Strategic discussion on funding and access to therapies targeting rare diseases in Spain: an expert consensus paper

BACKGROUND

In recent years, significant advances have been made in the field of rare diseases (RDs). However, there is a large number of RDs without specific treatment and half of these treatments have public funding in Spain. The aim of the FINEERR project was to carry out a multidisciplinary strategic discussion on the challenge of funding and access to RD-targeted drugs in Spain, in order to agree on specific proposals for medium-term improvement and hence support decision-making in the Spanish National Healthcare System (SNHS).

RESULTS

The FINEERR Project was organized around a CORE Advisory Committee, which provided an overview, agreed on the design and scope of the project, and selected the members within each of four working groups (WG). Overall, 40 experts discussed and reached a consensus on different relevant aspects, such as conditioning factors for initial funding and access, evaluation and access to RD-targeted therapies, funding of these therapies, and implementation of a new funding and access model. From these meetings, 50 proposals were defined and classified by their level of relevance according to the experts. A descriptive analysis of responses was performed for each proposal. Thereafter, experts completed another questionnaire where they ranked the 25 most relevant proposals according to their level of feasibility of being implemented in the SNHS. The most relevant and feasible proposals were to improve: process of referral of patients with RDs, control over monitoring mechanisms, and communication between healthcare professionals and patients.

CONCLUSIONS

The FINEERR project may provide a starting point for stakeholders involved in the process of funding and access to RD-targeted therapies in Spain to provide the necessary resources and implement measures to improve both the quality of life and life expectancy of patients with RDs.

Abstract 3440: Novel in vitro TME platform for rapid cancer therapeutic and target discovery

The tumor microenvironment (TME) plays an important role in malignances as tumors react with a multitude of changes and microenvironmental cues. TME components modulate tumor profiles and treatment responses, thereby affecting sensitivity to anti-cancer agents. The limited clinical success of therapeutics, including immunotherapies, emphasizes an unmet need to identify new targets and develop preclinical platforms to accelerate anti-cancer drug discovery. Although in vitro methods are essential in early drug development, standard approaches, which do not capture the complexity of TME, have been historically favored for both discovery and evaluation of potential therapeutics.

Resonant's IMPACT TME platform couples proprietary high-fidelity TME models with deep data-driven analytics for rapid and cost-effective discovery of novel targets and antibody-based therapeutics. Target and candidate selection is based upon a biology-forward approach driven by live animal immune systems and functional screening prior to target identification. Identified candidates are then prioritized via integration of publicly available information with internal functional and multi-omic data. Resultant targets display attributes, such as tumor selectivity and immune-modulatory capabilities, that are amenable to several therapeutic modalities, including antibody-drug conjugates (ADCs) and bispecifics. To date, Resonant has interrogated a variety of solid tumor types and thousands of candidates resulting in an expanding library of actionable antibodies and targets. Representative examples of in vitro and in vivo efficacy of selected candidates derived from the IMPACT TME platform are presented, highlighting their individual potential and validating the Resonant approach. As technological advances transform the landscape of therapeutics, the need for novel targets is burgeoning, and Resonant’s TME-driven platform provides a valuable tool to meet these demands.

Citation Format: Polina R. Matre, Byung-Kwon Choi, Oliver Delgado, John K. Westwick. Novel in vitro TME platform for rapid cancer therapeutic and target discovery [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 3440.

Mutational Activation of the NRF2 Pathway Upregulates Kynureninase Resulting in Tumor Immunosuppression and Poor Outcome in Lung Adenocarcinoma

Activation of the NRF2 pathway through gain-of-function mutations or loss-of-function of its suppressor KEAP1 is a frequent finding in lung cancer. NRF2 activation has been reported to alter the tumor microenvironment. Here, we demonstrated that NRF2 alters tryptophan metabolism through the kynurenine pathway that is associated with a tumor-promoting, immune suppressed microenvironment. Specifically, proteomic profiles of 47 lung adenocarcinoma (LUAD) cell lines (11 KEAP1 mutant and 36 KEAP1 wild-type) revealed the tryptophan-kynurenine enzyme kynureninase (KYNU) as a top overexpressed protein associated with activated NRF2. The siRNA-mediated knockdown of NFE2L2, the gene encoding for NRF2, or activation of the NRF2 pathway through siRNA-mediated knockdown of KEAP1 or via chemical induction with the NRF2-activator CDDO-Me confirmed that NRF2 is a regulator of KYNU expression in LUAD. Metabolomic analyses confirmed KYNU to be enzymatically functional. Analysis of multiple independent gene expression datasets of LUAD, as well as a LUAD tumor microarray demonstrated that elevated KYNU was associated with immunosuppression, including potent induction of T-regulatory cells, increased levels of PD1 and PD-L1, and resulted in poorer survival. Our findings indicate a novel mechanism of NRF2 tumoral immunosuppression through upregulation of KYNU.

Dynamic testing in columns for soil heavy metal removal for a car park SUDS

The increase in urban runoff brought about by a rise in impermeable surfaces has triggered the alteration and pollution of many aquatic systems. The overall goal of this research was to design a 'Sustainable Urban Drainage System' (SUDS) for the retention of heavy metals from a car park consisting of mixing autochthonous soil (70%) with sand (30%) to improve the hydrological conductivity and adsorption capacity. To quantify the retention of metals we characterize the adsorption kinetics and isotherms of the soil mixture and perform dynamic experiments. The proposed methodology allowed us to work out the amount of heavy metal retention by the adsorbent and the retention mechanisms. The retention capacity of the adsorbent mixture was as follows: Cr³⁺ ≈ Cu²⁺ ≫ Zn²⁺ > Ni²⁺ > Cd²⁺. Chromium and copper ions were mainly retained by precipitation, whereas zinc, nickel and cadmium were retained by ionic exchange with calcium ions that saturate the soil colloids. The soil mixture buffered pH was found to change when fed with an acid solution of metallic ions.

