Reconstructing mutational lineages in breast cancer by multi-patient-targeted single-cell DNA sequencing

Single-cell DNA sequencing (scDNA-seq) methods are powerful tools for profiling mutations in cancer cells; however, most genomic regions sequenced in single cells are non-informative. To overcome this issue, we developed a multi-patient-targeted (MPT) scDNA-seq method. MPT involves first performing bulk exome sequencing across a cohort of cancer patients to identify somatic mutations, which are then pooled together to develop a single custom targeted panel for high-throughput scDNA-seq using a microfluidics platform. We applied MPT to profile 330 mutations across 23,500 cells from 5 patients with triple negative-breast cancer (TNBC), which showed that 3 tumors were monoclonal and 2 tumors were polyclonal. From these data, we reconstructed mutational lineages and identified early mutational and copy-number events, including early TP53 mutations that occurred in all five patients. Collectively, our data suggest that MPT can overcome a major technical obstacle for studying tumor evolution using scDNA-seq by profiling information-rich mutation sites.

Abstract 6088: Reconstructing mutational lineages in breast cancer by multi-patient-targeted single cell DNA sequencing

Single cell DNA sequencing (scDNA-seq) methods are powerful tools for profiling mutations in cancer cells, however most genomic regions characterized in single cells are non-informative. To overcome this issue, we developed a Multi-Patient-Targeted (MPT) scDNA-seq sequencing method. MPT involves first performing bulk exome sequencing across a cohort of cancer patients to identify somatic mutations, which are then pooled together to develop a single custom targeted panel for high-throughput scDNA-seq using a microfluidics platform. We applied MPT to profile 330 mutations across 23,500 cells from 5 TNBC patients, which showed that 3 tumors were monoclonal and 2 tumors were polyclonal. From this data, we reconstructed mutational lineages and identified early mutational and copy number events, including early TP53 mutations that occurred in all five patients. Collectively, our data suggests that MPT can overcome technical obstacles for studying tumor evolution using scDNA-seq by profiling information-rich mutation sites.

Citation Format: Jake Leighton, Min Hu, Emi Sei, Funda Meric-Bernstam, Nicholas Navin. Reconstructing mutational lineages in breast cancer by multi-patient-targeted single cell DNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6088.

Abstract 2501: Delineating mutational lineages with single cell DNA sequencing using multi-patient specific panels

Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with high rates of metastasis. Although copy number aberrations (CNAs) and genome doubling have been extensively studied in relation to TNBC initiation, little is known regarding the timing and impact of point mutations during tumor initiation, outside of TP53. A major challenge in sequencing mutations in single cells is the significant cost of unbiased whole-exome analysis of many cells. To address this challenge, we developed an approach called multi-patient-panel (MPP) sequencing which involves first performing bulk deep-exome sequencing of many patient's tumors, after which hundreds of mutations are identified and pooled across patients to design a targeted panel for high-throughput single cell DNA sequencing. We applied MPP sequencing to profile 330 mutations across 23,000 single cells from 5 TNBC patients using a microdroplet system (Mission Bio). From this data we identified 1-4 major clonal subpopulations in each tumor which shared a common evolutionary lineage. Copy number data was inferred from the targeted panel coverage depth, which showed that CNAs were correlated with different subpopulations in the tumor. By integrating both the mutation and copy number data, we inferred phylogenetic lineages and identified the timing of mutations during primary tumor growth, which detected early truncal mutations (in addition to TP53) that were involved in the initiation of TNBC tumors. The MPP approach provides a powerful method to scale-up single cell DNA sequencing to tens of thousands of cells to detect mutations and infer cancer lineages and clonal substructure.

Citation Format: Jake Leighton, Min Hu, Alexander Davis, Emi Sei, Yong Wang, Nicholas Navin. Delineating mutational lineages with single cell DNA sequencing using multi-patient specific panels [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2501.

SIRT6-mediated transcriptional suppression of Txnip is critical for pancreatic beta cell function and survival in mice

AIMS/HYPOTHESIS

Better understanding of how genetic and epigenetic components control beta cell differentiation and function is key to the discovery of novel therapeutic approaches to prevent beta cell dysfunction and failure in the progression of type 2 diabetes. Our goal was to elucidate the role of histone deacetylase sirtuin 6 (SIRT6) in beta cell development and homeostasis.

METHODS

Sirt6 endocrine progenitor cell conditional knockout and beta cell-specific knockout mice were generated using the Cre-loxP system. Mice were assayed for islet morphology, glucose tolerance, glucose-stimulated insulin secretion and susceptibility to streptozotocin. Transcriptional regulatory functions of SIRT6 in primary islets were evaluated by RNA-Seq analysis. Reverse transcription-quantitative (RT-q)PCR and immunoblot were used to verify and investigate the gene expression changes. Chromatin occupancies of SIRT6, H3K9Ac, H3K56Ac and active RNA polymerase II were evaluated by chromatin immunoprecipitation.

RESULTS

Deletion of Sirt6 in pancreatic endocrine progenitor cells did not affect endocrine morphology, beta cell mass or insulin production but did result in glucose intolerance and defective glucose-stimulated insulin secretion in mice. Conditional deletion of Sirt6 in adult beta cells reproduced the insulin secretion defect. Loss of Sirt6 resulted in aberrant upregulation of thioredoxin-interacting protein (TXNIP) in beta cells. SIRT6 deficiency led to increased acetylation of histone H3 lysine residue at 9 (H3K9Ac), acetylation of histone H3 lysine residue at 56 (H3K56Ac) and active RNA polymerase II at the promoter region of Txnip. SIRT6-deficient beta cells exhibited a time-dependent increase in H3K9Ac, H3K56Ac and TXNIP levels. Finally, beta cell-specific SIRT6-deficient mice showed increased sensitivity to streptozotocin.

CONCLUSIONS/INTERPRETATION

Our results reveal that SIRT6 suppresses Txnip expression in beta cells via deacetylation of histone H3 and plays a critical role in maintaining beta cell function and viability.

DATA AVAILABILITY

Sequence data have been deposited in the National Institutes of Health (NIH) Gene Expression Omnibus (GEO) with the accession code GSE104161.

