Screening of Variants in the Transcript Profile of Eutopic Endometrium from Infertile Women with Endometriosis during the Implantation Window

Broi, Michele Gomes Da; Plaça, Jessica Rodrigues; Silva Jr, Wilson Araújo da; Ferriani, Rui Alberto; Navarro, Paula Andrea

doi:10.1055/s-0041-1730287

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Revista Brasileira de Ginecologia e Obstetrícia

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Sumário

Original Article • Rev. Bras. Ginecol. Obstet. 43 (06) • June 2021 • https://doi.org/10.1055/s-0041-1730287 copy

Screening of Variants in the Transcript Profile of Eutopic Endometrium from Infertile Women with Endometriosis during the Implantation Window

Rastreio de variantes no perfil de tanscritos do endométrio eutópico de mulheres inférteis com endometriose durante a janela de implantação

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Objective

Abnormalities in the eutopic endometrium of women with endometriosis may be related to disease-associated infertility. Although previous RNA-sequencing analysis did not show differential expression in endometrial transcripts of endometriosis patients, other molecular alterations could impact protein synthesis and endometrial receptivity. Our aim was to screen for functional mutations in the transcripts of eutopic endometria of infertile women with endometriosis and controls during the implantation window.

Methods

Data from RNA-Sequencing of endometrial biopsies collected during the implantation window from 17 patients (6 infertile women with endometriosis, 6 infertile controls, 5 fertile controls) were analyzed for variant discovery and identification of functional mutations. A targeted study of the alterations found was performed to understand the data into disease’s context.

Results

None of the variants identified was common to other samples within the same group, and no mutation was repeated among patients with endometriosis, infertile and fertile controls. In the endometriosis group, nine predicted deleterious mutations were identified, but only one was previously associated to a clinical condition with no endometrial impact. When crossing the mutated genes with the descriptors endometriosis and/or endometrium, the gene CMKLR1 was associated either with inflammatory response in endometriosis or with endometrial processes for pregnancy establishment.

Conclusion

Despite no pattern of mutation having been found, we ponder the small sample size and the analysis on RNA-sequencing data. Considering the purpose of the study of screening and the importance of the CMKLR1 gene on endometrial

Keywords:
endometriosis; infertility; eutopic endometrium; RNA-sequencing; mutation

Group	Pacient ID	Variants		Indel		SNV		Total after filtering/ prediction
Group	Pacient ID	Before filtering	After filtering/ prediction	Before filtering	After filtering/ prediction	Before filtering	After filtering/ prediction	Total after filtering/ prediction
Endometriosis	1	72239	5	1286	0	70953	5	9
	2	16482	0	975	0	15507	0
	3	14955	0	210	0	14745	0
	4	84156	1	4743	0	79413	1
	5	69363	2	1111	0	68252	2
	6	146610	1	8595	0	138015	1
Fertile control	1	79967	4	4694	0	75273	4	14
	2	66279	5	1505	0	64774	5
	3	98901	2	5775	0	93126	2
	4	157215	1	9525	0	147690	1
	5	84380	2	4940	0	79440	2
Infertile control	1	149952	2	9262	0	140690	2	19
	2	118616	4	7285	0	111331	4
	3	97232	2	5600	0	91632	2
	4	89246	1	5148	0	84098	1
	5	88790	7	1906	0	86884	7
	6	84869	3	4976	0	79893	3

