Arthrogryposis as a Syndrome: Gene Ontology Analysis

Abstract

Arthrogryposis by definition has multiple congenital contractures. All types of arthrogryposis have decreased in utero fetal movement. Because so many things are involved in normal fetal movement, there are many causes and processes that can go awry. In this era of molecular genetics, we have tried to place the known mutated genes seen in genetic forms of arthrogryposis into biological processes or cellular functions as defined by gene ontology. We hope this leads to better identification of all interacting pathways and processes involved in the development of fetal movement in order to improve diagnosis of the genetic forms of arthrogryposis, to lead to the development of molecular therapies, and to help better define the natural history of various types of arthrogryposis.

Arthrogryposis is the term that has been used for the last century to describe individuals born with multiple congenital contractures (e.g., 2 or more areas in different body parts with limitation of movement present at birth) [Hall, 2014]. Multiple congenital contractures have been recognized at birth for hundreds of years, particularly because there is often difficulty with delivery, and the contractures are obviously present in the newborn. Often in the past, severely affected individuals did not survive. During the last century, the term arthrogryposis multiplex congenita was often used for multiple congenital contractures. However, arthrogryposis and arthrogryposis multiplex congenita are both descriptive terms or signs rather than a specific diagnosis [Hall, 2012, 2014].

What makes arthrogryposis so interesting is that anything which interferes with normal fetal movement may lead to congenital contractures. In the severest form, fetal akinesia deformation sequence, secondary deformations of multiple tissues are seen (craniofacial changes, pulmonary hypoplasia, polyhydramnios, decreased gut mobility and shortened gut, short umbilical cord, skin changes, and multiple joints with limitation of movement, including limbs, jaw, and spine) [Hall, 2009].

Nowadays, the recognition of an affected infant is possible prenatally utilizing real-time ultrasound studies; however, the presence of joint contractures is most often missed [Filges and Hall, 2013]. In arthrogryposis, delivery is often breech and difficult, leading to C-section. In spite of a C-section, fractures of the long bones occur in the perinatal period in at least 10% of affected infants [Hall et al., 2014].

Arthrogryposis is not all that infrequent occurring in about 1/3,000 pregnancies [Lowry et al., 2010]. Of these children, about 1/3 will primarily have limbs affected, 1/3 will have limbs plus other body areas affected with normal intelligence, and 1/3 will have central nervous system dysfunction (in the past, half of these would die at birth or in the first year, or have such severe involvement as to be lethal) [Hall, 2012]. Amyoplasia is the most common form of arthrogryposis occurring in about 1/10,000 live births [Hall et al., 2014]. Amyoplasia is recognized by its unique clinical features. Individuals with this form usually do surprisingly well and have normal to high intelligence, but it appears to be totally sporadic (although increased in one of monozygotic twins). Most other recognizable types of arthrogryposis have a genetic basis (i.e., single gene mutation) [Michalk et al., 2008; Hall, 2014; Hunter et al., 2015; Bayram et al., 2016].

Over the last 40 years, the heterogeneity and diversity of specific disorders has begun to be recognized and delineated. Over 400 different specific conditions with arthrogryposis have been recognized and over 320 genes implicated [Michalk et al., 2008; Hall, 2014; Hunter et al., 2015; Bayram et al., 2016]. There is a need to annotate and functionally group these genes into known pathways and biological processes. Such a grouping has potential for identification and prioritization of other candidate disease genes. Additionally, it should inform the development of better molecular diagnostic techniques and specific therapeutic options. Until now, nonspecific physical therapy to loosen contractures and realign joints, casting, and surgeries to improve joint function have been the standard therapy.

It is clear that anything which limits or interferes with fetal movement may lead to congenital contractures (limitation of joint movement) [Hall, 2012, 2014]. These include myopathic processes with structural elements, ion channels, and mechanosensing elements; neuropathic processes including central and peripheral nerves, anterior horn cells, and brain organization and function; myelin deficiency; neuromotor endplate abnormalities; connective tissue disorders; limitation of space and constraint in utero; vascular compromise (decreased blood flow to the placenta or to the embryo/fetus); teratogenic exposure, and maternal illnesses. Any of the above-mentioned processes or clinical situations may lead to decreased fetal movement. Even hypotonia of the fetus may be severe enough to decrease in utero movement sufficiently, leading to contractures at birth.

