Targeting alternative splicing as a novel approach to chemotherapy induced peripheral neuropathy

Chemotherapy induced peripheral neuropathy (CIPN) is one of the most prevalent adverse effects of many chemotherapy drugs. It is estimated that up to 85% of patients suffer from CIPN during treatment and in many patients, painful neuropathy can continue beyond cessation of chemotherapy. Common symptoms of CIPN include, thermal and mechanical allodynia and painful sensations that are commonly described as burning and shooting pain. CIPN is often a dose limiting factor in the provision of chemotherapy. Currently, there are no effective treatments capable of preventing or treating CIPN. Consequently, CIPN is becoming an increasingly significant healthcare burden. As a result of this burden, there is a pressing need to develop novel therapeutic approaches with which to prevent and treat CIPN. In addition to this, development of chemotherapy agents that are as effective as traditional compounds but lack the severe adverse effects is also desirable. Recently, the neuroprotective and antinociceptive properties of alternatively spliced VEGF-A isoforms were identified in the context of diabetic and platinum chemotherapy neuropathy. VEGF-A isoform expression is governed by the activity of splicing kinase SRPK1 which phosphorylates splicing factor SRSF1 and controls the expression of VEGF-A isoforms by selection of the proximal or distal splicing site of exon 8 of the VEGFA gene. Inhibition of SRPK1 leads to distal splice site selection and the expression of VEGF-Axxxb isoforms which are neuroprotective and anti-nociceptive. Other splicing kinases with confirmed or putative roles in VEGF-A alternative splicing control include CLK1/CLK2 and DYRK1A. Therefore it has been proposed that novel compounds that inhibit these splicing kinases could have potential utility in preventing the onset of CIPN or be capable of reversing the neuropathy therapeutically via VEGF, or alternative splicing pathways. This thesis investigated the anti-nociceptive and neuroprotective properties of 4 novel splicing kinase inhibitors in in vitro models of vincristine induced neuronal sensitisation and vincristine induced neurite dieback, using dissociated primary DRG neurons. Additionally, an early stage chemotherapy agent, jerantinine was used in the same models and was compared to the neurotoxic and sensitising effects of a traditional agent, vincristine. Alteration of splicing kinases SRPK1, CLK1, CLK2 and DYRK1A with the 4 compounds was able to significantly inhibit vincristine induced sensitisation, in addition to preventing neurite dieback in response to chemotherapy challenge whilst having little or no detrimental effect as independent treatments. Furthermore, jerantinine did not sensitise neurons to the same degree as vincristine and caused a milder degree of neurite dieback. Using a 3D tumour spheroid model, inhibition of all 4 kinases combined with vincristine treatment significantly reduced spheroid growth whilst inhibitors had no effect on spheroid growth in the absence of vincristine. These findings suggest that these compounds will not inhibit chemotherapy activity and appease concerns that they could drive tumour growth. These results demonstrate that control of alternative splicing via inhibition of multiple kinases could be a potentially beneficial in preventing or treating CIPN, and that the novel chemotherapy agent jerantinine is worth developing further due to its reduced adverse effects

Targeting alternative splicing as a novel approach to chemotherapy induced peripheral neuropathy

Chemotherapy induced peripheral neuropathy (CIPN) is one of the most prevalent adverse effects of many chemotherapy drugs. It is estimated that up to 85% of patients suffer from CIPN during treatment and in many patients, painful neuropathy can continue beyond cessation of chemotherapy. Common symptoms of CIPN include, thermal and mechanical allodynia and painful sensations that are commonly described as burning and shooting pain. CIPN is often a dose limiting factor in the provision of chemotherapy. Currently, there are no effective treatments capable of preventing or treating CIPN. Consequently, CIPN is becoming an increasingly significant healthcare burden. As a result of this burden, there is a pressing need to develop novel therapeutic approaches with which to prevent and treat CIPN. In addition to this, development of chemotherapy agents that are as effective as traditional compounds but lack the severe adverse effects is also desirable. Recently, the neuroprotective and antinociceptive properties of alternatively spliced VEGF-A isoforms were identified in the context of diabetic and platinum chemotherapy neuropathy. VEGF-A isoform expression is governed by the activity of splicing kinase SRPK1 which phosphorylates splicing factor SRSF1 and controls the expression of VEGF-A isoforms by selection of the proximal or distal splicing site of exon 8 of the VEGFA gene. Inhibition of SRPK1 leads to distal splice site selection and the expression of VEGF-Axxxb isoforms which are neuroprotective and anti-nociceptive. Other splicing kinases with confirmed or putative roles in VEGF-A alternative splicing control include CLK1/CLK2 and DYRK1A. Therefore it has been proposed that novel compounds that inhibit these splicing kinases could have potential utility in preventing the onset of CIPN or be capable of reversing the neuropathy therapeutically via VEGF, or alternative splicing pathways. This thesis investigated the anti-nociceptive and neuroprotective properties of 4 novel splicing kinase inhibitors in in vitro models of vincristine induced neuronal sensitisation and vincristine induced neurite dieback, using dissociated primary DRG neurons. Additionally, an early stage chemotherapy agent, jerantinine was used in the same models and was compared to the neurotoxic and sensitising effects of a traditional agent, vincristine. Alteration of splicing kinases SRPK1, CLK1, CLK2 and DYRK1A with the 4 compounds was able to significantly inhibit vincristine induced sensitisation, in addition to preventing neurite dieback in response to chemotherapy challenge whilst having little or no detrimental effect as independent treatments. Furthermore, jerantinine did not sensitise neurons to the same degree as vincristine and caused a milder degree of neurite dieback. Using a 3D tumour spheroid model, inhibition of all 4 kinases combined with vincristine treatment significantly reduced spheroid growth whilst inhibitors had no effect on spheroid growth in the absence of vincristine. These findings suggest that these compounds will not inhibit chemotherapy activity and appease concerns that they could drive tumour growth. These results demonstrate that control of alternative splicing via inhibition of multiple kinases could be a potentially beneficial in preventing or treating CIPN, and that the novel chemotherapy agent jerantinine is worth developing further due to its reduced adverse effects

