Nucleolus activity-dependent recruitment and biomolecular condensation by pH sensing

DEAD-box ATPases are major regulators of biomolecular condensates and orchestrate diverse biochemical processes that are critical for the functioning of cells. How DEAD-box proteins are selectively recruited to their respective biomolecular condensates is unknown. We explored this in the context of the nucleolus and DEAD-box protein DDX21. We find that the pH of the nucleolus is intricately linked to the transcriptional activity of the organelle and facilitates the recruitment and condensation of DDX21. We identify an evolutionarily conserved feature of the C terminus of DDX21 responsible for nucleolar localization. This domain is essential for zebrafish development, and its intrinsically disordered and isoelectric properties are necessary and sufficient for the ability of DDX21 to respond to changes in pH and form condensates. Molecularly, the enzymatic activities of poly(ADP-ribose) polymerases contribute to maintaining the nucleolar pH and, consequently, DDX21 recruitment and nucleolar partitioning. These observations reveal an activity-dependent physicochemical mechanism for the selective recruitment of biochemical activities to biomolecular condensates.

SBDSR126T rescues survival of sbds -/- zebrafish in a dose-dependent manner independently of Tp53

Defects in ribosomal biogenesis profoundly affect organismal development and cellular function, and these ribosomopathies produce a variety of phenotypes. One ribosomopathy, Shwachman-Diamond syndrome (SDS) is characterized by neutropenia, pancreatic exocrine insufficiency, and skeletal anomalies. SDS results from biallelic mutations in SBDS, which encodes a ribosome assembly factor. Some individuals express a missense mutation, SBDS R126T , along with the common K62X mutation. We reported that the sbds-null zebrafish phenocopies much of SDS. We further showed activation of Tp53-dependent pathways before the fish died during the larval stage. Here, we expressed SBDS R126T as a transgene in the sbds -/- background. We showed that one copy of the SBDS R126T transgene permitted the establishment of maternal zygotic sbds-null fish which produced defective embryos with cdkn1a up-regulation, a Tp53 target involved in cell cycle arrest. None survived beyond 3 dpf. However, two copies of the transgene resulted in normal development and lifespan. Surprisingly, neutropenia persisted. The surviving fish displayed suppression of female sex differentiation, a stress response in zebrafish. To evaluate the role of Tp53 in the pathogenesis of sbds -/- fish phenotype, we bred the fish with a DNA binding deficient allele, tp53 M214K Expression of the loss-of-function tp53 M214K did not rescue neutropenia or survival in sbds-null zebrafish. Increased expression of cdkn1a was abrogated in the tp53 M214K/M214K ;sbds -/- fish. We conclude that the amount of SBDSR126T protein is important for development, inactivation of Tp53 fails to rescue neutropenia or survival in the sbds-null background, and cdkn1a up-regulation was dependent on WT tp53 We hypothesize that additional pathways are involved in the pathophysiology of SDS.

Impact of surgical left atrial appendage closure during coronary bypass on clinical outcomes and readmissions

Background

Whether surgical left atrial appendage closure (sLAAC) during coronary artery bypass (CABG)surgery improves post-operative outcome including stroke and atrial fibrillation (AF) occurrence is largely unknown.

Objective

To analyze the impact of concomitant sLAAC during CABG in terms of outcomes and readmissions over the following year.

Methods

We analyzed the Nationwide Readmissions Database (2016–2019) using ICD-10 codes to identify hospitalizations for CABG. Patients were subcategorized based on whether sLAAC was performed or not. Among patients who survived their index admission, we employed propensity matching (1:3) to adjust for age, sex, comorbidities, CHA2DS2-VASc scores, previous AF history, heart failure and hospital characteristics. Primary outcomes included unplanned AF and stroke-related readmissions at 1 year.

Results

A total of 58,311 patients with CABG and sLAAC were identified with 175,940 propensity matched controls. Patients undergoing sLAAC were older with higher CHA2DS2-VASc scores and comorbidity burdens. Confounders were well balanced following propensity matching. Over a mean follow-up of 152 days, sLAAC was associated with higher risk of readmission due to AF at one year (HR 1.71 [1.49–1.96] p<0.001). This association is independent of previous AF history. Lower rates of stroke-related readmission was associated with perfomance of sLAAC (HR 0.80 (0.65–0.97) p=0.026), however the association was not observed when accounting for AF history.

