Minimized combinatorial CRISPR screens identify genetic interactions in autophagy

Combinatorial CRISPR-Cas screens have advanced the mapping of genetic interactions, but their experimental scale limits the number of targetable gene combinations. Here, we describe 3Cs multiplexing, a rapid and scalable method to generate highly diverse and uniformly distributed combinatorial CRISPR libraries. We demonstrate that the library distribution skew is the critical determinant of its required screening coverage. By circumventing iterative cloning of PCR-amplified oligonucleotides, 3Cs multiplexing facilitates the generation of combinatorial CRISPR libraries with low distribution skews. We show that combinatorial 3Cs libraries can be screened with minimal coverages, reducing associated efforts and costs at least 10-fold. We apply a 3Cs multiplexing library targeting 12,736 autophagy gene combinations with 247,032 paired gRNAs in viability and reporter-based enrichment screens. In the viability screen, we identify, among others, the synthetic lethal WDR45B-PIK3R4 and the proliferation-enhancing ATG7-KEAP1 genetic interactions. In the reporter-based screen, we identify over 1,570 essential genetic interactions for autophagy flux, including interactions among paralogous genes, namely ATG2A-ATG2B, GABARAP-MAP1LC3B and GABARAP-GABARAPL2. However, we only observe few genetic interactions within paralogous gene families of more than two members, indicating functional compensation between them. This work establishes 3Cs multiplexing as a platform for genetic interaction screens at scale.

Acetylsalicylic acid enhances antiproliferative effects of the EGFR inhibitor gefitinib in the absence of activating mutations in gastric cancer

The epidermal growth factor receptor (EGFR) is highly expressed in gastric cancer indicating its suitability as a target for receptor tyrosine kinase (RTK) inhibitors. In the current study we explored the role of EGFR and its potential use as a therapeutic target in gastric cancer. First we analyzed 66 gastric cancer samples of Asian and Caucasian patients for the presence of EGFR mutations. No activating EGFR mutations were found and gefitinib alone was only weakly effective in gastric cancer cell lines. However, acetylsalicylic acid (ASA) significantly enhanced the inhibitory effects of gefitinib indicating synergistic action. Whole genome expression profiling indicated significant regulation of 120 genes in the case of co-administration of gefitinib and ASA (32 induced, 88 repressed) in gastric adenocarcinoma cells. Further analyses indicated that several important signalling pathways were effectively inhibited by simultaneous exposure to gefitinib and ASA. Our findings indicate that although gastric cancer does not seem to harbour mutations which render the cancer cells constitutively susceptible to gefitinib, the co-administration of ASA can strengthen RTK inhibitor activity in adenocarcinoma cells by EGFR activation. This is the first report of effective modulation of EGFR-inhibition activity in cancer.

[Mutations of growth factor receptor Flt3 in acute myeloid leukemia: transformation of myeloid cells by Ras-dependent and Ras-independent mechanisms]

BACKGROUND AND OBJECTIVE

The tyrosine kinase receptor Flt3 mediates important functions in early hematopoietic progenitors. Recently mutations of a growth factor receptor have been identified in about 30 % of patients with acute myeloid leukemia (AML). These mutations are associated with a poor prognosis. In-vitro and animal data show their involvement in leukemic transformation. Experiments analyzing the effects of these mutations on signal transduction and gene expression patterns of myeloid cells allow for the classification of this receptor as an oncogene. Furthermore, they help to define the receptor and its signaling intermediates as therapeutic targets.

METHODS

In order to analyze the signaling properties of mutated FLT3 receptors, we isolated the receptor mRNA from two patients with AML. Wild-type and mutant Flt3 isoforms were expressed in 32D cells that were subsequently analyzed for proliferation, survival, activation of signaling intermediates and gene expression levels. Also, the effects of of Ras-, MAP-Kinase and PI3-Kinase inhibition were analyzed.

RESULTS

The expression of mutated Flt3 (Flt3-ITD) induced factor-independent proliferation and survival in the myeloid progenitor cell line 32D. Flt3-ITD activated Ras- and PI3-kinase-dependent signaling pathways, as well as STAT5 and STAT3. Activation of STAT proteins was followed by the induction of known STAT target genes like SOCS2, SOCS3 and CIS. Inhibition of Ras-dependent signal transduction by a dominant negative Ras construct inhibited some, but not all biological effects of Flt3-ITD. Similar results were obtained by chemical inhibition of the MAP kinases. In contrast, inhibition of PI3 kinase activity inhibited growth factor-independent growth and apoptosis resistance of 32D cells.

