Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation

Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.

A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA

Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11-19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.

Rehospitalizations, repeated aortic surgery, and death in initial survivors of surgery for Stanford type A aortic dissection and the significance of age – a nationwide registry-based cohort study

Background

All patients with type A aortic dissections, regardless of age, are recommended urgent aortic surgery. However, studies exploring long term outcomes in survivors are sparse, and especially, the significance of age on long-term outcomes remain unclear.

Purpose

We described and compared incidences across age groups of post-discharge readmission, repeated aortic surgery, and death in patients who survived surgery and hospitalization for type A aortic dissection.

Methods

Using data from Danish nationwide registries, we identified patients hospitalized with Stanford type A aortic dissections from 2006–2018. Survivors of hospitalization and surgery on the ascending aorta and/or aortic arch comprised the study population (Figure 1). Using cumulative incidence plots taking death into account as a competing risk and Cox regression analysis, we described long-term outcomes (rehospitalizations, repeated aortic surgery, and death) and compared different age groups. The diagnosis of type A aortic dissection in the registries used, was validated from 191 clinical records to have a positive predictive value of 94.8%.

Results

Of 606 initial survivors of surgery and hospitalization with type A aortic dissection, 236 (38.9%) were <60 years old (group I), 194 (32.0%) were 60–69 years old (group II), and 176 (29.1%) were >69 years old (group III). Figure 2 shows cumulative incidences of outcomes according to age. During the first year, 62.5% were re-hospitalized (median number of days hospitalized was 2 days (IQR 1–8 days) and 1.4% underwent repeated aortic surgery with no significant differences across age groups (P=0.68 and P=0.39, respectively). Further, 5.9% died (group I: 3.0%, group II: 8.3%, group III: 7.4%, P=0.04). After 10 years of follow up, 8.0% had undergone repeated aortic surgery (group I: 11.5%, group II: 8.5%, group III: 1.6%, P=0.04) and 10.2% (group I), 17.0% (group II), and 22.2% (group III) had died (P=0.01). In adjusted analyses, no age differences were found in one-year outcomes, while age >69 years (group III) compared with age <60 years (group I) was associated with a lower rate of repeated aortic surgery (hazard ratio 0.17, 95% confidence interval 0.04–0.78) and a higher rate of all-cause mortality (hazard ratio 2.44, 95% confidence interval 1.37–4.34) in the 10-years analysis.

Conclusion

Among survivors of type A aortic dissections, rehospitalizations the first year after discharge were common among all age groups, but survival was high. Repeated aortic surgery was rare, and significantly more common among younger than older patients. Evaluations of quality of life in survivors of type A aortic dissections are needed.

Funding Acknowledgement

Type of funding sources: None.

A theoretical analysis of taxonomic binning accuracy

Many metagenomic and environmental DNA studies require the taxonomic assignment of individual reads or sequences by aligning reads to a reference database, known as taxonomic binning. When a read aligns to more than one reference sequence, it is often classified based on sequence similarity. This step can assign reads to incorrect taxa, at a rate which depends both on the assignment algorithm and on underlying population genetic and database parameters. In particular, as we move towards using environmental DNA to study eukaryotic taxa subject to regular recombination, we must take into account issues concerning gene tree discordance. Though accuracy is often compared across algorithms using a fixed data set, the relative impact of these population genetic and database parameters on accuracy has not yet been quantified. Here, we develop both a theoretical and simulation framework in the simplified case of two reference species, and compute binning accuracy over a wide range of parameters, including sequence length, species-query divergence time, divergence times of the reference species, reference database completeness, sample age and effective population size. We consider two assignment methods and contextualize our results using parameters from a recent ancient environmental DNA study, comparing them to the commonly used discriminative k-mer-based method Clark (Current Biology, 31, 2021, 2728; BMC Genomics, 16, 2015, 1). Our results quantify the degradation in assignment accuracy as the samples diverge from their closest reference sequence, and with incompleteness of reference sequences. We also provide a framework in which others can compute expected accuracy for their particular method or parameter set. Code is available at https://github.com/bdesanctis/binning-accuracy.

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

Environmental genomics of Late Pleistocene black bears and giant short-faced bears

Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.