Conclusion

CABG with concomitant sLAAC is maybe associated with lower stroke risk at the cost of higher risk of AF readmissions.

Funding Acknowledgement

Type of funding sources: None.

Calmodulin inhibitors improve erythropoiesis in Diamond-Blackfan anemia

Diamond-Blackfan anemia (DBA) is a rare hematopoietic disease characterized by a block in red cell differentiation. Most DBA cases are caused by mutations in ribosomal proteins and characterized by higher than normal activity of the tumor suppressor p53. Higher p53 activity is thought to contribute to DBA phenotypes by inducing apoptosis during red blood cell differentiation. Currently, there are few therapies available for patients with DBA. We performed a chemical screen using zebrafish ribosomal small subunit protein 29 (rps29) mutant embryos that have a p53-dependent anemia and identified calmodulin inhibitors that rescued the phenotype. Our studies demonstrated that calmodulin inhibitors attenuated p53 protein amount and activity. Treatment with calmodulin inhibitors led to decreased p53 translation and accumulation but does not affect p53 stability. A U.S. Food and Drug Administration-approved calmodulin inhibitor, trifluoperazine, rescued hematopoietic phenotypes of DBA models in vivo in zebrafish and mouse models. In addition, trifluoperazine rescued these phenotypes in human CD34⁺ hematopoietic stem and progenitor cells. Erythroid differentiation was also improved in CD34⁺ cells isolated from a patient with DBA. This work uncovers a potential avenue of therapeutic development for patients with DBA.

Loss of Sbds in zebrafish leads to neutropenia and pancreas and liver atrophy

Shwachman-Diamond syndrome (SDS) is characterized by exocrine pancreatic insufficiency, neutropenia, and skeletal abnormalities. Biallelic mutations in SBDS, which encodes a ribosome maturation factor, are found in 90% of SDS cases. Sbds^–/– mice are embryonic lethal. Using CRISPR/Cas9 editing, we created sbds-deficient zebrafish strains. Sbds protein levels progressively decreased and became undetectable at 10 days postfertilization (dpf). Polysome analysis revealed decreased 80S ribosomes. Homozygous mutant fish developed normally until 15 dpf. Mutant fish subsequently had stunted growth and showed signs of atrophy in pancreas, liver, and intestine. In addition, neutropenia occurred by 5 dpf. Upregulation of tp53 mRNA did not occur until 10 dpf, and inhibition of proliferation correlated with death by 21 dpf. Transcriptome analysis showed tp53 activation through upregulation of genes involved in cell cycle arrest, cdkn1a and ccng1, and apoptosis, puma and mdm2. However, elimination of Tp53 function did not prevent lethality. Because of growth retardation and atrophy of intestinal epithelia, we studied the effects of starvation on WT fish. Starved WT fish showed intestinal atrophy, zymogen granule loss, and tp53 upregulation — similar to the mutant phenotype. In addition, there was reduction in neutral lipid storage and ribosomal protein amount, similar to the mutant phenotype. Thus, loss of Sbds in zebrafish phenocopies much of the human disease and is associated with growth arrest and tissue atrophy, particularly of the gastrointestinal system, at the larval stage. A variety of stress responses, some associated with Tp53, contribute to pathophysiology of SDS.

Loss of ribosome maturation factor sbds in the zebrafish phenocopies human Shwachman-Diamond syndrome and is associated with p53 activation, but lethality cannot be rescued by p53 mutation.

Abstract P3-01-08: HER2-negative metastatic breast cancer with HER2-positive circulating tumor cells (CTCs): A new CTC-defined HER2-positive subgroup

Introduction: CTCs can overexpress HER2 discordant from tumor HER2 expression. We aimed to describe characteristics of a CTC-defined group of pts with metastatic breast cancer (MBC) that is tumor HER2- and CTC HER2+ (HER2 tumor- CTC+).

