MALAT1 in Liquid Biopsy: The Diagnostic and Prognostic Promise for Colorectal Cancer and Adenomas?

Figures & data

Figure 1 Schematic workflow of the study. RT-qPCR analysis of MALAT1 was performed in the tumour tissue and adjacent mucosa of CA patients (n=14) who were part of the pilot study and further in the plasma of CFI (n=48), CA patients (n=97) and CRC patients (n=101).

Abbreviations: CFI, cancer-free individuals; CA patients, colorectal adenoma; CRC, colorectal cancer.

Table 1 CA Patient’s Clinical Characteristics

		CA Patients (aCGH Group)	CA Patients (Plasma Study)
		N (Total=14)	N (total=97)
Age	Years ± SD	54±11	62±11
Gender	Male	8	62
	Female	6	35
Localization	Colon	10	75
	Rectum	4	22
Histology type of adenoma^a	Tubular	9	50
	Tubulovillous	5	30
	Hyperplastic	0	9
Grade^a	Low	11	59
	High	3	23

Notes: ^aNumbers may not add up to 100% of available subjects because of missing data.

Abbreviations: CA, colorectal adenoma; aCGH, array comparative genomic hybridization; SD, standard deviation.

Table 2 CRC Patient’s Clinical Characteristics

		N (Total=101)
Age	Years ± SD	65±10
Gender	Male	69
	Female	32
Localization	Colon	24
	Rectum	77
CRC TNM ^a,b	I	4
	II	33
	III	44
	IV	11
Grade^a	1	5
	2	57
	3	34
Survival status^a	Dead	18
	Alive	79
Response to therapy^a	Good	52
	Poor	42
Presence of a local recurrence^a	Yes	13
	No	84
Neoadjuvant therapy^a	Yes	51
	No	50
Adjuvant therapy^a	Yes	52
	No	44

Notes: ^aNumbers may not add up to 100% of available subjects because of missing data. ^bStaging was based on pathological staging according to the tumor–node–metastasis (TNM) system Union for International Cancer Control (UICC).

Figure 2 The expression levels of MALAT1 in the tissue of CA patients from the pilot phase. No significant difference was observed between the groups with and without MALAT1 amplification (p=0.08, 2.08-fold-change).

Figure 3 The expression level of MALAT1 in plasma. There are significant differences between CA and CRC patients compared to CFI (CA vs CFI – p<0.001, 5.25- fold change; CRC vs CFI – p<0.001, 5.16-fold change). The asterisk indicator (***) represents p ≤ 0.001.

Figure 4 The expression level of MALAT1 in different types of adenomas. There was a significant difference between hyperplastic (H; n=9) and tubulovillous/villous (TLV; n=30) adenomas (p=0.002, 6.14-fold change). Tubular (T; n=50) adenomas did not show a significant difference in MALAT1 expression (p=0.15, 3.09-fold change). The asterisk indicator (**) represents p ≤ 0.01.

Figure 5 The expression level of MALAT1 in CRC patients divided according to therapy response. There was a significant difference between good (n=52) and poor responders (n=42; p=0.04, 1.86-fold change). The asterisk indicator (*) represents p ≤ 0.05.

Table 3 The List of MALAT1 Targets Related to Biological Processes

GO ID	GO name	Fold Enrichment	p-val	Adjusted p-val	Number of Genes	Genes
GO:0015988	Energy coupled proton transmembrane transport, against electrochemical gradient	27,97	0.00057	0.04470	3	MT-ND5, MT-CO1, MT-ND4
GO:0015990	Electron transport coupled proton transport	27,97	0.00057	0.04492	3	MT-ND5, MT-CO1, MT-ND4
GO:0002486	Antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent	18,65	0.00019	0.01924	4	HLA-C, HLA-E, HLA-A, HLA-B
GO:0002484	Antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway	16,58	0.00027	0.02558	4	HLA-C, HLA-E, HLA-A, HLA-B
GO:0002483	Antigen processing and presentation of endogenous peptide antigen	11,78	0.00004	0.00496	6	B2M, HLA-DRA, HLA-C, HLA-E, HLA-A, HLA-B
GO:0019885	Antigen processing and presentation of endogenous peptide antigen via MHC class I	10,97	0.00022	0.02115	5	B2M, HLA-C, HLA-E, HLA-A, HLA-B
GO:0033119	Negative regulation of RNA splicing	10,29	0.00000	0.00090	8	PTBP1, PCBP4, RPS13, SRSF9, SRSF6
GO:0002181	Cytoplasmic translation	8,72	0.00000	0.00000	29	EIF3L, RPS16, RPL18A, RPL28, RPS13, RPL24…
GO:0019883	Antigen processing and presentation of endogenous antigen	8,61	0.00016	0.01638	6	B2M, HLA-DRA, HLA-C, HLA-E, HLA-A, HLA-B
GO:0032069	Regulation of nuclease activity	8,48	0.00060	0.04572	5	OAS3, OAS2, TMBIM6, RPS3, PRKCD