Generation of endoderm lineages from pluripotent stem cells

Definitive endoderm is the cellular precursor to respiratory- and digestive-related organs such as lungs, stomach, liver, pancreas and intestine. Endodermal lineage cells derived from pluripotent stem cells (PSCs) in vitro are a potentially unlimited resource for regenerative medicine. These cells are useful tools for studying the physiology, pathogenesis and medical therapies involving these tissues, and great progress has been achieved in PSCs differentiation protocols. In this review, we will focus on the most common and/or advanced differentiation strategies currently used in generating endodermal lineage cells from PSCs. A brief discussion about the effect of early definitive endoderm differentiation on the final development products will follow.

Extracellular Matrix and Integrins in Embryonic Stem Cell Differentiation

Embryonic stem cells (ESCs) are pluripotent cells with great therapeutic potentials. The in vitro differentiation of ESC was designed by recapitulating embryogenesis. Significant progress has been made to improve the in vitro differentiation protocols by toning soluble maintenance factors. However, more robust methods for lineage-specific differentiation and maturation are still under development. Considering the complexity of in vivo embryogenesis environment, extracellular matrix (ECM) cues should be considered besides growth factor cues. ECM proteins bind to cells and act as ligands of integrin receptors on cell surfaces. Here, we summarize the role of the ECM and integrins in the formation of three germ layer progenies. Various ECM–integrin interactions were found, facilitating differentiation toward definitive endoderm, hepatocyte-like cells, pancreatic beta cells, early mesodermal progenitors, cardiomyocytes, neuroectoderm lineages, and epidermal cells, such as keratinocytes and melanocytes. In the future, ECM combinations for the optimal ESC differentiation environment will require substantial study.

Modifiable factors that influence colorectal cancer lymph nodes sampling and examination

4047

Background: Colorectal cancer is the fourth most common malignancy in the United States. The single most important prognostic factor is lymph node involvement. Multiple guidelines recommend a minimum of 12 nodes should be sampled in order to insure accurate staging and treatment. However this standard of care requirement is not always achieved. The objective of this study is to identify potential modifiable factors that may explain this inadequacy between the optimal approach and routine practice. Methods: The medical charts of all patients treated for colorectal cancer stage I-III between 1999–2007 at Albert Einstein Medical Center were reviewed. The association between multiple variables and the presence of ≥12 lymph nodes reported were examined using logistic regression models. Results: A total of 337 patients were included; 173 (51%) had ≥12 lymph nodes retrieved with a mean of 12.7 (SD±7.6). Demographic characteristics: 78% older than 60 years old; 161 patients (47.8%) male; white (27%), black (67%) and other race (6%). Using a univariate analysis the following variables were statistically associated with ≥12 lymph nodes reported: Colon size (20.6±14.7 vs. 29.9±23.1 cm, P<.001); Mesocolon thickness (3.8±0.9 vs. 4.2±0.9 cm, P<.001); Tumor size (4.14±2.3 vs. 4.6±2.1, P=.03); Site of tumor (Right vs. Left, P<.001); Pathologist (P=.06); Pathologist's Assistant (P=.006); Type of surgery (Right or Sub-Total Colectomy vs. Others, P<.001), Individual Surgeon (P=.009). The results of the multivariate logistic regression analysis, adjusting for age, sex and race, are presented in the Table . Conclusions: This studied showed that multiple factors influence the number of lymph nodes sampled. The role of the surgeon, the pathologist and specially the pathologist's assistant are potentially improvable factors with appropriate education.

[Table: see text]

No significant financial relationships to disclose.

The public health surveillance of asthma

Asthma is a highly prevalent disease that affects the quality of life of many people in the United States. Yet there is limited descriptive epidemiological understanding of the disease, particularly at the state and local levels. Minimal surveillance of asthma is occurring across the country. Surveillance of a disease requires that public health workers have the ability to accurately identify cases, have access to needed data, and have adequate resources so that they can collect, assess, report, and use the data-all considerable challenges in the case of asthma. We consider four groups of questions that asthma surveillance should address: (1) How much asthma is there and what are the trends in asthma occurrence over time? (2) How severe is the asthma and what are the trends in asthma severity over time? (3) How well is asthma controlled and what are the trends in asthma management over time? (4) What is the cost of asthma? Because wise decision making in public health depends on the availability of appropriate data for program planning, implementation, and evaluation, we encourage increased surveillance of asthma in jurisdictions across the country.

Molecular controls of radiation-induced apoptosis in the neonatal rat kidney

The incidence of cell death due to radiation was examined in a neonatal in vivo model. Differences in the induction of apoptosis, amount of cell proliferation, S-phase cell death, Bcl-2 and p-53 expression could best be explained by the differences in the zonal state of differentiation and development. The present in vivo model may thus be useful in testing radiation therapies for renal cancer.

Radiation-induced apoptosis and gene expression in neonatal kidney and testis with and without protein synthesis inhibition

PURPOSE

To analyse the incidence of radiation-induced apoptosis, expression of two apoptosis-related genes, Bcl-2 and p53, and post-radiation levels of cell proliferation in the neonatal rat (4-5 days old) kidney and testis.

MATERIALS AND METHODS

Apoptosis was quantified in control or treated kidney or testis at 2, 4, 6, 8 and 24h after 5 Gy of whole body X-irradiation (n=4 per group). Morphology (light and electron microscopy) and DNA gel electrophoresis were used to assess apoptosis. Temporal and spatial expression of Bcl-2 or p53 were analysed using immunohistochemistry. Administration of cycloheximide (1.5mg/kg) was used to determine whether new protein synthesis had a role in induction of apoptosis. Tritiated thymidine uptake and autoradiography were used to indicate alterations in cell proliferation (radiolabel administered 1 h prior to tissue collection) or S-phase cells undergoing radiation-induced apoptosis (radiolabel administered 1 h prior to irradiation).

RESULTS

Apoptosis peaked at 4 h in the testis and 6 h in the kidney and was significantly higher in the renal nephrogenic zone than in the testis (p<0.05). Mitosis was almost completely negated after irradiation in both tissues. A higher proportion (almost fivefold) of the apoptotic cells died in S phase in the kidney than in the testis. Cycloheximide negated induction of apoptosis in the kidney, and markedly decreased apoptosis in the testis. Bcl-2 expression was highest in the differentiated zone of control kidneys and increased after irradiation in the nephrogenic zone, particularly near foci of apoptosis in developing nephrons. In the control testis, Sertoli cells had moderate expression of Bcl-2. After irradiation, there was complete absence of Bcl-2 expression in apoptotic Sertoli cells, with surviving cells increasing Bcl-2 expression. Irradiated kidney had more intense nuclear p53 expression compared with controls. In the testis, p53 that was present in controls continued to be expressed in surviving cells but not apoptotic cells in radiation-treated animals.

