Elevated serum CEA is associated with liver metastasis and distinctive circulating tumor DNA alterations in patients with castration-resistant prostate cancer.

BACKGROUND: Elevated serum carcinoembryonic antigen (CEA) is used to identify "treatment emergent" forms of castration-resistant prostate cancer (CRPC) such as aggressive variant prostate cancer (AVPC). However, its individual utility as a prognostic marker and the genetic alterations associated with its expression have not been extensively studied in CRPC. METHODS: This study retrospectively analyzed clinical outcomes and circulating tumor DNA profiles in 163 patients with CRPC and elevated or normal serum CEA. These same patients were then classified as AVPC or non-AVPC and compared to determine the uniqueness of CEA-associated gene alterations. RESULTS: Patients with elevated CEA demonstrated higher rates of liver metastasis (37.5% vs. 19.1%, p = 0.02) and decreased median overall survival from CRPC diagnosis (28.7 vs. 73.2 mo, p < 0.0001). In addition, patients with elevated CEA were more likely to harbor copy number amplifications (CNAs) in AR, PIK3CA, MYC, BRAF, CDK6, MET, CCNE1, KIT, RAF1, and KRAS. Based on variant allele frequency we also defined "clonal" single-nucleotide variants (SNVs) thought to be driving disease progression in each patient and found that CEA expression was negatively correlated with clonal AR SNVs and positively correlated with clonal TP53 SNVs. Of these genetic associations, only the increases in clonal TP53 SNVs and KRAS amplifications were recapitulated among patients with AVPC when compared to patients without AVPC. CONCLUSIONS: Together these findings suggest that CEA expression in CRPC is associated with aggressive clinical behavior and gene alterations distinct from those in AVPC.

Quantum battles in attoscience: tunnelling.

ABSTRACT: What is the nature of tunnelling? This yet unanswered question is as pertinent today as it was at the dawn of quantum mechanics. This article presents a cross section of current perspectives on the interpretation, computational modelling, and numerical investigation of tunnelling processes in attosecond physics as debated in the Quantum Battles in Attoscience virtual workshop 2020.

Phlebotomus papatasi sand fly predicted salivary protein diversity and immune response potential based on in silico prediction in Egypt and Jordan populations.

Phlebotomus papatasi sand flies inject their hosts with a myriad of pharmacologically active salivary proteins to assist with blood feeding and to modulate host defenses. In addition, salivary proteins can influence cutaneous leishmaniasis disease outcome, highlighting the potential of the salivary components to be used as a vaccine. Variability of vaccine targets in natural populations influences antigen choice for vaccine development. Therefore, the objective of this study was to investigate the variability in the predicted protein sequences of nine of the most abundantly expressed salivary proteins from field populations, testing the hypothesis that salivary proteins appropriate to target for vaccination strategies will be possible. PpSP12, PpSP14, PpSP28, PpSP29, PpSP30, PpSP32, PpSP36, PpSP42, and PpSP44 mature cDNAs from field collected P. papatasi from three distinct ecotopes in the Middle East and North Africa were amplified, sequenced, and in silico translated to assess the predicted amino acid variability. Two of the predicted sequences, PpSP12 and PpSP14, demonstrated low genetic variability across the three geographic isolated sand fly populations, with conserved multiple predicted MHCII epitope binding sites suggestive of their potential application in vaccination approaches. The other seven predicted salivary proteins revealed greater allelic variation across the same sand fly populations, possibly precluding their use as vaccine targets.

Author Correction: Attosecond angular streaking and tunnelling time in atomic hydrogen.

In this Letter, the statement 'I.I. and A.B. performed computations at the NCI Australia' was missing from the Acknowledgements section. This has been corrected online.

Attosecond angular streaking and tunnelling time in atomic hydrogen.

The tunnelling of a particle through a potential barrier is a key feature of quantum mechanics that goes to the core of wave-particle duality. The phenomenon has no counterpart in classical physics, and there are no well constructed dynamical observables that could be used to determine 'tunnelling times'. The resulting debate1-5 about whether a tunnelling quantum particle spends a finite and measurable time under a potential barrier was reignited in recent years by the advent of ultrafast lasers and attosecond metrology6. Particularly important is the attosecond angular streaking ('attoclock') technique7, which can time the release of electrons in strong-field ionization with a precision of a few attoseconds. Initial measurements7-10 confirmed the prevailing view that tunnelling is instantaneous, but later studies11,12 involving multi-electron atoms-which cannot be accurately modelled, complicating interpretation of the ionization dynamics-claimed evidence for finite tunnelling times. By contrast, the simplicity of the hydrogen atom enables precise experimental measurements and calculations13-15 and makes it a convenient benchmark. Here we report attoclock and momentum-space imaging16 experiments on atomic hydrogen and compare these results with accurate simulations based on the three-dimensional time-dependent Schrödinger equation and our experimental laser pulse parameters. We find excellent agreement between measured and simulated data, confirming the conclusions of an earlier theoretical study17 of the attoclock technique in atomic hydrogen that presented a compelling argument for instantaneous tunnelling. In addition, we identify the Coulomb potential as the sole cause of the measured angle between the directions of electron emission and peak electric field: this angle had been attributed11,12 to finite tunnelling times. We put an upper limit of 1.8 attoseconds on any tunnelling delay, in agreement with recent theoretical findings18 and ruling out the interpretation of all commonly used 'tunnelling times'19 as 'time spent by an electron under the potential barrier'20.