We performed an enrichment analysis (EA) to identify overrepresented functional biological groupings within the list of assembled 320 genes (table 1). EA is a common bioinformatic technique to describe common biological aspects associated with a list of genes. Gene lists are often the output of high-throughput genomics experiment or, in the case here, a listing of genes associated with a disease process. EA involves computing an enrichment statistic across a corpus of gene sets to identify over- and/or underrepresented gene sets in the gene list being interrogated. A corpus of gene sets is a collection of genes categorized together based on some biological aspect or property. The outcome of EA results in a list of statistically enriched gene sets describing the biological properties common within the given gene list. This allows for biologist interpretation of gene lists, whether it is a differential gene expression list or a list of genes associated with a disease state, such as the syndrome of arthrogryposis detailed in this review.

Table 1.

Gene table

Gene	Entrez Gene ID	Aliases	Functions
ABCC8	6833	ABC36, HHF1, HI, HRINS, MRP8, PHHI, SUR, SUR1, SUR1delta2, TNDM2	sarcolemma, synaptic transmission
ACTA1	58	ACTA, ASMA, CFTD, CFTD1, CFTDM, MPFD, NEM1, NEM2, NEM3	striated muscle thin filament, muscle filament sliding
ACTB	60	BRWS1, PS1TP5BP1	axon guidance, regulation of body fluid levels
ACTG1	71	ACT, ACTG, BRWS2, DFNA20, DFNA26, HEL-176	striated muscle cell development, muscle cell development
ADAMTS10	81794	ADAM-TS10, ADAMTS-10, WMS, WMS1	proteinaceous extracellular matrix
ADAMTSL2	9719	GPHYSD1	lung development, respiratory system development
ADCY6	112	AC6, LCCS8	sarcolemma, regulation of neurogenesis
ADGRG6	57211	APG1, DREG, GPR126, PS1TP2, VIGR	axon ensheathment
ADSL	158	AMPS, ASASE, ASL	carbohydrate derivative biosynthetic process
AIMP1	9255	EMAP2, EMAPII, HLD3, SCYE1, p43	regulation of epithelial cell proliferation, epithelial cell proliferation
AKT1	207	AKT, CWS6, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA	Schwann cell development, Schwann cell differentiation
ALG2	85365	CDGIi, CMS14, CMSTA3, NET38, hALPG2	mannosylation, glycoprotein biosynthetic process
ALG3	10195	CDG1D, CDGS4, CDGS6, D16Ertd36e, NOT56L, Not56, not	mannosylation, glycoprotein biosynthetic process
ANTXR2	118429	CMG-2, CMG2, HFS, ISH, JHF	endoplasmic reticulum part
AP1S2	8905	DC22, MRX59, MRXS21, MRXS5, MRXSF, PGS, SIGMA1B	neuromuscular process, connective tissue development
APLNR	187	AGTRL1, APJ, APJR, HG11	heart development, embryonic morphogenesis
ARX	170302	CT121, EIEE1, ISSX, MRX29, MRX32, MRX33, MRX36, MRX38, MRX43, MRX54, MRX76, MRX87, MRXS1, PRTS	cerebral cortex cell migration, cerebral cortex development
ASXL1	171023	BOPS, MDS	bone development, lung development
ATM	472	AT1, ATA, ATC, ATD, ATDC, ATE, TEL1, TELO1	neuron apoptotic process, regulation of neuron death
ATN1	1822	B37, D12S755E, DRPLA, HRS, NOD	neuron apoptotic process, neuron death
ATP7A	538	DSMAX, MK, MNK, SMAX3	collagen fibril organization, central nervous system neuron differentiation
ATRX	546	ATR2, JMS, MRX52, MRXHF1, RAD54, RAD54L, SFM1, SHS, XH2, XNP, ZNF-HX	limb morphogenesis, limb development