CONCLUSIONS

Unique differences can be identified between the incidence and biomolecular control of radiation-induced apoptosis in the normal neonatal kidney and testis. These results may find application for minimizing damage to these normal neonatal tissues in the development of, for example, cancer treatment regimens.

Expression and intracellular localisation of odorant receptors in mammalian cell lines using Semliki Forest virus vectors

Odorant receptors are members of the G protein-coupled receptor superfamily. They are expressed on the surface of cilia of olfactory neurons, where they bind ligand (odorant). Studies of the molecular mechanisms of olfaction are complicated by the extremely large number of receptor genes, and difficulties in pairing a particular mammalian receptor to a specific odorant ligand in vivo. Here we report expression and localisation studies of two rat odorant receptor genes (17 and OR5), and C. elegans odr-10, using the Semliki Forest virus (SFV) system. All receptors were epitope-tagged at the N- or C-terminus in order to facilitate their detection in infected cells, and determine the localisation and membrane-orientation of recombinant proteins. The immortalised mouse olfactory neuronal cell line OLF 442, rat cortical and striatal primary neuron cultures, and the baby hamster kidney (BHK) cells, were infected and tested. Immunofluorescence and confocal microscopy studies performed on permeabilised, non-permeabilised and native cells revealed that in BHK cells the rat receptors 17 and OR5 were not targeted to the plasma membrane and remained in the endoplasmic reticulum. In contrast, in the mouse olfactory cell line OLF 442 both rat receptors were correctly inserted into the plasma membrane. Similar results were obtained using primary neurons, indicating that like mature neurons, the immortalised OLF 442 cells are capable of providing for correct odorant receptor processing and targeting.

Phase II study of N-phosphonacetyl-L-aspartate, recombinant interferon-alpha, and fluorouracil infusion in advanced squamous cell carcinoma of the head and neck

BACKGROUND

5-Fluorouracil (5-FU), as a single agent, produces a 15% response rate in advanced squamous cell carcinoma of the head and neck (SCCHN). N-phosphonacetyl-L-aspartate (PALA) inhibits pyrimidine biosynthesis and increases incorporation of 5-FU metabolites into ribonucleic acid (RNA). Recombinant alpha interferon-2b (rIFN-alpha-2b) may inhibit 5-FU clearance and blunt reflex rise in thymidylate synthetase, therefore enhancing inhibition of the target enzyme of 5-FU.

METHODS

In an attempt to exploit their potential therapeutic synergy, we initiated a phase II trial combining PALA 250 mg/m2 by intravenous (IV) bolus day 1 with 5-FU 2600 mg/m2 24-hour IV infusion initiated 24 hours after PALA, followed by rIFNalpha-2b 10 million units (MU) by subcutaneous injection days 2, 3, and 4 in patients with advanced, measurable SCCHN incurable with surgery or radiotherapy. Treatment was repeated weekly; patients were assessed every 4-6 weeks. Pretreatment tumor specimens were analyzed for p53 mutations in exons 5-8 and for protein expression using the p53 polyclonal antibody CM-1.

RESULTS

Nineteen patients were enrolled from November 1991 through February 1994. Median age was 59 years (range, 31-72 years). All had previously received definitive radiotherapy, and all but two had undergone surgical resection. Seven patients (37%) had received prior adjuvant chemotherapy. Median time from initial diagnosis to protocol enrollment was 17 months (range, 5 months to 10 years). Median performance status (PS) was 1. Primary tumor sites included oral cavity (8 patients), larynx (7 patients), oropharynx (3 patients), and hypopharynx (1 patient). The median serum transferrin was 241 (range, 141-333). Sixteen patients (84%) had sufficient pretreatment biopsy material for p53 analysis. Patients received a median of 6 weeks of treatment (range, 2-30 weeks). Six patients (32%) in the absence of disease progression failed to finish the first 6 weeks of treatment: 3 died of pulmonary insufficiency or pneumonia and 3 were removed from study during the first 6 weeks due to toxicity. Grade 2-3 flulike symptoms occurred in 17 patients (89%); grade > or = 3 fatigue occurred in 12 patients (63%), and grade > or = 2 stomatitis occurred in 5 (26%). Gastrointestional toxicity was minimal and myelosuppression mild. Of 13 evaluable patients, there were 2 partial responses (15%) lasting 3 months and 20 months; 5 patients with stable disease lasting 2, 2, 2.5, 3, and 4.5 months; and 6 with disease progression. For all 19 patients, the overall response rate was 11%, the median survival was 6 months and 1-year survival rate 26%. Lower transferrin values (< or =241) were associated with shortened median survival 2.5 vs 11 months). Increased p53 protein expression but not p53 mutations in pretreatment specimens also predicted inferior survival (median, 6 vs 11 months) after enrollment in study (p = .0124).

CONCLUSIONS

Biochemical modulation of 5-FU by rIFNalpha-2b and PALA does not enhance its efficacy in patients with advanced SCCHN whose disease has progressed after prior radiotherapy. Serum transferrin and p53 protein expression segregate outcome in this group of uniformly treated patients.

Human mammary cancer cell lines and other epithelial cells cultured as organoid tissue in lenticular pouches of reinforced collagen membranes

A system has been developed for the culture of cells that provides conditions favoring the formation of tissues comparable to conditions existing in nature. The culture chamber is a lens-shaped pouch composed of two thin-walled, reinforced, waffled collagen membranes facing each other. The chamber is immersed in medium in a closed transparent container and incubated on a rocker. On histologic study, after days to weeks in culture, human mammary cancer cell lines BT-20, MCF-7, MDA-231, MDA-468, and T47D grow in the chamber as distinctive structured epithelial tissue. Dog kidney cell line MDCK grows as a papillary adenocarcinoma and rat bladder cancer line NBT-II as an epidermoid carcinoma; cells from clinical effusion tumors produce distinct tissue. Changes in histologic phenotype may be driven by molecular changes at the level of the genome. Resulting alteration of the biochemical functions essential for the integrity of specific durable tissue organization should alter or reset the pattern of tissue organization and of biological behavior, including malignancy and response to cytotoxic chemicals. Lenticular pouch culture promises to be an effective tool for exploring the molecular changes associated with histogenesis and malignancy.

