Peer review of: Enhancing chemotherapy response through augmented synthetic lethality by co-targeting nucleo (2020)


RR2
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
  The paper by Kong et al has undergone substantial revision, including new experiments to address
 my, and the other reviewer’s, comments. Overall, the paper is substantially improved. The authors
 should modify the text (lines 184-188), in describing the strength/synergism of the trigenic
 interaction between MK2, PKA, and p53 in the presence of cis-platin, that they have called ASL.
 The work demonstrates a synthetic lethal relationship between MK2 and XPA in presence of cis-
 platin in the adenocarcinoma cell line (Fig2A). The authors have addressed my concern about their
 claim that the lethality is dependent on the p53 status of the line by testing for synthetic
 sensitivity to cis-platin in three p53-minus cell lines as compared to one p53+ cell line (Fig S2).
 This is supportive of their model, but not conclusive, given that the genetic backgrounds of the
 four cell lines certainly differ in many ways in addition to their p53 status. A better experiment is
 presented in the rebuttal document (comparing results obtained in a matched cell line pair, ie.,
 HCT116 p53+ vs HCT116 p53-). This experiment should be included in the paper (e.g. as Fig S2
 E,F). In this case the p53 null line shows significantly reduced growth for the double KD, as
 compared to either single KD. The effect appears slightly greater than additive. One thing to note:
 the “expected” growth of the double KD in the p53 null HCT116 in 25μm Cisplatin appears too high
 relative to the single KD’s (dotted line).
 I would suggest modifying the sentence (lines 183-188) by deleting “similar synergistic killing” and
 as follows:
 Additive or greater than additive killing by cisplatin after combined MK2 and XPA knockdown,
 compared to individual knockdowns, was also observed in three p53 negative human NSLC tumor
 cell lines (H2009, H1299, K97B), but not observed in a p53+ NSCLC cell line.
 I would also suggest adding the HCT116 matched pair cell line results here.
Reviewer #3 (Remarks to the Author):
The authors have address my major concerns.
Reviewer #4 (Remarks to the Author):
 As noted previously, trigenic negative genetic interactions are not a novel concept, so I am not
 convinced that a conditional trigenic interaction (causing drug sensitivity to a sub-lethal dose of a
 DNA damaging agent) warrants creating a new nomenclature term (ASL), although this is not a
 major concern. The authors should at least reference somewhere the trigenic genetic interaction
 paper published recently in Science from the Boone/Andrews labs (PMID: 29674565).
    In the revised manuscript and accompanying rebuttal letter, the authors have adequately
 responded and in a satisfactory manner to all major concerns and questions of this reviewer and to
 the comments of the reviewers as well as fa as I can judge.
 With these changes and additions to the manuscript has certainly gained in quality and impact.
 I do have a few additional remarks, not raised before by the other reviewers, concerning mainly
 the DNA repair aspects.
 1) On page 5, lines 143-144; the authors state that: ‘...resulting in the cancer-prone syndromes XP
 and CS.’, which is not correct and should be corrected. Indeed, CS is caused by a defect in a sub
 pathway of NER (TC-NER), but CS patients are not cancer-prone (PMID: 1308368; PMID:
 
19809470; PMID: 23428416; PMID: 26204423).
 2) lines 181-182, the authors state: “Cells depleted of either MK2 or XPA alone showed modestly
 increased sensitivity to cisplatin as expected...”. I do not understand this statement, as it is
 opposite to expectation, when XPA is depleted (which interferes with the major pathway to remove
 the major Cis-Pt DNA adduct (intra-strand crosslinks), as the authors state on lines 138-14300 it is
 expected that cells are severely sensitized towards this agent. Similarly, it is surprising to note in
 2B that after depletion of XPA removal of Cis-Pt adducts is hardly affected, which again does not
 match with their statement that NER: ‘Cells genetically lacking key NER proteins are unable to
 repair Pt-induced lesions...” (line 142). The authors should explain.
 3) The rebuttal to reviewer #1, point 4 is important to include in the revised manuscript, as it is
 indeed enigmatic to the reader (including this reviewer) why the nanoparticles would specifically
 target cancer cells.