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: PSMD10

Gene summary for PSMD10

Gene summary.

Gene information	Species	Human
	Gene symbol	PSMD10
	Gene ID	5716
	Gene name	proteasome 26S subunit, non-ATPase 10
	Gene Alias	dJ889N15.2
	Cytomap	Xq22.3
	Gene Type	protein-coding
	GO ID	GO:0000079
	UniProtAcc	O75832

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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
5716	PSMD10	LZE4T	Human	Esophagus	ESCC	2.26e-10	4.22e-01	0.0811
5716	PSMD10	LZE7T	Human	Esophagus	ESCC	1.35e-11	9.05e-01	0.0667
5716	PSMD10	LZE8T	Human	Esophagus	ESCC	9.59e-05	2.11e-01	0.067
5716	PSMD10	LZE20T	Human	Esophagus	ESCC	9.57e-09	3.39e-01	0.0662
5716	PSMD10	LZE22D1	Human	Esophagus	HGIN	4.15e-06	2.44e-01	0.0595
5716	PSMD10	LZE22T	Human	Esophagus	ESCC	9.15e-05	2.99e-01	0.068
5716	PSMD10	LZE24T	Human	Esophagus	ESCC	7.98e-36	1.08e+00	0.0596
5716	PSMD10	LZE6T	Human	Esophagus	ESCC	1.81e-10	8.56e-01	0.0845
5716	PSMD10	P1T-E	Human	Esophagus	ESCC	1.45e-07	7.82e-01	0.0875
5716	PSMD10	P2T-E	Human	Esophagus	ESCC	9.17e-57	9.32e-01	0.1177
5716	PSMD10	P4T-E	Human	Esophagus	ESCC	1.09e-31	6.83e-01	0.1323
5716	PSMD10	P5T-E	Human	Esophagus	ESCC	1.51e-15	3.84e-01	0.1327
5716	PSMD10	P8T-E	Human	Esophagus	ESCC	5.10e-39	6.00e-01	0.0889
5716	PSMD10	P9T-E	Human	Esophagus	ESCC	3.30e-15	4.36e-01	0.1131
5716	PSMD10	P10T-E	Human	Esophagus	ESCC	1.92e-25	5.77e-01	0.116
5716	PSMD10	P11T-E	Human	Esophagus	ESCC	8.48e-10	5.90e-01	0.1426
5716	PSMD10	P12T-E	Human	Esophagus	ESCC	9.91e-26	4.24e-01	0.1122
5716	PSMD10	P15T-E	Human	Esophagus	ESCC	1.64e-23	4.84e-01	0.1149
5716	PSMD10	P16T-E	Human	Esophagus	ESCC	2.20e-30	5.48e-01	0.1153
5716	PSMD10	P17T-E	Human	Esophagus	ESCC	4.45e-09	5.29e-01	0.1278

