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: MTHFD1

Gene summary for MTHFD1

Gene summary.

Gene information	Species	Human
	Gene symbol	MTHFD1
	Gene ID	4522
	Gene name	methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1
	Gene Alias	CIMAH
	Cytomap	14q23.3
	Gene Type	protein-coding
	GO ID	GO:0000096
	UniProtAcc	P11586

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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
4522	MTHFD1	LZE4T	Human	Esophagus	ESCC	7.94e-08	2.44e-01	0.0811
4522	MTHFD1	LZE7T	Human	Esophagus	ESCC	8.17e-05	2.94e-01	0.0667
4522	MTHFD1	LZE22D1	Human	Esophagus	HGIN	1.28e-02	8.92e-02	0.0595
4522	MTHFD1	LZE24T	Human	Esophagus	ESCC	1.24e-06	1.72e-01	0.0596
4522	MTHFD1	LZE6T	Human	Esophagus	ESCC	3.55e-04	1.30e-01	0.0845
4522	MTHFD1	P2T-E	Human	Esophagus	ESCC	5.69e-21	4.34e-01	0.1177
4522	MTHFD1	P4T-E	Human	Esophagus	ESCC	6.99e-12	3.86e-01	0.1323
4522	MTHFD1	P5T-E	Human	Esophagus	ESCC	2.11e-11	2.55e-01	0.1327
4522	MTHFD1	P8T-E	Human	Esophagus	ESCC	2.65e-10	3.40e-01	0.0889
4522	MTHFD1	P9T-E	Human	Esophagus	ESCC	5.87e-13	1.35e-01	0.1131
4522	MTHFD1	P10T-E	Human	Esophagus	ESCC	3.91e-19	3.97e-01	0.116
4522	MTHFD1	P11T-E	Human	Esophagus	ESCC	5.82e-07	1.92e-01	0.1426
4522	MTHFD1	P12T-E	Human	Esophagus	ESCC	2.51e-20	4.55e-01	0.1122
4522	MTHFD1	P15T-E	Human	Esophagus	ESCC	1.02e-20	6.32e-01	0.1149
4522	MTHFD1	P16T-E	Human	Esophagus	ESCC	3.26e-19	4.84e-01	0.1153
4522	MTHFD1	P17T-E	Human	Esophagus	ESCC	5.38e-06	5.48e-01	0.1278
4522	MTHFD1	P19T-E	Human	Esophagus	ESCC	7.91e-06	6.00e-01	0.1662
4522	MTHFD1	P20T-E	Human	Esophagus	ESCC	1.21e-15	3.43e-01	0.1124
4522	MTHFD1	P21T-E	Human	Esophagus	ESCC	1.12e-20	4.98e-01	0.1617
4522	MTHFD1	P22T-E	Human	Esophagus	ESCC	1.11e-18	2.77e-01	0.1236

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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
Thyroid		ATC: Anaplastic thyroid cancer
		HT: Hashimoto's thyroiditis
		PTC: Papillary thyroid cancer

∗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:00351487	Cervix	CC	tube formation	31/2311	148/18723	2.07e-03	1.51e-02	31
GO:00018417	Cervix	CC	neural tube formation	23/2311	102/18723	2.80e-03	1.87e-02	23
GO:00605626	Cervix	CC	epithelial tube morphogenesis	57/2311	325/18723	3.79e-03	2.41e-02	57
GO:00140206	Cervix	CC	primary neural tube formation	21/2311	94/18723	4.68e-03	2.82e-02	21
GO:00219156	Cervix	CC	neural tube development	30/2311	152/18723	6.00e-03	3.43e-02	30
GO:00018435	Cervix	CC	neural tube closure	19/2311	88/18723	1.01e-02	4.91e-02	19
GO:0006575	Colorectum	AD	cellular modified amino acid metabolic process	59/3918	188/18723	4.80e-04	5.27e-03	59
GO:0006730	Colorectum	AD	one-carbon metabolic process	18/3918	40/18723	5.36e-04	5.74e-03	18
GO:0060562	Colorectum	AD	epithelial tube morphogenesis	93/3918	325/18723	5.65e-04	6.00e-03	93
GO:0043648	Colorectum	AD	dicarboxylic acid metabolic process	34/3918	96/18723	7.22e-04	7.28e-03	34
GO:0014020	Colorectum	AD	primary neural tube formation	33/3918	94/18723	1.02e-03	9.50e-03	33
GO:0001841	Colorectum	AD	neural tube formation	35/3918	102/18723	1.16e-03	1.05e-02	35
GO:0001843	Colorectum	AD	neural tube closure	30/3918	88/18723	2.83e-03	2.12e-02	30
GO:0060606	Colorectum	AD	tube closure	30/3918	89/18723	3.42e-03	2.49e-02	30
GO:0042398	Colorectum	AD	cellular modified amino acid biosynthetic process	18/3918	46/18723	3.67e-03	2.60e-02	18
GO:0035148	Colorectum	AD	tube formation	45/3918	148/18723	4.13e-03	2.87e-02	45
GO:0001838	Colorectum	AD	embryonic epithelial tube formation	38/3918	121/18723	4.40e-03	3.01e-02	38
GO:0048568	Colorectum	AD	embryonic organ development	112/3918	427/18723	4.60e-03	3.14e-02	112
GO:0072175	Colorectum	AD	epithelial tube formation	40/3918	132/18723	6.98e-03	4.29e-02	40
GO:0021915	Colorectum	AD	neural tube development	45/3918	152/18723	7.05e-03	4.31e-02	45