Methods: We retrospectively analyzed data from pts treated at Northwestern University who had serial evaluation of CTCs and circulating tumor DNA (ctDNA). We included pts with pathologically confirmed HER2- MBC and HER2+ CTCs. CTCs were enumerated with the CellSearch immunomagnetic kit (Menarini Silicon Biosystems), HER2 expression on CTCs was determined using the CellSearch CXC Kit in 7.5 cc whole blood, and ctDNA was analyzed using the Guardant360 NGS assay (Guardant Health).

Results: Among 98 pts with HER2- MBC and CTC analysis, 46 (47%) had at least 1 HER2+ CTC. In this cohort the median age was 53. At initial BC diagnosis, 80% had early stage or locally advanced BC and 20% had de-novo metastatic disease. Baseline histology was 65% ductal, 20% lobular, 2% mixed ductal and lobular, and 13% unknown. Pathology of metastatic tumor was hormone receptor positive (HR+)/HER2- in 78% and triple negative in 22%. Detailed HER2 immunohistochemistry (IHC) and FISH results from metastases were available from 63% of pts of whom 72% had an IHC score of 0 or 1 and 28% had an IHC score of 2 with negative FISH testing. The median time from the most recent pathologic metastatic tumor assessment to the detection of a HER2+ CTC was 6.5 mo. Twenty-two pts had simultaneous (within 8 weeks) HER2- tumor confirmation and HER2+ CTC detection. The median lines of endocrine therapy (ET) for MBC prior to detection of HER2+ CTCs was 1 (range 0-5, 41% no ET, 17% 1 line, 41% >2 lines). Pts received a median of 2 (range 0-10) prior systemic therapies for MBC prior to detection of HER2+ CTCs, (20% 0 lines, 41% 1-3 lines, and 39% >4 lines). Among these 46 pts, CTCs were analyzed longitudinally in 104 samples, with HER2+ CTCs detected in 77 samples. Number of HER2+ CTCs at initial detection ranged from <5 in 24%, 5-50 in 43%, and >50 in 33%, with a median of 11.5 HER2+ CTCs. CTC clusters were noted in 37% of pts. At initial detection the proportion of CTCs that were HER2+ was 0-25% in 13% of pts, 26-50% in 46% of pts, and 51-100% in 41% of pts. Seven pts had ERBB2 aberrations in ctDNA. Of 12 pts with tumor sequencing, 2 had ERBB2 mutations, 1 had ERBB3 amplification, and 1 had overexpression of ERBB3 RNA. After detection of HER2+ CTCs, 18 pts received HER2 directed therapy (with chemotherapy in 13 pts, with endocrine therapy in 4 pts, and as monotherapy in 1 pt). Imaging demonstrated a partial response or stable disease in 9 pts (clinical benefit rate 50%), including in 1 pt with trastuzumab monotherapy, progressive disease in 8 pts, and not evaluated in 1 pt.

Conclusions: HER2+ CTCs are frequently detected simultaneously or soon after HER2- tumor assessment in MBC. Within this newly defined subgroup, the several responses seen with HER2 targeted therapy serve as a proof of concept that HER2 tumor- CTC+ patients can benefit from HER2 targeted therapy. Future studies are needed to determine a clinically relevant threshold for HER2+ CTCs to guide further study of HER2 therapy combinations in HER2 tumor- CTC+ pts.

Citation Format: Shah AN, Gerratana L, Zhang Q, Davis AA, Zhang Y, Flaum L, Behdad A, Platanias L, Gradishar WJ, Cristofanilli M. HER2-negative metastatic breast cancer with HER2-positive circulating tumor cells (CTCs): A new CTC-defined HER2-positive subgroup [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-01-08.

Abstract P1-16-08: Response to subsequent therapy after dual immune checkpoint blockade in metastatic breast cancer

Introduction: While initial studies have found that combining chemotherapy with immune checkpoint blockade (ICB) can augment responses, additional toxicity has been observed. The optimal sequencing of chemotherapy and ICB has not yet been described. Sequential responses to chemotherapy after ICB have been reported in various tumor types; however, data is limited, and this has not been described in breast cancer to date.