Abstract 1447: Aberrant tryptophan catabolism marked by high kynureninase expression contributes to immunosuppression and poor outcome in lung adenocarcinoma

Low tryptophan levels promote tumor immune evasion by suppressing immune function. Elucidation of the immunomodulatory effects of altered tryptophan catabolism has relevance to cancer immunotherapy. Previous studies have largely focused on the role of the rate-limiting enzyme indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan depletion in the microenvironment. However, IDO1 levels are highly heterogeneous in different cancers, and numerous other downstream tryptophan catabolites have also been shown to have immunomodulatory activity. We surveyed the proteomes of 123 cancer cell lines for regulators of tryptophan metabolism which revealed overexpression of kynureninase (KYNU) in KEAP1 mutant lung adenocarcinomas. Functional analysis indicated that KYNU expression is regulated through nuclear factor, erythroid 2-like (Nrf2) activation. KYNU-high cell lines exhibited increased secretion of KYNU-derived anthranilate/3-hydroxyanthranilate. Ex-vivo studies using isolated PBMCs demonstrated that 3-hydroxyanthranilate reduced CD8+ T-cell viability. KYNU mRNA expression in three independent datasets of lung adenocarcinomas and additionally KYNU protein expression in lung adenocarcinoma tissue microarrays revealed that high KYNU expression predicts poor survival and disease recurrence. Our findings indicate that KYNU promotes immune suppression and is an independent prognostic marker for lung adenocarcinoma.

Citation Format: Edwin J. Ostrin, Johannes F. Fahrmann, Ichidai Tanaka, Muge Celiktas, Clemente Aguilar, Mitzi Aguilar, Jennifer B. Dennison, Eunice Murage, Satyendra C. Tripathi, Oliver Delgado, Hong Wang, Jaime Rodriguez-Canales, Carmen Behrens, Ignacio I. Wistuba, Ayumu Taguchi, Samir M. Hanash. Aberrant tryptophan catabolism marked by high kynureninase expression contributes to immunosuppression and poor outcome in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1447.

Thermal diffusivity measurement in thin metallic filaments using the mirage method with multiple probe beams and a digital camera

Photothermal beam deflection is a well-established technique for measuring thermal diffusivity. In this technique, a pump laser beam generates temperature variations on the surface of the sample to be studied. These variations transfer heat to the surrounding medium, which may be air or any other fluid. The medium in turn experiences a change in the refractive index, which will be proportional to the temperature field on the sample surface when the distance to this surface is small. A probe laser beam will suffer a deflection due to the refractive index periodical changes, which is usually monitored by means of a quadrant photodetector or a similar device aided by lock-in amplification. A linear relationship that arises in this technique is that given by the phase lag of the thermal wave as a function of the distance to a punctual heat source when unidimensional heat diffusion can be guaranteed. This relationship is useful in the calculation of the sample's thermal diffusivity, which can be obtained straightforwardly by the so-called slope method, if the pump beam modulation frequency is well-known. The measurement procedure requires the experimenter to displace the probe beam at a given distance from the heat source, measure the phase lag at that offset, and repeat this for as many points as desired. This process can be quite lengthy in dependence of the number points. In this paper, we propose a detection scheme, which overcomes this limitation and simplifies the experimental setup using a digital camera that substitutes all detection hardware utilizing motion detection techniques and software digital signal lock-in post-processing. In this work, the method is demonstrated using thin metallic filaments as samples.

Reduced IL-6 levels and tumor-associated phospho-STAT3 are associated with reduced tumor development in a mouse model of lung cancer chemoprevention with myo-inositol

Several promising chemopreventive agents have for lung cancer emerged in preclinical models and in retrospective trials. These agents have been shown to modulate pathways altered in carcinogenesis and reduce markers of carcinogenesis in animal and cell culture models. Cancer-prone transgenic mice with oncogenic Kras expressed in the airway epithelium (Ccsp^Cre/+ ; Kras^LSL-G12D/+ ) were raised on diets compounded with myo-inositol. These animals form lung premalignant lesions in a stereotypical fashion over the ten weeks following weaning. Mice raised on myo-inositol containing diets showed potent reduction in the number, size, and stage of lesions as compared to those raised on control diets. myo-inositol has previously been reported to inhibit phosphoinositide 3-kinase (PI3K) signaling. However, in mice raised on myo-inositol, total PI3K signaling was largely unaffected. Proteomic and cytokine analyses revealed large reduction in IL-6 related pathways, including STAT3 phosphorylation. This effect was not due to direct inhibition of IL-6 production and autocrine signaling within the tumor cell, but rather through alteration in macrophage recruitment and in phenotype switching, with an increase in antitumoral M1 macrophages.

Role of CPS1 in Cell Growth, Metabolism and Prognosis in LKB1-Inactivated Lung Adenocarcinoma

Background

Liver kinase B1 ( LKB1 ) is a tumor suppressor in lung adenocarcinoma (LADC). We investigated the proteomic profiles of 45 LADC cell lines with and without LKB1 inactivation. Carbamoyl phosphate synthetase 1 (CPS1), the first rate-limiting mitochondrial enzyme in the urea cycle, was distinctively overexpressed in LKB1-inactivated LADC cell lines. We therefore assessed the role of CPS1 and its clinical relevance in LKB1-inactivated LADC.

