Multimodal machine learning models identify chemotherapy drugs with prospective clinical efficacy in dogs with relapsed B-cell lymphoma.

Dogs with B-cell lymphoma typically respond well to first-line CHOP-based chemotherapy, but there is no standard of care for relapsed patients. To help veterinary oncologists select effective drugs for dogs with lymphoid malignancies such as B-cell lymphoma, we have developed multimodal machine learning models that integrate data from multiple tumor profiling modalities and predict the likelihood of a positive clinical response for 10 commonly used chemotherapy drugs. Here we report on clinical outcomes that occurred after oncologists received a prediction report generated by our models. Remarkably, we found that dogs that received drugs predicted to be effective by the models experienced better clinical outcomes by every metric we analyzed (overall response rate, complete response rate, duration of complete response, patient survival times) relative to other dogs in the study and relative to historical controls.

Dynamics of DNA replication in a eukaryotic cell.

Each genomic locus in a eukaryotic cell has a distinct average time of replication during S phase that depends on the spatial and temporal pattern of replication initiation events. Replication timing can affect genomic integrity because late replication is associated with an increased mutation rate. For most eukaryotes, the features of the genome that specify the location and timing of initiation events are unknown. To investigate these features for the fission yeast, Schizosaccharomyces pombe, we developed an integrative model to analyze large single-molecule and global genomic datasets. The model provides an accurate description of the complex dynamics of S. pombe DNA replication at high resolution. We present evidence that there are many more potential initiation sites in the S. pombe genome than previously identified and that the distribution of these sites is primarily determined by two factors: the sequence preferences of the origin recognition complex (ORC), and the interference of transcription with the assembly or stability of prereplication complexes (pre-RCs). We suggest that in addition to directly interfering with initiation, transcription has driven the evolution of the binding properties of ORC in S. pombe and other eukaryotic species to target pre-RC assembly to regions of the genome that are less likely to be transcribed.

Does transcription-associated DNA damage limit lifespan?

Small mammals undergo an aging process similar to that of larger mammals, but aging occurs at a dramatically faster rate. This phenomenon is often assumed to be the result of damage caused by reactive oxygen species generated in mitochondria. An alternative explanation for the phenomenon is suggested here. The rate of RNA synthesis is dramatically elevated in small mammals and correlates quantitatively with the rate of aging among different mammalian species. The rate of RNA synthesis is reduced by caloric restriction and inhibition of TOR pathway signaling, two perturbations that increase lifespan in multiple metazoan species. From bacteria to man, the transcription of a gene has been found to increase the rate at which it is damaged, and a number of lines of evidence suggest that DNA damage is sufficient to induce multiple symptoms associated with normal aging. Thus, the correlations frequently found between the rate of RNA synthesis and the rate of aging could potentially reflect an important role for transcription-associated DNA damage in the aging process.

Coordination of DNA damage tolerance mechanisms with cell cycle progression in fission yeast.

DNA damage tolerance (DDT) mechanisms allow cells to synthesize a new DNA strand when the template is damaged. Many mutations resulting from DNA damage in eukaryotes are generated during DDT when cells use the mutagenic translesion polymerases, Rev1 and Polζ, rather than mechanisms with higher fidelity. The coordination among DDT mechanisms is not well understood. We used live-cell imaging to study the function of DDT mechanisms throughout the cell cycle of the fission yeast Schizosaccharomyces pombe. We report that checkpoint-dependent mitotic delay provides a cellular mechanism to ensure the completion of high fidelity DDT, largely by homology-directed repair (HDR). DDT by mutagenic polymerases is suppressed during the checkpoint delay by a mechanism dependent on Rad51 recombinase. When cells pass the G2/M checkpoint and can no longer delay mitosis, they completely lose the capacity for HDR and simultaneously exhibit a requirement for Rev1 and Polζ. Thus, DDT is coordinated with the checkpoint response so that the activity of mutagenic polymerases is confined to a vulnerable period of the cell cycle when checkpoint delay and HDR are not possible.

Postreplication gaps at UV lesions are signals for checkpoint activation.

Exposure of eukaryotic cells to UV light induces a checkpoint response that delays cell-cycle progression after cells enter S phase. It has been hypothesized that this checkpoint response provides time for repair by signaling the presence of structures generated when the replication fork encounters UV-induced DNA damage. To gain insight into the nature of the signaling structures, we used time-lapse microscopy to determine the effects of deficiencies in translesion DNA polymerases on the checkpoint response of the fission yeast Schizosaccharomyces pombe. We found that disruption of the genes encoding translesion DNA polymerases Polkappa and Poleta significantly prolonged the checkpoint response, indicating that the substrates of these enzymes are signals for checkpoint activation. Surprisingly, we found no evidence that the translesion polymerases Rev1 and Polzeta repair structures that are recognized by the checkpoint despite their role in maintaining viability after UV irradiation. Quantitative flow cytometry revealed that cells lacking translesion polymerases replicate UV-damaged DNA at the same rate at WT cells, indicating that the enhanced checkpoint response of cells lacking Polkappa and Poleta is not the result of stalled replication forks. These observations support a model in which postreplication DNA gaps with unrepaired UV lesions in the template strand act both as substrates for translesion polymerases and as signals for checkpoint activation.

Shedding light on the DNA damage checkpoint.

DNA damage checkpoint genes are required to restrain cell cycle progression during DNA repair and to maintain chromosome stability. Checkpoint mutants are highly sensitive to killing by UV light, so the responses mediated by these genes are likely to be essential for survival during exposure to solar radiation. Yet it is still unclear exactly how checkpoint responses coordinate the cell cycle with DNA repair in the presence of UV lesions. At high doses, the UV response shares features with the ionizing radiation response, such as G1/S and G2/M checkpoints. At lower doses, only a postreplication checkpoint is evident. In this perspective we attempt to reconcile these observations and address their physiological meaning, with an emphasis on insights gained from direct cell-cycle measurements and recent studies in yeast.

UV irradiation induces a postreplication DNA damage checkpoint.

Eukaryotic cells irradiated with high doses of UV exhibit cell-cycle responses referred to as G(1)/S, intraS, and G(2)/M checkpoints. After a moderate UV dose that approximates sunlight exposure and is lethal to fission yeast checkpoint mutants, we found unexpectedly that these cell-cycle responses do not occur. Instead, cells at all stages of the cell cycle carry lesions into S phase and delay cell-cycle progression for hours after the completion of bulk DNA synthesis. Both DNA replication and the checkpoint kinase, Chk1, are required to generate this cell-cycle response. UV-irradiation of Deltachk1 cells causes chromosome damage and loss of viability only after cells have replicated irradiated DNA and entered mitosis. These data suggest that an important physiological role of the cell-cycle response to UV is to provide time for postreplication repair.