Methods: We identified patients (pts) from a small pilot study in HER2-negative metastatic breast cancer (MBC) who received at least 1 cycle of durvalumab (PD-L1 inhibitor) and tremelimumab (CTLA-4 inhibitor). We excluded pts without follow up data or if they did not receive subsequent systemic therapy. Comparison of differences between subgroups was calculated by Fisher's exact test for categorical variables and Wilcoxon rank-sum test for continuous variables. Time to treatment failure (TTF) of subsequent therapy and overall survival (OS) were assessed by the Kaplan-Meier method and differences between breast cancer subtype were compared by log-rank tests.

Results: Twenty-three pts received at least 1 cycle of ICB of whom 14 pts were eligible for this analysis. Nine had estrogen receptor positive (ER+) BC and 5 had triple negative (TN) BC. There were no statistically significant differences between the ER+ and TN subgroups in age, race, ethnicity, ECOG performance status (PS) at end of ICB, or sites of metastatic disease except for more lymph node metastases in the TN cohort (p=0.003). Overall response rates to ICB in this cohort was higher in TN vs ER+ (40% vs 0%, p=0.11). Pts received a median of 4 lines of systemic therapy for MBC prior to ICB. Subsequent therapy after ICB was eribulin in 29%, carboplatin/gemcitabine in 21%, palbociclib + endocrine therapy (ET) in 14%, anthracycline in 14%, ixabepilone +/- capecitabine in 14%, and paclitaxel in 7%. Clinical response was seen in 8 pts (57%), of whom 5 had ER+ BC and 3 had TNBC. The median TTF of subsequent therapy was 3.0 mo (1.9, 5.5), which compared to a median TTF for therapy prior to ICB of 2.5 mo. The median OS was 12.3 mo (2.3-13.3). There were no significant differences between the ER+ and TN cohorts (log-rank test p=0.74 and 0.90 for TTF and OS, respectively. Subsequent therapy was discontinued due to progressive disease in 44%, decline in PS in 19%, liver failure in 6%, treatment related adverse event in 6%, and unknown cause in 13%. Two pts remain on subsequent therapy with palbociclib + ET beyond 6 mo without disease progression. There were no statistically significant differences between TTF >3 mo (n=5) and TTF <3 mo (n=9) subgroups. Pts with TTF >3 mo were numerically more likely to have a PS 0-1 (100 vs 78%), liver metastases (80 vs 56%), and ER+ BC (80 vs 56%). Pts with TTF <3 mo had more lymphopenia (66% vs 20%) and more lines of prior systemic therapy for MBC (median 6 vs 4).

Conclusions: While median duration of response on subsequent therapy was short, a subset of pts had significant clinical responses. These findings provide rationale for prospective validation as they provide strategies for sequencing ICB with standard therapies.

Citation Format: Shah AN, Yalamanchili A, Helenowski I, Bhole S, Woodman J, Gradishar WJ, Cristofanilli M, Santa-Maria CA. Response to subsequent therapy after dual immune checkpoint blockade in metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-16-08.

Abstract P3-01-19: HER2-positive circulating tumor cells (CTCs) in advanced breast cancer (BC): A feature independent of BC subtype

Introduction: HER2 overexpression is observed on CTCs in advanced BC (ABC), but their significance is not known. We aimed to describe clinical, pathologic, and molecular associations with HER2 overexpression on CTCs in ABC patients (pts).

Methods: We conducted a retrospective analysis of data from ABC pts treated at Thomas Jefferson University and Northwestern University who had evaluation of CTCs and circulating tumor DNA (ctDNA). CTCs were enumerated with the CellSearch immunomagnetic kit (Menarini Silicon Biosystems), HER2 expression on CTCs was evaluated using the CellSearch CXC Kit, and ctDNA was analyzed using the Guardant360 NGS assay (Guardant Health). Associations with the presence of HER2+ CTCs were explored through univariate and multivariate logistic regression. Kruskal-Wallis testing evaluating HER2+ CTCs as a continuous variable was also conducted to confirm consistency of findings. Time to development of HER2+ CTCs was evaluated using Cox proportional hazards regression analysis.