Methods

Mass spectrometric profiling of proteome and metabolome and function of CPS1 were analyzed in LADC cell lines. CPS1 and LKB1 expression in tumors from 305 LADC and 160 lung squamous cell carcinoma patients was evaluated by immunohistochemistry. Kaplan-Meier and Cox regression analyses were applied to assess the association between overall survival and CPS1 and LKB1 expression. All statistical tests were two-sided.

Results

CPS1 knockdown reduced cell growth, decreased metabolite levels associated with nucleic acid biosynthesis pathway, and contributed an additive effect when combined with gemcitabine, pemetrexed, or CHK1 inhibitor AZD7762. Tissue microarray analysis revealed that CPS1 was expressed in 65.7% of LKB1-negative LADC, and only 5.0% of LKB1-positive LADC. CPS1 expression showed statistically significant association with poor overall survival in LADC (hazard ratio = 3.03, 95% confidence interval = 1.74 to 5.25, P < .001).

Conclusions

Our findings suggest functional relevance of CPS1 in LKB1-inactivated LADC and association with worse outcome of LADC. CPS1 is a promising therapeutic target in combination with other chemotherapy agents, as well as a prognostic biomarker, enabling a personalized approach to treatment of LADC.

Abstract 2775: CPS1 as a therapeutic target and prognostic indicator in LKB1-inactivated lung adenocarcinoma

Liver Kinase B1 (LKB1), encoded by STK11, is a tumor suppressor and somatically mutated in approximately 20% of lung adenocarcinoma. Aside from the effects of LKB1 inactivation on tumor initiation, LKB1-mutant cancers are biologically distinct from cancer with functional LKB1, and the loss of LKB1 uniquely confers invasive and metastatic properties in genetically engineered mouse models of cancer. While various pathways, including energy metabolism, cell polarity, and cell growth, are regulated by LKB1 and can play a pleiotropic role in cancer initiation and progression, no therapies are currently available for clinical use that specifically target LKB1 inactivation. Therefore, elucidation of the functional mechanisms associated with LKB1 inactivation has translational relevance.

We analyzed proteomic profiles of 45 lung adenocarcinoma cell lines with and without LKB1 inactivation to identify molecular features associated with LKB1 inactivation. Carbamoyl phosphate synthase 1 (CPS1) was identified as a markedly overexpressed protein in LKB1-inactivated lung adenocarcinoma cell lines. CPS1 is the first rate-limiting mitochondrial enzyme in the urea cycle, and plays an intricate role in arginine and pyrimidine metabolism. CPS1 knockdown reduced cell growth, decreased levels of metabolites associated with nucleic acid biosynthesis pathway, and contributed an additive effect when combined with conventional chemotherapy agents including gemcitabine, pemetrexed, or CHK1 inhibitor AZD7762. Tissue microarray analysis using 305 lung adenocarcinoma tumors revealed that CPS1 was expressed in 65.7% of LKB1-negative and only 5.0% of LKB1-positive lung adenocarcinomas. In addition, CPS1 expression was significantly and independently associated with poor overall survival of lung adenocarcinoma patients (P &lt; 0.0001, HR = 3.03, 95% CI 1.74-5.25). Concordant with the results of tissue microarray, analysis of the Cancer Genome Atlas (TCGA) dataset consisting 403 lung adenocarcinomas revealed that high CPS1 mRNA expression was significantly associated with worse overall survival and is an independent prognostic indicator of lung adenocarcinoma (P = 0.005, HR = 2.31, 95% CI 1.28-4.16). Our findings suggest functional relevance of CPS1 and its association with worse outcome in LKB1-inactivated lung adenocarcinoma. Therefore, CPS1 is a promising therapeutic target in combination with other chemotherapy agents, as well as a prognostic biomarker, enabling us to personalize the treatment of LKB1-inactivated lung adenocarcinoma.

Citation Format: Muge Celiktas, Ichidai Tanaka, Satyendra Chandra Tripathi, Johannes F. Fahrmann, Clemente Aguilar-Bonavides, Pamela Villalobos, Oliver Delgado, Dilsher Dhillon, Jennifer B. Dennison, Edwin J. Ostrin, Hong Wang, Carmen Behrens, Kim-Anh Do, Adi F. Gazdar, Samir M. Hanash, Ayumu Taguchi. CPS1 as a therapeutic target and prognostic indicator in LKB1-inactivated lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2775. doi:10.1158/1538-7445.AM2017-2775

CDDO-Me protects normal lung and breast epithelial cells but not cancer cells from radiation

Although radiation therapy is commonly used for treatment for many human diseases including cancer, ionizing radiation produces reactive oxygen species that can damage both cancer and healthy cells. Synthetic triterpenoids, including CDDO-Me, act as anti-inflammatory and antioxidant modulators primarily by inducing the transcription factor Nrf2 to activate downstream genes containing antioxidant response elements (AREs). In the present series of experiments, we determined if CDDO-Me can be used as a radioprotector in normal non-cancerous human lung and breast epithelial cells, in comparison to lung and breast cancer cell lines. A panel of normal non-cancerous, partially cancer progressed, and cancer cell lines from both lung and breast tissue was exposed to gamma radiation with and without pre-treatment with CDDO-Me. CDDO-Me was an effective radioprotector when given ∼18 hours before radiation in epithelial cells (average dose modifying factor (DMF) = 1.3), and Nrf2 function was necessary for CDDO-Me to exert these radioprotective effects. CDDO-Me did not protect cancer lines tested from radiation-induced cytotoxicity, nor did it protect experimentally transformed human bronchial epithelial cells (HBECs) with progressive oncogenic manipulations. CDDO-Me also protected human lymphocytes against radiation-induced DNA damage. A therapeutic window exists in which CDDO-Me protects normal cells from radiation by activating the Nrf2 pathway, but does not protect experimentally transformed or cancer cell lines. This suggests that use of this oral available, non-toxic class of drug can protect non-cancerous healthy cells during radiotherapy, resulting in better outcomes and less toxicity for patients.

