Rockefeller University Press

Table II.

L&H cell–specific genes

	FC	Gene symbol	Affymetrix probe set ID	Gene function
Genes up-regulated in NLPHL compared with normal B cells and B-NHL
	13	MMP12	204580_at	matrix metalloprotease; involved in ECM degradation, metastasis and angiogenesis
	9.8	CHIT1	208168_s_at
	8.5	CTSK	202450_s_at	involved in ECM degradation and tumor invasion
	7.6	CYP27B1	205676_at
	7.1	ZBED2	219836_at
	6.7	ALPK2	228367_at
	6.3		230741_at
	6.2	KISS1R	242517_at	involved in ERK activation; overexpressed in several cancers
	5.5	RGS4	204337_at	regulator of G protein signaling
	5	TPD52L1	203786_s_at	member of the tumor protein D52 family; involved in cell proliferation and calcium signaling
	4.6	PLA2G7	206214_at
	4.6	NPL	221210_s_at
	2.9		240449_at
	4.5	UBD	205890_s_at	may modulate tumorigenesis; high levels of UBD in cells lead to increased mitotic nondisjunction and chromosome instability
	4.5	SLC1A3	202800_at
	4.3	VCAM1	203868_s_at	mediates leukocyte–endothelial cell adhesion
	4.2	MAF	206363_at	oncogene; transcription factor; overexpressed in multiple myelomas
	4	CD2	205831_at
	4	DRAM	218627_at
	3.8		230391_at
	3.8	TMEM163	223503_at
	3.7	CTSB	227961_at	involved in ECM degradation and apoptosis; overexpressed in several cancers
	3.5	SCARB2	224983_at
	3.4	PTGDS	211663_x_at
	3.4	SERPING1	200986_at	complement component C1 inhibitor
	3.4	IGF2R	201392_s_at	involved in tumor cell surveillance
	3.4	ALAS1	205633_s_at
	3.4	SLC31A1	203971_at
	3.3	RASGEF1A	230563_at
	3.3	SLC26A11	226679_at
	3.2	CTTN	201059_at	oncogene; involved in tumor cell invasion and metastasis; overexpressed in several cancers
	3.1	SCPEP1	218217_at
	3	EOMES	231776_at	transcription factor highly homologous to T-bet
	3	RAB42	1552846_ s_at	member of the RAS oncogene family
	3	C1orf54	219506_at
	2.9	PLA2G2D	220423_at
	2.9	LOC642705	228066_at
	2.9	NPC1	202679_at
	2.9	LMNA	203411_s_at	lamin proteins are thought to be involved in nuclear stability and chromatin structure
	2.9	EGR2	205249_at	transcription factor
	2.9	FPR1	205119_s_at	appears to mediate motility, growth and angiogenesis of human glioblastoma
	2.7	PRKCZ	202178_at	serine/threonine kinase; involved in proliferation and differentiation; activates NF-κB
	2.7	TPCN2	229250_at
	2.6	ADFP	209122_at
	2.5	SQSTM1	201471_s_at
	2.4	VPS37C	219053_s_at
	2.3	PNKD	233177_s_at
	2.3	RTN4	214629_x_at
	2.1	SLIC1	228869_at
	2	ABCC1	202804_at	involved in multidrug resistance
Genes down-regulated in NLPHL compared with normal B cells and B-NHL
	−2.3	CD79B	205297_s_at	B lineage–specific gene
	−3.8	BCNP1	230983_at	B lineage–specific gene
	−4.3	IGHM	209374_s_at	B lineage–specific gene
	−4/−4	TCL1A	39318_at	B lineage–specific gene
			209995_s_at
	−2.8	FCRL2	1563674_at	B lineage–specific gene