Results: Baseline CTCs were evaluated in 209 pts (10% stage III, 90% stage IV) of whom 41% had no detectable CTCs, 23% had 1-4 CTCs, and 36% had >5 CTCs (stage IV aggressive). Twelve percent had CTC clusters. At least 1 HER2+ CTC was seen in 33% of pts at baseline draw. Of 39 patients with HER2+ BC, only 18% had HER2+ CTCs. Of patients with HER2+ CTCs, 55% had hormone receptor positive BC, 28% had triple negative BC, and 18% had HER2+ BC. On univariate logistic analysis, BC subtype or HER2 status was not associated with the presence of HER2+ CTCs. IBC pts represented 52% of pts and were less likely to have HER2+ CTCs (OR 0.40 95% CI 0.19-0.84). Bone metastases were associated with an increased likelihood of HER2+ CTCs (OR 2.46, 95% CI 1.12-5.38); however, other sites of metastases and number of metastatic sites were not correlated with HER2+ CTCs. Aggressive disease features including >5 CTCs and presence of CTC clusters were strongly associated with HER2+ CTCs (OR 15.72, 95% CI 6.89-35.8 and 8.97, 95% CI 3.23-24.89, respectively). Of 168 pts with ctDNA analysis, ERRB2 aberrations were seen in 22% of pts and were significantly associated with HER2+ CTCs (OR of 3.74, 95% CI 1.45-9.63). On multivariate analysis, the associations with >5 CTCs and ERBB2 alterations in ctDNA remained statistically significant. The associations of HER2+ CTCs with bone disease, >5 CTCs, CTC clusters, and ERBB2 alterations in ctDNA, and the inverse relationship with IBC were consistent when HER2+ CTCs were evaluated as a continuous variable with Kruskal-Wallis testing. Among pts without HER2+ CTCs at baseline, the time to detection of HER2+ CTCs correlated with the presence of bone metastases (HR 3.40, 95% CI 1.14-10.19), >5 CTCs (3.77, 95% CI 1.33-10.70), and visceral disease (HR 3.00, 95% CI 1.07-8.44).

Conclusions: HER2+ CTCs are common in ABC, independent of HER2 status of the tumor, and, in fact, common in the luminal BC. HER2+ CTCs were also strongly associated with CTC characteristics of aggressive disease with poor survival (CTCs clusters and >5 CTCs) and ERBB2 aberrations in ctDNA. Further studies will be investigating the role of HER2+ CTCs in endocrine resistance and the potential of anti-HER2 therapy in this unique CTC-defined setting.

Citation Format: Shah AN, Gerratana L, Davis AA, Zhang Q, Zhang Y, Rossi G, Wang C, Strickland K, Yang H, Flaum L, Abu-Khalaf M, Behdad A, Ye Z, Platanias L, Gradishar WJ, Cristofanilli M. HER2-positive circulating tumor cells (CTCs) in advanced breast cancer (BC): A feature independent of BC subtype [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-01-19.

Tuberculosis infection control measures at health care facilities offering HIV and tuberculosis services in India: A baseline assessment

BACKGROUND

Tuberculosis (TB) is one of world's oldest infectious disease and ranks alongside HIV as leading infectious killer. Tuberculosis infection control especially in HIV and TB care facilities has warranted attention after the recent health care-associated outbreaks in South Africa. The aim of this study was to describe the tuberculosis infection control measures implemented by HIV and TB care facilities in five high HIV burden provinces in India.

METHODS

Baseline assessment of 30 high burden Antiretroviral centers and TB facilities was conducted during Oct 2015-Dec 2015 by AIC trained staff using a structured format.

RESULTS

Thirty HIV and TB care facilities in five high HIV burden provinces were enrolled. Facility infrastructure and airborne infection control practices were highly varied between facilities. TB screening and fast tracking at ART centers is happening at majority of centers however inadequate TB infection control training, poor compliance to administrative and personal protective measures and lack of mechanism for health care workers surveillance need attention.

CONCLUSIONS

Local specific TB infection control interventions to be designed and implemented at HIV and TB care facilities including implementation of administrative, environmental and use of personal protective equipment's with the training of staff members. Health care workers surveillance needs to be prioritized considering the rising instances of tuberculosis among Health care workers.