Proteomic signatures associated with p53 mutational status in lung adenocarcinoma

p53 is commonly mutated in lung adenocarcinoma. Mutant p53 loses wild-type function and some missense mutations further acquire oncogenic functions, while p53 wild-type may also induce pro-survival signaling. Therefore identification of signatures based on p53 mutational status has relevance to our understanding of p53 signaling pathways in cancer and identification of new therapeutic targets. To this end, we compared proteomic profiles of three cellular compartments (whole-cell extract, cell surface, and media) from 28 human lung adenocarcinoma cell lines that differ based on p53 mutational status. In total, 11,598, 11,569, and 9090 protein forms were identified in whole-cell extract, cell surface, and media, respectively. Bioinformatic analysis revealed that representative pathways associated with epithelial adhesion, immune and stromal cells, and mitochondrial function were highly significant in p53 missense mutations, p53 loss and wild-type p53 cell lines, respectively. Of note, mRNA levels of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1-α), a transcription coactivator that promotes mitochondrial oxidative phosphorylation and mitochondrial biogenesis, was substantially higher in p53 wild-type cell lines compared to either cell lines with p53 loss or with missense mutation. Small interfering RNA targeting PGC1-α inhibited cell proliferation in p53 wild-type cell lines, indicative of PGC1-α and its downstream molecules as potential therapeutic targets in p53 wild-type lung adenocarcinoma.

Branching morphogenesis of immortalized human bronchial epithelial cells in three-dimensional culture

While mouse models have contributed in our understanding of lung development, repair and regeneration, inherent differences between the murine and human airways requires the development of new models using human airway epithelial cells. In this study, we describe a three-dimensional model system using human bronchial epithelial cells (HBECs) cultured on reconstituted basement membrane. HBECs form complex budding and branching structures on reconstituted basement membrane when co-cultured with human lung fetal fibroblasts. These structures are reminiscent of the branching epithelia during lung development. The HBECs also retain markers indicative of epithelial cell types from both the central and distal airways suggesting their multipotent potential. In addition, we illustrate how the model can be utilized to understand respiratory diseases such as lung cancer. The 3D novel cell culture system recapitulates stromal-epithelial interactions in vitro that can be utilized to understand important aspects of lung development and diseases.

Radiation-enhanced lung cancer progression in a transgenic mouse model of lung cancer is predictive of outcomes in human lung and breast cancer

PURPOSE

Carcinogenesis is an adaptive process between nascent tumor cells and their microenvironment, including the modification of inflammatory responses from antitumorigenic to protumorigenic. Radiation exposure can stimulate inflammatory responses that inhibit or promote carcinogenesis. The purpose of this study is to determine the impact of radiation exposure on lung cancer progression in vivo and assess the relevance of this knowledge to human carcinogenesis.

EXPERIMENTAL DESIGN

K-ras(LA1) mice were irradiated with various doses and dose regimens and then monitored until death. Microarray analyses were performed using Illumina BeadChips on whole lung tissue 70 days after irradiation with a fractionated or acute dose of radiation and compared with age-matched unirradiated controls. Unique group classifiers were derived by comparative genomic analysis of three experimental cohorts. Survival analyses were performed using principal component analysis and k-means clustering on three lung adenocarcinoma, three breast adenocarcinoma, and two lung squamous carcinoma annotated microarray datasets.

RESULTS

Radiation exposure accelerates lung cancer progression in the K-ras(LA1) lung cancer mouse model with dose fractionation being more permissive for cancer progression. A nonrandom inflammatory signature associated with this progression was elicited from whole lung tissue containing only benign lesions and predicts human lung and breast cancer patient survival across multiple datasets. Immunohistochemical analyses suggest that tumor cells drive predictive signature.

CONCLUSIONS

These results demonstrate that radiation exposure can cooperate with benign lesions in a transgenic model of cancer by affecting inflammatory pathways, and that clinically relevant similarities exist between human lung and breast carcinogenesis.

[Programs for optimizing the use of antibiotics (PROA) in Spanish hospitals: GEIH-SEIMC, SEFH and SEMPSPH consensus document]

The antimicrobial agents are unique drugs for several reasons. First, their efficacy is higher than other drugs in terms of reduction of morbidity and mortality. Also, antibiotics are the only group of drugs associated with ecological effects, because their administration may contribute to the emergence and spread of microbial resistance. Finally, they are used by almost all medical specialties. Appropriate use of antimicrobials is very complex because of the important advances in the management of infectious diseases and the spread of antibiotic resistance. Thus, the implementation of programs for optimizing the use of antibiotics in hospitals (called PROA in this document) is necessary. This consensus document defines the objectives of the PROA (namely, to improve the clinical results of patients with infections, to minimise the adverse events associated to the use of antimicrobials including the emergence and spread of antibiotic resistance, and to ensure the use of the most cost-efficacious treatments), and provides recommendations for the implementation of these programs in Spanish hospitals. The key aspects of the recommendations are as follows. Multidisciplinary antibiotic teams should be formed, under the auspices of the Infection Committees. The PROA need to be considered as part of institutional programs and the strategic objectives of the hospital. The PROA should include specific objectives based on measurable indicators, and activities aimed at improving the use of antimicrobials, mainly through educational activities and interventions based more on training activities directed to prescribers than just on restrictive measures.