Paclitaxel and carboplatin in the treatment of advanced non-small cell lung cancer

Based on the superior response rates (21% to 24%) of patients treated with single-agent paclitaxel (Taxol; Bristol-Myers Squibb Company, Princeton, NJ) in Eastern Cooperative Oncology Group and M.D. Anderson Cancer Center trials in non-small cell lung cancer (NSCLC) and on the superior 1-year survival rates of NSCLC patients treated with carboplatin in a randomized study of cisplatin combination and analogues, we initiated a phase II trial of paclitaxel/carboplatin in patients with stage IV or effusion-positive stage III NSCLC. Eligibility stipulated chemotherapy-naive patients with measurable disease, good performance status, and adequate hematologic, hepatic, and renal function. Previous radiotherapy was restricted to < or = 30% of marrow-bearing bone. Paclitaxel was initially given at 135 mg/m2 over 24 hours followed by carboplatin dosed to a targeted area under the concentration versus time curve (AUC) of 7.5, with treatment repeated at 3-week intervals for six cycles. Granulocyte colony-stimulating factor was introduced during the second and subsequent cycles, with the paclitaxel dose sequentially escalated in 40 mg/m2 increments to a maximum dose of 215 mg/m2 in patients with less than grade 4 granulocytopenia and less than grade 3 thrombocytopenia. Of 54 patients enrolled, 30 currently are evaluable for response, 23 for toxicity. Myelosuppression has been the principal toxicity, with grade 3 or 4 granulocytopenia occurring in 70% of patients after the first cycle. After the introduction of granulocyte colony-stimulating factor, granulocytopenia decreased to 37% during the second cycle and then consistently to 20% or lower during subsequent cycles. Only 22% of cycles have been delayed for 1 week or more. Neutropenic fever has occurred in five (5%) of 100 evaluable cycles. Other grade 3 or 4 toxicities include thrombocytopenia (13%), anemia (9%), fatigue (9%), and hemorrhagic cystitis (1%). The paclitaxel dose was boosted to 215 mg/m2 in 12 (70%) of 17 patients by cycle 3 or 4. At an AUC of 7.5, the median first-cycle carboplatin dose was 434 mg/m2 (range, 293 to 709 mg/m2). The objective response rate is 50%, with three complete, 12 partial, and five minor responses. We conclude that the paclitaxel/carboplatin combination is active in advanced NSCLC and, with AUC-based dosing of carboplatin, can be given at 3-week intervals. Although dose limiting at a paclitaxel dose of 135 mg/m2, granulocytopenia can be reduced substantially with granulocyte colony-stimulating factor, allowing sequential dose escalation of paclitaxel to 175 mg/m2 and 215 mg/m2 in 70% of patients receiving three or more cycles.

An ABC transporter in the mitochondrial inner membrane is required for normal growth of yeast

In an attempt to identify a mitochondrial ATP binding cassette (ABC) transporter, we have used the polymerase chain reaction to amplify 10 DNA fragments homologous to members of the ABC family from the yeast Saccharomyces cerevisiae. We disrupted five of the corresponding genes and found that one of the resulting null mutants barely grew on rich medium and failed to grow on minimal medium. This gene, termed ATM1, encodes a putative 'half-transporter' of 694 amino acids. Atm1p is synthesized with an N-terminal mitochondrial matrix-targeting signal and is located in the mitochondrial inner membrane, with its C-terminal ATPase domain exposed to the matrix. Cells lacking a functional ATM1 gene have an unstable mitochondrial genome and have white mitochondria that completely lack cytochromes. Atm1p is the first mitochondrial member of the ABC family to be identified and the only eukaryotic ABC transporter that has been shown to be necessary for normal cellular growth.

Exploring processes of organization of normal and neoplastic epithelial tissues in gradient culture

The biology of animal cells in culture is often studied in individual cells or in sheets of cells. The relevance of such studies to the intact animal is unclear, since the spatial conditions encountered by cells in animals is one of dense three-dimensional masses of cells, with limits to migration, and with gradients both of diffusion of metabolites and of morphologic maturation. These spatial requisites have gradually been met in culture. A brief account describes sponge matrix culture for three-dimensional growth and unilaminar, bilaminar, and radial histophysiologic gradient cultures. Some of the common neoplastic abnormalities of surface epithelial tissues are considered. Proposals for investigating the histokinetic mechanisms regulating some epithelial tissue processes are suggested. In the most recent development of gradient culture methods, a thin permeable transparent collagen membrane is intrinsically strengthened by producing a waffle membrane pattern for histophysiologic gradient culture.

Structural biology of epithelial tissue in histophysiologic gradient culture

Epithelial cells proliferate, forming organized tissues, when positioned in the lumen of a thin-walled, transparent, elongated cylindrical, cystlike culture chamber. The closed chamber, 2.5 mm in diameter and 25 mm long, bathed in medium, incubated with continuous gentle agitation, enables the inoculum to exchange metabolites including oxygen by diffusion across the thin, nylon filament-reinforced collagen membrane wall of the chamber. After periods of culture of a week or more, using inocula derived from urothelium, the inner surface of the cystic chamber is lined by a stratified epithelium. Proliferation of cells is seen in the basal zone, which is attached to the collagen substrate. The development of the model is briefly described. Some of the applications of the procedure are illustrated using cell lines, chick embryo tissues, and clinical tissues. Implications of the procedure are considered for studying categories of tissue biology, e.g., problems of aging, neoplasia, and toxicology.