Community assembly processes underlying the temporal dynamics of glacial stream and lake bacterial communities

Community assembly processes are important in structuring aquatic microbial communities; however, the influence of these processes on the dynamics of bacterial communities in glacial streams and lakes remains largely unstudied. To investigate the assembly processes underlying the temporal variation of the bacterial community, we collected 50 water samples over five months in an ephemeral glacial stream and its downstream lake at the terminus of the Qiangyong glacier on the Tibetan Plateau. Using the V4 hypervariable region of the bacterial 16S rRNA gene combined with environmental measurements, such as water temperature, pH, total nitrogen (TN), dissolved organic carbon (DOC) and water conductivity, we found that temporal variation in the environmental factors promoted the shift in the proglacial stream and the lake bacterial communities. The quantification of ecological processes showed that the stream microbial communities were influenced by the ecological drift (40%) in June, then changed to homogeneous selection (40%) in July and variable selection (60%) in September, while the dynamic pattern of proglacial lake bacterioplankton was governed by homogeneous selection (≥ 50%) over the time. Overall, the dynamic of bacterial community in the proglacial stream and lake water is influenced by environmental factors, and the community composition assembly of the Qiangyong glacial stream and lake could be dynamic and primarily governed by deterministic processes.

Evidence of human occupation in Mexico around the Last Glacial Maximum

The initial colonization of the Americas remains a highly debated topic¹, and the exact timing of the first arrivals is unknown. The earliest archaeological record of Mexico-which holds a key geographical position in the Americas-is poorly known and understudied. Historically, the region has remained on the periphery of research focused on the first American populations². However, recent investigations provide reliable evidence of a human presence in the northwest region of Mexico^3,4, the Chiapas Highlands⁵, Central Mexico⁶ and the Caribbean coast^7-9 during the Late Pleistocene and Early Holocene epochs. Here we present results of recent excavations at Chiquihuite Cave-a high-altitude site in central-northern Mexico-that corroborate previous findings in the Americas^10-17of cultural evidence that dates to the Last Glacial Maximum (26,500-19,000 years ago)¹⁸, and which push back dates for human dispersal to the region possibly as early as 33,000-31,000 years ago. The site yielded about 1,900 stone artefacts within a 3-m-deep stratified sequence, revealing a previously unknown lithic industry that underwent only minor changes over millennia. More than 50 radiocarbon and luminescence dates provide chronological control, and genetic, palaeoenvironmental and chemical data document the changing environments in which the occupants lived. Our results provide new evidence for the antiquity of humans in the Americas, illustrate the cultural diversity of the earliest dispersal groups (which predate those of the Clovis culture) and open new directions of research.

Ancient Plant Genomics in Archaeology, Herbaria, and the Environment

The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.

A 5700 year-old human genome and oral microbiome from chewed birch pitch

The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA.

137 ancient human genomes from across the Eurasian steppes

For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century BC, forming the Hun traditions in the fourth-fifth century AD, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry.

Ancient Biomolecules and Evolutionary Inference

Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.

Ancient plant DNA in lake sediments

Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.

Abstract P6-12-09: Pan-HER, an antibody mixture with antitumor activity against drug-resistant HER2-overexpressing breast cancers with high ERBB ligand expression

Background: Amplification/overexpression of ERBB receptors and/or ligands has been associated with resistance to anti-HER2 therapies. Pan-HER is a mixture of six antibodies targeting each of the ERBB receptors, EGFR, HER2 and HER3, with synergistic pairs of antibodies. Each pair of antibodies simultaneously blocks ligand binding and/or induces target degradation, thus preventing compensatory mechanisms to anti-ERBB therapies. We examined the antitumor activity of Pan-HER against drug-sensitive and -resistant HER2+ breast cancer cells and xenografts.

