Multiple Sox genes are expressed in stem cells or in differentiating neuro-sensory cells in the hydrozoan Clytia hemisphaerica

<p>Abstract</p> <p>Background</p> <p>The <it>Sox </it>genes are important regulators of animal development belonging to the HMG domain-containing class of transcription factors. Studies in bilaterian models have notably highlighted their pivotal role in controlling progression along cell lineages, various <it>Sox </it>family members being involved at one side or the other of the critical balance between self-renewing stem cells/proliferating progenitors, and cells undergoing differentiation.</p> <p>Results</p> <p>We have investigated the expression of 10 <it>Sox </it>genes in the cnidarian <it>Clytia hemisphaerica</it>. Our phylogenetic analyses allocated most of these <it>Clytia </it>genes to previously-identified Sox groups: SoxB (<it>CheSox2, CheSox3, CheSox10, CheSox13, CheSox14</it>), SoxC (<it>CheSox12</it>), SoxE (<it>CheSox1, CheSox5</it>) and SoxF (<it>CheSox11</it>), one gene (<it>CheSox15</it>) remaining unclassified. In the planula larva and in the medusa, the <it>SoxF </it>orthologue was expressed throughout the endoderm. The other genes were expressed either in stem cells/undifferentiated progenitors, or in differentiating (-ed) cells with a neuro-sensory identity (nematocytes or neurons). In addition, most of them were expressed in the female germline, with their maternal transcripts either localised to the animal region of the egg, or homogeneously distributed.</p> <p>Conclusions</p> <p>Comparison with other cnidarians, ctenophores and bilaterians suggest ancient evolutionary conservation of some aspects of gene expression/function at the <it>Sox </it>family level: (i) many <it>Sox </it>genes are expressed in stem cells and/or undifferentiated progenitors; (ii) other genes, or the same under different contexts, are associated with neuro-sensory cell differentiation; (iii) <it>Sox </it>genes are commonly expressed in the germline; (iv) <it>SoxF </it>group genes are associated with endodermal derivatives. Strikingly, total lack of correlation between a given <it>Sox </it>orthology group and expression/function in stem cells/progenitors <it>vs</it>. in differentiating cells implies that <it>Sox </it>genes can easily switch from one side to the other of the balance between these fundamental cellular states in the course of evolution.</p

Assessment of the pathogenicity of fusarium euwallaceae to grapevine and deciduous fruit trees in South Africa and its rapid detection in woody tissues