Table 4 The List of MALAT1 Targets Related to Molecular Functions

GO ID	GO Name	Fold Enrichment	p-val	Adjusted p-val	Number of Genes	Genes
GO:0023026	MHC class II protein complex binding	9,670,089	0.00002	0.00444	7	PKM, HSP90AB1, YWHAE, HSPA8, ANXA11…
GO:0023023	MHC protein complex binding	7,252,566	0.00011	0.01822	7	PKM, HSP90AB1, YWHAE, HSPA8, ANXA11…
GO:0003735	Structural constituent of ribosome	6,66,052	0.00000	0.00000	30	MRPL43, RPS16, RPL18A, RPL28, RPS13…
GO:0015453	Oxidoreduction-driven active transmembrane transporter activity	5,328,416	0.00004	0.00799	10	COX6A1, COX6B1, NDUFB8, NDUFV1, UQCRH…
GO:0043022	Ribosome binding	4,47,587	0.00034	0.04723	9	SEC61A1, ETF1, EIF5A, SRP68, RPSA…
GO:0045296	Cadherin binding	4,016806	0.00000	0.00000	35	CTNNA1, PKM, ENO1, EZR, HSP90AB1…
GO:0009055	Electron transfer activity	4,007321	0.00005	0.00897	13	AKR7A2, TSTA3, COX6A1, COX6B1, NDUFB8…
GO:0005200	Structural constituent of cytoskeleton	3,76,411	0.00031	0.04413	11	ACTB, DSP, ACTR3, TUBA1B, TUBA4A…
GO:0045182	Translation regulator activity	3,576,608	0.00008	0.01401	14	PABPC1, IGF2BP2, AARS, EIF3L, GTPBP1…
GO:0031625	Ubiquitin protein ligase binding	3,34,575	0.00000	0.00005	27	TOLLIP, HSP90AB1, HM13, GPI, CASC3…

Table 5 The List of MALAT1 Targets Related to Cellular Components

GO ID	GO name	Fold Enrichment	p-val	Adjusted p-val	Number of Genes	Genes
GO:0042612	MHC class I protein complex	20,72	0.00002	0.00057	5	SZRD1, FAM117A DEF8, LRRC58, B2M
GO:0005915	Zonula adherens	12,43	0.00327	0.04733	3	CTNNA1, JUP, CTNND1
GO:0042824	MHC class I peptide loading complex	12,43	0.00327	0.04700	3	B2M, CALR, HLA-A
GO:0008250	Oligosaccharyltransferase complex	10,66	0.00105	0.01917	4	MAGT1, DAD1, STT3B, OST4
GO:0045263	Proton-transporting ATP synthase complex	10,66	0.00105	0.01900	4	ATP5MC2, MT-ATP, MT-ATP8, ATP5PO
GO:0022627	Cytosolic small ribosomal subunit	9,95	0.00000	0.00000	12	RPS16, RPS13, RPS6, RPS2, RPS3 …
GO:0022625	Cytosolic large ribosomal subunit	9,48	0.00000	0.00000	15	RPL18A, RPL28, RPL24, RPL23, RPL13A…
GO:0098554	Cytoplasmic side of endoplasmic reticulum membrane	9,32	0.00160	0.02696	4	HM13, EPM2AIP1, PTPN1, RPS26
GO:0098576	Lumenal side of membrane	9,32	0.00000	0.00007	9	HM13, HSPA8, BDH1, CALR, HLA-DRA
GO:0022626	Cytosolic ribosome	9,24	0.00000	0.00000	26	RPS16, RPL18A, RPL28, RPS13, RPL24…