Description: Background Treatment options for patients with nonbulky stage IA–IIA Hodgkin lymphoma include combined modality therapy (CMT) using doxorubicin, bleomycin, vinblastine and dacarbazine (ABVD) plus involved-field radiation therapy (IFRT), and chemotherapy with ABVD alone. There are no mature randomized data comparing ABVD with CMT using modern radiation techniques. Patients and methods Using German Hodgkin Study Group HD10/HD11 and NCIC Clinical Trials Group HD.6 databases, we identified 588 patients who met mutually inclusive eligibility criteria from the preferred arms of HD10 or 11 ( n = 406) and HD.6 ( n = 182). We evaluated time to progression (TTP), progression-free (PFS) and overall survival, including in three predefined exploratory subset analyses. Results With median follow-up of 91 (HD10/11) and 134 (HD.6) months, respective 8-year outcomes were for TTP, 93% versus 87% [hazard ratio (HR) 0.44, 95% confidence interval (CI) 0.24–0.78]; for PFS, 89% versus 86% (HR 0.71, 95% CI 0.42–1.18) and for overall survival, 95% versus 95% (HR 1.09, 95% CI 0.49–2.40). In the exploratory subset analysis including HD10 eligible patients who achieved complete response (CR) or unconfirmed complete response (CRu) after two cycles of ABVD, 8-year PFS was 87% (HD10) versus 95% (HD.6) (HR 2.8; 95% CI 0.64–12.5) and overall survival 96% versus 100%. In contrast, among those without CR/CRu after two cycles of ABVD, 8-year PFS was 88% versus 74% (HR 0.35; 95% CI 0.16–0.79) and overall survival 95% versus 91%, respectively (HR 0.42; 95% CI 0.12–1.44). Conclusions In patients with nonbulky stage IA–IIA Hodgkin lymphoma, CMT provides better disease control than ABVD alone, especially among those not achieving complete response after two cycles of ABVD. Within the follow-up duration evaluated, overall survivals were similar. Longer follow-up is required to understand the implications of radiation and chemotherapy-related late effects. Clinical trials The trials included in this analysis were registered at ClinicalTrials.gov: HD10 - NCT00265018, HD11 - NCT00264953, HD.6 - NCT00002561.

Description: Cellular processes are typically carried out by protein complexes and functional modules. Identifying them plays an important role for our attempt to reveal principles of cellular organizations and functions. In this article, we review computational algorithms for identifying protein complexes and/or functional modules from protein–protein interaction (PPI) networks. We first describe issues and pitfalls when interpreting PPI networks. Then based on types of data used and main ideas involved, we briefly describe protein complex and/or functional module identification algorithms in four categories: (i) those based on topological structures of unweighted PPI networks; (ii) those based on characters of weighted PPI networks; (iii) those based on multiple data integrations; and (iv) those based on dynamic PPI networks. The PPI networks are modelled increasingly precise when integrating more types of data, and the study of protein complexes would benefit by shifting from static to dynamic PPI networks.

Description: The ataxia telangiectasia mutated and Rad3-related (ATR)-checkpoint kinase 1 (Chk1) axis is the major signaling pathway activated in response to replication stress and is essential for the intra-S checkpoint. ATR phosphorylates and activates a number of molecules to coordinate cell cycle progression. Chk1 is the major effector downstream from ATR and plays a critical role in intra-S checkpoint on replication stress. Activation of Chk1 kinase also requires its association with Claspin, an adaptor protein essential for Chk1 protein stability, recruitment and ATR-dependent Chk1 phosphorylation. We have previously reported that, on replication stress, the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is rapidly phosphorylated by ATR at the stalled replication forks and is required for cellular resistance to replication stresses although the impact of DNA-PKcs onto the ATR signaling pathway remains elusive. Here we report that ATR-dependent Chk1 phosphorylation and Chk1 signaling are compromised in the absence of DNA-PKcs. Our investigation reveals that DNA-PKcs is required to maintain Chk1–Claspin complex stability and transcriptional regulation of Claspin expression. The impaired Chk1 activity results in a defective intra-S checkpoint response in DNA-PKcs–deficient cells. Taken together, these results suggest that DNA-PKcs, in addition to its direct role in DNA damage repair, facilitates ATR-Chk1 signaling pathway in response to replication stress.