	FC	Gene symbol	Affymetrix probe set ID	Gene function
Genes up-regulated in NLPHL compared with normal B cells and B-NHL
	13	MMP12	204580_at	matrix metalloprotease; involved in ECM degradation, metastasis and angiogenesis
	9.8	CHIT1	208168_s_at
	8.5	CTSK	202450_s_at	involved in ECM degradation and tumor invasion
	7.6	CYP27B1	205676_at
	7.1	ZBED2	219836_at
	6.7	ALPK2	228367_at
	6.3		230741_at
	6.2	KISS1R	242517_at	involved in ERK activation; overexpressed in several cancers
	5.5	RGS4	204337_at	regulator of G protein signaling
	5	TPD52L1	203786_s_at	member of the tumor protein D52 family; involved in cell proliferation and calcium signaling
	4.6	PLA2G7	206214_at
	4.6	NPL	221210_s_at
	2.9		240449_at
	4.5	UBD	205890_s_at	may modulate tumorigenesis; high levels of UBD in cells lead to increased mitotic nondisjunction and chromosome instability
	4.5	SLC1A3	202800_at
	4.3	VCAM1	203868_s_at	mediates leukocyte–endothelial cell adhesion
	4.2	MAF	206363_at	oncogene; transcription factor; overexpressed in multiple myelomas
	4	CD2	205831_at
	4	DRAM	218627_at
	3.8		230391_at
	3.8	TMEM163	223503_at
	3.7	CTSB	227961_at	involved in ECM degradation and apoptosis; overexpressed in several cancers
	3.5	SCARB2	224983_at
	3.4	PTGDS	211663_x_at
	3.4	SERPING1	200986_at	complement component C1 inhibitor
	3.4	IGF2R	201392_s_at	involved in tumor cell surveillance
	3.4	ALAS1	205633_s_at
	3.4	SLC31A1	203971_at
	3.3	RASGEF1A	230563_at
	3.3	SLC26A11	226679_at
	3.2	CTTN	201059_at	oncogene; involved in tumor cell invasion and metastasis; overexpressed in several cancers
	3.1	SCPEP1	218217_at
	3	EOMES	231776_at	transcription factor highly homologous to T-bet
	3	RAB42	1552846_ s_at	member of the RAS oncogene family
	3	C1orf54	219506_at
	2.9	PLA2G2D	220423_at
	2.9	LOC642705	228066_at
	2.9	NPC1	202679_at
	2.9	LMNA	203411_s_at	lamin proteins are thought to be involved in nuclear stability and chromatin structure
	2.9	EGR2	205249_at	transcription factor
	2.9	FPR1	205119_s_at	appears to mediate motility, growth and angiogenesis of human glioblastoma
	2.7	PRKCZ	202178_at	serine/threonine kinase; involved in proliferation and differentiation; activates NF-κB
	2.7	TPCN2	229250_at
	2.6	ADFP	209122_at
	2.5	SQSTM1	201471_s_at
	2.4	VPS37C	219053_s_at
	2.3	PNKD	233177_s_at
	2.3	RTN4	214629_x_at
	2.1	SLIC1	228869_at
	2	ABCC1	202804_at	involved in multidrug resistance
Genes down-regulated in NLPHL compared with normal B cells and B-NHL
	−2.3	CD79B	205297_s_at	B lineage–specific gene
	−3.8	BCNP1	230983_at	B lineage–specific gene
	−4.3	IGHM	209374_s_at	B lineage–specific gene
	−4/−4	TCL1A	39318_at	B lineage–specific gene
			209995_s_at
	−2.8	FCRL2	1563674_at	B lineage–specific gene

49 genes specifically up-regulated by L&H cells compared with normal and other malignant B cells were identified according to the following criteria: (a) expression above background level in ≥4 out of 5 L&H cell profiles and in ≤6 out of the 50 normal and other malignant B cell profiles; and (b) greater than or equal to twofold up-regulation in L&H cells and with a t test p-value of ≤0.05. Five genes specifically down-regulated in L&H cells were identified according to the following criteria: (a) expression above background level in ≤1 out of 5 L&H cell profiles and in ≥33 out of the 50 normal and other malignant B cell profiles; and (b) greater than or equal to twofold down-regulation in L&H cells and with a t test p-value ≤0.05. The 12 cHL profiles were excluded from the comparison (see Results). For genes with known gene functions, these are indicated.

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