A large-scale RNAi screen reveals that mitochondrial function is important for meiotic chromosome organization in oocytes

In prophase of the first meiotic division, chromatin forms a compact spherical cluster called the karyosome within the enlarged oocyte nucleus in Drosophila melanogaster. Similar clustering of chromatin has been widely observed in oocytes in many species including humans. It was previously shown that the proper karyosome formation is required for faithful chromosome segregation, but knowledge about its formation and maintenance is limited. To identify genes involved in karyosome formation, we carried out a large-scale cytological screen using Drosophila melanogaster oocytes. This screen comprised 3916 genes expressed in ovaries, of which 106 genes triggered reproducible karyosome defects upon knockdown. The karyosome defects in 24 out of these 106 genes resulted from activation of the meiotic recombination checkpoint, suggesting possible roles in DNA repair or piRNA processing. The other genes identified in this screen include genes with functions linked to chromatin, nuclear envelope, and actin. We also found that silencing of genes with mitochondrial functions, including electron transport chain components, induced a distinct karyosome defect typically with de-clustered chromosomes located close to the nuclear envelope. Furthermore, mitochondrial dysfunction not only impairs karyosome formation and maintenance, but also delays synaptonemal complex disassembly in cells not destined to become the oocyte. These karyosome defects do not appear to be mediated by apoptosis. This large-scale unbiased study uncovered a set of genes required for karyosome formation and revealed a new link between mitochondrial dysfunction and chromatin organization in oocytes.

Validation of MYC and BCL6 rapid break apart digital fluorescence in situ hybridization assays for clinical use

OBJECTIVE

Detection of gene rearrangements in MYC (a family of regulator genes and proto-oncogenes) and human B-cell lymphoma 6 (BCL6) using fluorescence in situ hybridization (FISH) are important in the evaluation of lymphomas, in particular diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma. Our current clinical MYC and BCL6 FISH workflow involves an overnight hybridization of probes with digital analysis using the GenASIs Scan and Analysis instrument (Applied Spectral Imaging). In order to improve assay turnaround time SureFISH probes were validated to reduce the hybridization time from 16 hours down to 1.5 hours.

METHODS

Validation was a four-phase process involving initial development of the assays by testing new probes in a manual protocol, and cytogenetic studies to confirm the probe specificity, sensitivity, and localization. In the next phase, the assays were validated as a manual assay. The third phase involved development of the digital FISH assays by testing and optimizing the GenASIs Scan and Analysis instrument. In the final phase, the digital FISH assays were validated.

RESULTS

Cytogenetic studies confirmed 100% probe sensitivity/specificity, and localization patterns. Negative reference range cutoffs calculated from 20 normal lymph nodes using the inverse of the beta cumulative probability density function (Excel BETAINV calculation) were 11% inclusive for both manual and digital MYC and BCL6 assays. There was 100% concordance between the manual and digital methods. The shortened hybridization time decreased the overall workflow time by 14.5 hours.

CONCLUSIONS

This study validates the use of the SureFISH MYC and BCL6 probes on formalin fixed paraffin embedded (FFPE) tissue sections using a hybridization time of 1.5 hours that shortened the overall workflow by 14.5 hours. The process described also provides a standardized framework for validating digital FISH assays in the future.

Evaluating newly approved drugs for multidrug-resistant tuberculosis (endTB): study protocol for an adaptive, multi-country randomized controlled trial

BACKGROUND

Treatment of multidrug- and rifampin-resistant tuberculosis (MDR/RR-TB) is expensive, labour-intensive, and associated with substantial adverse events and poor outcomes. While most MDR/RR-TB patients do not receive treatment, many who do are treated for 18 months or more. A shorter all-oral regimen is currently recommended for only a sub-set of MDR/RR-TB. Its use is only conditionally recommended because of very low-quality evidence underpinning the recommendation. Novel combinations of newer and repurposed drugs bring hope in the fight against MDR/RR-TB, but their use has not been optimized in all-oral, shorter regimens. This has greatly limited their impact on the burden of disease. There is, therefore, dire need for high-quality evidence on the performance of new, shortened, injectable-sparing regimens for MDR-TB which can be adapted to individual patients and different settings.

