Integrating contextual miRNA and protein signatures for diagnostic and treatment decisions in cancer

Figures & data

Figure 1. Contextual miRNA and protein signatures for cancer diagnostics and treatment.

On the left is a flow chart of a conceptual high-density marker detection platform. Physical compartmentalization yields four contiguous but insulated compartments for the parallel detection of independent biomarkers from the tumor core to adjacent normal tissue. Specific locked nucleid acid-modified DNA probes are dispensed in each compartment (marker panel) and tissue slides are subjected to in situ hybridization assay. miRNA signal is revealed by tyramide signal amplification (TSA) reactions with green fluorochrome-tyramine substrate (color 1; detection assay). After hydrogen peroxide incubation to inactivate HRP from the preceding TSA reaction, protein expression is revealed by a new round of TSA reactions with a different fluorochrome–tyramine substrate (color 2). After heat-induced epitope retrieval, expression of additional proteins is revealed by sequential TSA reactions with other fluorochrome–tyramine substrates (colors 3 and 4). In this example, the colorized tissue cartoon provides a virtual rendition of the expected staining pattern for each marker on an ER⁺PR⁺HER2^- breast cancer specimen (multiplex staining). On the right are tentative and speculative multimarker panels based on biomarkers already incorporated in routine clinical practice and promising translational biomarkers. Computer-assisted image analysis will be used to quantitate the expression levels of each marker. This information will be used to generate contextual signatures that reflect molecular changes within the cancer cells (CK19⁺) or other cellular compartments of the tumor microenvironment, such as reactive fibroblast (vimentin⁺) and immune cells (CD45⁺), to inform treatment selection and intensity in prevalent solid tumors.

AdCa: Adenocarcinoma; EGFR: EGF receptor; ER: Estrogen receptor; H: High; HER2: Human EGF receptor 2; HRP: Horseradish peroxidase; L: Low; M: Medium; MMP: Matrix metalloproteinase; MSI: Microsatellite instable: MSS: Microsatellite stable; PR: Progesterone receptor; SCC: Squamous cell carcinoma.

Table 1. Diagnostic and prognostic applications of miRNA signatures in solid tumors.

Signature	Clinical application(s)	Number in study (n)	Ref.
Breast cancer
miR-7, -128a, -210, -516-3p	Disease progression (distant metastasis) in ER^+LN^- cases	147	[88]
miR-30a-3p, -30c, -182	Response to adjuvant tamoxifen in advanced ER^+ cases	246	[155]
miR-128a, -135a, -767-3p, -769-3p	Recurrence-free survival in ER^+ cases	207	[90]
miR-27b, -30c, -144, -150, -210, -342	Recurrence-free survival in ER^- cases	207	[90]
miR-21, -181a	Recurrence-free and overall survival in all-comers	291	[156]
miR-21, -210, -221, -222	Recurrence-free and overall survival in ER^-PR^-HER2^- cases	49	[91]
Colorectal cancer
miR-142-3p, -144, -151, -212	Subtype classification: MSS vs MSI-high	59	[50]
miR-17, -20, -25, -32, -92, -93, -106a, -125a, -155, -191, -192, -203, -215, -223	Subtype classification: MSS vs MSI-high	39	[100]
miR-320, -498	Recurrence-free survival in stage II MSS cases	37	[50]
Lung cancer
let-7a, -7b, -7c, -7d, -7e, -7f, -7g, -7i; miR-16, -17, -19b, -20a, -26a, -26b, -29a, -29b, -29c, -30b, -30d, -98, -103, -106a, -106b, -107, -146b-5p, -181a, -191, -195, -453, -491-5p, -498, -509-3p, -654-5p, -663	Subtype classification: AdCa vs SCC in male smokers	205	[125]
let-7a; miR-221, 137, -182*, -372	Recurrence-free and overall survival in NSCLC cases	112	[157]
let-7e; miR-17-5p, -20a, -20b, -21, -93, -106a, -106b, -126, -146b, -155, -182, -183, -191, -200a, -200c, -203, -210, -224	Overall survival in SCC cases	54	[158]
let-7e; miR-34a, -34c-5p, -25, -191	Overall survival in male smoker SCC cases	107	[125]

AdCa: Adenocarcinoma; ER: Estrogen receptor; HER2: Human EGF receptor 2; LN: Lymph node; MSI: Microsatellite instable; MSS: Microsatellite stable; NSCLC: Non-small-cell lung cancer; PR: Progesterone receptor; SCC: Squamous cell carcinoma.

Table 2. Diagnostic and prognostic applications of single miRNAs in solid tumors.

miRNA	Clinical application(s)	Number in study (n)	Ref.
Breast cancer
miR-21	Response to neoadjuvant trastuzumab treatment	32	[159]
	Recurrence-free survival in stage I/II all-comers	270	[160]
	Overall survival in all-comers	113	[161]
miR-205	Disease-recurrence and overall survival in ER^-PR^-HER2^- cases	20	[40]
miR-210	Disease progression (distant metastasis) in ER^-LN^- cases	114	[88]
	Disease progression (distant metastasis) in ER^-PR^-HER2^-LN^- cases	69	[88]
	Recurrence-free and overall survival in all-comers	219, 79	[80,89]
	Response to tamoxifen in ER^+ cases	89	[80]
Colorectal cancer
miR-21	Response to neoadjuvant chemoradiotherapy in advanced rectal cancer	40	[162]
	Recurrence-free survival in stage II colon cases	130	[51]
	Recurrence-free survival in all-comers	44	[101]
	Recurrence-free and overall in all-comers	156	[103]
	Overall survival in all-comers	84 (training) + 113 (validation)	[102]
miR-106a	Recurrence-free and overall survival in all-comers	110	[163]
miR-125b	Overall survival in all-comers	89	[164]
miR-145	Response to neoadjuvant chemoradiotherapy in advanced rectal cancer	40	[162]
miR-155	Recurrence-free and overall survival in all-comers	156	[103]
Lung cancer
let-7a	Overall survival in NSCLC cases	143	[165]
	Overall survival in AdCa cases	52	[131]
miR-21	Overall survival in NSCLC cases	48	[166]
	Overall survival in SCC cases	30	[167]
miR-34a	Recurrence-free and overall survival in NSCLC cases	70	[168]
miR-155	Overall survival in AdCa cases	55	[131]
miR-205	Subtype classification: AdCa vs SCC	122, 102, 31	[126,127,130]

AdCa: Adenocarcinoma; ER: Estrogen receptor; HER2: Human EGF receptor 2; LN: Lymph node; NSCLC: Non-small-cell lung cancer; PR: Progesterone receptor; SCC: Squamous cell carcinoma.

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