Results: Pan-HER exhibited potent growth inhibitory activity against a panel of HER2+ breast cancer cells (BT474, MDA-453, MDA-361, SUM190, HCC1954, UACC893 and SKBR3). Growth inhibition was associated with internalization and degradation of EGFR, HER2 and HER3. Pan-HER was superior to the combination of trastuzumab/pertuzumab (TP) against HER2+/PIK3CA mutant MDA-361, HCC1954, UACC893 and MDA-453 cells. We next compared the effect of Pan-HER against BT474, HCC1954 and MDA-361 xenografts established in nude mice to that of trastuzumab/lapatinib (TL), TP and T-DM1. All treatments were effective across the panel of xenografts. In mice with MDA-361 tumors, Pan-HER and TP were superior to TL. Immunoblot analysis showed significant downregulation of EGFR, HER2 and HER3 only in tumors treated with Pan-HER. After a complete response, treatment was discontinued. Among mice with BT474 xenografts treated with TP, TL and T-DM1, 25-50% of mice exhibited a tumor recurrence within 50 weeks of follow-up, while no recurrences were registered in mice treated with Pan-HER. Tumors recurring after TP and T-DM1 expressed significantly higher HER3 and P-HER3 protein levels and NRG1 mRNA levels. HCC1954 xenografts recurring after T-DM1 also overexpressed NRG1 mRNA compared to tumors before therapy.

We next examined the effect of Pan-HER against trastuzumab-resistant HR6 (BT474) cells (Ritter et al. CCR 2007) and HCC1954 and UACC893 cells with acquired resistance to T-DM1 (TDR; IC50 >5-, >6- and 600-fold in HR6, UACC893-TDR and HCC1954-TDR cells, respectively, vs. parental cells). All T-DM1-resistant cells expressed significantly higher HER3 and P-HER3 protein levels and NRG1 mRNA and protein levels. Treatment with the HER3 neutralizing antibody LJM716 resensitized HR6 and HCC1954-TDR cells to T-DM1, suggesting a causal association between the NRG1-HER3 axis and drug resistance. Mice with HR6 tumors were treated with Pan-HER, TL, TP and T-DM1. Only Pan-HER arrested HR6 tumor growth and downregulated EGFR, HER2, HER3, P-HER3 and P-AKT. Finally, HCC1954-TDR tumors rapidly grew in vivo despite treatment with T-DM1. Administration of Pan-HER to mice bearing HCC1954-TDR xenografts growing in the presence of T-DM1, induced rapid tumor regressions.

Conclusions: These data suggest that multitarget therapeutic interventions, such as Pan-HER, which simultaneously remove and/or block all ERBB receptors and ligands, are a feasible and effective approach against HER2-overexpressing cancers both sensitive and resistant to anti-HER2 therapies.

Citation Format: Schwarz LJ, Hutchinson KE, Estrada MV, Sanders ME, Dugger TC, Formisano L, Guerrero AL, Red-Brewer M, Young CD, Lantto J, Pedersen MW, Kragh M, Horak ID, Arteaga CL. Pan-HER, an antibody mixture with antitumor activity against drug-resistant HER2-overexpressing breast cancers with high ERBB ligand expression [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-12-09.

Detection and strain differentiation of infectious bronchitis virus in tracheal tissues from experimentally infected chickens by reverse transcription-polymerase chain reaction. Comparison with an immunohistochemical technique

Oligonucleotide pairs were constructed for priming the amplification of fragments of nucleocapsid (N) protein and spike glycoprotein (S) genes of avian infectious bronchitis virus (IBV) by reverse transcriptionpolymerase chain reaction (RT-PCR). One oligonucleotide pair amplified a common segment of the N-gene and could detect various strains of IBV in allantoic fluid from inoculated chicken embryos, and in tracheal tissue preparations from experimentally infected chickens. Four pairs of oligonucleotides selectively primed the amplification of the S1 gene of Massachusetts/Connecticut, D1466, D274/D3896 and 793B strains of IBV, respectively. Groups of specific pathogen free chickens were experimentally inoculated with the Massachusetts (H120, M41), the D1466 and the 793B strains of IBV, and tracheal tissue preparations were made from each bird for RT-PCR and for immunohistochemistry (IHC) up to 3 days post-inoculation. The N-gene RT-PCR detected IBV in 82% of the chickens, while IHC only detected IBV in 60%. This difference was significant (P<0.02). The detection rate by N-gene RT-PCR varied from 67 to 100% for the various strains of IBV inoculated. The S1 gene oligonucleotide pairs were applied to the same tissue preparations and they detected specifically the Massachusetts (M41 and H120), the D1466 and the 793B strains of IBV at rates varying between 58 and 92%. When the mixtures of the primers were applied, the detection rate in tissue preparations was reduced to the level of 50 to 67%. It is concluded that the direct detection of IBV in tracheal tissues by RT-PCR is more sensitive than IHC and that the RT-PCR technique is able to distinguish between types of IBV.