Keldysh-Rutherford Model for the Attoclock.

We demonstrate a clear similarity between attoclock offset angles and Rutherford scattering angles taking the Keldysh tunneling width as the impact parameter and the vector potential of the driving pulse as the asymptotic velocity. This simple model is tested against the solution of the time-dependent Schrödinger equation using hydrogenic and screened (Yukawa) potentials of equal binding energy. We observe a smooth transition from a hydrogenic to "hard-zero" intensity dependence of the offset angle with variation of the Yukawa screening parameter. Additionally, we make a comparison with the attoclock offset angles for various noble gases obtained with the classical-trajectory Monte Carlo method. In all cases we find a close correspondence between the model predictions and numerical calculations. This suggests a largely Coulombic origin of the attoclock offset angle and casts further doubt on its interpretation in terms of a finite tunneling time.

Photoionization delays in xenon using single-shot referencing in the collinear back-focusing geometry.

Attosecond photoemission delays for all the valence (5p3/2, 5p1/2, 5s, 4d5/2, 4d3/2) subshells of xenon have been accessed using the interferometric RABBITT technique. The 4d subshell delays in Xe have been accessed for the first time, to the best of our knowledge, due to the high photon energy used. A novel technique of single-shot referencing in the collinear back-focusing geometry has been introduced. This enables us to distinguish the signal from principal photoelectron peaks due to ionization by extreme ultraviolet radiation only and infrared-induced sideband contributions, especially in the regions of spectral overlap.

Population genetics analysis of Phlebotomus papatasi sand flies from Egypt and Jordan based on mitochondrial cytochrome b haplotypes.

BACKGROUND: Phlebotomus papatasi sand flies are major vectors of Leishmania major and phlebovirus infection in North Africa and across the Middle East to the Indian subcontinent. Population genetics is a valuable tool in understanding the level of genetic variability present in vector populations, vector competence, and the development of novel control strategies. This study investigated the genetic differentiation between P. papatasi populations in Egypt and Jordan that inhabit distinct ecotopes and compared this structure to P. papatasi populations from a broader geographical range. METHODS: A 461 base pair (bp) fragment from the mtDNA cytochrome b (cyt b) gene was PCR amplified and sequenced from 116 individual female sand flies from Aswan and North Sinai, Egypt, as well as Swaimeh and Malka, Jordan. Haplotypes were identified and used to generate a median-joining network, F ST values and isolation-by-distance were also evaluated. Additional sand fly individuals from Afghanistan, Iran, Israel, Jordan, Libya, Tunisia and Turkey were included as well as previously published haplotypes to provide a geographically broad genetic variation analysis. RESULTS: Thirteen haplotypes displaying nine variant sites were identified from P. papatasi collected in Egypt and Jordan. No private haplotypes were identified from samples in North Sinai, Egypt, two were observed in Aswan, Egypt, four from Swaimeh, Jordan and two in Malka, Jordan. The Jordan populations clustered separately from the Egypt populations and produced more private haplotypes than those from Egypt. Pairwise F ST values fall in the range 0.024-0.648. CONCLUSION: The clustering patterns and pairwise F ST values indicate a strong differentiation between Egyptian and Jordanian populations, although this population structure is not due to isolation-by-distance. Other factors, such as environmental influences and the genetic variability in the circulating Le. major parasites, could possibly contribute to this heterogeneity. The present study aligns with previous reports in that pockets of genetic differentiation exists between populations of this widely dispersed species but, overall, the species remains relatively homogeneous.

Mitochondrial DNA mutations and cardiovascular disease.

PURPOSE OF REVIEW: Cardiovascular disease (CVD) is responsible for more morbidity and mortality worldwide than any other ailment. Strategies for reducing CVD prevalence must involve identification of individuals at high risk for these diseases, and the prevention of its initial development. Such preventive efforts are currently limited by an incomplete understanding of the genetic determinants of CVD risk. In this review, evidence for the involvement of inherited mitochondrial mutations in development of CVD is examined. RECENT FINDINGS: Several forms of CVD have been documented in the presence of pathogenic mitochondrial DNA (mtDNA) mutations, both in isolation and as part of larger syndromes. Other 'natural' mtDNA polymorphisms not overtly tied to any pathology have also been associated with alterations in mitochondrial function and individual risk for CVD, but until very recently these studies have been merely correlative. Fortunately, novel animal models are now allowing investigators to define a causal relationship between inherited 'natural' mtDNA polymorphisms, and cardiovascular function and pathology. SUMMARY: Cardiovascular involvement is highly prevalent among patients with pathogenic mtDNA mutations. The relationship between CVD susceptibility and 'natural' mtDNA polymorphisms requires further investigation, but will be aided in the near future by several novel experimental models.