Selective immunosuppression by administration of major histocompatibility complex (MHC) class II-binding peptides. I. Evidence for in vivo MHC blockade preventing T cell activation

Draining lymph node cells (LNC) from mice immunized with hen egg white lysozyme (HEL) display at their surface antigen-MHC complexes able to stimulate, in the absence of any further antigen addition, HEL peptide-specific, class II-restricted T cell hybridomas. Chloroquine addition to these LNC cultures fails to inhibit antigen presentation, indicating that antigenic complexes of class II molecules and HEL peptides are formed in vivo. MHC class II restriction of antigen presentation by LNC from HEL-primed mice was verified by the use of anti-class II monoclonal antibodies. Coinjection of HEL and the I-Ak-binding peptide HEL 112-129 in mice of H-2k haplotype inhibits the ability of LNC to stimulate I-Ak-restricted, HEL 46-61-specific T cell hybridomas. Similar results are obtained in mice coinjected with the HEL peptides 46-61 and 112-129. Inhibition of T hybridoma activation can also be observed using as antigen-presenting cells irradiated, T cell-depleted LNC from mice coinjected with HEL 46-61 and HEL 112-129, ruling out the possible role of either specific or nonspecific suppressor T cells. Inhibition of T cell proliferation is associated with MHC-specific inhibition of antigen presentation and with occupancy by the competitor of class II binding sites, as measured by activation of peptide-specific T cell hybridomas. These results demonstrate that administration of MHC class II binding peptide competitors selectively inhibits antigen presentation to class II-restricted T cells, indicating competitive blockade of class II molecules in vivo.

Expression of messenger RNA for insulin-like growth factors and insulin-like growth factor binding proteins by experimental breast cancer and normal breast tissue in vivo

We report the expression of insulin-like growth factors (IGFs) and their binding proteins (IGFBPs) by breast cancer cells and normal breast tissue in vivo. N-nitrosomethyl-urea (NMU)-induced rat mammary tumors synthesize mRNAs for IGF-II and IGFBP-2, -3, and -4. In contrast, normal lactating breast contains only IGFBP-2 and IGF-II messages; IGFBP-3 and -4 mRNAs are absent in this tissue. IGF-I and IGFBP-1 mRNAs are not expressed in either NMU tumors or in normal breast. This is the first report of in vivo expression of IGFBPs and IGF-II messages in breast tumors.

Radial histophysiologic gradient culture chamber: rationale and preparation

Histophysiologic gradient culture methods reconstitute important spatial relationships that occur in nature between a parenchyma and its supporting stroma. At the epithelial-stromal interface, epithelia are firmly attached to the stromal substrate, initiation of renewal takes place, and metabolites are exchanged by a process of diffusion between epithelium and substrate. Other spatial imperatives characteristic of stratified epithelium are high density of cells, gradients of maturation, and continuity of epithelia along the entire course of the stromal-parenchymal interface. In radial gradient culture these relationships of epithelial cells, and supporting substrates are reconstituted. The culture chamber consists of a thin-walled cylinder, 2 to 3 mm in diameter and 3 cm long. The wall is a transparent collagen membrane in whose substance is embedded a reinforcing nylon mesh. To prepare a culture, one end of the cylinder is ligated, 1 or 2 particulate inocula are inserted in the open end of the cylinder, guided toward the ligature, and the open end is ligated. Subsequently, during incubation in a container with medium, the explants attach and proliferate. Proliferation and migration result in the cylinder being completely lined by a complex organoid tissue with structural characteristics of the original tissue. The tissue patterns in radial gradient culture of two human cell lines, RT-4, a bladder cancer, and 87 x 50, an ovarian cancer, are illustrated.

Comparison of structural requirements for interaction of the same peptide with I-Ek and I-Ed molecules in the activation of MHC class II-restricted T cells

We have analyzed the interaction of the hen egg-white lysozyme (HEL) peptide 107-116 with the MHC class II molecule I-Ek, using truncated and single residue substitution analogues to measure activation of I-Ek-restricted, 107-116-specific T cell hybridomas and competition for Ag presentation by I-Ek molecules. These results have been compared with previous findings on the interaction of the same peptide with the I-Ed molecule. Stimulation of T cell hybridomas by truncated peptides defines the sequence 108-116 as the minimum epitope necessary for activation of both I-Ek- and I-Ed-restricted T cell hybridomas. Substitution analysis pinpoints three residues (V109, A110, and K116) in the sequence 108-116 as being critical for binding to I-Ek molecules and demonstrates the involvement of most other residues in recognition by T cells. Results previously obtained for binding of HEL 107-116 to I-Ed molecules indicated that peptide residues R112, R114, and K116 were critical for interaction with I-Ed. Comparison of these results indicates a difference in the likely MHC contact residues between the HEL sequence 108-116 and I-Ed or I-Ek molecules, suggesting that the same HEL peptide assumes a different conformation in the binding site of these two MHC molecules. This in turn affects residues interacting with the specific T cell receptor. According to the hypothetical tridimensional structure predicted for class II molecules, the difference in MHC contact residues observed within the sequence 108-116 can be related to polymorphic amino acids in the binding site of I-Ek and I-Ed molecules. A search through published binding data for a common pattern in this and other I-Ek-binding peptides has permitted us to derive a possible motif for predicting peptide binding to I-Ek molecules. This putative motif was tested by determining binding to I-Ek of an unbiased panel of about 150 synthetic peptides. Binding data indeed demonstrate the presence of this motif in the majority of good binders to I-Ek molecules.

Comparison of structural requirements for interaction of the same peptide with I-Ek and I-Ed molecules in the activation of MHC class II-restricted T cells

We have analyzed the interaction of the hen egg-white lysozyme (HEL) peptide 107-116 with the MHC class II molecule I-Ek, using truncated and single residue substitution analogues to measure activation of I-Ek-restricted, 107-116-specific T cell hybridomas and competition for Ag presentation by I-Ek molecules. These results have been compared with previous findings on the interaction of the same peptide with the I-Ed molecule. Stimulation of T cell hybridomas by truncated peptides defines the sequence 108-116 as the minimum epitope necessary for activation of both I-Ek- and I-Ed-restricted T cell hybridomas. Substitution analysis pinpoints three residues (V109, A110, and K116) in the sequence 108-116 as being critical for binding to I-Ek molecules and demonstrates the involvement of most other residues in recognition by T cells. Results previously obtained for binding of HEL 107-116 to I-Ed molecules indicated that peptide residues R112, R114, and K116 were critical for interaction with I-Ed. Comparison of these results indicates a difference in the likely MHC contact residues between the HEL sequence 108-116 and I-Ed or I-Ek molecules, suggesting that the same HEL peptide assumes a different conformation in the binding site of these two MHC molecules. This in turn affects residues interacting with the specific T cell receptor. According to the hypothetical tridimensional structure predicted for class II molecules, the difference in MHC contact residues observed within the sequence 108-116 can be related to polymorphic amino acids in the binding site of I-Ek and I-Ed molecules. A search through published binding data for a common pattern in this and other I-Ek-binding peptides has permitted us to derive a possible motif for predicting peptide binding to I-Ek molecules. This putative motif was tested by determining binding to I-Ek of an unbiased panel of about 150 synthetic peptides. Binding data indeed demonstrate the presence of this motif in the majority of good binders to I-Ek molecules.