Multipotent capacity of immortalized human bronchial epithelial cells

While the adult murine lung utilizes multiple compartmentally restricted progenitor cells during homeostasis and repair, much less is known about the progenitor cells from the human lung. Translating the murine stem cell model to humans is hindered by anatomical differences between species. Here we show that human bronchial epithelial cells (HBECs) display characteristics of multipotent stem cells of the lung. These HBECs express markers indicative of several epithelial types of the adult lung when experimentally tested in cell culture. When cultured in three different three-dimensional (3D) systems, subtle changes in the microenvironment result in unique responses including the ability of HBECs to differentiate into multiple central and peripheral lung cell types. These new findings indicate that the adult human lung contains a multipotent progenitor cell whose differentiation potential is primarily dictated by the microenvironment. The HBEC system is not only important in understanding mechanisms for specific cell lineage differentiation, but also for examining changes that correlate with human lung diseases including lung cancer.

Efecto de tres dietas en el crecimiento de crías de cocodrilo americano Crocodylus acutus

Se estudió el efecto de tres dietas con sustitución de pescado marino (20 y 40%) por hígado de res en el crecimiento y supervivencia, así como el efecto de la temperatura en el consumo de alimento de crías de Crocodylus acutus. Los cocodrilos alimentados con la dieta de 40% de hígado tuvieron el mayor crecimiento y un 100% de supervivencia, con potencial de mayor tolerancia a condiciones invernales.

Irreparable complex DNA double-strand breaks induce chromosome breakage in organotypic three-dimensional human lung epithelial cell culture

DNA damage and consequent mutations initiate the multistep carcinogenic process. Differentiated cells have a reduced capacity to repair DNA lesions, but the biological impact of unrepaired DNA lesions in differentiated lung epithelial cells is unclear. Here, we used a novel organotypic human lung three-dimensional (3D) model to investigate the biological significance of unrepaired DNA lesions in differentiated lung epithelial cells. We showed, consistent with existing notions that the kinetics of loss of simple double-strand breaks (DSBs) were significantly reduced in organotypic 3D culture compared to kinetics of repair in two-dimensional (2D) culture. Strikingly, we found that, unlike simple DSBs, a majority of complex DNA lesions were irreparable in organotypic 3D culture. Levels of expression of multiple DNA damage repair pathway genes were significantly reduced in the organotypic 3D culture compared with those in 2D culture providing molecular evidence for the defective DNA damage repair in organotypic culture. Further, when differentiated cells with unrepaired DNA lesions re-entered the cell cycle, they manifested a spectrum of gross-chromosomal aberrations in mitosis. Our data suggest that downregulation of multiple DNA repair pathway genes in differentiated cells renders them vulnerable to DSBs, promoting genome instability that may lead to carcinogenesis.

Immortalized epithelial cells derived from human colon biopsies express stem cell markers and differentiate in vitro

BACKGROUND & AIMS

Long-term propagation of human colonic epithelial cells (HCEC) of adult origin has been a challenge; currently used HCEC lines are of malignant origin and/or contain multiple cytogenetic changes. We sought to immortalize human colon biopsy-derived cells expressing stem cell markers and retaining multilineage epithelial differentiation capability.

METHODS

We isolated and cultured cells from biopsy samples of 2 patients undergoing routine screening colonoscopy. Cells were immortalized by expression of the nononcogenic proteins cyclin-dependent kinase 4 (Cdk4) and the catalytic component of human telomerase (hTERT) and maintained for more than 1 year in culture.

RESULTS

The actively proliferating HCECs expressed the mesenchymal markers vimentin and alpha-smooth muscle actin. Upon growth arrest, cells assumed a cuboidal shape, decreased their mesenchymal features, and expressed markers of colonic epithelial cells such as cytokeratin 18, zonula occludens-1, mucins-1 and -2, antigen A33, and dipeptidyl peptidase 4. Immortalized cells expressed stem cell markers that included LGR5, BMI1, CD29, and CD44. When placed in Matrigel in the absence of a mesenchymal feeder layer, individual cells divided and formed self-organizing, cyst-like structures; a subset of cells exhibited mucin-2 or polarized villin staining.

CONCLUSIONS

We established immortalized HCECs that are capable of self-renewal and multilineage differentiation. These cells should serve as valuable reagents for studying colon stem cell biology, differentiation, and pathogenesis.

Fluvastatin as co-medication in heart transplant recipients with elevated creatine-kinase

BACKGROUND

Statins reduce the risk for transplant vasculopathy and mortality among heart transplant recipients. Interactions between commonly used statins (ie, simvastatin, atorvastatin) and immunosuppressant drugs lead to side effects or withdrawal of statin therapy. Fluvastatin shows fewer interactions with the immunosuppressant agents because it is not metabolized via the cytochrome P-450 3A4 pathway like most immunosuppressants, steroids, or other statins. This study investigated the impact of a switch from other statins to fluvastatin in heart transplant recipients who revealed elevated creatine-kinase levels.

METHODS

A total of 23 heart transplant patients with elevated creatine-kinase levels were included in this study. Statins were replaced with an equal dosage of fluvastatin. We measured on the day of replacement as well as there after at 3, 6, 9, and 12 months creatine-kinase, lipid status, ALT, AST, and creatinine levels.

RESULTS

After 6 months creatine-kinase showed a significant reduction of 25% (P < .05) and after 9 months of 38% (P < .05). The HDL-cholesterol levels were significantly reduced at 6 months (8%; P < .05) and 9 months (23%; P < .05). At 3 months, triglyceride levels were significantly elevated (18%; P < .05). No differences were observed in ALT, AST, creatinine, total, and LDL-cholesterol at any time.