Description: The female genital epithelium plays a protective role against invading pathogens; however, sexual transmission of human immunodeficiency virus type 1 (HIV-1) still occurs in healthy women. To model virus–cell interactions in this barrier during sexual transmission, we studied the uptake and infection of ectocervical and endocervical cell lines with cell-free fluorescent protein-expressing recombinant HIV-1 carrying primary transmitted/founder envelope genes. We observed that a subset of both the ectocervical and endocervical epithelial cells become productively infected with cell-free HIV-1 in a CD4-independent manner. In addition, the ability of the semen-derived enhancer of virus infection (SEVI) to enhance virus-epithelial cell interactions was studied. This infection is increased approximately 2–5 fold when inoculation occurs in the presence of SEVI fibrils. Once infected, the epithelial cells are capable of transmitting the virus to target CD4 T cells in coculture in a contact-dependent manner that uses conventional CD4- and coreceptor-dependent entry. The infection of target CD4 T cells only occurs when de novo HIV-1 is produced within the epithelial cells. These findings suggest that a subset of cervical epithelial cells may be actively involved in establishing a systemic HIV infection and should be a target when designing prevention strategies to protect against HIV-1 sexual transmission.

Description: Motivation: Identification of altered pathways that are clinically relevant across human cancers is a key challenge in cancer genomics. Precise identification and understanding of these altered pathways may provide novel insights into patient stratification, therapeutic strategies and the development of new drugs. However, a challenge remains in accurately identifying pathways altered by somatic mutations across human cancers, due to the diverse mutation spectrum. We developed an innovative approach to integrate somatic mutation data with gene networks and pathways, in order to identify pathways altered by somatic mutations across cancers. Results: We applied our approach to The Cancer Genome Atlas (TCGA) dataset of somatic mutations in 4790 cancer patients with 19 different types of tumors. Our analysis identified cancer-type-specific altered pathways enriched with known cancer-relevant genes and targets of currently available drugs. To investigate the clinical significance of these altered pathways, we performed consensus clustering for patient stratification using member genes in the altered pathways coupled with gene expression datasets from 4870 patients from TCGA, and multiple independent cohorts confirmed that the altered pathways could be used to stratify patients into subgroups with significantly different clinical outcomes. Of particular significance, certain patient subpopulations with poor prognosis were identified because they had specific altered pathways for which there are available targeted therapies. These findings could be used to tailor and intensify therapy in these patients, for whom current therapy is suboptimal. Availability and implementation: The code is available at: http://www.taehyunlab.org . Contact: jhcheong@yuhs.ac or taehyun.hwang@utsouthwestern.edu or taehyun.cs@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: In order to elucidate the functional organization of the genome, it is vital to directly visualize the interactions between genomic elements in living cells. For this purpose, we engineered the Cas9 protein from Staphylococcus aureus (SaCas9) for the imaging of endogenous genomic loci, which showed a similar robustness and efficiency as previously reported for Streptococcus pyogenes Cas9 (SpCas9). Imaging readouts allowed us to characterize the DNA-binding activity of SaCas9 and to optimize its sgRNA scaffold. Combining SaCas9 and SpCas9, we demonstrated two-color CRISPR imaging with the capability to resolve genomic loci spaced by 〈300 kb. Combinatorial color-mixing further enabled us to code multiple genomic elements in the same cell. Our results highlight the potential of combining SpCas9 and SaCas9 for multiplexed CRISPR-Cas9 applications, such as imaging and genome engineering.

Description: Aims Over the past decade, catheter ablation (CA) has become an established therapy for symptomatic atrial fibrillation (AF). Atrial fibrillation is common in hypertrophic cardiomyopathy (HCM) patients, and restoring sinus rhythm is of great clinical benefit to them. Therefore, we conducted a systematic review and meta-analysis of the available data to evaluate the effectiveness and safety of CA for AF in patients with HCM. Methods and Results Six databases were searched to identify studies describing outcomes of CA of AF in HCM patients with a mean follow-up of ≥12 months after the index procedure. The following data were extracted: (i) single-procedure success, (ii) multiple-procedure success, and (iii) drug-free success. Fifteen studies involving 531 patients were included. Single-procedure freedom from atrial arrhythmia at the latest follow-up was 45.5% [95% confidence interval (CI): 34.8–56.2%]. With multiple procedures, the final success rate was 66.1% (95% CI: 55.3–76.9%) overall, 71.8% (95% CI: 61.6–82.0%) in paroxysmal AF, and 47.5% (95% CI: 36.0–59.0%) in non-paroxysmal AF. Without anti-arrhythmic drugs (AADs), single-procedure success rate at latest follow-up was 32.9% (95% CI: 21.7–41.1%); after multiple procedures, this raised to 50.4% (95% CI: 39.2–61.6%). The incidence of serious periprocedural complications was acceptable [5.1% (95% CI: 2.8–9.6%)]. Substantial heterogeneity ( I 2 〉 50%) was noted in the above groups. Conclusions Catheter ablation of AF in patients with HCM is feasible, although more repeat procedures and AAD are needed to prevent AF recurrence.

Description: The rotation curve (RC) of the Milky Way out to ~100 kpc has been constructed using ~16 000 primary red clump giants (PRCGs) in the outer disc selected from the LAMOST Spectroscopic Survey of the Galactic Anti-centre (LSS-GAC) and the Sloan Digital Sky Survey (SDSS)-III/APOGEE survey, combined with ~5700 halo K giants (HKGs) selected from the SDSS/SEGUE survey. To derive the RC, the PRCG sample of the warm disc population and the HKG sample of halo stellar population are, respectively, analysed using a kinematical model allowing for the asymmetric drift corrections and re-analysed using the spherical Jeans equation along with measurements of the anisotropic parameter β currently available. The typical uncertainties of RC derived from the PRCG and HKG samples are, respectively, 5–7 km s –1 and several tens km s –1 . We determine a circular velocity at the solar position, V c ( R 0 ) = 240 ± 6 km s –1 and an azimuthal peculiar speed of the Sun, V = 12.1 ± 7.6 km s –1 , both in good agreement with the previous determinations. The newly constructed RC has a generally flat value of 240 km s –1 within a Galactocentric distance r of 25 kpc and then decreases steadily to 150 km s –1 at r  ~ 100 kpc. On top of this overall trend, the RC exhibits two prominent localized dips, one at r  ~ 11 kpc and another at r  ~ 19 kpc. From the newly constructed RC, combined with other constraints, we have built a parametrized mass model for the Galaxy, yielding a virial mass of the Milky Way's dark matter halo of $0.90^{+0.07}_{-0.08} \times 10^{12}$  M and a local dark matter density, $\rho _{\rm {\odot }, dm} = 0.32^{+0.02}_{-0.02}$  GeV cm –3 .

Description: Motivation: Sequencing of matched tumor and normal samples is the standard study design for reliable detection of somatic alterations. However, even very low levels of cross-sample contamination significantly impact calling of somatic mutations, because contaminant germline variants can be incorrectly interpreted as somatic. There are currently no sequence-only based methods that reliably estimate contamination levels in tumor samples, which frequently display copy number changes. As a solution, we developed Conpair, a tool for detection of sample swaps and cross-individual contamination in whole-genome and whole-exome tumor–normal sequencing experiments. Results: On a ladder of in silico contaminated samples, we demonstrated that Conpair reliably measures contamination levels as low as 0.1%, even in presence of copy number changes. We also estimated contamination levels in glioblastoma WGS and WXS tumor–normal datasets from TCGA and showed that they strongly correlate with tumor–normal concordance, as well as with the number of germline variants called as somatic by several widely-used somatic callers. Availability and Implementation: The method is available at: https://github.com/nygenome/conpair . Contact: egrabowska@gmail.com or mczody@nygenome.org Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Background Grade II and III gliomas have variable clinical behaviors, showing the distinct molecular genetic alterations from glioblastoma (GBM), many of which eventually transform into more aggressive tumors. Since the classifications of grade II/III gliomas based on the genetic alterations have been recently emerging, it is now a trend to include molecular data into the standard diagnostic algorithm of glioma. Methods Here we sequenced TERT promoter mutational status ( TERT p-mut) in the DNA of 377 grade II/III gliomas and analyzed the clinical factors, molecular aberrations, and transcriptome profiles. Results We found that TERT p-mut occurred in 145 of 377 grade II and III gliomas (38.5%), mutually exclusive with a TP53 mutation ( TP53 -mut; P 〈 .001) and coincident with a 1p/19q co-deletion ( P = .002). TERT p-mut was an independent predictive factor of a good prognosis in all patients ( P = .048). It has been an independent factor associated with a good outcome in the IDH mutation ( IDH -mut) subgroup ( P = .018), but it has also been associated with a poor outcome in the IDH wild-type ( IDH -wt) subgroup ( P = .049). Combining TERTp -mut and IDH -mut allowed the grade II/III malignancies to be reclassified into IDH -mut/ TERTp -mut, IDH -mut only, TERTp -mut only, and IDH -wt/ TERTp -wt. 1p/19q co-deletion, TP53 -muts, Ki-67 expression differences, and p-MET expression differences characterized IDH -mut/ TERTp- mut, IDH- mut only, TERTp- mut only, and IDH -wt/ TERTp -wt subtypes, respectively. Conclusions Our results showed that TERT p-mut combined with IDH -mut allowed simple classification of grade II/III gliomas for stratifying patients and clarifying diagnostic accuracy by supplementing standard histopathological criteria.