Cyclic AMP mimics, but does not mediate, interleukin-1- and tumour-necrosis-factor-stimulated phospholipase A2 secretion from rat renal mesangial cells

We have previously shown that recombinant interleukin 1 (IL-1) and recombinant tumour necrosis factor (TNF) synergistically stimulate phospholipase A2 release from mesangial cells. We now report that treatment of mesangial cells with the beta-agonist salbutamol, prostaglandin E2 (PGE2), cholera toxin or forskolin, which all activate adenylate cyclase, increased release of phospholipase A2 activity. Likewise, addition of a membrane-permeant cyclic AMP (cAMP) analogue or the phosphodiesterase inhibitor 3-isobutyl-1-methylxanthine enhanced release of phospholipase A2 activity from mesangial cells. There was a lag period of about 8 h before a significantly enhanced secretion could be detected. Furthermore, actinomycin D or cycloheximide completely suppressed cAMP-stimulated secretion of phospholipase A2. Angiotensin II, the phorbol ester phorbol 12-myristate 13-acetate, the Ca2+ ionophore A23187 and a membrane-permeant cGMP analogue did not stimulate phospholipase A2 release from the cells. Treatment with indomethacin completely inhibited IL-1 beta- and TNF-stimulated PGE2 synthesis, without having any effect on phospholipase A2 secretion, thus excluding cytokine-induced PGE2 synthesis as the mediator of phospholipase A2 release. Neither IL-1 beta nor TNF induced any increase in intracellular cAMP in mesangial cells. Furthermore, incubation of the cells with 2',5'-dideoxyadenosine, an inhibitor of adenylate cyclase, did not block cytokine-stimulated phospholipase A2 secretion. In addition, IL-1 beta and TNF synergistically interacted with forskolin to stimulate phospholipase A2 release from the cells. The protein kinase inhibitors H-8, staurosporine, K252a and amiloride inhibited IL-1 beta- and TNF-stimulated phospholipase A2 secretion. However, high concentrations that inhibit other protein kinases were needed. These observations suggest that IL-1 beta and TNF cause secretion of phospholipase A2 by a mechanism independent of cAMP. The signalling pathways used by IL-1 beta and TNF may involve a protein kinase that is probably different from protein kinase A or protein kinase C.

Recovery of cyclic antidepressants with gastric lavage

The role of lavage fluid volume in recovery of cyclic antidepressant with gastric lavage was determined in 13 patients treated for moderate to severe cyclic antidepressant intoxication. An orogastric tube was placed, gastric contents aspirated, and gastric lavage performed with 60 to 180 mL aliquots of tap water or 0.9% NaCl for irrigation. A volume of 12.8 +/- 4.4 liters of lavage fluid was instilled, and 97.6 +/- 6.9% of this volume was recovered. The recovered aspirate and lavage fluid were inspected for the presence of particulate matter and saved in 4 to 5 liter collections. Determination of cyclic antidepressant and metabolite concentrations was performed using gas chromatography-mass spectrometry, and the amount of cyclic antidepressant recovered was calculated. The mean total amount recovered was 110 mg and ranged from 2.4 mg to 342 mg. Of the total amount recovered, 88% +/- 13% was recovered in the first 4 to 5 liters of lavage fluid. An estimate of the dose ingested was available in 7 patients, with 8.7% (0.4% to 21.7%) of the estimated dose recovered by lavage. There were no cases of significant drug recovery in clear lavage fluid. We conclude that if gastric lavage is undertaken in cyclic antidepressant intoxications, it should utilize 5 liters initially and then continue only if particulate matter is seen.

Reconstitution of the malignant phenotype of genitourinary cancer in gradient culture

The diagnosis of cancer is made on histologic examination by recognizing the characteristics of the malignant phenotype, i.e. abnormal cells in abnormal groupings, often in abnormal locations. Histophysiologic gradient culture reconstitutes conditions that meet the spatial imperatives of tissues in nature. A variety of carcinomas arise in the genitourinary system involving both glandular and stratified epithelium. To be considered here are the contrasting polarizations of proliferation of normal and neoplastic rat urothelium, the continuity of sheets of epithelium in nature, the poorly understood stable and unstable interepithelial boundaries, and the formation of organoid endocrinelike tissue in histophysiologic gradient culture of normal human amnion epithelium.

The National WIC Evaluation: evaluation of the Special Supplemental Food Program for Women, Infants, and Children. VI. Study of infants and children

The major associations with the Special Supplemental Food Program for Women, Infants, and Children (WIC) in preschool children were better dietary intake associated with current WIC participation, especially for Fe, vitamin A, and vitamin C, but there were no increases in energy intake and, after infancy, no residual benefits from past WIC participation; strongest dietary effects among children who were poor, black, or in single-parent or large families (children lost to WIC were as needy as those currently enrolled); shorter stature, suggesting effective targeting (with enrollment in utero there was no parallel deficit in head circumference, which is consistent with results for newborns); better immunization and more frequent regular source of health care but no more frequent use of preventive health services; and better vocabulary with WIC participation begun in utero; better digit memory with entry into the program after the first birthday (differences that emerged only after statistical adjustment for sociodemographic factors); and more advantageous child behavior (NS).

