Note for: The therapeutic significance of mutational signatures from DNA repair deficiency in cancer

Note for: The therapeutic significance of mutational signatures from DNA repair deficiency in cancer

doi: 10.1038/s41467-018-05228-y

1. Computational analysis on PAN cancer has revealed mutational patterns which could identify cancer types.

2. Development of DNA repair deficiency biomarkers -- critical to determine therapeutic choice to treat repair-deficient tumours -- those therapeutic choices could be damaging agents/immunotherapy for personalized medicine

In the post genomics era which sequencing tech is cheap -- there have been huge amounts of study of the sequencing of genetic instability and DNa repair deficiency in cancer.

Phenotypic changes of defective DNA repair pathway can be detected through the sequencing data.

Study of mutational pattern changes and copy number changes can be used to portray mutational contribution to genomic instability.

2/3 of mutation in cancers occur from error in replication

1. Passenger mutations

1. Not relate to oncogenesis

2. Driver mutations

1. Drive oncogenesis

This paper will review:

1. the relationship between mutational profiles vs type of DNA repair defect. By knowing which pathway is defect -- it facilitates a precision oncology approach by which it could take advantage of synthetic lethality.

2. Various DNA repair defect also influences micro-environmental phenotype of tumour -- thus affecting tumor’s vulnerability to micro-environtally directed therapies like immunotherapy

DNA repair pathway

• Many DNA repair pathways and there are crosstalk among them.

• Specific lesions

• Determine method detection of DNA repair defects in pathway

• Influencing microenvironmental phenotype of the resulting malignancy

Functionally detection of DNA repair deficiency

• Genomic level

• Sequencing and looking at mutational profiles/structural changes

• In vitro/in vivo testing tumor material

• Foci formation of HR ky player in HR

• Introduction HR/NHEJ reporter to tumor tissue and measure activity

Mutation signature

• Mutational signatures

• Somatic mutations and copy number alteration

• Defect in DNA repair

• More evidence shows pattern in passenger mutations

• Passenger mutations -- randomly occur but found out later that it relates to defect in  DNA repair machinery

• Structural change at chromosome level -- relates to DNA repair defective

• Example of the passenger changes

• Lynch syndrome

• Cancer predisposition syndrome

• Risk of colon and endometrial cancers

• Caused by germline mutation of MMR

• Microsatellite regions are prone target for this defect

• Unstable microsatellites -- phenotype which represents MMR-deficient tumors

• Genomic technologies

• Assary-based comparative genomic hybridization

• SNP array -- copy number changes

• Example of this tech

• Detecting breast cancer

• Changes in copies number between WT and BRCA1/2 mutated

• Genomic signature of HR

• HR is the most studied in term of mutational signatures

• Signature 3 

• HR defective tumors are enriched in breast, ovarian and prostate but 5-10% could be found in other cancers

• Signature 3 is more related to BRCA1/2 mutation-related DNA repair deficiency

• However, there might be HR-deficiency tumour which does have Sig 3 phenotype due to the etiological agent is different (not related BRAC1/2)

• PAN cancer analysis revealed

• Defective in DNA replication could be therapeutically targeted in the same way as DNA-repair based defective? -- further research may answer

• Chromosomal instability is related to anaphase defects of chromosomal separation rather than underlying DNA repair defect

• APOBEC family also results in specific signature if the activity is abnormal -- analysis showed prominent source of mutagenesis in bladder, breast, cervical, head and neck cancers

• More and more genes related to DNA damage repair pathway if mutated -- result in specific signature and found in tumour

• Limitation on analysis of signature in tumour

• Signature represent an archeological history of tumour during development and it might not be a good representation whether the pathway is currently deficient in tumour

• Mutation could retain the other pathway facilitating the restoration of previously DNA repair defective pathway

• Functional assay has come to complete the gap of mutational signature

• IHC visualize recruitment of repair protein

• Mutational signatures associated with HR-def -- associated with RAD51 deficiency -- but mutational signatures based on exomes -- not capture all cases of HR def

• Gene expression signature

• Provide the real-time expression of DNA repair genes -- thus could provide HR status

DNA repair deficiency in cancer

• Remain in the active area of research for which pathway is defect and related to individual cancer