Thesis (MScConsEcol)--Stellenbosch University, 2022.ENGLISH ABSTRACT: A myriad of different tree species in South Africa are under threat from the invasive woodboring beetle, Euwallacea fornicatus (Coleoptera: Curculionidae: Scolytinae), the polyphagous shot hole borer, PSHB. While constructing galleries in the wood of hosts these beetles release spores of a mutualistic fungus, Fusarium euwallaceae (Hypocreales; Nectriaceae).The fungus colonises the xylem tissues and acts as the primary food source for the beetle, but colonisation can lead to Fusarium dieback disease in susceptible hosts. Many economically important fruit tree species have been identified as possible hosts; however, no assessments have specifically tested the pathogenicity of F. euwallaceae towards these. The work presented in this thesis set out to evaluate the susceptibility of different deciduous fruit trees (plum, nectarine and apple) and grapevine to F. euwallaceae. The effect of branch diameter and increased inoculum load on the rate of lesion development was also assessed. Fusarium euwallaceae was pathogenic to all fruit tree species and cultivars tested but no evidence of disease development was recorded in grapevine. There were no significant differences in virulence between the different isolates. There was also no evidence that differences in branch diameter or differences in the number of inoculation points on a branch can affect the growth rate of F. euwallaceae. For monitoring, the presence of PSHB is often determined by positive identification of F. euwallaceae without collection of the beetle, particularly when beetles are not able to establish viable colonies. Standard approaches to identify F. euwallaceae are costly and labour- and time intensive as the fungus needs to be isolated and cultivated from freshly collected material, the DNA needs to be extracted and purified, and the DNA needs to be sequenced for a marker that can be used to identify it. In this thesis a faster, more accessible, and cheaper tool for the identification of F. euwallaceae in both fresh and dried wood samples which increases monitoring capacity when resources are limited is presented. A species-specific marker was identified from literature and an optimized PCR protocol for the identification of F. euwallaceae was developed that removes requirements to rear the fungus, purify its DNA and to sequence a DNA marker. This protocol was tested on eleven different hosts, all but one of which that produced positive results in at least one of the replicates. Amplification was not possible in one of the hosts likely due to the high concentration of PCR inhibitory compounds. In cases like this, a secondary measure based on the protocol developed here can be used where fungal isolates are first obtained from diseased woody tissues and these subjected to the rapid detection protocol. Amplification of F. euwallaceae DNA using this approach had a 100% reproducibility rate.AFRIKAANSE OPSOMMING: 'n Magdom verskillende boomspesies in Suid Afrika is bedreig deur die indringer stamboorder, Euwallacea fornicatus (Coleoptera: Curcilonidae: Scolutinae), die polifage stompkopboorder , (PSHB). Terwyl die kewer gate deur die hout boor van gashere stel dit spore van sy mutualistiese swam, Fusarium euwallaceae (Hypocreales; Nectriaceae), vry. Die swam koloniseer die xileem weevsel en dien as die primêre voedingsbron vir die kewer, maar kolonisering kan lei tot Fusarium afsterwe siekte in vatbare gashere. Baie boom spesies wat ekonomies belangrik is, is al identifiseer as moontlike gashere; maar geen assesserings wat spesefiek die patogenisiteit van F. euwallaceae op hierdie gashere toets was al uitgevoer nie. Die werk wat in hierdie tesis aangebied word stel om die vatbaarheid van verskillende sagtevrugtebome (pruim, nektarien en apple) en wingerdstokke aan F. euwallaceae te evalueer. Die effek wat tak diameter en toegeneemde inokulum lading het op die koers van letsel groei was ook geassesseer. Fusarium euwallaceae was patogenies tot alle vrugteboom spesies en kultivars wat getoets is, maar geen bewyse van siekte ontwikkeling was waargeneem in wingerd nie. Daar was geen verskille in virulensie tussen verskillende isolate gevind wat betekenisvol was nie. Daar was ook geen bewyse dat verskille in tak diameter of verskille in die nommer van inokulasiepunte die koers van F. euwallaceae groei affekteer nie. Vir monitering, is die teenwoordigheid van PSHB vas gestel deur positiewe identifiikasie van F. euwallaceae sonder versameling van die beesie, veral wanneer beesies nie lewensvatbare kolonies vestig nie. Standaard benaderings om F. euwallaceae te identifiseer is duur en arbeids- en tyd intensief omdat die swam eers geisoleer en gekweek moet word vanaf vars versamelde plant material, dan word DNA ekstraksie uitgevoer en DNA word gesuiwer. Daarna moet volgordebapaling uitgevoer word met ‘n merker wat kan gebruik word om F. euwallaceae te identifiseer. In hierdie tesis word ‘n vinniger, meer toeganklikke en goedkoper metode vir die identifikasie van F. euwallaceae in beide vars en gedroogte plantmateriaal aangebied. ‘n Spesies-spesefieke merker was identifiseer vanaf literatuur en ‘n geoptimiseerde PCR protokol was ontwikkel vir die identifikasie van F. euwallaceae wat die vereistes verwyder om die swam eers te kweek dan DNA ekstraksie- en DNA merker volgordebepaling uit te voer. Hierdie protokol was getoets op elf verskillende gashere, waarvan almal behalwe een positiewe resultate in ten minste een van vyf replikate positiewe resultate gegee het. Versterking was nie moontlik in een van die gashere nie, waarskynlik omdat daar hoë konsentrasies van inihiberende verbindings teenwoordig is. In gevalle soos hierdie is daar ‘n sekondêre benadering wat gebasseer is op die protokol wat hier ontwikkel is; die vinnige opsprong protokol kan toegepas word op swam isolate wat vooraf verkry is vanaf siek houtagtige weevsels. Versterking van F. euwallaceae DNA met hierdie benadering het ‘n 100% reproduseerbaarheid.Master

Effects of chemotherapy on contralateral breast cancer risk in BRCA1 and BRCA2 mutation carriers:A nationwide cohort study