The National WIC Evaluation: evaluation of the Special Supplemental Food Program for Women, Infants, and Children. IV. Study methodology and sample characteristics in the longitudinal study of pregnant women, the study of children, and the food expenditures study

The longitudinal study of pregnant women enrolled a national probability sample of 5,205 women first certified for WIC and 1,358 comparable low-income pregnant women in 174 WIC clinics located in 58 areas in the contiguous 48 states and in 55 prenatal clinics without WIC programs in counties with low program coverage. The women completed 24-h dietary recalls, histories of food expenditures, health care utilization, health and sociodemographic status, and anthropometric assessment. At late-pregnancy follow-up 3,967 WIC and 1043 control women were interviewed and 853 WIC and 762 control women completed 1-wk food expenditure diaries. Birth outcome was abstracted (from hospital records) for 3,863 WIC and 1058 control women. Anthropometry, dietary intake, health, and use of health services were related to WIC among 2,619 random low-income preschoolers. Psychological development was assessed in 526 children aged 4 and 5 y. Control women had higher income, education, and employment status; therefore, WIC program benefits probably were underestimated.

The National WIC Evaluation: evaluation of the Special Supplemental Food Program for Women, Infants, and Children. I. Background and introduction

The Special Supplemental Food Program for Women, Infants, and Children (WIC) aims to improve the nutrition and health of low-income, nutritionally at-risk pregnant women and preschool children with supplemental food, nutrition education, and coordination of health care. Started in 1972, it recently served greater than 3.4 million persons monthly and at a cost of $1.66 billion annually. The National WIC Evaluation (NWE) consisted of four studies: The historical study estimated changes in birth outcome attributable to WIC from 1972 to 1980 in 19 states and the District of Columbia from WIC program data and vital statistics. The longitudinal study of pregnant women compared dietary intake, weight gain, anthropometry, duration of gestation, birth weight, and infant length and head circumference between a representative national sample of WIC participants and economically comparable women. The cross-sectional study of preschool children related WIC to dietary intake, anthropometry, and psychological development. The food expenditures study estimated the impact of WIC on family grocery and other food expenditures.

The National WIC Evaluation: evaluation of the Special Supplemental Food Program for Women, Infants, and Children. II. Review of past studies of WIC

We reviewed past work relating WIC benefits to birth weight, perinatal and infant survival, anemia, child growth, and dietary intake. Despite many uncertainties, the probable range of reduction in the rate of low birth weight was approximately 1-2% and the increase in mean birth weight ranged from 0 to approximately 60 g. There was too little information to securely estimate effects of WIC on perinatal and infant mortality nor on the dietary intake of women or children. Although the number of studies was small, there probably were important effects of WIC on rates of childhood anemia. There is too little evidence to come to any conclusion on effects during pregnancy. There is little evidence that the WIC program has affected children's linear growth.

The National WIC Evaluation: evaluation of the Special Supplemental Food Program for Women, Infants, and Children. V. Longitudinal study of pregnant women

The major associations with the Special Supplemental Food Program for Women, Infants, and Children (WIC) in pregnancy were increased intake of protein, iron, calcium, and vitamin C (four of five targeted nutrients) and of energy, magnesium, phosphorus, thiamin, riboflavin, niacin, vitamin B-6, and vitamin B-12; reversal of low weight gain in early pregnancy; smaller fat stores in late pregnancy; reduced frequency of premature rupture of the uterine membranes; larger infant head circumference with no effect on birth weight and length; increased birth weight and head circumference with better program quality; and lower fetal mortality of appreciable but not significant magnitude. Incremental energy intake was comparable to that in most small-scale supplementation trials. There was no evidence of effects on frequency of prenatal care, use of alcohol or tobacco, the intention to breast-feed, or the rate of breast-feeding. Maternal alcohol intake was associated with depressed infant head circumference, over and above effects on birth weight and length.

Interactions between newly formed endothelial channels and carcinoma cells in plasma clot culture

Bovine capillary endothelial cells (BCEC), cultured in suspension on a rotary shaker, formed aggregates ranging from 50 to 300 micron in diameter. In plasma clot these aggregates sprouted in multiple directions and gave rise to vascular channels. Aggregates of the squamous cell carcinoma line of rat bladder NBT-II-81, cultured in plasma clot, formed solid spheroids that grew slowly by expansion. When cultured together with BCEC, however, NBT-II-81 infiltrated the plasma clot extensively. The tumor cells, after establishing contacts with the vascular channels, spread into the fibrin meshwork using the subendothelial space as their path of propagation. Endothelial cells that were separated from the surrounding matrix by invading tumor cells degenerated, leaving behind channels lined only by neoplastic epithelium. The adhesive properties of the subendothelial matrix were studied by seeding NBT-II-81 cells on dishes coated with the extracellular matrix produced by BCEC. Tumor cells attached readily and in large numbers to dishes coated with the subendothelial matrix. In contrast they attached poorly to dishes coated with fibrin. We conclude that the spread of carcinoma cells into plasma clot is markedly enhanced by endothelial channels, developed in the absence of blood flow. The production of a highly adhesive extracellular matrix by the capillary endothelium during angiogenesis may represent an important element in the preferential growth of the tumor along the vascular route.

Evaluation of an enkephalin analog in men with castor oil-induced diarrhea

This study was a parallel, double-blind, placebo-controlled evaluation of acute doses of nifalatide, an enkephalin analog, in subjects with castor oil-induced diarrhea. Seventy-two subjects completed the study. The time to first stool after castor oil administration was significantly greater after the 16 and 48 mg doses of nifalatide as compared with placebo dosing. The same doses of nifalatide also decreased the overall stool frequency, the frequency of abdominal cramping, and the incidence of nausea and vomiting. There were no clinically significant, drug-related changes in the physical examination results, ECG, vital signs, or clinical laboratory parameters. The only increased adverse experiences that appeared to be related to the drug were dizziness and mild dry mouth.

Radial gradient culture on the inner surface of collagen tubes: organoid growth of normal rat bladder and rat bladder cancer cell line NBT-II

Radial histophysiologic gradient culture uses thin walled, permeable collagen tubes to house inocula in the form of either tissue explants, aggregates of cells, or dissociated cells. The outgrowth from these inocula spreads on the inner surface of the cylindrical tube, completely lining the lumen. Metabolites are exchanged through the wall of the collagen tube by diffusion from the pool of medium surrounding the cylinder. Urothelial cells form organoid stratified epithelium. A histophysiologic gradient occurs with the basal surface of the epithelium attached to the collagen wall. At this interface, for normal bladder, the initiation of epithelial renewal is seen in the basal zone, as shown by incorporation of tritiated thymidine. The simulation of conditions in nature is attained by the exchange of metabolites between the pool of medium and the basal zone of the epithelium. NBT-II appears as two concentric stratified epithelia. Isotopic labelling is seen throughout the epithelium attached to the collagen membrane. In the superficial stratified epithelium remnants of nuclei are seen without isotopic labelling. Preparation of living cultures and, after fixation, of histologic sections is technically easy.