ATXN2	6311	ASL13, ATX2, SCA2, TNRC13	neuromuscular process, central nervous system neuron differentiation
ATXN3	4287	AT3, ATX3, JOS, MJD, MJD1, SCA3	actin filament-based process, synaptic transmission
B3GAT3	26229	GLCATI, glcUAT-I	chondroitin sulfate metabolic process, proteoglycan metabolic process
BAG3	9531	BAG-3, BIS, CAIR-1, MFM6	spinal cord development, I band
BICD2	23299	SMALED2, bA526D8.1	organelle localization
BIN1	274	AMPH2, AMPHL, SH3P9	sarcolemma, I band
CANT1	124583	DBQD, SCAN-1, SCAN1, SHAPY	proteoglycan metabolic process, glycoprotein biosynthetic process
CAPN3	825	CANP3, CANPL3, LGMD2, LGMD2A, nCL-1, p94	muscle cell cellular homeostasis, sarcolemma
CASK	8573	CAGH39, CAMGUK, CMG, FGS4, LIN2, MICPCH, MRXSNA, TNRC8	regulation of cellular response to growth factor stimulus, synaptic membrane
CD24	100133941	CD24A	neuromuscular synaptic transmission, neuroblast proliferation
CD6	923	TP120	response to wounding
CDK5	1020	LIS7, PSSALRE	Schwann cell development, Schwann cell differentiation
CHAT	1103	CHOACTASE, CMS1A, CMS1A2, CMS6	developmental growth, synaptic transmission
CHMP1A	5119	CHMP1, PCH8, PCOLN3, PRSM1, VPS46-1, VPS46A	organelle localization
CHRNA1	1134	ACHRA, ACHRD, CHRNA, CMS1A, CMS1B, CMS2A, FCCMS, SCCMS	muscle cell cellular homeostasis, neuromuscular synaptic transmission
CHRNB1	1140	ACHRB, CHRNB, CMS1D, CMS2A, CMS2C, SCCMS	neuromuscular synaptic transmission, skeletal muscle contraction
CHRND	1144	ACHRD, CMS2A, CMS3A, CMS3B, CMS3C, FCCMS, SCCMS	neuromuscular synaptic transmission, skeletal muscle contraction
CHRNE	1145	ACHRE, CMS1D, CMS1E, CMS2A, CMS4A, CMS4B, CMS4C, FCCMS, SCCMS	neuromuscular synaptic transmission, skeletal muscle contraction
CHRNG	1146	ACHRG	neuromuscular synaptic transmission, chemical synaptic transmission, postsynaptic
CHST14	113189	ATCS, D4ST1, EDSMC1, HNK1ST	chondroitin sulfate metabolic process, proteoglycan metabolic process
CHST3	9469	C6ST, C6ST1, HSD	chondroitin sulfate metabolic process, proteoglycan metabolic process
CHUK	1147	IKBKA, IKK-alpha, IKK1, IKKA, NFKBIKA, TCF16	skeletal muscle contraction, striated muscle contraction
CNTN1	1272	F3, GP135, MYPCN	positive regulation of epithelial cell proliferation, regulation of epithelial cell proliferation
CNTNAP1	8506	CASPR, CNTNAP, NRXN4, P190	axon ensheathment, neuromuscular process, regulation of membrane potential
COG7	91949	CDG2E	glycoprotein biosynthetic process, glycoprotein metabolic process
COL11A2	1302	DFNA13, DFNB53, FBCG2, HKE5, PARP, STL3	fibrillar collagen trimer, complex of collagen trimers
COL1A1	1277	EDSC, OI1, OI2, OI3, OI4	fibrillar collagen trimer, complex of collagen trimers
COL1A2	1278	OI4	fibrillar collagen trimer, complex of collagen trimers
COL2A1	1280	ANFH, AOM, COL11A3, SEDC, STL1	fibrillar collagen trimer, complex of collagen trimers
COL3A1	1281	EDS4A	fibrillar collagen trimer, complex of collagen trimers
COL6A1	1291	OPLL	complex of collagen trimers, collagen metabolic process
COL6A2	1292	PP3610	collagen metabolic process, sarcolemma
COL6A3	1293	DYT27	complex of collagen trimers, collagen metabolic process
COL7A1	1294	EBD1, EBDCT, EBR1, NDNC8	complex of collagen trimers, collagen metabolic process
CRLF1	9244	CISS, CISS1, CLF, CLF-1, NR6, zcytor5	neuron apoptotic process, regulation of neuron death