AIM: BRCA1/2 mutation carriers with primary breast cancer (PBC) are at high risk of contralateral breast cancer (CBC). In a nationwide cohort, we investigated the effects of chemotherapeutic agents given for PBC on CBC risk separately in BRCA1 and BRCA2 mutation carriers. PATIENTS AND METHODS: BRCA1 or BRCA2 mutation carriers with an invasive PBC diagnosis from 1990 to 2017 were selected from a Dutch cohort. We estimated cumulative CBC incidence using competing risks analysis. Hazard ratios (HR) for the effect of neo-adjuvant or adjuvant chemotherapy and different chemotherapeutic agents on CBC risk were estimated using Cox regression. RESULTS: We included 1090 BRCA1 and 568 BRCA2 mutation carriers; median follow-up was 8.9 and 8.4 years, respectively. Ten-year cumulative CBC incidence for treatment with and without chemotherapy was 6.7% [95%CI: 5.1–8.6] and 16.7% [95%CI: 10.8–23.7] in BRCA1 and 4.8% [95%CI: 2.7–7.8] and 16.0% [95%CI: 9.3–24.4] in BRCA2 mutation carriers, respectively. Chemotherapy was associated with reduced CBC risk in BRCA1 (multivariable HR: 0.46, 95%CI: 0.29–0.74); a similar trend was observed in BRCA2 mutation carriers (HR: 0.63, 95%CI: 0.29–1.39). In BRCA1, risk reduction was most pronounced in the first 5 years (HR: 0.32, 95%CI: 0.17–0.61). Anthracyclines and the combination of anthracyclines with taxanes were associated with substantial CBC risk reduction in BRCA1 carriers (HR: 0.34, 95%CI: 0.17–0.68 and HR: 0.22, 95%CI: 0.08–0.62, respectively). CONCLUSION: Risk-reducing effects of chemotherapy are substantial for at least 5 years and may be used in personalised CBC risk prediction in any case for BRCA1 mutation carriers

Are Hox Genes Ancestrally Involved in Axial Patterning? Evidence from the Hydrozoan Clytia hemisphaerica (Cnidaria)

Background: The early evolution and diversification of Hox-related genes in eumetazoans has been the subject of conflicting hypotheses concerning the evolutionary conservation of their role in axial patterning and the pre-bilaterian origin of the Hox and ParaHox clusters. The diversification of Hox/ParaHox genes clearly predates the origin of bilaterians. However, the existence of a "Hox code' predating the cnidarian-bilaterian ancestor and supporting the deep homology of axes is more controversial. This assumption was mainly based on the interpretation of Hox expression data from the sea anemone, but growing evidence from other cnidarian taxa puts into question this hypothesis. Methodology/Principal Findings: Hox, ParaHox and Hox-related genes have been investigated here by phylogenetic analysis and in situ hybridisation in Clytia hemisphaerica, an hydrozoan species with medusa and polyp stages alternating in the life cycle. Our phylogenetic analyses do not support an origin of ParaHox and Hox genes by duplication of an ancestral ProtoHox cluster, and reveal a diversification of the cnidarian HOX9-14 genes into three groups called A, B, C. Among the 7 examined genes, only those belonging to the HOX9-14 and the CDX groups exhibit a restricted expression along the oralaboral axis during development and in the planula larva, while the others are expressed in very specialised areas at the medusa stage. Conclusions/Significance: Cross species comparison reveals a strong variability of gene expression along the oral-aboral axis and during the life cycle among cnidarian lineages. The most parsimonious interpretation is that the Hox code, collinearity and conservative role along the antero-posterior axis are bilaterian innovations

A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers.

Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10-8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707

The predictive ability of the 313 variant–based polygenic risk score for contralateral breast cancer risk prediction in women of European ancestry with a heterozygous BRCA1 or BRCA2 pathogenic variant

Abstract: Purpose: To evaluate the association between a previously published 313 variant–based breast cancer (BC) polygenic risk score (PRS313) and contralateral breast cancer (CBC) risk, in BRCA1 and BRCA2 pathogenic variant heterozygotes. Methods: We included women of European ancestry with a prevalent first primary invasive BC (BRCA1 = 6,591 with 1,402 prevalent CBC cases; BRCA2 = 4,208 with 647 prevalent CBC cases) from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), a large international retrospective series. Cox regression analysis was performed to assess the association between overall and ER-specific PRS313 and CBC risk. Results: For BRCA1 heterozygotes the estrogen receptor (ER)-negative PRS313 showed the largest association with CBC risk, hazard ratio (HR) per SD = 1.12, 95% confidence interval (CI) (1.06–1.18), C-index = 0.53; for BRCA2 heterozygotes, this was the ER-positive PRS313, HR = 1.15, 95% CI (1.07–1.25), C-index = 0.57. Adjusting for family history, age at diagnosis, treatment, or pathological characteristics for the first BC did not change association effect sizes. For women developing first BC < age 40 years, the cumulative PRS313 5th and 95th percentile 10-year CBC risks were 22% and 32% for BRCA1 and 13% and 23% for BRCA2 heterozygotes, respectively. Conclusion: The PRS313 can be used to refine individual CBC risks for BRCA1/2 heterozygotes of European ancestry, however the PRS313 needs to be considered in the context of a multifactorial risk model to evaluate whether it might influence clinical decision-making

A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

Abstract: Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10−8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers

Author Correction: A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers.

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-23162-4