CONCLUSIONS

Inhibition of Ras-dependent signaling pathways is not sufficient to abrogate the functional consequences of Flt3-mutations in myeloid cells. Therefore, therapeutic intervention by Ras-Inhibitors may not be sufficient to treat Flt3-driven disease.

Declining chloroquine resistance of Plasmodium falciparum in Lambaréné, Gabon from 1992 to 1998

Plasmodium falciparum malaria continues to threaten human populations in the tropics and travellers in endemic areas. Drug resistance of the parasite is a major problem in treating this devastating disease. In a prospective trial we investigated the in vitro sensitivity of Plasmodium falciparum to chloroquine, quinine and mefloquine in the Albert Schweitzer Hospital in Lambaréné, Gabon every second year from 1992 to 1998. We used the standard WHO in vitro sensitivity assay. Parasite sensitivity to quinine and mefloquine remained stable over the years. However, parasite resistance to chloroquine decreased highly significantly with the change in local malaria treatment policy. In 1992, 100% of parasite isolates showed resistance to chloroquine, whereas in 1998 only 45% were found resistant.

5' phospholipid phosphatase SHIP-2 causes protein kinase B inactivation and cell cycle arrest in glioblastoma cells

The tumor suppressor protein PTEN is mutated in glioblastoma multiform brain tumors, resulting in deregulated signaling through the phosphoinositide 3-kinase (PI3K)-protein kinase B (PKB) pathway, which is critical for maintaining proliferation and survival. We have examined the relative roles of the two major phospholipid products of PI3K activity, phosphatidylinositol 3,4-biphosphate [PtdIns(3,4)P2] and phosphatidylinositol 3,4,5-triphosphate [PtdIns(3,4,5)P3], in the regulation of PKB activity in glioblastoma cells containing high levels of both of these lipids due to defective PTEN expression. Reexpression of PTEN or treatment with the PI3K inhibitor LY294002 abolished the levels of both PtdIns(3, 4)P2 and PtdIns(3,4,5)P3, reduced phosphorylation of PKB on Thr308 and Ser473, and inhibited PKB activity. Overexpression of SHIP-2 abolished the levels of PtdIns(3,4,5)P3, whereas PtdIns(3,4)P2 levels remained high. However, PKB phosphorylation and activity were reduced to the same extent as they were with PTEN expression. PTEN and SHIP-2 also significantly decreased the amount of PKB associated with cell membranes. Reduction of SHIP-2 levels using antisense oligonucleotides increased PKB activity. SHIP-2 became tyrosine phosphorylated following stimulation by growth factors, but this did not significantly alter its phosphatase activity or ability to antagonize PKB activation. Finally we found that SHIP-2, like PTEN, caused a potent cell cycle arrest in G(1) in glioblastoma cells, which is associated with an increase in the stability of expression of the cell cycle inhibitor p27(KIP1). Our results suggest that SHIP-2 plays a negative role in regulating the PI3K-PKB pathway.

Prediction of accelerated cure in Plasmodium falciparum malaria by the elevated capacity of tumor necrosis factor production

Cytokine regulation was compared in three groups of Gabonese patients with Plasmodium falciparum malaria before and after therapy; adults with uncomplicated malaria, children with uncomplicated malaria, and children with severe malaria. Plasma levels of tumor necrosis factor (TNF), interleukin-6 (IL-6), IL-8, TNF receptors (TNF R), and the TNF/TNF R ratios were significantly higher in severe malaria compared with uncomplicated malaria. High plasma levels of all immunoregulatory molecules were associated with slow cure after therapy. In all patients, phytohemagglutinin-induced cytokine production was depressed on admission compared with convalescence. A significant difference was the higher TNF production capacity in patients with severe malaria on day 2 and day 5 compared with that in patients with uncomplicated malaria. In contrast to IL-6 and IL-8, a high TNF production capacity during the acute phase of malaria predicted a rapid clinical and parasitologic cure in the patients. These findings illustrate the dual role of TNF in the protection and pathology of malaria.