Group	Patient ID	Chromosome	Reference allele	Mutant allele	Genotype	Depth	SNV score	Gene	1000 g	dbSNP NCBI	CADD
CF	1	2	C	T	het	10	62.77	TTN	0.076877	rs4894028	24.0
		3	A	G	het	10	52.77	ZNF502	0.10603	rs56084453	17.61
		17	G	A	het	10	109.77	EVPL	0.0081869	rs150149800	33.0
		19	G	A	het	10	106.77	DOCK6	0.519569	rs12978266	22.9
	5	1	G	A	het	10	103.77	ATAD3B	0.00239617	rs141377718	23.5
		3	C	T	het	10	32.77	DNAH1	0.0299521	rs419752	34.0
		6	T	C	het	10	66.77	GSTA3	0.000199681	rs139422505	21.8
		8	C	A	het	10	58.77	MAPK15	0.095647	rs60732298	28.2
		12	A	C	het	10	71.77	CLEC7A	0.00858626	rs16910527	25.2
	8	1	C	T	het	10	124.77	OXCT2	−	rs150795467	22.6
	8	19	T	C	het	10	81.77	ZNF836	0.0129792	rs61739527	18.91
	9	1	A	C	het	10	24.78	PLEKHN1	−	rs181207265	20.5
	32	1	G	C	het	10	224.77	ANKRD45	0.00199681	rs191985325	24.7
	32	10	A	G	het	10	30.77	PPP1R3C	0.00199681	rs143318107	24.6
CI	2	1	C	T	het	10	127.77	KMO	0.000798722	rs200044625	28.8
	2	11	A	T	het	10	166.77	CCDC88B	0.000399361	rs572682028	29.4
	6	5	G	A	het	10	93.77	PCDHB5	0.0297524	rs17844422	18.71
		11	G	A	het	10	54.77	SLC25A45	0.0101837	rs34400381	26.0
		16	C	A	het	10	204.77	MT1A	0.470647	rs11640851	18.37
		18	G	A	het	10	69.77	ALPK2	0.0203674	rs79863383	24.1
	7	1	C	G	het	10	56.77	TRAF3IP3	0.00139776	rs147791408	22.8
	7	10	G	A	het	10	31.77	CFAP58	−	rs143080879	29.2
	17	1	G	A	het	10	67.77	C1orf87	−	rs772501233	26.5
	19	3	G	A	het	10	234.77	CCDC13	0.167732	rs17238798	24.8
		3	C	G	het	10	59.77	IQCG	0.281749	rs67877771	26.2
		5	C	T	het	10	91.77	C5orf51	0.00159744	rs151191974	33.0
		6	T	C	het	10	190.77	CRYBG1	0.0201677	rs61741114	27.0
		6	G	A	het	10	113.77	LAMA4	0.0309505	rs11757455	34.0
		11	C	T	het	10	152.77	RIN1	0.0183706	rs140145986	24.7
		17	G	A	het	10	94.77	ITGAE	0.265375	rs1716	25.0
	22	8	C	T	het	10	184.77	MICU3	0.000399361	rs201776772	26.8
		9	G	A	het	10	140.77	FAM166B	0.0333466	rs75679360	33.0
		12	G	C	het	10	49.77	CAPRIN2	0.0111821	rs73079976	28.0
END	3	4	C	T	het	10	136.77	NSG1	0.00139776	rs142822048	32.0
		12	G	A	het	10	111.77	CMKLR1	0.000199681	rs201809939	29.0
		14	G	A	hom	10	241.41	AHNAK2	0.538538	rs10438247	24.7
		17	A	T	het	10	108.77	EFCAB13	0.0892572	rs72825679	24.7
		20	T	C	het	10	97.77	DHX35	0.014976	rs36053162	23.0
	27	4	C	T	het	10	227.77	SLC2A9	0.294129	rs3733591	22.8
	28	17	G	A	het	10	44.77	ASB16	0.0141773	rs74491716	24.2
	28	19	A	T	het	10	131.77	IZUMO4	0.0107827	rs45506200	25.6
	31	5	C	T	het	10	224.77	JMY	0.0141773	rs116121324	24.5