CTSA	5476	GLB2, GSL, NGBE, PPCA, PPGB	lysosomal lumen, glycoprotein biosynthetic process
CTSL	1514	CATL, CTSL1, MEP	lysosomal lumen, collagen metabolic process
DCX	1641	DBCN, DC, LISX, SCLH, XLIS	cerebral cortex cell migration, hippocampus development
DES	1674	CSM1, CSM2, LGMD2R	muscle filament sliding, actin filament-based movement
DHCR24	1718	DCE, Nbla03646, SELADIN1, seladin-1	skin development, regulation of neuron death
DHCR7	1717	SLOS	lung development, respiratory system development
DMPK	1760	DM, DM1, DM1PK, DMK, MDPK, MT-PK	skeletal muscle contraction, chemical synaptic transmission, postsynaptic
DNM2	1785	CMT2M, CMTDI1, CMTDIB, DI-CMTB, DYN2, DYNII, LCCS5	regulation of cellular response to growth factor stimulus, synaptic membrane
DPAGT1	1798	ALG7, CDG-Ij, CDG1J, CMS13, CMSTA2, D11S366, DGPT, DPAGT, DPAGT2, G1PT, GPT, UAGT, UGAT	glycoprotein biosynthetic process, glycoprotein metabolic process
DPM1	8813	CDGIE, MPDS	mannosylation, glycoprotein biosynthetic process
DST	667	BP240, BPA, BPAG1, CATX-15, CATX15, D6S1101, DMH, DT, EBSB2, HSAN6, MACF2	I band, contractile fiber
DYM	54808	DMC, SMC	bone development, skeletal system development
DYNC1H1	1778	CMT2O, DHC1, DHC1a, DNCH1, DNCL, DNECL, DYHC, Dnchc1, HL-3, SMALED1, p22	organelle localization, glycoprotein biosynthetic process
DYSF	8291	FER1L1, LGMD2B, MMD1	sarcolemma, muscle contraction
EBP	10682	CDPX2, CHO2, CPX, CPXD, MEND	skeletal system development, endoplasmic reticulum part
EGR2	1959	AT591, CMT1D, CMT4E, KROX20	Schwann cell differentiation, peripheral nervous system development
EMD	2010	EDMD, LEMD5, STA	skeletal muscle tissue development, skeletal muscle organ development
ERBB3	2065	ErbB-3, HER3, LCCS2, MDA-BF-1, c-erbB-3, c-erbB3, erbB3-S, p180-ErbB3, p45-sErbB3, p85-sErbB3	Schwann cell differentiation, peripheral nervous system development
ERCC1	2067	COFS4, RAD10, UV20	developmental growth, embryo development
ERCC2	2068	COFS2, EM9, TFIIH, TTD, TTD1, XPD	glial cell development, spinal cord development
ERCC6	2074	ARMD5, CKN2, COFS, COFS1, CSB, RAD26, UVSS1	developmental growth
ERLIN2	11160	C8orf2, Erlin-2, NET32, SPFH2, SPG18	endoplasmic reticulum part
ESCO2	157570	2410004I17Rik, EFO2, RBS	animal organ development
EZH2	2146	ENX-1, ENX1, EZH1, EZH2b, KMT6, KMT6A, WVS, WVS2	hippocampus development, limbic system development
FAM20C	56975	DMP-4, DMP4, GEF-CK, RNS	bone development, osteoblast differentiation
FBN1	2200	ACMICD, ECTOL1, FBN, GPHYSD2, MASS, MFS1, OCTD, SGS, SSKS, WMS, WMS2	extracellular matrix disassembly, regulation of cellular response to growth factor stimulus
FBN2	2201	CCA, DA9, EOMD	embryonic limb morphogenesis, extracellular matrix disassembly
FBN3	84467		regulation of cellular response to growth factor stimulus, proteinaceous extracellular matrix
FGD1	2245	AAS, FGDY, MRXS16, ZFYVE3	actin filament-based process, cellular response to growth factor stimulus
FGF9	2254	FGF-9, GAF, HBFG-9, HBGF-9, SYNS3	chondrocyte differentiation, regulation of stem cell proliferation, embryonic skeletal system development
FGFR1	2260	BFGFR, CD331, CEK, FGFBR, FGFR-1, FLG, FLT-2, FLT2, HBGFR, HH2, HRTFDS, KAL2, N-SAM, OGD, bFGF-R-1	cerebral cortex cell migration, neuroblast proliferation
FGFR2	2263	BBDS, BEK, BFR-1, CD332, CEK3, CFD1, ECT1, JWS, K-SAM, KGFR, TK14, TK25	prostate gland epithelium morphogenesis, neuroblast proliferation
