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: MTHFD1L

Gene summary for MTHFD1L

Gene summary.

Gene information	Species	Human
	Gene symbol	MTHFD1L
	Gene ID	25902
	Gene name	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like
	Gene Alias	FTHFSDC1
	Cytomap	6q25.1
	Gene Type	protein-coding
	GO ID	GO:0001501
	UniProtAcc	B7ZM99

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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
25902	MTHFD1L	CCI_1	Human	Cervix	CC	5.58e-14	1.12e+00	0.528
25902	MTHFD1L	CCI_2	Human	Cervix	CC	1.74e-02	6.66e-01	0.5249
25902	MTHFD1L	CCI_3	Human	Cervix	CC	4.38e-11	6.79e-01	0.516
25902	MTHFD1L	HTA11_1391_2000001011	Human	Colorectum	AD	5.50e-04	7.06e-01	-0.059
25902	MTHFD1L	HTA11_99999970781_79442	Human	Colorectum	MSS	2.43e-04	5.07e-01	0.294
25902	MTHFD1L	HTA11_99999965062_69753	Human	Colorectum	MSI-H	5.87e-04	1.27e+00	0.3487
25902	MTHFD1L	HTA11_99999965104_69814	Human	Colorectum	MSS	1.70e-11	9.06e-01	0.281
25902	MTHFD1L	HTA11_99999971662_82457	Human	Colorectum	MSS	1.44e-21	1.01e+00	0.3859
25902	MTHFD1L	HTA11_99999974143_84620	Human	Colorectum	MSS	3.48e-02	2.90e-01	0.3005
25902	MTHFD1L	A015-C-203	Human	Colorectum	FAP	1.62e-05	-2.85e-01	-0.1294
25902	MTHFD1L	A002-C-205	Human	Colorectum	FAP	1.40e-03	-1.62e-01	-0.1236
25902	MTHFD1L	A002-C-114	Human	Colorectum	FAP	1.07e-02	-1.64e-01	-0.1561
25902	MTHFD1L	A015-C-104	Human	Colorectum	FAP	3.30e-06	-2.58e-01	-0.1899
25902	MTHFD1L	A002-C-016	Human	Colorectum	FAP	1.54e-02	-1.63e-01	0.0521
25902	MTHFD1L	A002-C-116	Human	Colorectum	FAP	4.56e-04	-1.48e-01	-0.0452
25902	MTHFD1L	A018-E-020	Human	Colorectum	FAP	9.31e-06	-2.64e-01	-0.2034
25902	MTHFD1L	AEH-subject1	Human	Endometrium	AEH	1.95e-13	5.35e-01	-0.3059
25902	MTHFD1L	AEH-subject2	Human	Endometrium	AEH	8.20e-13	5.07e-01	-0.2525
25902	MTHFD1L	AEH-subject4	Human	Endometrium	AEH	7.41e-05	3.55e-01	-0.2657
25902	MTHFD1L	AEH-subject5	Human	Endometrium	AEH	1.20e-06	3.89e-01	-0.2953

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
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
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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
hsa00670	Colorectum	MSI-H	One carbon pool by folate	7/797	20/8465	1.65e-03	1.73e-02	1.45e-02	7
hsa006701	Colorectum	MSI-H	One carbon pool by folate	7/797	20/8465	1.65e-03	1.73e-02	1.45e-02	7
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
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

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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

MTHFD1L

SNV

Missense_Mutation

c.1213G>C

p.Glu405Gln

p.E405Q

protein_coding

tolerated(0.1)

possibly_damaging(0.502)

TCGA-AR-A0TX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MTHFD1L

SNV

Missense_Mutation

c.1087N>A

p.Asp363Asn

p.D363N

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-BH-A0E1-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MTHFD1L

SNV

Missense_Mutation

c.658N>T

p.Asp220Tyr

p.D220Y

protein_coding

deleterious(0.02)

benign(0.255)

TCGA-C8-A1HK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MTHFD1L

SNV

Missense_Mutation

c.631C>G

p.Leu211Val

p.L211V

protein_coding

deleterious(0.04)

benign(0.028)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

MTHFD1L

SNV

Missense_Mutation

rs759525027

c.1847N>G

p.Val616Gly

p.V616G

protein_coding

deleterious(0)

probably_damaging(0.977)

TCGA-D8-A1JT-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

MTHFD1L

SNV

Missense_Mutation

c.2278N>A

p.Gly760Ser

p.G760S

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-E2-A14Z-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

arimidex

MTHFD1L

SNV

Missense_Mutation

c.1073C>G

p.Ser358Cys

p.S358C

protein_coding

deleterious(0.05)

benign(0.009)

TCGA-E9-A226-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

tamoxiphen

MTHFD1L

insertion

Nonsense_Mutation

novel

c.2689_2690insTCTAGATGTCAAAGAAGAGGATGCTCACATGTGC

p.Thr897IlefsTer2

p.T897Ifs*2

protein_coding

TCGA-BH-A0E7-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

MTHFD1L

deletion

Frame_Shift_Del

c.1124_1145delNNNNNNNNNNNNNNNNNNNNNN

p.Val377CysfsTer21

p.V377Cfs*21

protein_coding

TCGA-E2-A1LS-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Cyclophosphamide

MTHFD1L

SNV

Missense_Mutation

novel

c.2425G>A

p.Ala809Thr

p.A809T

protein_coding

deleterious(0.02)

probably_damaging(0.995)

TCGA-2W-A8YY-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

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