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa012405	Esophagus	ESCC	Biosynthesis of cofactors	97/4205	153/8465	3.88e-04	1.35e-03	6.94e-04	97
hsa0124012	Esophagus	ESCC	Biosynthesis of cofactors	97/4205	153/8465	3.88e-04	1.35e-03	6.94e-04	97
hsa01240	Liver	Cirrhotic	Biosynthesis of cofactors	66/2530	153/8465	3.11e-04	1.99e-03	1.23e-03	66
hsa012401	Liver	Cirrhotic	Biosynthesis of cofactors	66/2530	153/8465	3.11e-04	1.99e-03	1.23e-03	66
hsa012402	Liver	HCC	Biosynthesis of cofactors	103/4020	153/8465	4.67e-07	5.05e-06	2.81e-06	103
hsa006702	Liver	HCC	One carbon pool by folate	17/4020	20/8465	6.04e-04	2.50e-03	1.39e-03	17
hsa012403	Liver	HCC	Biosynthesis of cofactors	103/4020	153/8465	4.67e-07	5.05e-06	2.81e-06	103
hsa0067011	Liver	HCC	One carbon pool by folate	17/4020	20/8465	6.04e-04	2.50e-03	1.39e-03	17
hsa012404	Oral cavity	OSCC	Biosynthesis of cofactors	88/3704	153/8465	3.84e-04	1.20e-03	6.12e-04	88
hsa0124011	Oral cavity	OSCC	Biosynthesis of cofactors	88/3704	153/8465	3.84e-04	1.20e-03	6.12e-04	88
hsa0124021	Oral cavity	LP	Biosynthesis of cofactors	57/2418	153/8465	1.17e-02	3.91e-02	2.52e-02	57
hsa0124031	Oral cavity	LP	Biosynthesis of cofactors	57/2418	153/8465	1.17e-02	3.91e-02	2.52e-02	57

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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
MTHFD1	LUMP	Breast	IDC	SAMD9,MCM3,TRAP1, etc.	2.02e-01
MTHFD1	STM	Endometrium	EEC	TAB1,ZNF133,STON2, etc.	4.90e-01

∗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

MTHFD1

SNV

Missense_Mutation

c.1691N>G

p.Ser564Cys

p.S564C

P11586

protein_coding

deleterious(0.01)

probably_damaging(0.919)

TCGA-A2-A04P-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxol

MTHFD1

SNV

Missense_Mutation

c.808N>G

p.Pro270Ala

p.P270A

P11586

protein_coding

deleterious(0.02)

probably_damaging(0.999)

TCGA-A2-A04T-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

MTHFD1

SNV

Missense_Mutation

novel

c.1850N>T

p.Asp617Val

p.D617V

P11586

protein_coding

deleterious(0)

probably_damaging(0.995)

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MTHFD1

SNV

Missense_Mutation

c.1466N>A

p.Phe489Tyr

p.F489Y

P11586

protein_coding

deleterious(0)

probably_damaging(0.993)

TCGA-A8-A07L-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

MTHFD1

SNV

Missense_Mutation

c.782C>T

p.Ala261Val

p.A261V

P11586

protein_coding

tolerated(0.14)

benign(0.139)

TCGA-BH-A0HA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MTHFD1

SNV

Missense_Mutation

novel

c.560N>T

p.Trp187Leu

p.W187L

P11586

protein_coding

tolerated(0.72)

possibly_damaging(0.547)

TCGA-C8-A26Z-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

MTHFD1

SNV

Missense_Mutation

c.236N>G

p.Ser79Cys

p.S79C

P11586

protein_coding

tolerated(0.07)

benign(0.336)

TCGA-C8-A274-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

MTHFD1

SNV

Missense_Mutation

novel

c.1238N>T

p.Ser413Phe

p.S413F

P11586

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-OL-A5RW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

MTHFD1

SNV

Missense_Mutation

novel

c.2645N>T

p.Thr882Ile

p.T882I

P11586

protein_coding

deleterious(0.01)

benign(0.436)

TCGA-S3-AA10-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cytoxan

MTHFD1

insertion

Nonsense_Mutation

novel

c.1852_1853insTGCTCTAAAATAGTCTAGAATGGATTTCTCACAT

p.Ala618ValfsTer3

p.A618Vfs*3

P11586

protein_coding

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

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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

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