Ancient and modern environmental DNA

DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.

Analysing migrations of Atlantic cod Gadus morhua in the north-east Atlantic Ocean: then, now and the future

The application of data storage tags bears the potential for a quantum leap in the research on fish migrations, because not only first-capture and recapture positions are known, but at least theoretically, the migration path during the period at large can be reconstructed. Position, however, cannot be measured directly but has to be estimated using the available data on light, temperature, pressure and salinity. The reconstructed locations based on advanced estimation techniques have been termed geolocations. Examples are discussed which illustrate the applicability of geolocations in individual path descriptions, separation of reproductively isolated populations, timing and areas of spawning, tidal transport and use of protected areas. The examples are based on archival tag data from the North Sea, the Baltic Sea, the Barents Sea and Faroese and Icelandic Waters. Besides presenting the state-of-the-art geolocations for cod Gadus morhua in the north-east Atlantic Ocean, the major aim of this review is to raise awareness of gaps in knowledge and to identify ideas for new research.

Differential response to gefitinib of cells expressing normal EGFR and the mutant EGFRvIII

Epidermal growth factor receptor (EGFR) is frequently amplified and/or mutated in a number of human tumours and abnormal signalling from this receptor is believed to contribute to the malignant phenotype seen in these tumours. Gefitinib is a small molecule inhibitor that specifically binds and inhibits the EGFR tyrosine kinase and has been shown to inhibit the growth, proliferation, survival and invasion of a range of tumour cells overexpressing EGFR. However, clinical response to gefitinib has failed to correlate with EGFR levels and activity, indicating that other molecular mechanisms such as downstream signalling and mutations could be of importance in predicting clinical response. We therefore investigated the effect of the specific EGFR inhibitor gefitinib on the phosphorylation level, signalling and growth of cells expressing the naturally occurring constitutively active EGFR variant EGFRvIII, a low nontransforming level of EGFR and a high transforming level of EGFR. Results show that levels of gefitinib sufficient to suppress EGFR phosphorylations, EGFR-mediated proliferation and EGFR-mediated anchorage-independent growth are not sufficient to inhibit these features in cells expressing EGFRvIII. Furthermore, the data indicate that long-term exposure of EGFRvIII-expressing cells to low concentrations of gefitinib (0.01–0.1 μM) result in increased phosphotyrosine load of the receptor, increased signalling to ERK and stimulation of proliferation and anchorage-independent growth, presumably by inducing EGFRvIII dimerisation. Higher concentrations of gefitinib (1–2 μM), on the other hand, significantly decreased EGFRvIII phosphotyrosine load, EGFRvIII-mediated proliferation and anchorage-independent growth. Further studies are needed to investigate the implications of these important findings in the clinical setting.

The insulinoma-associated 1: a novel promoter for targeted cancer gene therapy for small-cell lung cancer

The insulinoma-associated 1 (INSM1) gene is expressed exclusively during early embryonal development, but has been found re-expressed at high levels in neuroendocrine tumors. The regulatory region of the INSM1 gene is therefore a potential candidate for regulating expression of a therapeutic gene in transcriptionally targeted cancer gene therapy against neuroendocrine tumors. We analyzed expression of a reporter gene from a 1.7 kb region of the INSM1 promoter in a large number of small-cell lung cancer (SCLC) cell lines. This INSM1 promoter region showed very high levels of expression in most of the SCLC cell lines and expression was absent in cell lines of non-neuroendocrine origin. Inclusion of the general transcriptional enhancer from SV40 compromised the specificity of the promoter and did not enhance transcription in most of the SCLC cell lines. For comparison, the region of the gastrin releasing peptide (GRP) previously suggested for SCLC gene therapy was analyzed in a similar manner. High expression was observed for a number of cell lines, but unlike for the INSM1 promoter, reporter gene expression from the GRP promoter did not correlate to the relative GRP mRNA levels, demonstrating that this region may not contain all necessary regulatory elements. Expression of the suicide gene herpes simplex virus thymidine kinase (HSV-TK) from the INSM1 promoter in combination with treatment with the prodrug ganciclovir (GCV) caused a significant increase in GCV sensitivity specifically in INSM1-expressing cell lines. The INSM1 promoter is therefore a potential novel tool for transcriptionally targeted gene therapy for neuroendocrine tumors.