Macrophage-Dependent Cytoplasmic Transfer during Melanoma Invasion In Vivo

Interactions between tumor cells and tumor-associated macrophages play critical roles in the initiation of tumor cell motility. To capture the cellular interactions of the tumor microenvironment with high-resolution imaging, we directly visualized tumor cells and their interactions with macrophages in zebrafish. Live imaging in zebrafish revealed that macrophages are dynamic, yet maintain sustained contact with tumor cells. In addition, the recruitment of macrophages to tumor cells promotes tumor cell dissemination. Using a Cre/LoxP strategy, we found that macrophages transfer cytoplasm to tumor cells in zebrafish and mouse models. Remarkably, macrophage cytoplasmic transfer correlated with melanoma cell dissemination. We further found that macrophages transfer cytoplasm to tumor cells upon cell contact in vitro. Thus, we present a model in which macrophage/tumor cell contact allows for the transfer of cytoplasmic molecules from macrophages to tumor cells corresponding to increased tumor cell motility and dissemination.

Why are HIV-infected people not started on antiretroviral therapy? A mixed-methods study from Gujarat, India

Setting: Five purposively selected antiretroviral therapy (ART) centres in Gujarat, India. Objectives: To assess the proportion of ART-eligible people living with the human immunodeficiency virus (PLHIV) who were not initiated on ART within 2 months of being recorded as eligible, to identify factors associated with non-initiation and to explore reasons from the provider's perspective. Design: We used a mixed-methods design (triangulation) of 1) a quantitative phase involving record reviews and cohort analysis (Poisson regression) of PLHIV registered during April 2014-March 2015, and 2) a qualitative phase involving one-to-one interviews with 25 providers. Results: Of 2079 ART-eligible PLHIV, 339 (16%) were not started on ART within 2 months. PLHIV with CD4 counts of <350 cells/μl and patients who were labourers, hospitalised, bedridden or registered with certain ART centres were more likely not to be initiated on ART. Qualitative results were categorised into two broad themes: government health system- and patient-related challenges, which validated and complemented the quantitative findings. Conclusion: Several patient subgroups at greater risk of ART non-initiation were identified, along with reasons for risk; this has important programme implications for achieving the UNAIDS 90-90-90 goal, and particularly the second 90 component of having 90% of diagnosed PLHIV start ART.

A genetic basis for molecular asymmetry at vertebrate electrical synapses

Neural network function is based upon the patterns and types of connections made between neurons. Neuronal synapses are adhesions specialized for communication and they come in two types, chemical and electrical. Communication at chemical synapses occurs via neurotransmitter release whereas electrical synapses utilize gap junctions for direct ionic and metabolic coupling. Electrical synapses are often viewed as symmetrical structures, with the same components making both sides of the gap junction. By contrast, we show that a broad set of electrical synapses in zebrafish, Danio rerio, require two gap-junction-forming Connexins for formation and function. We find that one Connexin functions presynaptically while the other functions postsynaptically in forming the channels. We also show that these synapses are required for the speed and coordination of escape responses. Our data identify a genetic basis for molecular asymmetry at vertebrate electrical synapses and show they are required for appropriate behavioral performance.

DOI:http://dx.doi.org/10.7554/eLife.25364.001

Are partners of HIV-infected people being tested for HIV? A mixed-methods research from Gujarat, India

Setting: Four selected antiretroviral therapy (ART) centres of Gujarat State, India, which accounts for 8% of the human immunodeficiency virus (HIV) burden in India. Objectives: 1) To assess the proportion of people living with HIV (PLHIV) whose partners were not tested for HIV; 2) to assess sociodemographic and clinical characteristics of index cases associated with partner testing; and 3) to understand perceived facilitators and barriers to partner testing and make suggestions on how to improve testing from the perspective of the health-care provider. Design: A mixed-method design with a quantitative phase that involved reviewing the programme records of married PLHIV enrolled during 2011-2015, followed by a qualitative phase of key informant interviews. Results: Of 3884 married PLHIV, 1279 (33%) did not have their partners tested for HIV. Factors including index cases being male, illiterate, aged >25 years, belonging to key populations, substance use and being in advanced clinical stages were more likely to be associated with partner non-testing. Non-disclosure of HIV status (due to fear of marital discord) and lack of awareness and risk perception were the key barriers to testing. Conclusion: One third of PLHIV did not have their partners tested for HIV. Several factors were identified as being associated with the non-testing of partners, and solutions were explored that need to be implemented urgently if we are to achieve the 90-90-90 targets and end HIV.

