From your example about using EntitySet<t> as query root, I tried:

var subTopic = (from topic in Query.All<Topic>() where topic.Name == topicName select topic).SingleOrDefault<Topic>();

EntitySet<Subscription> subscriptions = subTopic.Subscriptions;
var subscription = from sub in subscriptions where sub.ApplicationName == ApplicationName select sub;

but the where in the last line is highlighted with the following error:

"Delegate 'System.Func<nnet.broker.subscription,int,bool>' does not take '1' arguments"

[HierarchyRoot]
    [Index("Name")]
    public class Topic : Entity {
        [Field, Key]
        public long Id { get; private set; }

        [Field]
        public string Name { get; set; }

        [Field, Association(PairTo = "Topic", OnTargetRemove = OnRemoveAction.Clear)]
        public EntitySet<Event> Events { get; private set; }

        [Field, Association(OnTargetRemove = OnRemoveAction.Clear)]
        public EntitySet<Subscription> Subscriptions { get; private set; }
    }

    [HierarchyRoot]
    [Index("ApplicationName")]
    public class Subscription : Entity {
        [Field, Key]
        public long Id { get; private set; }

        [Field]
        public String ApplicationName { get; set; }

        [Field]
        public bool Persistent { get; set; }

        [Field, Key]
        public long LastEventId { get; private set; }
    }

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