Between roost contact is essential for maintenance of European bat lyssavirus type-2 in Myotis daubentonii bat reservoir: 'The Swarming Hypothesis'

Many high-consequence human and animal pathogens persist in wildlife reservoirs. An understanding of the dynamics of these pathogens in their reservoir hosts is crucial to inform the risk of spill-over events, yet our understanding of these dynamics is frequently insufficient. Viral persistence in a wild bat population was investigated by combining empirical data and in-silico analyses to test hypotheses on mechanisms for viral persistence. A fatal zoonotic virus, European Bat lyssavirus type 2 (EBLV-2), in Daubenton's bats (Myotis daubentonii) was used as a model system. A total of 1839 M. daubentonii were sampled for evidence of virus exposure and excretion during a prospective nine year serial cross-sectional survey. Multivariable statistical models demonstrated age-related differences in seroprevalence, with significant variation in seropositivity over time and among roosts. An Approximate Bayesian Computation approach was used to model the infection dynamics incorporating the known host ecology. The results demonstrate that EBLV-2 is endemic in the study population, and suggest that mixing between roosts during seasonal swarming events is necessary to maintain EBLV-2 in the population. These findings contribute to understanding how bat viruses can persist despite low prevalence of infection, and why infection is constrained to certain bat species in multispecies roosts and ecosystems

Berkeley Supernova Ia Program I: Observations, Data Reduction, and Spectroscopic Sample of 582 Low-Redshift Type Ia Supernovae

In this first paper in a series we present 1298 low-redshift (z\leq0.2) optical spectra of 582 Type Ia supernovae (SNe Ia) observed from 1989 through 2008 as part of the Berkeley SN Ia Program (BSNIP). 584 spectra of 199 SNe Ia have well-calibrated light curves with measured distance moduli, and many of the spectra have been corrected for host-galaxy contamination. Most of the data were obtained using the Kast double spectrograph mounted on the Shane 3 m telescope at Lick Observatory and have a typical wavelength range of 3300-10,400 Ang., roughly twice as wide as spectra from most previously published datasets. We present our observing and reduction procedures, and we describe the resulting SN Database (SNDB), which will be an online, public, searchable database containing all of our fully reduced spectra and companion photometry. In addition, we discuss our spectral classification scheme (using the SuperNova IDentification code, SNID; Blondin & Tonry 2007), utilising our newly constructed set of SNID spectral templates. These templates allow us to accurately classify our entire dataset, and by doing so we are able to reclassify a handful of objects as bona fide SNe Ia and a few other objects as members of some of the peculiar SN Ia subtypes. In fact, our dataset includes spectra of nearly 90 spectroscopically peculiar SNe Ia. We also present spectroscopic host-galaxy redshifts of some SNe Ia where these values were previously unknown. [Abridged]Comment: 34 pages, 11 figures, 11 tables, revised version, re-submitted to MNRAS. Spectra will be released in January 2013. The SN Database homepage (http://hercules.berkeley.edu/database/index_public.html) contains the full tables, plots of all spectra, and our new SNID template

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Rad21-Cohesin Haploinsufficiency Impedes DNA Repair and Enhances Gastrointestinal Radiosensitivity in Mice

Approximately half of cancer-affected patients receive radiotherapy (RT). The doses delivered have been determined upon empirical experience based upon average radiation responses. Ideally higher curative radiation doses might be employed in patients with genuinely normal radiation responses and importantly radiation hypersensitive patients would be spared the consequences of excessive tissue damage if they were indentified before treatment. Rad21 is an integral subunit of the cohesin complex, which regulates chromosome segregation and DNA damage responses in eukaryotes. We show here, by targeted inactivation of this key cohesin component in mice, that Rad21 is a DNA-damage response gene that markedly affects animal and cell survival. Biallelic deletion of Rad21 results in early embryonic death. Rad21 heterozygous mutant cells are defective in homologous recombination (HR)-mediated gene targeting and sister chromatid exchanges. Rad21+/− animals exhibited sensitivity considerably greater than control littermates when challenged with whole body irradiation (WBI). Importantly, Rad21+/− animals are significantly more sensitive to WBI than Atm heterozygous mutant mice. Since supralethal WBI of mammals most typically leads to death via damage to the gastrointestinal tract (GIT) or the haematopoietic system, we determined the functional status of these organs in the irradiated animals. We found evidence for GIT hypersensitivity of the Rad21 mutants and impaired bone marrow stem cell clonogenic regeneration. These data indicate that Rad21 gene dosage is critical for the ionising radiation (IR) response. Rad21 mutant mice thus represent a new mammalian model for understanding the molecular basis of irradiation effects on normal tissues and have important implications in the understanding of acute radiation toxicity in normal tissues