Approaching Perfection: New Developments in Zebrafish Genome Engineering

Programmable nucleases have revolutionized zebrafish genetics by enabling targeted genome modifications. In this issue of Developmental Cell, Hoshijima et al. (2016) take genome modification in the zebrafish to the next level, demonstrating the efficient use of homologous recombination to make genetic tools for a range of applications.

Targeted candidate gene screens using CRISPR/Cas9 technology

In the postgenomic era, the ability to quickly, efficiently, and inexpensively assign function to the zebrafish proteome is critical. Clustered regularly interspaced short palindromic repeats (CRISPRs) have revolutionized the ability to perform reverse genetics because of its simplicity and broad applicability. The CRISPR system is composed of an engineered, gene-specific single guide RNA (sgRNA) and a Cas9 enzyme that causes double-stranded breaks in DNA at the targeted site. This simple, two-part system, when injected into one-cell stage zebrafish embryos, efficiently mutates target loci at a frequency such that injected embryos phenocopy known mutant phenotypes. This property allows for CRISPR-based F0 screening in zebrafish, which provides a means to screen through a large number of candidate genes for their role in a phenotype of interest. While there are important considerations for any successful genetic screen, CRISPR screening has significant benefits over conventional methods and can be accomplished in any lab with modest molecular biology experience.

Rapid reverse genetic screening using CRISPR in zebrafish

Identifying genes involved in biological processes is critical for understanding the molecular building blocks of life. We used engineered CRISPR (clustered regularly interspaced short palindromic repeats) to efficiently mutate specific loci in zebrafish (Danio rerio) and screen for genes involved in vertebrate biological processes. We found that increasing CRISPR efficiency by injecting optimized amounts of Cas9-encoding mRNA and multiplexing single guide RNAs (sgRNAs) allowed for phenocopy of known mutants across many phenotypes in embryos. We performed a proof-of-concept screen in which we used intersecting, multiplexed pool injections to examine 48 loci and identified two new genes involved in electrical-synapse formation. By deep sequencing target loci, we found that 90% of the genes were effectively screened. We conclude that CRISPR can be used as a powerful reverse genetic screening strategy in vivo in a vertebrate system.

Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis

BACKGROUND

Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to directly identify point mutations in specific genes of interest in genomic DNA from a large chemically mutagenized population. Classical TILLING processes, based on enzymatic detection of mutations in heteroduplex PCR amplicons, are slow and labor intensive.

RESULTS

Here we describe a new TILLING strategy in zebrafish using direct next generation sequencing (NGS) of 250 bp amplicons followed by Paired-End Low-Error (PELE) sequence analysis. By pooling a genomic DNA library made from over 9,000 N-ethyl-N-nitrosourea (ENU) mutagenized F1 fish into 32 equal pools of 288 fish, each with a unique Illumina barcode, we reduce the complexity of the template to a level at which we can detect mutations that occur in a single heterozygous fish in the entire library. MiSeq sequencing generates 250 base-pair overlapping paired-end reads, and PELE analysis aligns the overlapping sequences to each other and filters out any imperfect matches, thereby eliminating variants introduced during the sequencing process. We find that this filtering step reduces the number of false positive calls 50-fold without loss of true variant calls. After PELE we were able to validate 61.5% of the mutant calls that occurred at a frequency between 1 mutant call:100 wildtype calls and 1 mutant call:1000 wildtype calls in a pool of 288 fish. We then use high-resolution melt analysis to identify the single heterozygous mutation carrier in the 288-fish pool in which the mutation was identified.

CONCLUSIONS

Using this NGS-TILLING protocol we validated 28 nonsense or splice site mutations in 20 genes, at a two-fold higher efficiency than using traditional Cel1 screening. We conclude that this approach significantly increases screening efficiency and accuracy at reduced cost and can be applied in a wide range of organisms.

