Determining the effects of loss of function mutations in human cell lines

Quantifying differences in the amount of protein and mRNA caused by missense mutations in a gene of interest can be challenging, especially when using patient-derived primary cells, which are intrinsically variable. In this protocol, we describe how to culture patient-derived lymphoblast and fibroblast cell lines for later mRNA and protein quantification. We also describe the steps to examine variants of PUM1 in HEK293T cells, but the protocol can be applied to other proteins of interest. For complete details on the use and execution of this protocol, please refer to Gennarino et al. (2018).

SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair

When transcribed DNA is damaged, the transcription and DNA repair machineries must interact to ensure successful DNA repair. The mechanisms of this interaction in the context of chromatin are still being elucidated. Here we show that the SIRT6 protein enhances non-homologous end joining (NHEJ) DNA repair by transiently repressing transcription. Specifically, SIRT6 mono-ADP ribosylates the lysine demethylase JHDM1A/KDM2A leading to rapid displacement of KDM2A from chromatin, resulting in increased H3K36me2 levels. Furthermore, we found that through HP1α binding, H3K36me2 promotes subsequent H3K9 tri-methylation. This results in transient suppression of transcription initiation by RNA polymerase II and recruitment of NHEJ factors to DNA double-stranded breaks (DSBs). These data reveal a mechanism where SIRT6 mediates a crosstalk between transcription and DNA repair machineries to promote DNA repair. SIRT6 functions in multiple pathways related to aging, and its novel function coordinating DNA repair and transcription is yet another way by which SIRT6 promotes genome stability and longevity.

SIRT6 promotes transcription of a subset of NRF2 targets by mono-ADP-ribosylating BAF170

SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) responsive genes during oxidative stress. However, while the mechanism of SIRT6-mediated silencing is well understood, the mechanism of SIRT6-mediated transcriptional activation is unknown. Here, we employed SIRT6 separation of function mutants to reveal that SIRT6 mono-ADP-ribosylation activity is required for transcriptional activation. We demonstrate that SIRT6 mono-ADP-ribosylation of BAF170, a subunit of BAF chromatin remodeling complex, is critical for activation of a subset of NRF2 responsive genes upon oxidative stress. We show that SIRT6 recruits BAF170 to enhancer region of the Heme oxygenase-1 locus and promotes recruitment of RNA polymerase II. Furthermore, SIRT6 mediates the formation of the active chromatin 10-kb loop at the HO-1 locus, which is absent in SIRT6 deficient tissue. These results provide a novel mechanism for SIRT6-mediated transcriptional activation, where SIRT6 mono-ADP-ribosylates and recruits chromatin remodeling proteins to mediate the formation of active chromatin loop.

Dangerous Entrapment for NRF2

Progerin, a mutated lamin A, causes the severe premature-aging syndrome Hutchinson-Gilford progeria (HGPS). Kubben et al. present a driving mechanism for HGPS involving trapping of NRF2 at the nuclear periphery by progerin. This local restriction results in impaired NRF2 signaling and chronic oxidative stress.

Designing a broad-spectrum integrative approach for cancer prevention and treatment

Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broad-spectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment. Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered.

Outcome of arthroscopic single-bundle anterior cruciate ligament reconstruction: anteromedial portal technique versus transtibial drilling technique

PURPOSE

Controversies exist about the femoral tunnel preparation technique in anterior cruciate ligament (ACL) reconstruction surgeries. The aim of this study was to evaluate mid-term outcomes of transtibial (TT) technique in comparison with anteromedial portal (AMP) one.

METHODS

Demographic data, height, weight, period of time from injury to surgery, and follow-up duration of patients underwent ACL reconstruction using single-bundle hamstring graft by the senior author between 2007 and 2011 were evaluated, retrospectively. Mid-quadriceps circumference difference, passive range of motion of the joint, anterior drawer test, Lachman test, and pivot shift test were assessed for each case. Function of the knee joint was calculated using International Knee Documentation Committee (IKDC), Lysholm, and Tegner scores.

RESULTS

Of 50 cases in the AMP group (age 30.6 ± 6.5), 45 were male and of the 44 patients in the TT group (age 30.0 ± 6.5), forty were male. Mean follow-up times in the AMP and TT group were 18.2 months (range 12-84 months) and 25.7 months (range 16-48 months), respectively. No statistically significant difference was found in mid-quadriceps circumference difference (P = 0.861). Also, functional knee scores (P values of IKDC = 0.329, Lysholm score = 0.08, Tegner = 0.504) and stability tests (P values of anterior drawer test = 0.07, Lachman test = 0.486, pivot shift test = 0.348) did not differ statistically between groups.

CONCLUSION

There is no superiority of AMP technique on TT technique in ACL reconstructive surgeries. It could be suggested that performing a well-done technique, either TT or AMP, may be more important than only choosing a technique.

Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition

Genomic instability can initiate cancer, augment progression, and influence the overall prognosis of the affected patient. Genomic instability arises from many different pathways, such as telomere damage, centrosome amplification, epigenetic modifications, and DNA damage from endogenous and exogenous sources, and can be perpetuating, or limiting, through the induction of mutations or aneuploidy, both enabling and catastrophic. Many cancer treatments induce DNA damage to impair cell division on a global scale but it is accepted that personalized treatments, those that are tailored to the particular patient and type of cancer, must also be developed. In this review, we detail the mechanisms from which genomic instability arises and can lead to cancer, as well as treatments and measures that prevent genomic instability or take advantage of the cellular defects caused by genomic instability. In particular, we identify and discuss five priority targets against genomic instability: (1) prevention of DNA damage; (2) enhancement of DNA repair; (3) targeting deficient DNA repair; (4) impairing centrosome clustering; and, (5) inhibition of telomerase activity. Moreover, we highlight vitamin D and B, selenium, carotenoids, PARP inhibitors, resveratrol, and isothiocyanates as priority approaches against genomic instability. The prioritized target sites and approaches were cross validated to identify potential synergistic effects on a number of important areas of cancer biology.

The healing effect of bioglue in articular cartilage defect of femoral condyle in experimental rabbit model

Background

The full-thickness articular cartilage defects of knee have a poor healing capacity that may progress to osteoarthritis and need a knee replacement. This study determines the healing effect of bioglue in fullthickness articular cartilage defect of femoral condyle in rabbit.

Methods

Forty-eight male rabbits were randomly divided into four equal groups. In group A, 4 mm articular cartilage defects were created in the right and left medial femoral condyles. Then a graft from xiphoid cartilage was transferred into the defect together with a designed bioglue and the knees were closed. In group B, an articular cartilage defect was created identical to group A, but the defect size was 6 mm. In group C, 4 and 6 mm articular cartilage defects were created in the right and left medial femoral condyles respectively. The graft was transferred into the defect and the knees were stitched. In group D, articular cartilage defects were created similar to group C, just filled with bioglue and closed. The rabbits were euthanized and subgroups were defined as A1, B1, C1 and D1 after 30 days and A2, B2, C2 and D2 after 60 days. The cartilages were macroscopically and histologically investigated for any changes.

Results

Microscopic and macroscopic investigations showed that bioglue had a significant healing effect in the femoral condyle.

Conclusion

Addition of bioglue can effectively promote the healing of articular cartilage defects.