In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

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The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people worldwide, igniting an unprecedented effort from the scientific community to understand the biological underpinning of COVID19 pathophysiology. In this Review, we summarize the current state of knowledge of innate and adaptive immune responses elicited by SARS-CoV-2 infection and the immunological pathways that likely contribute to disease severity and death. We also discuss the rationale and clinical outcome of current therapeutic strategies as well as prospective clinical trials to prevent or treat SARS-CoV-2 infection.

Patients with cancer can develop recurrent metastatic disease with latency periods that range from years even to decades. This pause can be explained by cancer dormancy, a stage in cancer progression in which residual disease is present but remains asymptomatic. Cancer dormancy is poorly understood, resulting in major shortcomings in our understanding of the full complexity of the disease. Here, I review experimental and clinical evidence that supports the existence of various mechanisms of cancer dormancy including angiogenic dormancy, cellular dormancy (G0-G1 arrest) and immunosurveillance. The advances in this field provide an emerging picture of how cancer dormancy can ensue and how it could be therapeutically targeted.The vast majority of cancer-related deaths are due to metastatic tumour growth that impairs the function of vital organs 1 . Metastatic lesions invariably originate from disseminated tumour cells, which often undergo a period of dormancy 2 (FIG. 1). Cancer recurrence after therapy and long periods of remission is frequent. For example, 20-45% of patients with breast or prostate cancer will relapse years or decades later 3-5 (FIGS 1,2). In fact, most cancer types are associated with disseminated disease that after treatment might persist as minimal residual disease (FIG 2; TABLE 1). However, the lack of mechanistic insight into this stage has been a major shortcoming in our understanding of the full complexities of metastatic growth. Functional characterization of disseminated dormant tumour cells is important because these cells most probably contain the information about the future progression of the disease (that is, metastasis development). To fully understand dormancy, cells must be characterized during the dormant state. Therefore, given that these cells are present in a wide variety of cancers, information gathered from studies of cancer dormancy might be applicable to a large number of patients.Cancer dormancy can be separated into mechanisms that antagonize the expansion of a dividing tumour cell population (tumour mass dormancy) and mechanisms that result in tumour cell growth arrest (tumour cell dormancy, or cellular dormancy) (FIG. 2). In the former, tumour cells usually divide but the lesion does not expand beyond a certain size because of either limitations in blood supply or an active immune system. Cellular dormancy can occur when tumour cells enter a state of quiescence (see BOX 1 for information on the relationship between quiescence, senescence and dormancy). These general mechanisms might explain the dormancy of residual cells that, following treatment, develop loco-regional or distant organ recurrences within different time frames. Box 1 Cancer dormancy: senescence or quiescence programmes?A common attempt to explain cellular dormancy is to catalogue it within known mechanisms of growth arrest such as senescence or quiescence. However, whether quiescence or senescence programmes drive tumour cell dormancy is still incompletely understood. NIH Public Access Author Ma...

Metastases arise from residual disseminated tumour cells (DTCs). This can happen years after primary tumour treatment because residual tumour cells can enter dormancy and evade therapies. As the biology of minimal residual disease seems to diverge from that of proliferative lesions, understanding the underpinnings of this new cancer biology is key to prevent metastasis. Analysis of approximately 7 years of literature reveals a growing focus on tumour and normal stem cell quiescence, extracellular and stromal microenvironments, autophagy and epigenetics as mechanisms that dictate tumour cell dormancy. In this Review, we attempt to integrate this information and highlight both the weaknesses and the strengths in the field to provide a framework to understand and target this crucial step in cancer progression.

Accumulating data suggest that metastatic dissemination often occurs early during tumour formation but the mechanisms of early metastatic spread have not yet been addressed. Here, we studied metastasis in a HER2-driven mouse breast cancer model and found that progesterone-induced signalling triggered migration of cancer cells from early lesions shortly after HER2 activation, but promoted proliferation in advanced primary tumour cells. The switch from migration to proliferation was regulated by elevated HER2 expression and increased tumour cell density involving miRNA-mediated progesterone receptor (PGR) down-regulation and was reversible. Cells from early, low-density lesions displayed more stemness features than cells from dense, advanced tumours, migrated more and founded more metastases. Strikingly, we found that at least 80% of metastases were derived from early disseminated cancer cells (DCC). Karyotypic and phenotypic analysis of human disseminated cancer cells and primary tumours corroborated the relevance of these findings for human metastatic dissemination.

In patients non-proliferative disseminated tumour cells (DTCs) can persist in the bone marrow (BM) while other organs (i.e. lung) present growing metastasis. This suggested that the BM might be a metastasis “restrictive soil” by encoding dormancy-inducing cues in DTCs. Here we show in a HNSCC model that strong and specific TGFβ2 signalling in the BM activates p38α/β, inducing a [ERK/p38]low signalling ratio. This results in induction of DEC2/SHARP1 and p27, downregulation of CDK4 and dormancy of malignant DTCs. TGFβ2-induced dormancy required TGFβ-receptor-I, TGFβ-receptor-III and SMAD1/5 activation to induce p27. In lungs, a metastasis “permissive soil” with low TGFβ2 levels, DTC dormancy was short lived and followed by metastatic growth. Importantly, systemic inhibition of TGFβ-receptor-I or p38α/β activities awakened dormant DTCs fueling multi-organ metastasis. Our work reveals a “seed and soil” mechanism where TGFβ2 and TGFβRIII signalling through p38α/β regulates DTC dormancy and defines restrictive (BM) and -permissive (lung) microenvironments for HNSCC metastasis.

Metastases can originate from disseminated tumor cells (DTCs), which may be dormant for years before reactivation. Here we find that the orphan nuclear receptor NR2F1 is epigenetically upregulated in experimental HNSCC dormancy models and in DTCs from prostate cancer patients carrying dormant disease for 7–18 years. NR2F1-dependent dormancy is recapitulated by a co-treatment with the DNA demethylating agent 5-Aza-C and retinoic acid across various cancer types. NR2F1-induced quiescence is dependent on SOX9, RARβ and CDK inhibitors. Intriguingly, NR2F1 induces global chromatin repression and the pluripotency gene NANOG, which contributes to dormancy of DTCs in the bone marrow. When NR2F1 is blocked in vivo, growth arrest or survival of dormant DTCs is interrupted in different organs. We conclude that NR2F1 is a critical node in dormancy induction and maintenance by integrating epigenetic programs of quiescence and survival in DTCs.