FGFR3	2261	ACH, CD333, CEK2, HSFGFR3EX, JTK4	glial cell development, bone morphogenesis
FHL1	2273	FHL-1, FHL1A, FHL1B, FLH1A, KYOT, SLIM, SLIM-1, SLIM1, SLIMMER, XMPMA	regulation of membrane potential, muscle organ development
FKBP10	60681	BRKS1, FKBP65, OI11, OI6, PPIASE, hFKBP65	endoplasmic reticulum part
FKRP	79147	LGMD2I, MDC1C, MDDGA5, MDDGB5, MDDGC5	mannosylation, sarcolemma
FKTN	2218	CMD1X, FCMD, LGMD2M, MDDGA4, MDDGB4, MDDGC4	mannosylation, muscle organ development
FLNA	2316	ABP-280, ABPX, CSBS, CVD1, FLN, FLN-A, FLN1, FMD, MNS, NHBP, OPD, OPD1, OPD2, XLVD, XMVD	protein import, actin cytoskeleton
FLNB	2317	ABP-278, ABP-280, AOI, FH1, FLN-B, FLN1L, LRS1, SCT, TABP, TAP	hippocampus development, limbic system development
FUCA1	2517	FUCA	lysosomal lumen, glycoprotein biosynthetic process
GAA	2548	LYAG	muscle cell cellular homeostasis, skeletal muscle contraction
GAD1	2571	CPSQ1, GAD, SCP	synaptic transmission
GBA	2629	GBA1, GCB, GLUC	lysosomal lumen, skin development
GBE1	2632	APBD, GBE, GSD4	carbohydrate metabolic process
GCK	2645	FGQTL3, GK, GLK, HHF3, HK4, HKIV, HXKP, LGLK, MODY2	actin cytoskeleton, carbohydrate derivative biosynthetic process
GDF5	8200	BDA1C, BMP-14, BMP14, CDMP1, LAP-4, LAP4, OS5, SYM1B, SYNS2	chondrocyte differentiation, embryonic limb morphogenesis
GJA1	2697	AVSD3, CMDR, CX43, EKVP, GJAL, HLHS1, HSS, ODDD, PPKCA	actin filament-based movement, embryonic limb morphogenesis
GLI3	2737	ACLS, GCPS, GLI3-190, GLI3FL, PAP-A, PAPA, PAPA1, PAPB, PHS, PPDIV	cerebral cortex cell migration, neuroblast proliferation
GLRA1	2741	HKPX1, STHE	chemical synaptic transmission, postsynaptic, neuromuscular process
GLRB	2743	HKPX2	neuromuscular process, synaptic membrane
GLUL	2752	GLNS, GS, PIG43, PIG59	positive regulation of epithelial cell proliferation, regulation of epithelial cell proliferation
GPC3	2719	DGSX, GTR2-2, MXR7, OCI-5, SDYS, SGB, SGBS, SGBS1	body morphogenesis, chondroitin sulfate metabolic process
GRHL3	57822	SOM, TFCP2L4, VWS2	skin development, embryonic organ morphogenesis
GRN	2896	CLN11, GEP, GP88, PCDGF, PEPI, PGRN	neural precursor cell proliferation, positive regulation of epithelial cell proliferation
GUSB	2990	BG, MPS7	lysosomal lumen, carbohydrate metabolic process
HEXA	3073	TSD	chondroitin sulfate metabolic process, lysosomal lumen
HEXB	3074	ENC-1AS, HEL-248, HEL-S-111	chondroitin sulfate metabolic process, lysosomal lumen
HLA-DRB1	3123	DRB1, DRw10, HLA-DR1B, HLA-DRB, SS1	negative regulation of cell proliferation, response to wounding
HOXA13	3209	HOX1, HOX1J	prostate gland epithelium morphogenesis, embryonic limb morphogenesis
HOXD13	3239	BDE, BDSD, HOX4I, SPD	prostate gland epithelium morphogenesis, embryonic limb morphogenesis
HRAS	3265	C-BAS/HAS, C-H-RAS, C-HA-RAS1, CTLO, H-RASIDX, HAMSV, HRAS1, RASH1, p21ras	positive regulation of epithelial cell proliferation, neuron apoptotic process
HSPG2	3339	HSPG, PLC, PRCAN, SJA, SJS, SJS1	chondroitin sulfate metabolic process, bone morphogenesis
IDS	3423	MPS2, SIDS	chondroitin sulfate metabolic process, lysosomal lumen
IGF2	3481	C11orf43, GRDF, IGF-II, PP9974	digestive system development, striated muscle cell differentiation