CONCLUSION

A conversion from commonly used statins to fluvastatin in heart transplant patients with elevated creatine-kinase was safe, leading to a significant reduction in creatine-kinase levels. Except for an initial raise in triglycerides and a lowering of HDL-cholesterol, no changes in lipid status were seen. This conversion might help to maintain lipid-lowering therapy in transplant recipients who show side effects using conventional statins.

The DNA sequence, annotation and analysis of human chromosome 3

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

The finished DNA sequence of human chromosome 12

Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.

The DNA sequence of the human X chromosome

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

Microbial characterization and hydrocarbon biodegradation potential of natural bilge waste microflora

Shipping operations produce oily wastes that must be managed properly to avoid environmental pollution. The aim of this study was to characterize microorganisms occurring in ship bilge wastes placed in open lagoons and, particularly, to assess their potential to degrade polycyclic aromatic hydrocarbons (PAHs). A first-order kinetic was suitable for describing hydrocarbon biodegradation after 17 days of treatment. The calculated rate constants were 0.0668 and 0.0513 day(-1) with a corresponding half-life of 10.3 and 13.5 days for the aliphatic and aromatic hydrocarbon fractions, respectively. At day 17, PAH removal percentages were: acenaphtylene 100, fluorene 95.2, phenanthrene 93.6, anthracene 70.3, and pyrene 71.5. Methyl phenanthrene removals were lower than that of their parent compound (3-methyl phenanthrene 83.6, 2-methyl phenanthrene 80.8, 1-methyl phenanthrene 77.3, 9-methyl phenanthrene 75.1, and 2,7-dimethyl phenanthrene 76.6). Neither pure cultures nor the microbial community from these wastes showed extracellular biosurfactant production suggesting that the addition of an exogenously produced biosurfactant may be important in enhancing hydrocarbon bioavailability and biodegradation. DNA analysis of bilge waste samples revealed a ubiquitous distribution of the nahAc genotype in the dump pools. Although almost all of the isolates grew on naphthalene as sole carbon source, only some of them yielded nahAc amplification under the experimental conditions used. The variety of PAHs in bilge wastes could support bacteria with multiple degradation pathways and a diversity of catabolic genes divergent from the classical nah-like type.

Isolation and characterization of solventogenic, cellulase-free xylanolytic Clostridia from cow rumen

Hemicellulolytic obligate anaerobes capable of converting a range of agricultural substrates and monomeric sugars of hemicellulose to solvents and acids were isolated from cow rumen fluid. The strains were identified as 5 strains of C. beijerinckii (3 different genotypes), 3 strains of C. acetobutylicum (2 different genotypes), 1 strain of C. butyricum and 3 strains of C. bifermentans (2 different genotypes). All of them produced cellulase-free xylanase activity. C. acetobutylicum LU1 produced solvent, a high of 5.1 gl(-1) and C.bifermentans LU1 produced xylanase activity a high of 4.2 IU ml(-1).

Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes

To meet the new challenge of generating the draft sequences of mammalian genomes, we describe the development of a novel high throughput 96-well method for the purification of plasmid DNA template using size-fractionated, acid-washed glass beads. Unlike most previously described approaches, the current method has been designed and optimized to facilitate the direct binding of alcohol-precipitated plasmid DNA to glass beads from alkaline lysed bacterial cells containing the insoluble cellular aggregate material. Eliminating the tedious step of separating the cleared lysate significantly simplifies the method and improves throughput and reliability. During a 4 month period of 96-capillary DNA sequencing of the Rattus norvegicus genome at the Baylor College of Medicine Human Genome Sequencing Center, the average success rate and read length derived from >1 800 000 plasmid DNA templates prepared by the direct lysis/glass bead method were 82.2% and 516 bases, respectively. The cost of this direct lysis/glass bead method in September 2001 was approximately 10 cents per clone, which is a significant cost saving in high throughput genomic sequencing efforts.

Beta-galactosidase from a cold-adapted bacterium: purification, characterization and application for lactose hydrolysis

The enzyme beta-galactosidase was purified from a cold-adapted organism isolated from Antarctica. The organism was identified as a psychotrophic Pseudoalteromonas sp. The enzyme was purified with high yields by a rapid purification scheme involving extraction in an aqueous two-phase system followed by hydrophobic interaction chromatography and ultrafiltration. The beta-galactosidase was optimally active at pH 9 and at 26 degrees C when assayed with o-nitrophenyl-beta-D-galactopyranoside as substrate for 2 min. The enzyme activity was highly sensitive to temperature above 30 degrees C and was undetectable at 40 degrees C. The cations Na+, K+, Mg2+ and Mn2+ activated the enzyme while Ca2+, Hg2+, Cu2+ and Zn2+ inhibited activity. The shelf life of the pure enzyme at 4 degrees C was significantly enhanced in the presence of 0.1% (w/v) polyethyleneimine. The pure beta-galactosidase was also evaluated for lactose hydrolysis. More than 50% lactose hydrolysis was achieved in 8 h in buffer at an enzyme concentration of 1 U/ml, and was increased to 70% in the presence of 0.1% (w/v) polyethyleneimine. The extent of lactose hydrolysis was 40-50% in milk. The enzyme could be immobilized to Sepharose via different chemistries with 60-70% retention of activity. The immobilized enzyme was more stable and its ability to hydrolyze lactose was similar to that of the soluble enzyme.

