Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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	Gene summary
	Malignant transformation analysis
	Malignant transformation related pathway analysis
	Cell-cell communication analysis
	Single-cell gene regulatory network inference analysis
	Somatic mutation of malignant transformation related genes
	Related drugs of malignant transformation related genes

Gene: NUAK2

Gene summary for NUAK2

Gene summary.

Gene information	Species	Human
	Gene symbol	NUAK2
	Gene ID	81788
	Gene name	NUAK family kinase 2
	Gene Alias	ANPH2
	Cytomap	1q32.1
	Gene Type	protein-coding
	GO ID	GO:0006464
	UniProtAcc	B4E0Y5

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Malignant transformation analysis

Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells

Malignant transformation involving gene list.

Entrez ID	Symbol	Replicates	Species	Organ	Tissue	Adj P-value	Log2FC	Malignancy
81788	NUAK2	HTA11_347_2000001011	Human	Colorectum	AD	4.14e-07	2.39e-01	-0.1954
81788	NUAK2	HTA11_1391_2000001011	Human	Colorectum	AD	2.73e-08	3.75e-01	-0.059
81788	NUAK2	HTA11_546_2000001011	Human	Colorectum	AD	1.61e-04	3.31e-01	-0.0842
81788	NUAK2	HTA11_866_3004761011	Human	Colorectum	AD	1.76e-08	3.23e-01	0.096
81788	NUAK2	LZE4T	Human	Esophagus	ESCC	6.92e-10	4.40e-01	0.0811
81788	NUAK2	LZE20T	Human	Esophagus	ESCC	2.06e-08	3.64e-01	0.0662
81788	NUAK2	LZE22T	Human	Esophagus	ESCC	1.01e-03	4.64e-01	0.068
81788	NUAK2	LZE21T	Human	Esophagus	ESCC	5.75e-05	3.18e-01	0.0655
81788	NUAK2	P1T-E	Human	Esophagus	ESCC	1.65e-19	9.96e-01	0.0875
81788	NUAK2	P2T-E	Human	Esophagus	ESCC	5.75e-13	3.39e-01	0.1177
81788	NUAK2	P4T-E	Human	Esophagus	ESCC	8.21e-20	5.29e-01	0.1323
81788	NUAK2	P5T-E	Human	Esophagus	ESCC	2.41e-34	8.13e-01	0.1327
81788	NUAK2	P8T-E	Human	Esophagus	ESCC	4.40e-10	2.37e-01	0.0889
81788	NUAK2	P9T-E	Human	Esophagus	ESCC	6.69e-05	1.76e-01	0.1131
81788	NUAK2	P10T-E	Human	Esophagus	ESCC	7.96e-03	6.94e-02	0.116
81788	NUAK2	P11T-E	Human	Esophagus	ESCC	1.98e-18	8.58e-01	0.1426
81788	NUAK2	P12T-E	Human	Esophagus	ESCC	2.74e-11	1.95e-01	0.1122
81788	NUAK2	P15T-E	Human	Esophagus	ESCC	3.87e-09	2.69e-01	0.1149
81788	NUAK2	P16T-E	Human	Esophagus	ESCC	1.21e-07	1.55e-01	0.1153
81788	NUAK2	P21T-E	Human	Esophagus	ESCC	9.02e-16	3.28e-01	0.1617

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma

∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer

Figure of enriched GO biological processes.

Tissue	Disease Stage	Enriched GO biological Processes
Colorectum	AD
Colorectum	SER
Colorectum	MSS
Colorectum	MSI-H
Colorectum	FAP

∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).

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Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:0031667	Colorectum	AD	response to nutrient levels	138/3918	474/18723	1.22e-05	2.68e-04	138
GO:0042594	Colorectum	AD	response to starvation	63/3918	197/18723	1.77e-04	2.38e-03	63
GO:0071496	Colorectum	AD	cellular response to external stimulus	94/3918	320/18723	1.98e-04	2.64e-03	94
GO:0009267	Colorectum	AD	cellular response to starvation	51/3918	156/18723	3.90e-04	4.44e-03	51
GO:0031668	Colorectum	AD	cellular response to extracellular stimulus	71/3918	246/18723	1.86e-03	1.52e-02	71
GO:0031669	Colorectum	AD	cellular response to nutrient levels	63/3918	215/18723	2.19e-03	1.73e-02	63
GO:0071496111	Esophagus	ESCC	cellular response to external stimulus	215/8552	320/18723	4.29e-15	2.43e-13	215
GO:0031668111	Esophagus	ESCC	cellular response to extracellular stimulus	168/8552	246/18723	4.93e-13	2.23e-11	168
GO:0031669110	Esophagus	ESCC	cellular response to nutrient levels	148/8552	215/18723	4.58e-12	1.76e-10	148
GO:0031667111	Esophagus	ESCC	response to nutrient levels	289/8552	474/18723	9.25e-12	3.47e-10	289
GO:0009267110	Esophagus	ESCC	cellular response to starvation	110/8552	156/18723	2.63e-10	7.37e-09	110
GO:004259419	Esophagus	ESCC	response to starvation	133/8552	197/18723	4.31e-10	1.14e-08	133
GO:00421492	Esophagus	ESCC	cellular response to glucose starvation	36/8552	48/18723	3.43e-05	2.80e-04	36
GO:007149620	Oral cavity	OSCC	cellular response to external stimulus	186/7305	320/18723	2.56e-12	1.05e-10	186
GO:003166819	Oral cavity	OSCC	cellular response to extracellular stimulus	141/7305	246/18723	3.99e-09	8.95e-08	141
GO:003166720	Oral cavity	OSCC	response to nutrient levels	245/7305	474/18723	1.02e-08	2.10e-07	245
GO:003166918	Oral cavity	OSCC	cellular response to nutrient levels	121/7305	215/18723	1.96e-07	3.17e-06	121
GO:004259416	Oral cavity	OSCC	response to starvation	111/7305	197/18723	5.68e-07	8.19e-06	111
GO:000926717	Oral cavity	OSCC	cellular response to starvation	91/7305	156/18723	7.55e-07	1.06e-05	91