IGHMBP2	3508	CATF1, CMT2S, HCSA, HMN6, SMARD1, SMUBP2, ZFAND7	spinal cord development, central nervous system neuron differentiation
IMPAD1	54928	GPAPP, IMP 3, IMP-3, IMPA3	chondroitin sulfate metabolic process, bone morphogenesis
INSR	3643	CD220, HHF5	digestive system development, regulation of developmental growth
IRF6	3664	LPS, OFC6, PIT, PPS, PPS1, VWS, VWS1	skin development, epithelial cell proliferation
ISPD	729920	MDDGA7, MDDGC7, Nip, hCG_1745121	mannosylation, glycoprotein biosynthetic process
ITGA6	3655	CD49f, ITGA6B, VLA-6	digestive tract development, digestive system development
ITGB4	3691	CD104	digestive tract development, digestive system development
KCNA1	3736	AEMK, EA1, HBK1, HUK1, KV1.1, MBK1, MK1, RBK1	neuroblast proliferation, hippocampus development
KCNJ11	3767	BIR, HHF2, IKATP, KIR6.2, MODY13, PHHI, TNDM3	sarcolemma, regulation of membrane potential
KCNK9	51305	K2p9.1, KT3.2, TASK-3, TASK3	regulation of membrane potential, synaptic transmission
KIAA0196	9897	RTSC, SPG8	cell development
KIF14	9928	MKS12	hippocampus development, limbic system development
KIF5C	3800	CDCBM2, KINN, NKHC, NKHC-2, NKHC2	axon guidance, axonogenesis
KIF7	374654	ACLS, AGBK, HLS2, JBTS12, UNQ340	heart development, blood vessel development
KLHL40	131377	KBTBD5, NEM8, SRYP, SYRP	muscle fiber development, I band
KLHL41	10324	KBTBD10, Krp1, SARCOSIN	muscle fiber development, striated muscle contraction, striated muscle cell development
KLKB1	3818	KLK3, PKK, PKKD, PPK	extracellular matrix disassembly, extracellular matrix organization
L1CAM	3897	CAML1, CD171, HSAS, HSAS1, MASA, MIC5, N-CAM-L1, N-CAML1, NCAM-L1, S10, SPG1	synaptic membrane, regulation of developmental growth
LAMA2	3908	LAMM	Schwann cell development, Schwann cell differentiation
LARGE	9215	MDC1D, MDDGA6, MDDGB6	muscle cell cellular homeostasis, mannosylation
LIFR	3977	CD118, LIF-R, SJS2, STWS, SWS	cell-type specific apoptotic process, neuron projection morphogenesis
LMBR1	64327	ACHP, C7orf2, DIF14, LSS, PPD2, THYP, TPT, ZRS	embryonic limb morphogenesis, limb morphogenesis
LMNA	4000	CDCD1, CDDC, CMD1A, CMT2B1, EMD2, FPL, FPLD, FPLD2, HGPS, IDC, LDP1, LFP, LGMD1B, LMN1, LMNC, LMNL1, PRO1	striated muscle cell development, muscle cell development
LMX1B	4010	LMX1.2, NPS1	chordate embryonic development, embryo development
LTBP2	4053	C14orf141, GLC3D, LTBP3, MSPKA, MSTP031, WMS3	regulation of stem cell proliferation, stem cell proliferation
MAGEL2	54551	NDNL1, PWLS, SHFYNG, nM15	actin filament-based process
MASP1	5648	3MC1, CRARF, CRARF1, MAP1, MASP, MASP3, MAp44, PRSS5, RaRF	response to wounding
MED12	9968	ARC240, CAGH45, FGS1, HOPA, MED12S, OHDOX, OKS, OPA1, TNRC11, TRAP230	Schwann cell development, Schwann cell differentiation
MEGF10	84466	EMARDD	muscle cell development, skeletal muscle tissue development
MFN2	9927	CMT2A, CMT2A2, CPRP1, HSG, MARF	organelle localization, chordate embryonic development
MMP2	4313	CLG4, CLG4A, MMP-2, MMP-II, MONA, TBE-1	face development, body morphogenesis
MNX1	3110	HB9, HLXB9, HOXHB9, SCRA1	spinal cord development, neuron migration
MTM1	4534	CNM, MTMX, XLMTM	muscle cell cellular homeostasis, I band
MUSK	4593	CMS9, FADS	neuron apoptotic process, regulation of neuron death
MYBPC2	4606	MYBPC, MYBPCF	muscle filament sliding, actin filament-based movement