The Science of Sungrazers, Sunskirters, and Other Near-Sun Comets

This review addresses our current understanding of comets that venture close to the Sun, and are hence exposed to much more extreme conditions than comets that are typically studied from Earth. The extreme solar heating and plasma environments that these objects encounter change many aspects of their behaviour, thus yielding valuable information on both the comets themselves that complements other data we have on primitive solar system bodies, as well as on the near-solar environment which they traverse. We propose clear definitions for these comets: We use the term near-Sun comets to encompass all objects that pass sunward of the perihelion distance of planet Mercury (0.307 AU). Sunskirters are defined as objects that pass within 33 solar radii of the Sun’s centre, equal to half of Mercury’s perihelion distance, and the commonly-used phrase sungrazers to be objects that reach perihelion within 3.45 solar radii, i.e. the fluid Roche limit. Finally, comets with orbits that intersect the solar photosphere are termed sundivers. We summarize past studies of these objects, as well as the instruments and facilities used to study them, including space-based platforms that have led to a recent revolution in the quantity and quality of relevant observations. Relevant comet populations are described, including the Kreutz, Marsden, Kracht, and Meyer groups, near-Sun asteroids, and a brief discussion of their origins. The importance of light curves and the clues they provide on cometary composition are emphasized, together with what information has been gleaned about nucleus parameters, including the sizes and masses of objects and their families, and their tensile strengths. The physical processes occurring at these objects are considered in some detail, including the disruption of nuclei, sublimation, and ionisation, and we consider the mass, momentum, and energy loss of comets in the corona and those that venture to lower altitudes. The different components of comae and tails are described, including dust, neutral and ionised gases, their chemical reactions, and their contributions to the near-Sun environment. Comet-solar wind interactions are discussed, including the use of comets as probes of solar wind and coronal conditions in their vicinities. We address the relevance of work on comets near the Sun to similar objects orbiting other stars, and conclude with a discussion of future directions for the field and the planned ground- and space-based facilities that will allow us to address those science topics

Ecosystem services from Southern African woodlands and their future under global change

Miombo and mopane woodlands are the dominant land cover in southern Africa. Ecosystem services from these woodlands support the livelihoods of 100 M rural people and 50 M urban dwellers, and others beyond the region. Provisioning services contribute $9 ± 2 billion yr(−1) to rural livelihoods; 76$780 M. Woodlands support much of the region's agriculture through transfers of nutrients to fields and shifting cultivation. Woodlands store 18–24 PgC carbon, and harbour a unique and diverse flora and fauna that provides spiritual succour and attracts tourists. Longstanding processes that will impact service provision are the expansion of croplands (0.1 M km(2); 2000–2014), harvesting of woodfuels (93 M tonnes yr(−1)) and changing access arrangements. Novel, exogenous changes include large-scale land acquisitions (0.07 M km(2); 2000–2015), climate change and rising CO(2). The net ecological response to these changes is poorly constrained, as they act in different directions, and differentially on trees and grasses, leading to uncertainty in future service provision. Land-use change and socio-political dynamics are likely to be dominant forces of change in the short term, but important land-use dynamics remain unquantified. This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’

The Origin and Evolution of Mutations in Acute Myeloid Leukemia

SummaryMost mutations in cancer genomes are thought to be acquired after the initiating event, which may cause genomic instability and drive clonal evolution. However, for acute myeloid leukemia (AML), normal karyotypes are common, and genomic instability is unusual. To better understand clonal evolution in AML, we sequenced the genomes of M3-AML samples with a known initiating event (PML-RARA) versus the genomes of normal karyotype M1-AML samples and the exomes of hematopoietic stem/progenitor cells (HSPCs) from healthy people. Collectively, the data suggest that most of the mutations found in AML genomes are actually random events that occurred in HSPCs before they acquired the initiating mutation; the mutational history of that cell is “captured” as the clone expands. In many cases, only one or two additional, cooperating mutations are needed to generate the malignant founding clone. Cells from the founding clone can acquire additional cooperating mutations, yielding subclones that can contribute to disease progression and/or relapse

Association of genetic variation with systolic and diastolic blood pressure among African Americans: the Candidate Gene Association Resource study

The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10−8) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10−8). The top IBC association for SBP was rs2012318 (P= 6.4 × 10−6) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10−6) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexit