Comprehensive mutational scanning of EGFR reveals TKI sensitivities of extracellular domain mutants

The epidermal growth factor receptor, EGFR, is frequently activated in lung cancer and glioblastoma by genomic alterations including missense mutations. The different mutation spectra in these diseases are reflected in divergent responses to EGFR inhibition: significant patient benefit in lung cancer, but limited in glioblastoma. Here, we report a comprehensive mutational analysis of EGFR function. We perform saturation mutagenesis of EGFR and assess function of ~22,500 variants in a human EGFR-dependent lung cancer cell line. This approach reveals enrichment of erlotinib-insensitive variants of known and unknown significance in the dimerization, transmembrane, and kinase domains. Multiple EGFR extracellular domain variants, not associated with approved targeted therapies, are sensitive to afatinib and dacomitinib in vitro. Two glioblastoma patients with somatic EGFR G598V dimerization domain mutations show responses to dacomitinib treatment followed by within-pathway resistance mutation in one case. In summary, this comprehensive screen expands the landscape of functional EGFR variants and suggests broader clinical investigation of EGFR inhibition for cancers harboring extracellular domain mutations.

Functional genomic analysis of CDK4 and CDK6 gene dependency across human cancer cell lines

Cyclin-dependent kinase 4 (CDK4) and cyclin-dependent kinase 6 (CDK6) are key cell cycle regulators that are frequently dysregulated in human malignancies. CDK4/6 inhibitors are clinically approved for the treatment of hormone receptor-positive, HER2-negative (HR+/HER2-) breast cancer, but improved specificity and reduced toxicity might expand their use to other indications. Through analysis of publicly available genome-wide loss-of-function data combined with single and dual-targeting CRISPR assays, we found differential cell proliferation vulnerability of cell lines to either CDK4 deletion alone, CDK6 deletion alone, combined CDK4/CDK6 deletion, or neither. CDK6 expression was the best single predictor of CDK4 (negatively correlated) and CDK6 (positively correlated) dependencies in the cancer cell lines, with adenocarcinoma cell lines being more sensitive to CDK4 deletion and hematologic and squamous cancer cell lines being more sensitive to CDK6 deletion. RB-E2F signaling was confirmed as a main downstream node of CDK4/6 in these experiments as shown by the survival effects of RB1 deletion. Finally, we show in a subset of cancer cell lines not dependent on CDK4/6 that CDK2-CCNE1 is an important alternative dependency for cell proliferation. Together, our comprehensive data exploration and functional experiments delineate the landscape of pan-cancer CDK4/6 gene dependencies and define unique cancer cell populations that might be sensitive to CDK4-selective or CDK6-selective inhibitors.

Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma

Genomic analysis of lung adenocarcinomas has revealed that the MGA gene, which encodes a heterodimeric partner of the MYC-interacting protein MAX, is significantly mutated or deleted in lung adenocarcinomas. Most of the mutations are loss of function for MGA, suggesting that MGA may act as a tumor suppressor. Here, we characterize both the molecular and cellular role of MGA in lung adenocarcinomas and illustrate its functional relevance in the MYC pathway. Although MGA and MYC interact with the same binding partner, MAX, and recognize the same E-box DNA motif, we show that the molecular function of MGA appears to be antagonistic to that of MYC. Using mass spectrometry-based affinity proteomics, we demonstrate that MGA interacts with a noncanonical PCGF6-PRC1 complex containing MAX and E2F6 that is involved in gene repression, while MYC is not part of this MGA complex, in agreement with previous studies describing the interactomes of E2F6 and PCGF6. Chromatin immunoprecipitation-sequencing and RNA sequencing assays show that MGA binds to and represses genes that are bound and activated by MYC. In addition, we show that, as opposed to the MYC oncoprotein, MGA acts as a negative regulator for cancer cell proliferation. Our study defines a novel MYC/MAX/MGA pathway, in which MYC and MGA play opposite roles in protein interaction, transcriptional regulation, and cellular proliferation. IMPLICATIONS: This study expands the range of key cancer-associated genes whose dysregulation is functionally equivalent to MYC activation and places MYC within a linear pathway analogous to cell-cycle or receptor tyrosine kinase/RAS/RAF pathways in lung adenocarcinomas.

p53 and ribosome biogenesis stress: the essentials

Cell proliferation and cell growth are two tightly linked processes, as the proliferation program cannot be executed without proper accumulation of cell mass, otherwise endangering the fate of the two daughter cells. It is therefore not surprising that ribosome biogenesis, a key element in cell growth, is regulated by many cell cycle regulators. This regulation is exerted transcriptionally and post-transcriptionally, in conjunction with numerous intrinsic and extrinsic signals. Those signals eventually converge at the nucleolus, the cellular compartment that is not only responsible for executing the ribosome biogenesis program, but also serves as a regulatory hub, responsible for integrating and transmitting multiple stress signals to the omnipotent cell fate gatekeeper, p53. In this review we discuss when, how and why p53 is activated upon ribosomal biogenesis stress, and how perturbation of this critical regulatory interplay may impact human disease.

RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation

Embryonic stem cells (ESCs) maintain high genomic plasticity, which is essential for their capacity to enter diverse differentiation pathways. Posttranscriptional modifications of chromatin histones play a pivotal role in maintaining this plasticity. We now report that one such modification, monoubiquitylation of histone H2B on lysine 120 (H2Bub1), catalyzed by the E3 ligase RNF20, increases during ESC differentiation and is required for efficient execution of this process. This increase is particularly important for the transcriptional induction of relatively long genes during ESC differentiation. Furthermore, we identify the deubiquitinase USP44 as a negative regulator of H2B ubiquitylation, whose downregulation during ESC differentiation contributes to the increase in H2Bub1. Our findings suggest that optimal ESC differentiation requires dynamic changes in H2B ubiquitylation patterns, which must occur in a timely and well-coordinated manner.

Importin 7 and exportin 1 link c-Myc and p53 to regulation of ribosomal biogenesis

Members of the β-karyopherin family mediate nuclear import of ribosomal proteins and export of ribosomal subunits, both required for ribosome biogenesis. We report that transcription of the β-karyopherin genes importin 7 (IPO7) and exportin 1 (XPO1), and several additional nuclear import receptors, is regulated positively by c-Myc and negatively by p53. Partial IPO7 depletion triggers p53 activation and p53-dependent growth arrest. Activation of p53 by IPO7 knockdown has distinct features of ribosomal biogenesis stress, with increased binding of Mdm2 to ribosomal proteins L5 and L11 (RPL5 and RPL11). Furthermore, p53 activation is dependent on RPL5 and RPL11. Of note, IPO7 and XPO1 are frequently overexpressed in cancer. Altogether, we propose that c-Myc and p53 counter each other in the regulation of elements within the nuclear transport machinery, thereby exerting opposing effects on the rate of ribosome biogenesis. Perturbation of this balance may play a significant role in promoting cancer.

DePICTing p53 activation: a new nucleolar link to cancer

p53 activation by ribosomal biogenesis stress is important for tumor suppression. In the August issue of Nature Medicine, Sasaki et al. identify PICT1 as a regulator of this process. PICT1 sequesters ribosomal protein RPL11 in the nucleolus, attenuating p53 induction. Excessive PICT1 may dampen the p53 response and promote cancer.

Different subcellular localizations and functions of Arabidopsis myosin VIII

BACKGROUND

Myosins are actin-activated ATPases that use energy to generate force and move along actin filaments, dragging with their tails different cargos. Plant myosins belong to the group of unconventional myosins and Arabidopsis myosin VIII gene family contains four members: ATM1, ATM2, myosin VIIIA and myosin VIIIB.

RESULTS

In transgenic plants expressing GFP fusions with ATM1 (IQ-tail truncation, lacking the head domain), fluorescence was differentially distributed: while in epidermis cells at the root cap GFP-ATM1 equally distributed all over the cell, in epidermal cells right above this region it accumulated in dots. Further up, in cells of the elongation zone, GFP-ATM1 was preferentially positioned at the sides of transversal cell walls. Interestingly, the punctate pattern was insensitive to brefeldin A (BFA) while in some cells closer to the root cap, ATM1 was found in BFA bodies. With the use of different markers and transient expression in Nicotiana benthamiana leaves, it was found that myosin VIII co-localized to the plasmodesmata and ER, colocalized with internalized FM4-64, and partially overlapped with the endosomal markers ARA6, and rarely with ARA7 and FYVE. Motility of ARA6 labeled organelles was inhibited whenever associated with truncated ATM1 but motility of FYVE labeled organelles was inhibited only when associated with large excess of ATM1. Furthermore, GFP-ATM1 and RFP-ATM2 (IQ-tail domain) co-localized to the same spots on the plasma membrane, indicating a specific composition at these sites for myosin binding.

CONCLUSION

Taken together, our data suggest that myosin VIII functions differently in different root cells and can be involved in different steps of endocytosis, BFA-sensitive and insensitive pathways, ER tethering and plasmodesmatal activity.