MYH2	4620	IBM3, MYH2A, MYHSA2, MYHas8, MYPOP, MyHC-2A, MyHC-IIa	muscle filament sliding, actin filament-based movement
MYH3	4621	HEMHC, MYHC-EMB, MYHSE1, SMHCE	muscle filament sliding, skeletal muscle contraction
MYH7B	57644	MHC14, MYH14	skeletal muscle contraction, actin filament-based movement
MYH8	4626	DA7, MyHC-peri, MyHC-pn, gtMHC-F	muscle filament sliding, skeletal muscle contraction
MYO18B	84700		muscle fiber development, I band
MYO9A	4649		actin cytoskeleton
MYOT	9499	LGMD1, LGMD1A, MFM3, TTID, TTOD	sarcolemma, I band
NALCN	259232	CLIFAHDD, CanIon, IHPRF, INNFD, VGCNL1, bA430M15.1	regulation of membrane potential
NEB	4703	NEB177D, NEM2	striated muscle thin filament, muscle filament sliding
NEFH	4744	NFH	hippocampus development, peripheral nervous system development
NEU1	4758	NANH, NEU, SIAL1	lysosomal lumen, glycoprotein biosynthetic process
NF1	4763	NFNS, VRNF, WSS	Schwann cell development, Schwann cell differentiation
NOG	9241	SYM1, SYNS1	prostate gland epithelium morphogenesis, face development
OCRL	4952	INPP5F, LOCR, NPHL2, OCRL-1, OCRL1	muscle system process, chordate embryonic development
OFD1	8481	71-7A, CXorf5, JBTS10, RP23, SGBS2	cell projection morphogenesis, cell part morphogenesis
ORC4	5000	ORC4L, ORC4P	actin cytoskeleton
ORC6	23594	ORC6L	actin cytoskeleton
PAFAH1B1	5048	LIS1, LIS2, MDCR, MDS, PAFAH	cerebral cortex cell migration, neuroblast proliferation
PANK2	80025	C20orf48, HARP, HSS, NBIA1, PKAN	regulation of membrane potential, carbohydrate derivative biosynthetic process
PAX3	5077	CDHS, HUP2, WS1, WS3	spinal cord development, central nervous system neuron differentiation
PEX1	5189	PBD1A, PBD1B, ZWS, ZWS1	protein targeting to peroxisome, intracellular protein transmembrane import
PEX10	5192	NALD, PBD6A, PBD6B, RNF69	integral component of peroxisomal membrane, protein targeting to peroxisome
PEX12	5193	PAF-3, PBD3A	integral component of peroxisomal membrane, protein targeting to peroxisome
PEX13	5194	NALD, PBD11A, PBD11B, ZWS	integral component of peroxisomal membrane, protein targeting to peroxisome
PEX14	5195	NAPP2, PBD13A, Pex14p, dJ734G22.2	protein targeting to peroxisome, intracellular protein transmembrane import
PEX2	5828	PAF1, PBD5A, PBD5B, PMP3, PMP35, PXMP3, RNF72, ZWS3	integral component of peroxisomal membrane, protein targeting to peroxisome
PEX26	55670	PBD7A, PBD7B, PEX26M1T, Pex26pM1T	integral component of peroxisomal membrane, protein targeting to peroxisome
PEX3	8504	PBD10A, TRG18	integral component of peroxisomal membrane, protein targeting to peroxisome
PEX5	5830	PBD2A, PBD2B, PTS1-BP, PTS1R, PXR1	protein targeting to peroxisome, intracellular protein transmembrane import
PEX6	5190	PAF-2, PAF2, PBD4A, PDB4B, PXAAA1	protein targeting to peroxisome, intracellular protein transmembrane import
PEX7	5191	PBD9B, PTS2R, RCDP1, RD	protein targeting to peroxisome, intracellular protein transmembrane import
PFKM	5213	ATP-PFK, GSD7, PFK-1, PFK1, PFKA, PFKX, PPP1R122	muscle cell cellular homeostasis, carbohydrate metabolic process
PIEZO2	63895	C18orf30, C18orf58, DA3, DA5, FAM38B, FAM38B2, HsT748, HsT771, MWKS	regulation of membrane potential
PIGT	51604	CGI-06, MCAHS3, NDAP, PNH2	neuron apoptotic process, neuron death
PIP5K1C	23396	LCCS3, PIP5K-GAMMA, PIP5K1-gamma, PIP5Kgamma	organelle localization, axon guidance
