C4 abolished the high affinity phase, but did not alter the ATP influence on the low affinity phase. In the absence of ATP, antibodies of line QA4 abolished the low affinity phase, leaving a high affinity phase similar to that induced by ATP. In the presence of ATP, QA4 abolished the high affinity phase, leaving a low affinity phase similar to that seen with ATP alone. This behavior is consistent with the dissection of two catalytic sites for cytochrome c and more than one ATP affector site.

Thermodynamics of reverse electron transfer across site 1: ATP/2e- is greater than one

ATP-driven, rotenone-sensitive, reverse electron transfer from succinate to acetoacetate was measured in rat liver mitochondria in the presence of cyanide. In the approach to equilibrium, the absolute ratio of the free energy change of electron transfer to that of ATP hydrolysis exceeded 1, tending towards about 1 1/4. The data support an H+/2e- stoichiometry of 5 for Site 1 as predicted by a thirteen-proton model of chemiosmotic coupling.

The mechanism of antibody inhibition of proton pumping by cytochrome oxidase vesicles

Antibodies previously shown to inhibit vectorial proton translocation through cytochrome oxidase vesicles were converted to F(ab')2 and Fab'. Neither fragment inhibited proton pumping, although binding capacity was present. However, when a surrogate Fc was added to F(ab')2, inhibition of proton translocation was restored; indicating that the inhibition is due to steric hindrance. These results provide insight into mechanisms of energy transduction by oxidase.

Interactions in cytochrome oxidase: functions and structure

Mitochondrial cytochrome c oxidase is an exceedingly complex multistructural and multifunctional membranous enzyme. In this review, we will provide an overview of the many interactions of cytochrome oxidase, stressing developments not covered by the excellent monograph of Wikström, Krab, and Saraste (1981), and continuing into early 1983. First we describe its functions (both in the nominal sense, as a transporter of electrons between cytochrome c and oxygen, and in its role in energy transduction). Then we describe its structure, emphasizing the protein (its structure as a whole, the number and stoichiometry of its subunits, their biosynthetic origin, and their interactions with each other, with other components of the enzyme complex, and with the membrane as a whole). Finally, we present a model in which the protein conformation serves as the focus for the dynamic interaction of its two major functions.

The effect of specific antibodies on oxygen uptake and H+ pumping by cytochrome c oxidase vesicles

Antibodies to solubilized cytochrome c oxidase and to subunit III were incubated with liposomal oxidase. In oxygen uptake experiments, the inhibiting effects on RCI of anti-oxidase (primarily anti- subunits II and IV) and anti-III were by different mechanisms: the former, by inhibiting the uncoupled rate; the later, by stimulating the coupled rate. In experiments with H+ translocation, anti-oxidase was without effect, while anti-III was a potent inhibitor of proton pumping. These results are conclusive evidence for redox-linked proton extrusion from the vesicles by the oxidase (and its subunit III).

Redox-dependent accessibility of subunit V of cytochrome oxidase. A novel use of ELISA as a probe of intact membranes

Beef heart cytochrome c oxidase subunit V was isolated by a new one-step procedure. The product was homogeneous to 99% and immunogenically competent. The resulting antibodies inhibited the whole enzyme. A variation of ELISA (enzyme-linked immunosorbent assay) is described which, using a homogeneous antigen, probes the surface of intact membranes to a high degree of specificity. We showed that the subunit is accessible on the surface of inside-out mitochondrial inner membrane particles only when the particles were reduced with ascorbate and N,N,N',N'-tetramethyl-p-phenylene-diamine but is inaccessible on the surface of right-side-out particles regardless of the presence of reductants. These findings have implications with respect to the topography of the enzyme per se and in relation to its neighbors, and with respect to the degree of coupling between electron transport and proton pumping by the enzyme.

Heme-associated subunit complex of cytochrome c oxidase identified by a new two-dimensional gel electrophoresis

A Novel two-dimensional system (isoelectric focusing in the first dimension and sodium dodecyl sulfate-urea electrophoresis in the second) was used to determine the pI values of beef heart subunits of cytochrome c oxidase. The results identified a heme-associated complex of Subunits I, II, and IV. Conditions mitigate against migration of free heme.

Biosynthesis of mitochondrial membrane proteins: co-ordination with special reference to cytochrome c oxidase

This paper reviews mechanisms by which the rate of synthesis of subunits of mitochondrial inner membrane protein complexes and the assembly of these subunits are co-ordinated. Current models are evaluated and critically discussed in the light of some recent evidences. The focus is on the incorporation of cytoplasmically-synthesized cytochrome c oxidase subunits in the development of a newer model, which introduces some twists into a combination of several current ideas. A mechanism which governs both organized assembly and the co-ordination of rates of polypeptide synthesis is illustrated and the principles of the model are applied to the elucidation of some odd features of certain mutants. The possibilities that mitochondrial ATPase and cytochrome c reductase may also be synthesized and assembled according to this model are discussed.