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ

∗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:003139816	Esophagus	ESCC	positive regulation of protein ubiquitination	82/8552	119/18723	2.41e-07	3.64e-06	82
GO:00510908	Esophagus	ESCC	regulation of DNA-binding transcription factor activity	252/8552	440/18723	5.22e-07	6.97e-06	252
GO:19040294	Esophagus	ESCC	regulation of cyclin-dependent protein kinase activity	69/8552	98/18723	6.04e-07	7.91e-06	69
GO:00000794	Esophagus	ESCC	regulation of cyclin-dependent protein serine/threonine kinase activity	66/8552	94/18723	1.24e-06	1.53e-05	66
GO:0030330110	Esophagus	ESCC	DNA damage response, signal transduction by p53 class mediator	53/8552	72/18723	1.34e-06	1.63e-05	53
GO:009019914	Esophagus	ESCC	regulation of release of cytochrome c from mitochondria	38/8552	48/18723	2.11e-06	2.43e-05	38
GO:00719029	Esophagus	ESCC	positive regulation of protein serine/threonine kinase activity	124/8552	200/18723	2.27e-06	2.61e-05	124
GO:004586018	Esophagus	ESCC	positive regulation of protein kinase activity	219/8552	386/18723	6.91e-06	6.97e-05	219
GO:003367420	Esophagus	ESCC	positive regulation of kinase activity	260/8552	467/18723	7.26e-06	7.22e-05	260
GO:001082315	Esophagus	ESCC	negative regulation of mitochondrion organization	36/8552	49/18723	7.24e-05	5.45e-04	36
GO:19040312	Esophagus	ESCC	positive regulation of cyclin-dependent protein kinase activity	26/8552	33/18723	1.06e-04	7.43e-04	26
GO:003030710	Esophagus	ESCC	positive regulation of cell growth	100/8552	166/18723	1.07e-04	7.55e-04	100
GO:200102112	Esophagus	ESCC	negative regulation of response to DNA damage stimulus	54/8552	81/18723	1.09e-04	7.64e-04	54
GO:00457372	Esophagus	ESCC	positive regulation of cyclin-dependent protein serine/threonine kinase activity	23/8552	29/18723	2.25e-04	1.40e-03	23
GO:0043409110	Esophagus	ESCC	negative regulation of MAPK cascade	105/8552	180/18723	4.13e-04	2.35e-03	105
GO:005122013	Esophagus	ESCC	cytoplasmic sequestering of protein	18/8552	22/18723	5.69e-04	3.10e-03	18
GO:004324811	Esophagus	ESCC	proteasome assembly	11/8552	12/18723	1.26e-03	6.06e-03	11
GO:009020112	Esophagus	ESCC	negative regulation of release of cytochrome c from mitochondria	16/8552	20/18723	1.85e-03	8.40e-03	16
GO:00434332	Esophagus	ESCC	negative regulation of DNA-binding transcription factor activity	103/8552	185/18723	3.86e-03	1.57e-02	103
GO:19017975	Esophagus	ESCC	negative regulation of signal transduction by p53 class mediator	22/8552	31/18723	3.90e-03	1.58e-02	22

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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

Cell Type

Tissue

Disease Stage

Target Gene

RSS

Regulon Activity

∗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

PSMD10

SNV

Missense_Mutation

novel

c.140N>T

p.Ala47Val

p.A47V

O75832

protein_coding

deleterious(0.02)

probably_damaging(0.983)

TCGA-AO-A1KS-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

PSMD10

SNV

Missense_Mutation

c.475C>A

p.Leu159Met

p.L159M

O75832

protein_coding

deleterious(0.02)

possibly_damaging(0.887)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PSMD10

SNV

Missense_Mutation

novel

c.352N>G

p.Arg118Gly

p.R118G

O75832

protein_coding

tolerated(0.08)

benign(0.084)

TCGA-AA-3949-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Unknown

PSMD10

SNV

Missense_Mutation

novel

c.175N>G

p.Leu59Val

p.L59V

O75832

protein_coding

deleterious(0)

probably_damaging(0.978)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

PSMD10

SNV

Missense_Mutation

novel

c.671N>G

p.Val224Gly

p.V224G

O75832

protein_coding

deleterious(0.01)

benign(0.026)

TCGA-A5-A2K5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

PSMD10

SNV

Missense_Mutation

novel

c.424N>A

p.Ala142Thr

p.A142T

O75832

protein_coding

deleterious(0)

benign(0.14)

TCGA-AX-A06F-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

PSMD10

SNV

Missense_Mutation

novel

c.239N>T

p.Ala80Val

p.A80V

O75832

protein_coding

deleterious(0)

probably_damaging(0.984)

TCGA-AX-A0J1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

PSMD10

SNV

Missense_Mutation

novel

c.466N>A

p.His156Asn

p.H156N

O75832

protein_coding

tolerated(0.22)

benign(0.023)

TCGA-B5-A0JY-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

PSMD10

SNV

Missense_Mutation

novel

c.657A>G

p.Ile219Met

p.I219M

O75832

protein_coding

tolerated(0.29)

benign(0.01)

TCGA-B5-A3FA-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

PSMD10

SNV

Missense_Mutation

c.462G>T

p.Met154Ile

p.M154I

O75832

protein_coding

tolerated(1)

benign(0.001)

TCGA-BS-A0UV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

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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
5716	PSMD10	TRANSCRIPTION FACTOR BINDING	inhibitor	BORTEZOMIB	BORTEZOMIB
5716	PSMD10	TRANSCRIPTION FACTOR BINDING	inhibitor	CARFILZOMIB	CARFILZOMIB

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