Early dynamic transcriptomic changes during preoperative radiotherapy in patients with rectal cancer: A feasibility study

Table 1 Patient characteristics

Patient	Age (yr)	Disease stage	> G1 radiotherapy	Surgical	Surgical stage	Outcome at 2 yr	Tumor purity	Mean RNA content (μg)
			toxicity	toxicity		of follow-up	in biopsies	Pre-RT biopsies	Early-RT biopsies
1	66	uT2Nx	No	No	ypT2N0	NED	100%	18.0	19.7
2	55	uT3N1	No	No	ypT4N1	NED	100%	27.0	12.6
3	84	uT3N1	No	No	ypT3N1	M1	100%	21.0	35.8
4	78	uT3N1	No	No	ypT2N0	NED	100%	37.1	28.7
5	60	uT3N0	No	No	ypT3N1	NED	100%	20.0	19.4
6	67	uT3N0	No	No	ypT2N1	NED	100%	14.2	19.9

NED: Non evolutive disease, M1: Metastatic disease; RT: Radiotherapy.

Table 2 Up- or down-regulated genes in rectal cancer biopsies

Fold	False discovery rate	ID	Gene title	Symbol
Up-regulated genes
2.649	0	AI827789	Anterior gradient homolog 3 (Xenopus)	AGR3
3.427	0	AA743462	-	-
2.524	0	NM_006472	Thioredoxin interacting protein	TXNIP
5.514	0	AB018305	Spondin 1, extracellular matrix protein	SPON1
2.95	7.551	NM_152315	Family with sequence similarity 55, A	FAM55A
3.289	7.551	AL536553	Neural precursor cell expressed, developmentally down-regulated 4-like	NEDD4L
2.684	7.551	AF055009	cAMP responsive element binding protein 3-like 1	CREB3L1
3.111	7.551	AL137063	A kinase (PRKA) anchor protein 7	AKAP7
2.717	7.551	AF266504	Chemokine (C-C motif) ligand 28	CCL28
2.546	8.39	BF589413	FERM domain containing 3	FRMD3
2.637	8.39	AA554045	Polypeptide N-acetylgalactosaminyltransferase 12	GALNT12
3.047	8.39	NM_030926	Integral membrane protein 2C	ITM2C
2.775	8.39	AW026379	Tumor necrosis factor receptor superfamily, member 11a	TNFRSF11A
2.609	8.39	U38654	RAB27A, member RAS family	RAB27A
2.629	8.39	NM_003570	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase pseudogene	CMAH
2.521	8.58	AV728268	Chromosome 11 open reading frame 32	C11orf32
2.579	8.58	NM_016929	Chloride intracellular channel 5	CLIC5
2.541	10.487	NM_016548	Golgi membrane protein 1	GOLM1
2.728	10.487	AW162846	Calcium/calmodulin-dependent protein kinase II inhibitor 1	CAMK2N1
2.806	10.487	AI659927	prostate androgen-regulated mucin-like protein 1	PARM1
2.896	10.487	NM_024709	Chromosome 1 open reading frame 115	C1orf115
3.333	10.487	NM_005629	Solute carrier family 6 member 8	SLC6A8
2.869	10.487	NM_019062	Ring finger protein 186	RNF186
3.174	10.487	AK025181	Intestine-specific homeobox	ISX
3.968	10.487	AB007899	Neural precursor cell expressed, developmentally down-regulated 4-like	NEDD4L
8.2	10.487	NM_001873	Carboxypeptidase E	CPE
4.845	10.487	NM_014479	ADAM-like, decysin 1	ADAMDEC1
2.56	10.487	BF195709	Calpain 5	CAPN5
2.601	10.487	NM_014456	Programmed cell death 4	PDCD4
2.931	10.787	AW971415	cDNA clone IMAGE:5745639	-
2.787	10.787	NM_005173	ATPase, Ca++ transporting, ubiquitous	ATP2A3
Down-regulated genes
0.265	8.58	AI378647	Coagulation factor II (thrombin) receptor-like 2	F2RL2
0.356	8.58	BG200951	Pvt1 oncogene homolog, MYC activator	PVT1
0.322	10.787	AL109839	Poly(A) binding protein, cytoplasmic 1-like	PABPC1L
0.356	10.787	NM_005978	S100 calcium binding protein A2	S100A2
0.373	10.787	AL041761	Transcribed locus	-
0.38	10.787	D86983	Peroxidasin homolog (Drosophila)	PXDN