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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Cell-cell communication analysis

Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states

Ligand

Receptor

LRpair

Pathway

Tissue

Disease Stage

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Single-cell gene regulatory network inference analysis

Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states

TF	Cell Type	Tissue	Disease Stage	Target Gene	RSS	Regulon Activity
NUAK2	GRA	Oral cavity	ADJ	TGM1,EVPL,ANXA1, etc.	2.46e-01
NUAK2	COR	Oral cavity	LP	TGM1,EVPL,ANXA1, etc.	2.21e-01
NUAK2	GRA	Oral cavity	LP	TGM1,EVPL,ANXA1, etc.	2.46e-01
NUAK2	COR	Oral cavity	OSCC	TGM1,EVPL,ANXA1, etc.	3.81e-01
NUAK2	ECC	Skin	AK	LGALSL,CALML5,SLURP1, etc.	4.91e-02
NUAK2	PIL	Skin	SCCIS	LGALSL,CALML5,SLURP1, etc.	1.34e-02
NUAK2	cDC	Skin	ADJ	BIRC3,CCR7,MARCKSL1, etc.	1.51e-01
NUAK2	PLA	Skin	ADJ	BIRC3,CCR7,MARCKSL1, etc.	1.36e-02
NUAK2	cDC	Skin	AK	BIRC3,CCR7,MARCKSL1, etc.	1.44e-01
NUAK2	PLA	Skin	AK	BIRC3,CCR7,MARCKSL1, etc.	2.49e-02

∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.

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Somatic mutation of malignant transformation related genes

Annotation of somatic variants for genes involved in malignant transformation

Hugo Symbol

Variant Class

Variant Classification

dbSNP RS

HGVSc

HGVSp

HGVSp Short

SWISSPROT

BIOTYPE

SIFT

PolyPhen

Tumor Sample Barcode

Tissue

Histology

Sex

Age

Stage

Therapy Types

Drugs

Outcome

NUAK2

SNV

Missense_Mutation

c.735N>G

p.His245Gln

p.H245Q

Q9H093

protein_coding

tolerated(0.64)

benign(0.003)

TCGA-AO-A128-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

NUAK2

SNV

Missense_Mutation

c.1262C>A

p.Ser421Tyr

p.S421Y

Q9H093

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-AR-A0TX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NUAK2

SNV

Missense_Mutation

c.842N>T

p.Gly281Val

p.G281V

Q9H093

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0DV-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxotere

NUAK2

SNV

Missense_Mutation

c.380N>C

p.Ile127Thr

p.I127T

Q9H093

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-C8-A26V-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

tamoxiphen

NUAK2

SNV

Missense_Mutation

c.497N>A

p.Ser166Asn

p.S166N

Q9H093

protein_coding

tolerated(0.17)

benign(0.052)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

NUAK2

insertion

Nonsense_Mutation

novel

c.1848_1849insCCAGGGATGGGAAATAGAAAAACTGCCGAATCAAAACAAACGTGA

p.Val616_Ser617insProGlyMetGlyAsnArgLysThrAlaGluSerLysGlnThrTer

p.V616_S617insPGMGNRKTAESKQT*

Q9H093

protein_coding

TCGA-A8-A06P-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unspecific

NUAK2

insertion

Frame_Shift_Ins

novel

c.1065_1066insCCCTTCTT

p.Gly356ProfsTer171

p.G356Pfs*171

Q9H093

protein_coding

TCGA-BH-A0BA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

NUAK2

SNV

Missense_Mutation

novel

c.988G>A

p.Val330Met

p.V330M

Q9H093

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

NUAK2

SNV

Missense_Mutation

novel

c.577N>A

p.Glu193Lys

p.E193K

Q9H093

protein_coding

deleterious(0)

probably_damaging(0.925)

TCGA-MA-AA3Z-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

NUAK2

SNV

Missense_Mutation

c.1421G>C

p.Ser474Thr

p.S474T

Q9H093

protein_coding

tolerated(0.23)

benign(0)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

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Related drugs of malignant transformation related genes

Identification of chemicals and drugs interact with genes involved in malignant transfromation

(DGIdb 4.0)

Entrez ID	Symbol	Category	Interaction Types	Drug Claim Name	Drug Name	PMIDs
81788	NUAK2	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME	inhibitor	249565727

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