The phenotypic landscape of essential human genes

Understanding the basis for cellular growth, proliferation, and function requires determining the roles of essential genes in diverse cellular processes, including visualizing their contributions to cellular organization and morphology. Here, we combined pooled CRISPR-Cas9-based functional screening of 5,072 fitness-conferring genes in human HeLa cells with microscopy-based imaging of DNA, the DNA damage response, actin, and microtubules. Analysis of >31 million individual cells identified measurable phenotypes for >90% of gene knockouts, implicating gene targets in specific cellular processes. Clustering of phenotypic similarities based on hundreds of quantitative parameters further revealed co-functional genes across diverse cellular activities, providing predictions for gene functions and associations. By conducting pooled live-cell screening of ∼450,000 cell division events for 239 genes, we additionally identified diverse genes with functional contributions to chromosome segregation. Our work establishes a resource detailing the consequences of disrupting core cellular processes that represents the functional landscape of essential human genes.

Alpha-satellite RNA transcripts are repressed by centromere-nucleolus associations

Although originally thought to be silent chromosomal regions, centromeres are instead actively transcribed. However, the behavior and contributions of centromere-derived RNAs have remained unclear. Here, we used single-molecule fluorescence in-situ hybridization (smFISH) to detect alpha-satellite RNA transcripts in intact human cells. We find that alpha-satellite RNA-smFISH foci levels vary across cell lines and over the cell cycle, but do not remain associated with centromeres, displaying localization consistent with other long non-coding RNAs. Alpha-satellite expression occurs through RNA polymerase II-dependent transcription, but does not require established centromere or cell division components. Instead, our work implicates centromere–nucleolar interactions as repressing alpha-satellite expression. The fraction of nucleolar-localized centromeres inversely correlates with alpha-satellite transcripts levels across cell lines and transcript levels increase substantially when the nucleolus is disrupted. The control of alpha-satellite transcripts by centromere-nucleolar contacts provides a mechanism to modulate centromere transcription and chromatin dynamics across diverse cell states and conditions.

Functional genetics reveals modulators of antimicrotubule drug sensitivity

Microtubules play essential roles in diverse cellular processes and are important pharmacological targets for treating human disease. Here, we sought to identify cellular factors that modulate the sensitivity of cells to antimicrotubule drugs. We conducted a genome-wide CRISPR/Cas9-based functional genetics screen in human cells treated with the microtubule-destabilizing drug nocodazole or the microtubule-stabilizing drug paclitaxel. We further conducted a focused secondary screen to test drug sensitivity for ∼1,400 gene targets across two distinct human cell lines and to additionally test sensitivity to the KIF11 inhibitor, STLC. These screens defined gene targets whose loss enhances or suppresses sensitivity to antimicrotubule drugs. In addition to gene targets whose loss sensitized cells to multiple compounds, we observed cases of differential sensitivity to specific compounds and differing requirements between cell lines. Our downstream molecular analysis further revealed additional roles for established microtubule-associated proteins and identified new players in microtubule function.

Functional genetics reveals modulators of anti-microtubule drug sensitivity

Microtubules play essential roles in diverse cellular processes and are important pharmacological targets for treating human disease. Here, we sought to identify cellular factors that modulate the sensitivity of cells to anti-microtubule drugs. We conducted a genome-wide CRISPR/Cas9-based functional genetics screen in human cells treated with the microtubule-destabilizing drug nocodazole or the microtubule-stabilizing drug taxol. We further conducted a focused secondary screen to test drug sensitivity for ~1400 gene targets across two distinct human cell lines and to additionally test sensitivity to the Kif11-inhibitor, STLC. These screens defined gene targets whose loss enhances or suppresses sensitivity to anti-microtubule drugs. In addition to gene targets whose loss sensitized cells to multiple compounds, we observed cases of differential sensitivity to specific compounds and differing requirements between cell lines. Our downstream molecular analysis further revealed additional roles for established microtubule-associated proteins and identified new players in microtubule function.

Retrospective audit of laparoscopic inguinal hernia repair at a South African tertiary academic hospital

BACKGROUND

Adoption of laparoscopic inguinal hernia repair (LIHR) in sub-Saharan Africa is poor. The aim of this study was to describe our experience of the feasibility and short-term efficacy of the LIHR service at a South African tertiary academic hospital.

METHODS

A retrospective audit of all the adult, elective, laparoscopic inguinal hernia cases that were done between November 2011 and 31 October 2016. Data were collected regarding the patient demographics, index side of hernia, type of repair, conversion rate, peri- and postoperative complications, postoperative hernia recurrence, persistent groin pain for more than three months and procedure-related mortality.

RESULTS

One hundred and eighty-six patients were evaluated. One hundred and twenty-six (68%) patients were followed up for a mean of 38 months (3.1 years; range 9-67 months). Sixty (32%) patients were lost to follow-up. Early hernia recurrence (onset in < 7 days) occurred in one case after a totally extra-peritoneal (TEP) repair had required conversion to a trans-abdominal pre-peritoneal (TAPP) repair. Late recurrence (onset in > 7 days) occurred in seven TEP repair cases (5.6%). Four recurrences (57%) occurred within the first two years. Recurrences in the next three years showed a 59% reduction giving a recurrence rate of 2.9%. At follow-up, six TEP cases (4.8%) had persistent groin pain persisting for 3-6 months in two cases and for more than one year in four cases. Five cases had seroma, six scrotal haematoma and one port-site sepsis. No death occurred.

CONCLUSION

LIHR could be safely offered in a South African tertiary academic centre with acceptable results that are comparable with the South African private sector setting. LIHR could be implemented in other surgical training centres within a resource-limited environment.