METHODS

endTB is a phase III, pragmatic, multi-country, adaptive, randomized, controlled, parallel, open-label clinical trial evaluating the efficacy and safety of shorter treatment regimens containing new drugs for patients with fluoroquinolone-susceptible, rifampin-resistant tuberculosis. Study participants are randomized to either the control arm, based on the current standard of care for MDR/RR-TB, or to one of five 39-week multi-drug regimens containing newly approved and repurposed drugs. Study participation in all arms lasts at least 73 and up to 104 weeks post-randomization. Randomization is response-adapted using interim Bayesian analysis of efficacy endpoints. The primary objective is to assess whether the efficacy of experimental regimens at 73 weeks is non-inferior to that of the control. A sample size of 750 patients across 6 arms affords at least 80% power to detect the non-inferiority of at least 1 (and up to 3) experimental regimens, with a one-sided alpha of 0.025 and a non-inferiority margin of 12%, against the control in both modified intention-to-treat and per protocol populations.

DISCUSSION

The lack of a safe and effective regimen that can be used in all patients is a major obstacle to delivering appropriate treatment to all patients with active MDR/RR-TB. Identifying multiple shorter, safe, and effective regimens has the potential to greatly reduce the burden of this deadly disease worldwide.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier NCT02754765. Registered on 28 April 2016; the record was last updated for study protocol version 3.3, on 27 August 2019.

A survey to understand the feelings towards and impact of COVID-19 on the households of juvenile dermato myositis patients from a parent or carer perspective

OBJECTIVES

This aim of this study was to gain a better understanding of how parents and carers feel about the effects and impact of the coronavirus disease 2019 (COVID-19) pandemic lockdown and how this impacted upon their child/young person with JDM.

METHOD

We approached 139 participants from the JDM Cohort Biomarker Study (JDCBS), with specific consent to approach electronically for research studies. A secure electronic questionnaire with study introduction was sent to participants for their parents and carers around the UK to complete. It consisted of 20 questions about the impact of the pandemic on their child or young person's clinical care. Data were analysed quantitatively and qualitatively.

RESULTS

There were 76 (55%) responses to the survey. More than 50% of participants were actively being treated for their JDM at the point of survey completion as recorded by their parent or carer. More than 40% attested to disrupted treatment owing to COVID-19. The biggest impact upon clinical care was cancellation of appointments, initiating virtual appointments and extension of time between blood tests. Parents and carers expressed their own feelings of worry, concern and anxiety, but also those of their child or young person.

CONCLUSION

Families who have a child or young person with JDM have been affected by COVID-19. Qualitative comments highlight that it has been a very difficult time. Further investigation is required into this area and could be compared with research on the effects of COVID-19 on other patient groups with chronic disease.

A Type 1 Diabetes Genetic Risk Score Predicts Progression of Islet Autoimmunity and Development of Type 1 Diabetes in Individuals at Risk

OBJECTIVE

We tested the ability of a type 1 diabetes (T1D) genetic risk score (GRS) to predict progression of islet autoimmunity and T1D in at-risk individuals.

RESEARCH DESIGN AND METHODS

We studied the 1,244 TrialNet Pathway to Prevention study participants (T1D patients' relatives without diabetes and with one or more positive autoantibodies) who were genotyped with Illumina ImmunoChip (median [range] age at initial autoantibody determination 11.1 years [1.2-51.8], 48% male, 80.5% non-Hispanic white, median follow-up 5.4 years). Of 291 participants with a single positive autoantibody at screening, 157 converted to multiple autoantibody positivity and 55 developed diabetes. Of 953 participants with multiple positive autoantibodies at screening, 419 developed diabetes. We calculated the T1D GRS from 30 T1D-associated single nucleotide polymorphisms. We used multivariable Cox regression models, time-dependent receiver operating characteristic curves, and area under the curve (AUC) measures to evaluate prognostic utility of T1D GRS, age, sex, Diabetes Prevention Trial-Type 1 (DPT-1) Risk Score, positive autoantibody number or type, HLA DR3/DR4-DQ8 status, and race/ethnicity. We used recursive partitioning analyses to identify cut points in continuous variables.