The chick embryo in toxicology: an alternative to the rabbit eye

The chorioallantoic membrane (CAM) of the chick embryo is readily accessible for experimentation. It is a complete tissue that responds to injury with classical inflammatory reactions. It is limited to the late phase of embryologic life, and is without the sense of pain. Focal topical application of various household products onto the CAM results in local injury and reactions that differ in severity from one product to another. For any single product, tested as a sequence of dilutions on a series of membranes, the CAM responds with decreasing intensity that parallels the decreasing dosage. The membrane is prepared for study according to the method of Zwilling (Transplantn Bull 1959, 6, 115). The test material is applied in a Teflon ring to the 14-day-old CAM, to localize the application site. The macroscopic response is scored on day 17 of incubation. The results of analysis of histological preparations are found to correlate with macroscopic appearance. When a series of preparations was ranked according to the severity of the response each induced on the CAM, there was a good correlation with the ranking of the same preparations in the Draize test.

Characterized full-length and truncated plasmid clones of the crystal protein of Bacillus thuringiensis subsp. kurstaki HD-73 and their toxicity to Manduca sexta

Bacillus thuringiensis subsp. kurstaki HD-73 produces a crystal protein which is lethal to many lepidopteran larvae. The gene encoding this crystal protein has been isolated from a 75-kb plasmid and engineered into a recombinant Escherichia coli plasmid for analysis. The complete nucleotide sequences of the coding region and 387-bp 5' and 376-bp 3' to the coding region have been determined. The 3537-bp of the coding region specify a protein of Mr 133 330. The full-length gene and several 3' -truncated derivatives of the gene were examined in both E. coli and in an E. coli minicell-expression system to determine if the carboxy end of the protein is essential for toxicity. The results presented here provide the primary structure of the crystal protein gene and show that the N-terminal 68-kDal peptide is toxic, but at a lower level than the full-length gene product.

Organoid structure of normal rat bladder in unilaminar and bilaminar histophysiologic gradient culture : methods and observations

In lining epithelium of mammals certain recurrent architectural patterns are recognized that may be critical for epithelial organization in culture. Among these structural imperatives are three dimensional growth, restricted migration of cells, histophysiologic gradients, and continuity of epithelial membranes. Histophysiologic gradient culture procedures have been developed to comply with requirements suggested by normal tissue architecture. In a small chamber, 5 mm diam, epithelium grows attached to a thin permeable transparent collagen membrane or sandwiched between two apposed collagen membranes. The chamber is held in a plastic capsule so that metabolic exchange is limited to substances that diffuse across the collagen membranes to the adherent basal layer of epithelium. On a single membrane after 2 wk of growth, normal urothelium appears as a diffusely hypercellular urothelium, 6 to 10 cells thick. As the culture period is extended by 2 or more wk, multiple nodules of urothelium extend from the basal surface into the subepithelial space between the epithelium and the collagen membrane. Normal bladder, cultured between two apposed collagen membranes, gives rise in a few days to confluent epithelium that contains many extracellular cysts. Through an apparent merging of cysts, after 2 wk the urothelium appears as a highly organoid structure, a flattened cyst lined by completely stratified polarized urothelium. Such microbladders consist of a stratified epithelium without interruption of continuity. With histophysiologic gradient culture, processes in carcinoma and precursor lesions are accessible to study at the level of tissue organization.

The propagation of cancer, a process of tissue remodeling

Effective study of the malignant phenotype at the tissue level requires model systems that are intelligible both to cell biologists and to pathologists, and that also observe the spatial imperatives intrinsic to tissues in nature. Malignant cells commonly appear in multicellular units, and growth of tumor tissue is seen as an increase in the number of cells and multicellular units. The supporting stroma frequently has an abnormal appearance, and this component of the tissue also increases in mass as the tumor enlarges and spreads. The direction of invasion is influenced by the direction of available metabolites. Histophysiologic gradient culture complies with nature's spatial rationale, since at the substrate-parenchymal interface three functions coincide. These are anchorage, initiation of epithelial renewal, and complete exchange of metabolites. Our model system provides a setting for reconstructing and manipulating many features of the malignant phenotype seen in cancer tissues in nature, such as abnormalities in the sequence of maturation of stratified epithelium, hyperplasias, dysplasias, interaction between different types of epithelium, aggregate formation, tumor angiogenesis, and neoplastic blockade.

Mitral valve E point to ventricular septal separation in infants and children

This investigation establishes heretofore unavailable norms that permit clinical application of mitral valve E point to ventricular septal separation (EPSS) as an ejection phase index in infants and children. The study consisted of 105 normal subjects (1 day through 15 years of age, mean 7.4 years) and 67 patients of comparable age. Fifty-seven patients had increased left ventricular (LV) volume with normal function (ventricular septal defect or patent ductus arteriosus) and 10 patients had increased LV volume with depressed function (dilated cardiomyopathy). In normal subjects, EPSS was 2.5 +/- 1.7 mm and "normalized" EPSS, that is, the ratio of EPSS to end-diastolic dimension (EPSS/EDD), was 0.08 +/- 0.06 (mean +/- standard deviation); there was no correlation between either of these indexes and age, body surface area, height or weight. In patients with ventricular septal defect or patent ductus arteriosus, or both, the EPSS and EPSS/EDD were similar to those of normal subjects (3.2 +/- 2.3 mm and 0.09 +/- 0.06 mm, respectively). In patients with dilated cardiomyopathy, these indexes were significantly increased (p greater than 0.05) (EPSS 16.5 +/- 5.1 mm; EPSS/EDD 0.39 +/- 0.09). The data provide normal values for EPSS and EPSS/EDD in infants and children and show that these indexes are independent of age, body surface area, height or weight. Mitral valve EPSS and EPSS/EDD can now be used in pediatric echocardiography as a simple, practical and accurate means of separating normal from abnormal LV function.