Attosecond Time Delay in Photoemission and Electron Scattering near Threshold.

We study the time delay in the primary photoemission channel near the opening of an additional channel and compare it with the Wigner time delay in elastic scattering of the photoelectron near the corresponding inelastic threshold. The photoemission time delay near threshold is significantly enhanced, to a measurable 40 as, in comparison to the corresponding elastic scattering delay. The enhancement is due to the different lowest order of interelectron interaction coupling the primary and additional photoemission channels. We illustrate these findings by considering photodetachment from the H^{-} negative ion, and compare it with electron scattering on the hydrogen atom near the first excitation threshold. Other threshold processes of atomic photoionization and molecular photofragmentation, where photoemission time delay is enhanced, are identified. This opens the possibility of studying threshold behavior utilizing attosecond chronoscopy.

Endothelial Cell Bioenergetics and Mitochondrial DNA Damage Differ in Humans Having African or West Eurasian Maternal Ancestry.

BACKGROUND: We hypothesized that endothelial cells having distinct mitochondrial genetic backgrounds would show variation in mitochondrial function and oxidative stress markers concordant with known differential cardiovascular disease susceptibilities. To test this hypothesis, mitochondrial bioenergetics were determined in endothelial cells from healthy individuals with African versus European maternal ancestries. METHODS AND RESULTS: Bioenergetics and mitochondrial DNA (mtDNA) damage were assessed in single-donor human umbilical vein endothelial cells belonging to mtDNA haplogroups H and L, representing West Eurasian and African maternal ancestries, respectively. Human umbilical vein endothelial cells from haplogroup L used less oxygen for ATP production and had increased levels of mtDNA damage compared with those in haplogroup H. Differences in bioenergetic capacity were also observed in that human umbilical vein endothelial cells belonging to haplogroup L had decreased maximal bioenergetic capacities compared with haplogroup H. Analysis of peripheral blood mononuclear cells from age-matched healthy controls with West Eurasian or African maternal ancestries showed that haplogroups sharing an A to G mtDNA mutation at nucleotide pair 10398 had increased mtDNA damage compared with those lacking this mutation. Further study of angiographically proven patients with coronary artery disease and age-matched healthy controls revealed that mtDNA damage was associated with vascular function and remodeling and that age of disease onset was later in individuals from haplogroups lacking the A to G mutation at nucleotide pair 10398. CONCLUSIONS: Differences in mitochondrial bioenergetics and mtDNA damage associated with maternal ancestry may contribute to endothelial dysfunction and vascular disease.

Mitochondrial Genetics Regulate Breast Cancer Tumorigenicity and Metastatic Potential.

Current paradigms of carcinogenic risk suggest that genetic, hormonal, and environmental factors influence an individual's predilection for developing metastatic breast cancer. Investigations of tumor latency and metastasis in mice have illustrated differences between inbred strains, but the possibility that mitochondrial genetic inheritance may contribute to such differences in vivo has not been directly tested. In this study, we tested this hypothesis in mitochondrial-nuclear exchange mice we generated, where cohorts shared identical nuclear backgrounds but different mtDNA genomes on the background of the PyMT transgenic mouse model of spontaneous mammary carcinoma. In this setting, we found that primary tumor latency and metastasis segregated with mtDNA, suggesting that mtDNA influences disease progression to a far greater extent than previously appreciated. Our findings prompt further investigation into metabolic differences controlled by mitochondrial process as a basis for understanding tumor development and metastasis in individual subjects. Importantly, differences in mitochondrial DNA are sufficient to fundamentally alter disease course in the PyMT mouse mammary tumor model, suggesting that functional metabolic differences direct early tumor growth and metastatic efficiency.

An ex-vivo model for evaluating bioenergetics in aortic rings.

Cardiovascular disease (CVD) is the leading cause of death worldwide and it exhibits a greatly increasing incidence proportional to aging. Atherosclerosis is a chronic condition of arterial hardening resulting in restriction of oxygen delivery and blood flow to the heart. Relationships between mitochondrial DNA damage, oxidant production, and early atherogenesis have been recently established and it is likely that aspects of atherosclerotic risk are metabolic in nature. Here we present a novel method through which mitochondrial bioenergetics can be assessed from whole aorta tissue. This method does not require mitochondrial isolation or cell culture and it allows for multiple technical replicates and expedient measurement. This procedure facilitates quantitative bioenergetic analysis and can provide great utility in better understanding the link between mitochondria, metabolism, and atherogenesis.