RESULTS

Higher T1D GRS significantly increased the rate of progression to T1D adjusting for DPT-1 Risk Score, age, number of positive autoantibodies, sex, and ethnicity (hazard ratio [HR] 1.29 for a 0.05 increase, 95% CI 1.06-1.6; P = 0.011). Progression to T1D was best predicted by a combined model with GRS, number of positive autoantibodies, DPT-1 Risk Score, and age (7-year time-integrated AUC = 0.79, 5-year AUC = 0.73). Higher GRS was significantly associated with increased progression rate from single to multiple positive autoantibodies after adjusting for age, autoantibody type, ethnicity, and sex (HR 2.27 for GRS >0.295, 95% CI 1.47-3.51; P = 0.0002).

CONCLUSIONS

The T1D GRS independently predicts progression to T1D and improves prediction along T1D stages in autoantibody-positive relatives.

A phase I study of CNTO328, an anti-interleukin (IL)-6 monoclonal antibody combined with docetaxel in subjects with metastatic castration-resistant prostate cancer (CRPC)

5063

Background: IL-6 is a potential mediator of prostate cancer morbidity and mortality and may protect prostate cancer cells from chemotherapy-induced apoptosis. CNTO328, a chimeric anti-IL-6 antibody, has been shown to inhibit prostate tumor growth in xenograft mouse models. Methods: Chemotherapy-naïve patients with metastatic CRPC were administered CNTO328 in combination with T (75 mg/m2 q3w) in 3 dose-escalation cohorts (6 mg/kg q2w, and 9 and 12 mg/kg q3w) following an initial run-in cycle of T alone to examine the effect of CNTO328 on T pharmacokinetics (PK). Safety was evaluated prior to each dose escalation. Prostate specific antigen (PSA), radiological response, and C-reactive protein (CRP), the best-known surrogate of serum IL-6 bioactivity, were also assessed. Results: This study is fully enrolled December 2008 with 38 patients. 36 patients with KPS ≥70, median age 66 (range 43–82) received 6 (median) cycles of T (range 1–37). 32 patients received at least one dose of CNTO328 in combination with T and are evaluable. Baseline patient characteristics included: median PSA of 59 ng/mL (range 12–1430) and median CRP was 3.85 mg/L (range <1 to 91.3). One DLT was observed in each cohort (grade 4 neutropenic infection, grade 3 syncope and dehydration, grade 3 GI bleeding), though MTD for the combination was not reached. Most frequent ≥grade 3 adverse events (AE) were neutropenia (69%); leukopenia (63%); lymphopenia (31%); dyspnea (19%); fatigue (16%). One patient died due to AE (sepsis) reported as possible related to T and unlikely related to CNTO328 by investigator. Preliminary data show CNTO328 does not appear to have a major effect on T PK. Preliminary efficacy data is shown in the table . Ongoing evaluation indicates 3/12 partial responses in patients with measurable disease reported thus far. Conclusions: CNTO328 with T is well tolerated and demonstrates biological and clinical activity in CRPC that warrants further study.

[Table: see text]

[Table: see text]

Phase II study of the farnesyl transferase inhibitor tipifarnib plus fulvestrant in postmenopausal patients with hormone receptor-positive breast cancer: New York Cancer Consortium Trial P6205

1037

Background: Tipifarnib and fulvestrant both have single agent activity in hormone receptor-positive (HR+) metastatic breast cancer (MBC), and tipifarnib enhances the activity of anti-estrogens in HR+ breast cancer cell lines. Methods: Eligibility criteria: measurable HR+ MBC, postmenopausal status, ECOG PS of 0–2, and no prior chemotherapy for MBC. Treatment: fulvestrant 250 mg IM on day 1 plus oral tipifarnib 300 mg BID on days 1–21 every 28 days (defined as one cycle). Response was evaluated by RECIST criteria every 3 cycles. The study was suspended for efficacy/futility analysis after 33 of 46 patients were accrued. It was designed to detect an improvement in clinical benefit rate (CBR; defined as objective response or stable disease for at least 24 weeks) from 50% to 70% (90% power, type I error 10%), and would require at least 26 of 42 eligible/evaluable patients to have clinical benefit (CB). The expected CBR for fulvestrant alone is 30% in aromatase inhibitor (AI) resistant disease (Ingle, 2006), 45% in tamoxifen (tam)-resistant disease (Osborne, 2002), and 60% when used as first line endocrine therapy (ET) (Howell, 2004). Results: Of 33 patients enrolled, 28 are currently assessable for CBR (2 were ineligible, and 3 have stable disease for < 6 months and remain on treatment). Grade 3/4 toxicity: neutropenia (15%), pain (11%) and gastrointestinal toxicity (11%). Tipifarnib was either reduced in dose (N=10) or discontinued (N=8) due to toxicity or non-compliance. The overall CBR is shown; should accrual continue, all 14 evaluable patients must have CB in order to meet the pre-specified efficacy objective. For the ET-resistant group, 18 were resistant to AI therapy (or AI plus tam in 5) and 2 to tam. * Number eligible/evaluable for CBR. Conclusions: The tipifarnib-fulvestrant combination is not likely to produce a CBR of at least 70%. The 45% CBR in ET-resistant disease may merit further evaluation in this setting.