Neurobeachin is required postsynaptically for electrical and chemical synapse formation

BACKGROUND

Neural networks and their function are defined by synapses, which are adhesions specialized for intercellular communication that can be either chemical or electrical. At chemical synapses, transmission between neurons is mediated by neurotransmitters, whereas at electrical synapses, direct ionic and metabolic coupling occur via gap junctions between neurons. The molecular pathways required for electrical synaptogenesis are not well understood, and whether they share mechanisms of formation with chemical synapses is not clear.

RESULTS

Here, using a forward genetic screen in zebrafish, we find that the autism-associated gene neurobeachin (nbea), which encodes a BEACH-domain-containing protein implicated in endomembrane trafficking, is required for both electrical and chemical synapse formation. Additionally, we find that nbea is dispensable for axonal formation and early dendritic outgrowth but is required to maintain dendritic complexity. These synaptic and morphological defects correlate with deficiencies in behavioral performance. Using chimeric animals in which individually identifiable neurons are either mutant or wild-type, we find that Nbea is necessary and sufficient autonomously in the postsynaptic neuron for both synapse formation and dendritic arborization.

CONCLUSIONS

Our data identify a surprising link between electrical and chemical synapse formation and show that Nbea acts as a critical regulator in the postsynaptic neuron for the coordination of dendritic morphology with synaptogenesis.

Early outcome of second line antiretroviral therapy in treatment-experienced human immunodeficiency virus positive patients

PURPOSE AND AIM

Multi-drug resistance in treatment-experienced human immune deficiency virus (HIV) patients has been a major cause to first line antiretroviral therapy (ART) failure, necessitating a switch to second line therapy. In India, the second line treatment program is still relatively new with little experience and unclear outcomes. It is therefore, critical to assess the clinical, virological and immunological effectiveness and treatment outcome over the 1(st) year of follow-up in the patients' switched to the second line ART at public sector tertiary care center.

MATERIALS AND METHODS

A prospective, observational study was carried out on HIV positive patients switched on second line ART from January 2010 to December 2010 at ART Centre, Civil Hospital, Ahmedabad. Demographic details, symptoms, adverse drug reactions (ADRs), second line ART regimens, CD4 count, and plasma viral load (PVL) were recorded in a case record form. Patients were followed-up monthly for 12 months. The data was analyzed by t-test, z-test, and Fisher-exact test.

RESULTS

Out of 126 patients, 82 received regimen V [zidovudine (ZDV) + lamivudine (3TC) + tenofovir (TDF) + boosted lopinavir (LPV/r)] and 44 received regimen Va [3TC + TDF + LPV/r]. A significant (P < 0.0001) increase in mean body weight and marked reduction in number of patients (7) categorized as WHO stage III/IV was observed at 12 months of second line ART. Moreover, a significant immune reconstitution with increase in mean CD4 count and viral suppression (PVL < 400 copies/ml) in 103 (82%) patients (P < 0.0001) was also observed. A total of 83 ADRs were observed in 69 (55%) patients, the most common being dyslipidemia (57) followed by anemia (9).

CONCLUSION

Early treatment outcome with second line ART was good with 82% success rate in treatment experienced HIV patients. Dyslipidemia and anemia were the common ADRs observed.

RNA-seq-based mapping and candidate identification of mutations from forward genetic screens

Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life; however, identifying the causal mutations from such screens has long been the bottleneck in the process, particularly in vertebrates. We have developed an RNA-seq-based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons, alter transcript splicing, or alter gene expression levels. Furthermore, we develop an easily accessible bioinformatics pipeline allowing for implementation of all steps of the method. Overall, we show that RNA-seq is a fast, reliable, and cost-effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.

Ocular loiasis in London 2008-2009: a case series

PURPOSE

To report three cases of Loa loa infestation presenting over the course of 12 months to ophthalmology departments in the South West Thames region around London.

METHODS

Case series (three case histories are described) and literature review.

RESULTS

All three patients had a history of travel to West Africa. All had worms surgically removed and were referred to an infectious diseases hospital, where these were confirmed as adult Loa loa nematodes and treatment was initiated.

CONCLUSIONS

Although ocular loiasis is endemic in West Africa, European ophthalmologists in areas of diverse ethnicity should be aware that it is presenting increasingly frequently, that there is often no history of recent travel abroad, and that loiasis is a differential diagnosis for any 'at-risk' patient with an unexplained foreign body sensation.