Malaria epidemiology in the province of Moyen Ogoov, Gabon

In the course of epidemiological and immunological baseline studies parasitological surveys were conducted, in 1992, in three localities situated in our near rain forest in the area of Lambaréné, Gabon, western Central Africa. Anopheles gambiae s.s. and A. funestus are considered to be the main vectors of malaria. The three localities represent strata with obvious differences in the intensity of malaria transmission. The lowest parasite rates were recorded in the village around the Albert-Schweitzer-Hospital where environmental sanitation and easy access to diagnostic and therapeutic facilities afford a fair measure of malaria control. The villages of Bellevue and Tchad show a much higher prevalence of Plasmodium falciparum, followed by P. malariae and P. ovale. In all three villages parasite rates and geometric mean parasite densities of P. falciparum showed the age pattern typical for areas with stable, hyperendemic malaria. Analysis by season showed the period of the long rains to be the epidemiologically calmest while the dry season and even more the short rainy season produced an increase of parasite rates and densities. In Tchad, the most affected of the three villages, the parasite rates in female adults were significantly lower than in male adults. This was accompanied by lower parasite densities in female adults.

Drug sensitivity of Plasmodium falciparum in Gabon. Activity correlations between various antimalarials

The sensitivity of Plasmodium falciparum to chloroquine, mefloquine, quinine, halofantrine, and sulfadoxine/pyrimethamine has been investigated at Lambaréné, in the Gabonese rain forest, between April and September 1992. WHO standard micro in vitro tests were performed. Of 43 isolates tested for response to chloroquine all were resistant to the drug with mean EC 50 and EC 90 values of 1.86 and 4.18 mumol/l blood, respectively, indicating the highest degree of resistance ever reported from Central Africa. With sulfadoxine/pyrimethamine 19 out of 27 isolates showed 90% inhibition of schizont maturation at a pyrimethamine concentration of at least 75 nmol/l blood medium mixture, indicating 30% of resistance to sulfadoxine/pyrimethamine. In contrast all isolates tested were fully inhibited by mefloquine at 3.2 mumol/l blood (40 isolates), quinine at 5.12 mumol/l blood medium mixture (41 isolates) and halofantrine at 3 nmol/l blood medium mixture (40 isolates) indicating full sensitivity to these drugs. A significant positive correlation was found between responses to quinine and mefloquine. The response to halofantrine was positively correlated with the responses to quinine and mefloquine, in the case of chloroquine and halofantrine an inverse relationship was observed. Compared with previous data from Gabon, the findings suggest a substantial increase of chloroquine resistance, in contrast to reports from neighbouring countries, which show stabilising or even declining chloroquine resistance patterns.

Clindamycin in combination with chloroquine or quinine is an effective therapy for uncomplicated Plasmodium falciparum malaria in children from Gabon

Multidrug resistance of Plasmodium falciparum is becoming common in Africa. In a randomized trial, four short-term regimens were compared for treating uncomplicated P. falciparum malaria in children 4-15 years old in Gabon. One hundred thirty patients received chloroquine (25 mg/kg over 48 h; group C), chloroquine (as above) plus clindamycin (5 mg/kg every 12 h for 6 doses; group CCl), quinine (12 mg/kg every 12 h for 6 doses; group Q), or quinine (as above) plus clindamycin (as above; group QCl). In group C, only 9% of patients were cured by day 28, 44% showed recrudescent malaria (RI), and 47% showed intermediate or high-grade resistance (RII/RIII). In group CCl, 70% of patients were cured and 30% showed recrudescences. In group Q, 32% were cured and 68% showed recrudescences. In group QCl, 88% were cured and 12% showed recrudescences after day 14. All treatment regimens were well tolerated. Thus, the combination of clindamycin with chloroquine or quinine enhances parasite clearance and improves response to therapy.

Curing of chloroquine-resistant malaria with clindamycin

A randomized comparative trial for treating adult patients with Plasmodium falciparum malaria was performed in Lambarene, Gabon. Forty-two patients received chloroquine (25 mg/kg for 48 hr) and 38 patients received clindamycin (5 mg/kg twice a day, for five days). Chloroquine treatment cured 15 patients (36%). Twenty patients (48%) showed recrudescent malaria by day 28 of follow-up (RI resistance) and seven patients (17%) showed persistent parasitemia after chloroquine treatment (RII/III resistance). In contrast, clindamycin treatment cured 37 of 38 patients (97%) and only one (3%) showed a recrudescence by day 28 (P < 0.001). Although the parasite clearance time was significantly longer after clindamycin treatment (median five days, range 3-6) than after chloroquine treatment (median four days, range 2-8) (P < 0.01), no differences were seen in the duration of symptoms after chemotherapy. In both treatment groups, no severe side effects occurred. Clindamycin can be used as a safe alternative to achieve radical cure in semi-immune adult patients with chloroquine-resistant P. falciparum malaria in Central Africa.