[Table: see text]

No significant financial relationships to disclose.

Phase II trial of FOLFOX6, bevacizumab and cetuximab in patients with Colorectal Cancer

4075

Background: Bevacizumab (B) + FOLFOX is widely accepted as a standard first-line therapy for metastatic colorectal cancer (mCRC). Recent treatment strategies have included the use of targeted therapies combined with chemotherapy to improve efficacy and to reduce chemotherapy-related toxicities. This Phase II study assesses first-line mFOLFOX6 + B + cetuximab (C), a monoclonal antibody approved for use in irinotecan-refractory mCRC. Methods: All pts had ECOG PS = 1, normal bone marrow, hepatic and renal function. Pts received mFOLFOX6 + B (5mg/kg) biweekly and C weekly (initially at 400 mg/m2, then subsequent doses at 250 mg/m2). Tumor assessment by imaging was done every 8 weeks. Primary endpoints are response rate, progression free-survival (PFS), overall survival (OS), and safety. The regimen would be considered promising if there were = 32 responses, or if = 60% of pts were progression-free for at least 8 months. Results: 67 pts (37 males, 30 females) were enrolled from 12/04–11/06. Median age was 57. Toxicities included Grade 4: neutropenia (6%), thrombosis/embolism (5%). Grade 3: neutropenia (13%), rash (13%), fatigue (11%), diarrhea (11%), abdominal pain (6%), neuropathy (5%), infection with ≤ Grade 2 ANC (4.5%). There were 2 deaths, 1 due to neutropenia and diarrhea and 1 to pulmonary fibrosis. As of 12/06, 9 pts were too early to evaluate. Of the remaining 58 pts, there were 32 responses (55%; 95% CI: 42%, 68%), including 3 CRs and 29 PRs; Median PFS was 9.6 months (95% CI: 8.8, 13.9 months), 71% were progression-free for at least 8 months, and median OS was not reached after a median follow-up of 11.4 months (range 1.5–25.2 months). Conclusions: Treatment with mFOLFOX6+ B + C met the pre-specified criteria for objective response and PFS to be considered promising. This regimen is associated with an acceptable toxicity profile and merits further evaluation. Supported by N01-CA-62204.

No significant financial relationships to disclose.

Detection of Escherichia coli Enterotoxins by Using Mouse Adrenal Cell and Suckling Mouse Assays: Collaborative Study

The ability of 10 Escherichia coli strains to produce heat-stable enterotoxin (ST) and heat-labile enterotoxin (LT) was determined by 8 analysts in a collaborative study. The suckling mouse model and the mouse adrenal cell line (Y-l) tests were used to detect ST and LT, respectively. Cultures for assay were grown 24 h in casamino acid-yeast extracttrace salts broth at 37°C in a shaker incubator at 250 rpm. Cell-free culture broth prepared by centrifugation and filtration was divided into 2 portions: One was heated for 30 min and used both for ST assay and as a heated control for LT assay; the other was used unheated for LT assay. Results were expressed as positive for ST, positive for LT, positive for ST and LT, or negative for both ST and LT; percent of correct estimates was calculated for each culture for each analyst. At the 95% confidence interval, the overall correct results were 96.3 ± 2.9 and 95.0 ± 3.4% for ST and LT, respectively. The test performances thus were satisfactory for detecting ST and LT produced in vitro by E. coli. The method has been adopted official first action.