Value of a dipstick based on recombinant RK39 antigen for differential diagnosis of American visceral leishmaniasis from other sympatric endemic diseases in Venezuela

A laboratory trial using recombinant rK39 dipsticks for differential diagnosis of American visceral leishmaniasis (AVL) from other sympatric endemic diseases which share similar clinic features (Chagas disease, malaria, schistosomiasis and toxoplasmosis) was conducted in Venezuela. The 100% specificity of the test previously obtained in other countries was confirmed. The use of this test at the primary health care level in Venezuela for a rapid diagnosis of active AVL cases, which may avoid deaths, is recommended.

Chlorin-type photosensitizers photochemically derived from vinyl porphyrins

The reaction of singlet oxygen with four vinyl-substituted dicarboxylic porphyrins, vinyldeuteroporphyrin (VD), ethylvinyldeuteroporphyrin (EVD), hydroxyethylvinyldeuteroporphyrin (HVD) and protoporphyrin (PP) in organic solutions is investigated. The main products, the "hydroxyaldehyde" chlorin-type derivatives, are formed with a concentration-dependent photochemical quantum yield that reaches a maximum of 7.4 +/- 1.6 x 10(-3). However, owing to the high turnover of singlet-oxygen production, these chlorin-type compounds are easily prepared photochemically with a chemical yield of 70% and little side product formation. In chemical ionization mass spectrometry, these compounds display an unusual fragmentation with a loss of 16 mass units. This is attributed to the loss of the oxygen bound to the saturated carbon of the modified pyrrole unit. All these compounds sensitize the formation of singlet oxygen with a yield around 0.8. They interact with singlet oxygen with rate constants of 5 x 10(6)-9 x 10(6) M-1 s-1, lower than those measured for vinyl porphyrins. These data are likely to help in the characterization of photoproducts of vinyl porphyrins relevant to photodynamic therapy (PP, HVD). As exemplified with VD and EVD, they also point out the reaction of singlet oxygen as an efficient route to chlorin-type photosensitizers.

Effects of trap design and CO2 presentation on the measurement of adult mosquito abundance using Centers for Disease Control-style miniature light traps

Centers for Disease Control miniature light traps augmented with CO2 provide an effective method of monitoring Culex abundance and may provide a useful supplement to New Jersey light traps used by the California Mosquito Surveillance Program. To assist in standardizing sampling protocols, the present research compared the catch of adult mosquitoes collected using 4 trap designs and 3 CO2 presentation methods. When augmented with dry ice, the Arbovirus Field Station (AFS) trap (consisting of a 3-in. fan mounted into a white polyvinyl chloride pipe and operated without a light source or rain shield) collected as many or more Culex females than similar traps purchased from John W. Hock and American Biophysics, or a trap with a 4.25-in. 2-bladed fan constructed by the Orange County Vector Control District (similar to the Encephalitis Virus Surveillance model distributed by Bioquip). Few blooded or gravid females and males were collected, indicating that CO2 released from the dry ice and not light probably was the primary attractant. Catch of Culex tarsalis females in traps baited with CO2 released at 0.5-1.5 liters/min from gas cylinders was significantly greater than in traps baited with dry ice, even though the CO2 release rates from the dry ice at dusk probably were comparable to that released from the cylinders and averaged 0.4-0).5 liters/min for the night. Traps baited with 0.5 liters/ min of CO2 gas released in 15 3- or 2-sec bursts per hour collected the fewest mosquitoes. In all experiments, trap location effects were significant and accounted for as much variability in catch size as trap design or CO2 presentation. Sampling efficiency of all trap designs or CO2 presentations were consistent over time, space, and different levels of mosquito abundance.

Targeting of HIV gp120 by oligonucleotide-photosensitizer conjugates. Light-induced damages

Some guanine-rich oligonucleotides inhibit HIV infectivity through interaction with the gp120 glycoprotein. Besides, photoinactivation of viruses attracts attention for blood decontamination. The feasibility of targeting a red light-absorbing chlorin-type photosensitizer to gp120 through covalent coupling with 8-mer phosphodiester oligodeoxynucleotides is investigated. Some conjugates inhibit binding of antibodies directed to gp120. Inhibition is significantly increased upon red light activation. The activity of the conjugates correlates with their ability to self-associate, a process strongly favored by the propensity of the hydrophobic chlorin moiety to dimerize. Thus, the photosensitizer moiety both promotes structures with a higher affinity for gp120 and, upon light activation, can induce site-directed damages to the protein.

Comparative effectiveness of three adult mosquito sampling methods in habitats representative of four different biomes of California

The effectiveness of New Jersey (NJ) light, dry ice baited, and gravid female traps for collecting adult mosquitoes was compared at representative habitats in the Coachella, San Joaquin, and Sacramento valleys and the Los Angeles basin of California. The NJ light traps effectively sampled Anopheles freeborni, Culex tarsalis, Psorophora columbiae, and several Aedes when abundance was high in rural areas with minimal competitive illumination. Dry ice-baited encephalitis virus surveillance or CDC style traps collected significantly more females of most species at most localities than did NJ light traps, regardless of background illumination. The Cummings modification of the Reiter gravid female trap baited with a bulrush (Schoenoplectus) infusion was the best method for collecting Culex pipiens complex females in most habitats. In the Los Angeles basin, gravid traps baited with bulrush infusion collected, on average, 4.5 times more Culex quinquefasciatus females than did traps baited with the Reiter infusion. The bulrush infusion in combination with the Cummings trap design seemed to provide resting site cues and collected males as well as empty and bloodfed females. Mosquito surveillance programs in California should include the systematic operation of dry ice-baited and gravid female traps to improve surveillance sensitivity for selected species in appropriate habitats.