Profile of differentially expressed genes mediated by the type III epidermal growth factor receptor mutation expressed in a small-cell lung cancer cell line

Previous studies have shown a correlation between expression of the EGF receptor type III mutation (EGFRvIII) and a more malignant phenotype of various cancers including: non-small-cell lung cancer, glioblastoma multiforme, prostate cancer and breast cancer. Thus, a detailed molecular genetic understanding of how the EGFRvIII contributes to the malignant phenotype is of major importance for future therapy. The GeneChip Hu6800Set developed by Affymetrix was used to identify changes in gene expression caused by the expression of EGFRvIII. The cell line selected for the study was an EGF receptor negative small-cell-lung cancer cell line, GLC3, stably transfected with the EGFRvIII gene in a Tet-On system. By comparison of mRNA levels in EGFRvIII-GLC3 with those of Tet-On-GLC3, it was found that the levels of mRNAs encoding several transcription factors (ATF-3, JunD, and c-Myb), cell adhesion molecules (CD36, CD24), signal transduction related molecules (MKP-1) and other molecules related to cancer (CD98, thymosin beta-10) were altered in the EGFRvIII transfected cell line. Northern hybridisations and Western blot analyses were used to verify selected results. The results indicate that expression of EGFRvIII alters expression of genes involved in the control of cell growth, survival and motility.

The type III epidermal growth factor receptor mutation. Biological significance and potential target for anti-cancer therapy

Mutations in the epidermal growth factor receptor occur frequently in a number of human tumours including gliomas, non-small-cell lung carcinomas, ovarian carcinomas and prostate carcinomas. The type III epidermal growth factor receptor mutation (variously named EGFRvIII, de2-7 EGFR or AEGFR), which lacks a portion of the extracellular ligand binding domain, is the most common. Here, we review the current status with regard to the role of EGFRvIII in human cancers. A detailed discussion of the formation of EGFRvIII and its structure at the protein level are likewise included along with a discussion of its more functional roles. The design and use (preclinical and clinical) of small molecule inhibitors, antibodies, and antisense oligonucleotides against wild-type EGFR are considered in detail as these strategies can be directly adapted to target EGFRvIII. Finally, the status of EGFRvIII targeted therapy is reviewed.

Coregulation of glucose uptake and vascular endothelial growth factor (VEGF) in two small-cell lung cancer (SCLC) sublines in vivo and in vitro

We examined the relationship between (18)F- labeled 2-fluro-2-deoxy-d-glucose (FDG) uptake, and expression of glucose transporters (GLUTs) in two human small-cell lung cancer (SCLC) lines CPH 54A and CPH 54B. Changes in the expression of GLUTs and vascular endothelial growth factor (VEGF) during 12-, 18-, and 24 hours of severe hypoxia in vivo (xenografts) and in vitro (cell cultures) were recorded for both tumor lines. The two SCLC lines are subpopulations of the same patient tumor. In spite of their common genomic origin they represent consistently different metabolic and microenvironmental phenotypes as well as treatment sensitivities. There were higher levels of Glut-1 protein in 54B and a correspondingly higher FDG uptake in this tumor line (P<.001). During hypoxia a significant upregulation of in VEGF mRNA, GLUT-1 mRNA, and Glut-1 and -3 protein occurred with a distinctly different time course in the two cell lines. A similar co-upregulation of GLUT and VEGF was seen in hypoxic tumors of both lines. There were no significant changes of HIF-1alpha mRNA during hypoxia in either of the cell lines. A more detailed understanding of such correlations between glucose metabolism, angiogenesis, and microenvironmental phenotype of tumors, by positron emission tomography (PET) and molecular techniques might further sophisticate our interpretation of glycolytic predominance in tumors as seen by 18FFDG PET.