Group	ID	Chr	Ref	Mut	NCBI register	Gene Symbol	Official name	Codon impact	Molecular consequence (dbSNP)	Interpretation(ClinVar)	Associated condition (ClinVar)
CF	1	2	C	T	rs4894028	TTN	titin	R (Arg) > H (His)	Missense variant	Benign / Likely benign	Dilated Cardiomyopathy, Myopathy, Hypertrophic cardiomyopathy, Limb-Girdle Muscular Dystrophy, Distal myopathy Markesbery-Griggs type
		3	A	G	rs56084453	ZNF502	zinc finger protein 502	Q (Gln) > R (Arg)	Missense variant	NR	−
		17	G	A	rs150149800	EVPL	envoplakin	R (Arg) > C (Cys)	Missense variant	NR	−
		19	G	A	rs12978266	DOCK6	dedicator of cytokinesis 6	P (Pro) > L (Leu)	Missense variant	Benign	Adams-Oliver syndrome 2
	2	1	G	A	rs141377718	ATAD3B	ATPase family AAA domain containing 3B	V (Val) > M (Met)	Missense variant	NR	−
		3	C	T	rs419752	DNAH1	dynein axonemal heavy chain 1	R (Arg) > C (Cys)	Missense variant	Benign	• Ciliary dyskinesia, Spermatogenic failure
		6	T	C	rs139422505	GSTA3	glutathione S-transferase α 3	N (Asn) > S (Ser)	Missense variant	NR	−
		8	C	A	rs60732298	MAPK15	Mitogen-activated protein kinase 15	T (Thr) > K (Lys)	Missense variant	NR	−
		12	A	C	rs16910527	CLEC7A	C-type lectin domain containing 7A	I (Ile) > S (Ser)	Missense variant	NR	−
	3	1	C	T	rs150795467	OXCT2	3-oxoacid CoA-transferase 2	D (Asp) > N (Asn)	Missense variant	NR	−
	3	19	T	C	rs61739527	ZNF836	zinc finger protein 836	E (Glu) > G (Gly)	Missense variant	NR	−
	4	1	A	C	rs181207265	PLEKHN1	pleckstrin homology domain containing N1	T (Thr) > P (Pro)	Missense variant	NR	−
	5	1	G	C	rs191985325	ANKRD45	ankyrin repeat domain 45	L (Leu) > V (Val)	Missense variant	NR	−
	5	10	A	G	rs143318107	PPP1R3C	protein phosphatase 1 regulatory subunit 3C	F (Phe) > S (Ser)	Missense variant	NR	−
CI	1	1	C	T	rs200044625	KMO	kynurenine 3-monooxygenase	T (Thr) > I (Ile)	Missense variant	NR	−
	1	11	A	T	rs572682028	CCDC88B	coiled-coil domain containing 88B	E (Glu) > V (Val)	Missense variant	NR	−
	2	5	G	A	rs17844422	PCDHB5	protocadherin β 5	S (Ser) > N (Asn)	Missense variant	NR	−
		11	G	A	rs34400381	SLC25A45	solute carrier family 25 member 45	R (Arg) > C (Cys)	Missense variant	NR	−
		16	C	A	rs11640851	MT1A	metallothionein 1A	T (Thr) > N (Asn)	Missense variant	NR	−
		18	G	A	rs79863383	ALPK2	α kinase 2	T (Thr) > I (Ile)	Missense variant	NR	−
	3	1	C	G	rs147791408	TRAF3IP3	TRAF3 interacting protein 3	D (Asp) > E (Glu)	Missense variant	NR	−
	3	10	G	A	rs143080879	CFAP58	cilia and flagella associated protein 58	R (Arg) > H (His)	Missense variant	NR	−
	4	1	G	A	rs772501233	C1orf87	chromosome 1 open reading frame 87	A (Ala) > V (Val)	Missense variant	NR	−
	5	3	G	A	rs17238798	CCDC13	coiled-coil domain containing 13	R (Arg) > W (Trp)	Missense variant	NR	−
		3	C	G	rs67877771	IQCG	IQ motif containing G	D (Asp) > H (His)	Missense variant	NR	−
		5	C	T	rs151191974	C5orf51	chromosome 5 open reading frame 51	P (Pro) > L (Leu)	Missense variant	NR	−
		6	T	C	rs61741114	CRYBG1	crystallin β-gamma domain containing 1	L (Leu) > P (Pro)	Missense variant	NR	−
		6	G	A	rs11757455	LAMA4	laminin subunit α 4	R (Arg) > W (Trp)	Missense variant	Benign	−
		11	C	T	rs140145986	RIN1	Ras and Rab interactor 1	A (Ala) > T (Thr)	Missense variant	NR	−
		17	G	A	rs1716	ITGAE	integrin subunit α E	R (Arg) > W (Trp)	Missense variant	NR	−
END	1	4	C	T	rs142822048	NSG1	neuronal vesicle trafficking associated 1	P (Pro) > S (Ser)	Missense variant	NR	−
		12	G	A	rs201809939	CMKLR1	chemerin chemokine-like receptor 1	R (Arg) > C (Cys)	Missense variant	NR	−
		14	G	A	rs10438247	AHNAK2	AHNAK nucleoprotein 2	P (Pro) > L (Leu)	Missense variant	NR	−
		17	A	T	rs72825679	EFCAB13	EF-hand calcium-binding domain-containing protein 13	D (Asp) > V (Val)	Missense variant	NR	−
		20	T	C	rs36053162	DHX35	DEAH-box helicase 35	I (Ile) > T (Thr)	Missense variant	NR	−
	4	4	C	T	rs3733591	SLC2A9	solute carrier family 2 member 9	R (Arg) > H (His)	Missense variant	Benign	Familial renal hypouricemia
	5	17	G	A	rs74491716	ASB16	ankyrin repeat and SOCS box containing 16	A (Ala) > T (Thr)	Missense variant	NR	−
		19	A	T	rs45506200	IZUMO4	IZUMO family member 4	Y (Tyr) > F (Phe)	Missense variant	NR	−
	6	5	C	T	rs116121324	JMY	junction mediating and regulatory protein, p53 cofactor	P (Pro) > L (Leu)	Missense variant	NR	−

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[1] Address for correspondence Michele Gomes Da Broi, PhD, University of São Paulo, Avenida Bandeirantes, 3900, 14049-900, Ribeirão Preto, SP, Brazil (e-mail: michi.dabroi@gmail.com).