The re-emergence of American visceral leishmaniasis in an old focus in Venezuela: present situation of human and canine infections

The report of a new autochthonous case of human American Visceral Leishmaniasis (AVL) in 1992 in the village of Guayabita, Aragua State, Venezuela (10 degrees 16'N, 67 degrees 28'W; 500 m asl), led us to undertake an epidemiological study in this locality. A demographic survey was conducted using a structured questionnaire in which data was collected regarding sex, age, occupation, length of residence in the area and migratory history. A leishmanin skin test (LST) was applied and samples of venous blood for counter immunoelectrophoresis (CIEP) and immunofluorescent antibodies (IFAT) tests were drawn. The prevalence of positive LST was 11.4%. The positivity was highest among males and increased with age. Young males seemed to be more exposed to infection than females. Since occupation per se did not seem to account for this association, it may be explained as a gender-associated behavior, leading to different degrees of exposure to sand flies. The canine population was also screened for leishmanial infection. One dog was shown to be parasitologically infected with Leishmania sp. Four out of 71 dogs (5.6%) were positive for FG, CIEP, IFAT and Western Blot and 11 (15.5%) were positive for CIEP. These results suggest that after almost 30 years of epidemiological silence, American visceral leishmaniasis has re-emerged in this focus.

Follow-up of a human accidental infection by Leishmania (Viannia) braziliensis using conventional immunologic techniques and polymerase chain reaction

The results of a two-year follow-up study of an accidental human infection with Leishmania (Viannia) braziliensis are presented. Western blots, indirect immunofluorescence, and intradermal reaction assays were not able to detect the infection before week 18 postinfection, whereas using the polymerase chain reaction (PCR) on blood samples, parasite DNA was detected at week 8. All test results, except the intradermal reaction followed the cure process and 12 weeks after the last chemotherapy injection (week 36 postinfection), all were negative. However, a year after cure, the PCR became positive again and has remained so for two years. To determine in which blood cell fraction the parasite was evident, enriched lymphocyte and monocyte fractions were assayed by the PCR. These results are discussed in the context of persistent infections.

Photodynamic inactivation of cell-free HIV strains by a red-absorbing chlorin-type photosensitizer

We have investigated the photodynamic activity of a new chlorin-type photosensitizer on a reference human immunodeficiency virus type 1 (HIV-1) strain, two wild-type HIV-1 isolates and two drug-resistant HIV-1 isolates. This chlorin was highly effective for the inactivation of free viruses, as assessed by two different quantitative cell culture assays. In the absence of blood components, all the HIV strains, including wild-type and drug-resistant mutant isolates, were totally inactivated using 30 micrograms ml-1 of chlorin and 0.75 J cm-2 of 661 nm light. Successful killing of HIV-1 strains in either plasma or whole blood was also obtained by increasing the chlorin concentration moderately. Our results demonstrate the antiviral efficiency of this chlorin, suggesting the potential application of dye-sensitized photoirradiation to decontaminate blood products.

Late seroconversion of C virus markers in hemodialysis patients

We examined the prevalence of the IgG C virus C 100-3 antibody (anti-HCV) in a group of 43 patients on hemodialysis in our center during three periods: A: 1988; B: 1989; C: 1990. During period A, the anti-HCV prevalence was 30% (13 of 43 patients), these patients being regarded as chronic carriers of these antibodies. In period B, two patients displayed seroconversion, and another seven during period C, all of whom had tested negative during period A. These patients were considered acute. During the three years under study, all of the patients shared the same hemodialysis monitors. High ALT values were found in four of nine acute patients (44.4%) and nine of thirteen (69.23%) of the chronic patients. In 10 anti-HCV patients, hypertransaminemia continued long-term (> 6 months). Two patients had been given contaminated blood, four were multi-transfused (> 14 transfusions), two less than 4 units, and one had never received a transfusion. The period between the initial high and/or maximum ALT and the determination of HCV Ac was up to 10 to 11 months in three patients. These findings indicate the lack of sensitivity of ALTs as a diagnostic tool for HCV, the possible late C 100-3 seroconversion, which makes it necessary to carry out periodic serological checks in hemodialysis patients and the decisive role transfusions in HCV transmission, without excluding other possible intra-dialysis contagion sources.

Leishmania colombiensis in Venezuela

Flagellate parasites isolated in Venezuela from bone marrow aspirates of a human (MHOM/VE/70/Chuao) and a dog (MCAN/VE/72/Talisman2) were subsequently identified by isozyme analysis as Leishmania colombiensis. Data are presented describing genetic similarity among Panama, Colombia, and Venezuela populations of this species.

In vitro uptake of dicarboxylic porphyrins by human atheroma. Kinetic and analytical studies

Human atheromatous aorta segments as well as presumably disease-free control aorta were obtained at autopsy. They were incubated with solutions of various purified dicarboxylic porphyrins including hematoporphyrin (HP) and hydroxyethylvinyldeuteroporphyrin (HVD), and with solutions of Photofrin. Selective labelling of the atheroma was shown by macroscopic and microscopic observations of the characteristic porphyrin fluorescence associated with the atheromatous plaques. The time dependence of the uptake, monitored by absorption spectrophotometry or by high performance liquid chromatography, was inferred from the disappearance of the porphyrins in the incubation medium. Significant binding was observed in the absence of albumin or serum proteins. The uptake of HP was less than that of the more hydrophobic compounds HVD or Photofrin when these porphyrins were used alone. The presence of albumin or serum drastically reduces atheroma labelling. Some competition between HP and HVD for binding sites is also seen. The present results do indicate that hydrophobic porphyrins have an intrinsic affinity for atheroma and that they can be taken up through passive processes. Taking into account previous data on animal models (Photochem. Photobiol. (1989), 731-737), it appears however that, in vivo, interactions with proteins and pharmacokinetics will primarily determine plaque labelling.