Relationship between vessel density and expression of vascular endothelial growth factor and basic fibroblast growth factor in small cell lung cancer in vivo and in vitro

In 21 human small cell lung cancer (SCLC) cell lines, we determined the expression of mRNA and secreted protein levels of vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF). The VEGF expression was highly variable between cell lines, with a > 100-fold variation, under identical in vitro conditions. The bFGF expression in cell lines was generally very low. Nine of the cell lines were further analyzed during growth as solid tumor xenografts in nude mice (in vivo). A more uniform VEGF protein expression was present in vivo. Compared with the variable in vitro expression, VEGF was relatively up-regulated in the tumor lines CPH 54A and CPH 54B and down-regulated in GLC 3. One line, DMS 79, had a high VEGF expression in vivo as well as in vitro. The vessel density was determined by Chalkley point counting on CD31 immunostained cryosections of tumors of each of the nine SCLC lines. We found a strong positive correlation between vessel density and tissue VEGF protein expression (r(s) = 0.75; P = 0.02) and a comparatively strong negative correlation (r(s) = -0.80; P = 0.01) between vessel density and tissue bFGF expression. No significant correlation was present between vessel density and in vitro VEGF expression. We conclude that VEGF and bFGF expression is dependent on microenvironmental conditions, as well as cell line-specific factors, and that a strong positive correlation exists between in vivo VEGF expression and vessel density, whereas high tissue levels of bFGF are not correlated with higher vessel densities in SCLC xenografts.

The effect of whisky and wine consumption on total phenol content and antioxidant capacity of plasma from healthy volunteers

OBJECTIVE

To assess whether consumption of 100 ml of whisky or red wine by healthy male subjects increased plasma total phenol content and antioxidant capacity.

DESIGN

A Latin square arrangement to eliminate ordering effects whereby, after an overnight fast, nine volunteers consumed 100 ml of red wine, malt whisky or unmatured 'new make' spirit. Each volunteer participated on three occasions one week apart, consuming one of the beverages each time. Blood samples were obtained from the anticubital vein at intervals up to 4h after consumption of the beverages when a urine sample was also obtained.

RESULTS

Within 30 min of consumption of the wine and whisky, there was a similar and significant increase in plasma total phenol content and antioxidant capacity as determined by the ferric reducing capacity of plasma (FRAP). No changes were observed following consumption of 'new make' spirit.

CONCLUSIONS

Consumption of phenolic-containing alcoholic beverages transiently raises total phenol concentration and enhances the antioxidant capacity of plasma. This is compatible with suggestions that moderate alcohol usage and increased antioxidant intake decrease the risk of coronary heart disease.

Mycoplasma hyopneumoniae infection in pigs: duration of the disease and evaluation of four diagnostic assays

200 SPF pigs were infected by aerosol with Mycoplasma hyopneumoniae and the development of clinical signs, serological and pathological reactions were studied. Mean time to onset of coughing was 13 days. A mean delay of 9 days was observed from onset of coughing until seroconversion against M. hyopneumoniae as measured by ELISA. At an individual level, the sensitivity for this ELISA was estimated to 98-100% and the specificity to 93-100%. Pasteurella multocida was isolated from the majority of the lungs 4 weeks post inoculation with M. hyopneumoniae and the lung lesions in pigs were significantly larger when P. multocida was present as compared to pigs with M. hyopneumoniae alone. An evaluation of cultivation, immunofluorescence, ELISA and polymerase chain reaction for demonstration of M. hyopneumoniae in lungs showed that all four methods have a high sensitivity in the acute stages of pneumonia. In the later stages the sensitivity of cultivation was superior to the other methods. No differences in specificity were observed between the methods. The antigen-ELISA OD values and the immunofluorescence scores revealed a strong positive correlation. Nasal swabs were additionally used for demonstration of M. hyopneumoniae and the polymerase chain reaction was found superior to the other methods.