• Defective in DNA repair -- currently shown by genetic and epigenetic mechanism

Genetic inactivation of DNA repair

• Check through germ-line and/or somatic alteration at DNA sequence (my guess they might do the experiment which correlate with DNA repair activity and mutation profiles)

• Germline mutation (familial syndrome)

Gene	Cancer	Genetic signature test
MMS defect	Hereditary nonpolyposis colorectal cancer (Lynch syndrome)
HR defect	Hereditary Breast and Ovarian Cancer Syndrome
	Fanconi anemia
	Bloom syndrome
	MUTYH-associated polyposis
	Xeroderma pigmentosum

Epigenetic inactivation

• DNA methylation

• Histone modification

• Nucleosome remodeling

• RNA-mediated targeting

• More and more investigation in this field due to the advancement of technology

• Epigenetic -- gene regulation and chromatin structure alterations

Gene	Cancer	Epigenetic signature test
MGMT (O-6-Methylguanine-DNA Methyltransferase)	Glioblastoma, colorectal, Hodgkin lymphoma	Methylation detection
MMR (MLH1)		Methylation detection
BRCA1, RAD51C		Methylation detection

Synthetic lethal -- focusing on DNA repair defect

Discovery of additional synthetic lethal relationship

Gene	Possible synthetic lethal partners	DNA repair pw involved
BRCA1/2	POLQ	Alternative-end joining
	RAD52	HR when no RAD51
	TLS polymerase	Post-replication gap repair
PARP1	Androgen receptor signaling

Uncover synthetic lethality through the observation on traditional cytotoxic therapies

• Traditional therapy -- mainly DNA damaging agent (alkylating, IR, certain targeted biologics)

• Those DNA damaging agents are good for DNA repair defect cancers

Gene	Cancer	Genetic signature test
ERCC2 (NER)	Bladder cancer	mutations

Synthetic viability as potential mechanism of PARP inhibitor resistance

• Occur when cancer cells resist to DNA damaging agents due to a reversion mutation reduce existing DNA repair defects (restoration of gene function)

Gene	Possible synthetic lethal (1st treatment)	Possible synthetic viable
BRCA1/2	PARP1	53BP1

• Thus, functional assay of HR is important for the possibility of reversion mutations

Targeting immune system in tumor with defective in DNA repair

• DNA repair plays an important role in immune systems

• For example -- generate diversity of immune repository

• Active investigation on the relationship between DNA repair defect and immune system during oncogenesis

• Defective in DNA repair results in different lesion in DNA and cause DNA sequence changes specifically -- these changes affect how cancer cells response to immune’s response (both innate and adaptive)

Defects in DDR -- improve recognition of tumours by adaptive immune system

• Adaptive immune system must recognize non-self antigen -- like neoantigens 

• Neoantigen -- novel proteins which are commonly a result of somatic mutations -- restrict to a tumour

• High-throughput sequencing could identify this neoantigen

• Number of neoantigens in a tumour -- directly proportional to number of non-synonymous mutations (mutation caused change in AA) in tumor

• Rate of mutation (result from defect in DNA repair) -- correlate with immune filtration

• Higher mutation load -- good respond to checkpoint blockade

• Different defects in DNA repair result in different sets of neoantigens - thus it influences the immune response.

• Possible treatment -- using mutagenic chemotherapeutic drugs to enrich neoantigens thus facilitating immune recognition

• Possible treatment based on concept of DNA repair deficiency

• DNA repair deficiency -- using synthetic lethality approach

• DNA repair deficiency -- using antigenicity of neoantigens approach

Defects in DNA repair activate innate immune system

• How innate immune system senses the presence of malignancy -- under investigated

• Evident shows it is mediated by activation of Stimulator of Interferon Genes (STING)

• STING

• Signaling molecule

• Involved with endoplasmic reticulum

• Central role in generating immune response to DNA-based viruses/bacteria

• Recent evidence suggests STING involves in innate immune response to malignancy

• Dying tumour cells are eaten by  phagocyte -- DNA from these dying cells triggers STING response -- innate immune response

• DNA damages by exogenous source (DNA damaging agents/IR) -- induce STING response (DNA is released from tumours)

• Defect in DNA repair caused the release of DNA to the cytosol (in dividing cells) -- thus activating STING

• Suggested therapy -- DNA damaging agents which introducing lots of micronuclei -- might synergize with anti-PD1 therapy by facilitating innate immune recognition