Identification of plant cytoskeleton-interacting proteins by screening for actin stress fiber association in mammalian fibroblasts

Taking advantage of the high conservation of the cytoskeleton building blocks actin and tubulin between plant and animal kingdoms, we developed a functional genomic screen for the isolation of new plant cytoskeleton-binding proteins that uses a mammalian cell expression system. A yellow fluorescent protein (YFP)-fusion cDNA library from Arabidopsis was inserted into rat fibroblasts and screened for fluorescent chimeras localizing to cytoskeletal structures. The high-throughput screen was performed by an automated microscope. An initial set of candidate genes identified in the screen was isolated, sequenced, the full-length cDNAs were synthesized by RT-PCR and tested by biochemical approaches to verify the ability of the genes to bind actin directly. Alternatively, indirect binding via interaction with other actin-binding proteins was studied. The full-length cDNAs were transferred back to plants as YFP chimeras behind the CAMV-35S promoter. We give here two examples of new plant cytoskeletal proteins identified in the pilot screen. ERD10, a member of the dehydrin family of proteins, was localized to actin stress fibers in rat fibroblasts. Its direct binding to actin filaments was confirmed by several biochemical approaches. Touch-induced calmodulin-like protein, TCH2, was also localized to actin stress fibers in fibroblasts, but was unable to bind actin filaments directly in vitro. Nevertheless, it did bind to the IQ domains of Arabidopsis myosin VIII in a calcium-dependent manner. Further evidence for a cytoskeletal function of ERD10 was obtained in planta; GFP-ERD10 was able to protect the actin cytoskeleton from latrunculin-mediated disruption in Nicotiana benthamiana leaves.

Supernaturalist curers and sorcery accusations in Thailand

Thailand's supernaturalist practitioners are both respected for their curative powers and feared as potential sorcerers. When sorcery is diagnosed, exorcists generally implicate other practitioners as the source of the supernatural aggression. Given the often grave nature of such accusations, how have supernaturalist curers been spared from persecution during times of adversity? This paper examines three different sets of restraints that have evolved in three different regions of Thailand to protect supernaturalist curers from excessive accusations that could lead to harassment. The unique local character of each set of restraints is shown to be shaped by such factors as the availability of modern medical facilities, local methods of conflict resolution, local spirit beliefs, and the presence or absence of ethnic outgroup practitioners.

The interplay of traditional therapies in south Thailand

Discernible among the diversity of folk-medical practitioners of Songkhla, Thailand, are three prominent therapeutic traditions: those of the herbalists, folk psychotherapists, and supernaturalists. Most curers describe themselves as specialists in one or another of these modes, but at the same time, many also recognize multiple levels of causation and multi-modal treatment alternatives for any specific affliction. Accordingly, they liberally apply their own therapeutic orientation to afflictions ordinarily diagnosed as calling for treatment in modes other than their own. To treat afflictions normally outside their own domain, they call on metaphorical principles to render their traditional techniques and paraphernalia applicable to a greater variety of illnesses. In this way they strive to attract a wider variety of clientele in the increasingly competitive environment created by the expansion of modern medical facilities. An analysis of this system contributes to our understanding of therapeutic pluralism in these times of rapid culture change.

Rivalry and diversity among Thai curer-magicians

In central and southern Thailand neighboring practitioners of the same folk-medical specialties were found to be remarkably inconsistent in their diagnostic interpretations of similar afflictions. There appears to be little or no direct communication between local competitors among Thailand's traditional curers. Those in search of tutelage from an established practitioner must often travel long distances to find a willing tutor. What results from this pattern is a system of master-disciple networks through which curative knowledge and patient referrals flow across provincial boundaries. Rivalry among neighboring curer-magicians is so pervasive that diagnostic decisions sometimes depend in part on the relative status of previous healers on a case. The paper concludes with a discussion of the competition found among a specific group of curer-magicians, namely, Thai-Buddhist monk-practitioners. The latter rivalry may play an important role in social relations within and among Buddhist monasteries.

Curing and sociocultural separatism in South Thailand

In much of Thailand animistic curing practices have lost ground to great tradition herbal medicine and modern scientific medicine as more people achieve literacy. Especially in urbanizing areas, Buddhist and Muslim Thais hold in the highest esteem traditional curers whose knowledge derives from patient experimentation and the study of ancient texts. However, among Malay-speaking Muslims in south Thailand, the most respected therapeutic knowledge is revelatory in nature. Southern Muslim curers are generally mystics or spirit-mediums whose direct channels of communication with the supernatural convey remedies for afflictions but also provide guidelines for maintaining sociocultural separatism.

The curer as cultural intermediary in southern Thailand

A glimpse at the life of an illustrious Buddhist monastic curer in Pattani, Thailand, reveals a significant multiethnic component of Southeast Asia's traditional medical systems. The prominence of this curer and the prosperity of his monastery derive in large part from his command of alien occult knowledge, which he uses to combat outside supernatural aggression. The paper concludes with a discussion of how centers of outside magical power are conceptualized among various groups in Thailand.