PITX1	5307	BFT, CCF, LBNBG, POTX, PTX1	embryonic limb morphogenesis, limb morphogenesis
PLEKHG5	57449	CMTRIC, DSMA4, GEF720, Syx, Tech	chemotaxis, cellular response to growth factor stimulus
PLOD1	5351	EDS6, LH, LH1, LLH, PLOD	extracellular matrix organization, endoplasmic reticulum part
PLOD2	5352	BRKS2, LH2, TLH	extracellular matrix organization, endoplasmic reticulum part
PLOD3	8985	LH3	collagen fibril organization, lung development
PLP1	5354	GPM6C, HLD1, MMPL, PLP, PLP/DM20, PMD, SPG2	glial cell development, axon ensheathment
PMM2	5373	CDG1, CDG1a, CDGS, PMI, PMI1, PMM 2	glycoprotein biosynthetic process, glycoprotein metabolic process
PMP22	5376	CMT1A, CMT1E, DSS, GAS-3, HMSNIA, HNPP, Sp110	peripheral nervous system development, axon ensheathment
POMGNT1	55624	GNTI.2, GnT I.2, LGMD2O, MEB, MGAT1.2, gnT-I.2	glycoprotein biosynthetic process, glycoprotein metabolic process
POMGNT2	84892	AGO61, C3orf39, GTDC2, MDDGA8	mannosylation, neuron migration
POMT1	10585	LGMD2K, MDDGA1, MDDGB1, MDDGC1, RT	mannosylation, extracellular matrix organization
POMT2	29954	LGMD2N, MDDGA2, MDDGB2, MDDGC2	mannosylation, glycoprotein biosynthetic process
POR	5447	CPR, CYPOR, P450R	bone morphogenesis, chondrocyte differentiation
PRG4	10216	CACP, HAPO, JCAP, MSF, SZP	stem cell proliferation, animal organ development
PRKAR1A	5573	ACRDYS1, ADOHR, CAR, CNC, CNC1, PKR1, PPNAD1, PRKAR1, TSE1	striated muscle cell development, muscle cell development
PRX	57716	CMT4F	axon ensheathment
PSD3	23362	EFA6D, EFA6R, HCA67	synaptic membrane
PTDSS1	9791	LMHD, PSS1, PSSA	carbohydrate derivative biosynthetic process, endoplasmic reticulum part
PTH1R	5745	PFE, PTHR, PTHR1	chondrocyte differentiation, cartilage development
RAB18	22931	RAB18LI1, WARBM3	brain development, head development
RAB3GAP1	22930	P130, RAB3GAP, RAB3GAP130, WARBM1	face development, body morphogenesis
RAPSN	5913	CMS11, CMS4C, FADS, RAPSYN, RNF205	neuromuscular synaptic transmission, neuron apoptotic process
RBM10	8241	DXS8237E, GPATC9, GPATCH9, S1-1, TARPS, ZRANB5	cell-type specific apoptotic process, negative regulation of cell proliferation
RELN	5649	ETL7, LIS2, PRO1598, RL	cerebral cortex cell migration, hippocampus development
RET	5979	CDHF12, CDHR16, HSCR1, MEN2A, MEN2B, MTC1, PTC, RET-ELE1, RET51	digestive tract development, digestive system development
RIPK4	54101	ANKK2, ANKRD3, DIK, NKRD3, PKK, PPS2, RIP4	morphogenesis of an epithelium, tissue morphogenesis
RMRP	6023	CHH, NME1, RMRPR, RRP2	hippocampus development, limbic system development
RNASEH2A	10535	AGS4, JUNB, RNASEHI, RNHIA, RNHL	osteoblast differentiation, ossification
RNASEH2B	79621	AGS2, DLEU8	chordate embryonic development, embryo development
RYR1	6261	CCO, MHS, MHS1, PPP1R137, RYDR, RYR, RYR-1, SKRR	muscle fiber development, sarcolemma
SCN4A	6329	CMS16, HOKPP2, HYKPP, HYPP, NAC1A, Na(V)1.4, Nav1.4, SkM1	muscle contraction, regulation of membrane potential
SEPN1	57190	CFTD, MDRS1, RSMD1, RSS, SELN	muscle fiber development, striated muscle cell development
SETX	23064	ALS4, AOA2, SCAR1, bA479K20.2	regulation of neurogenesis, regulation of nervous system development
SGCG	6445	35DAG, A4, DAGA4, DMDA, DMDA1, LGMD2C, MAM, SCARMD2, SCG3, gamma-SG	sarcolemma, muscle cell development
SHOX	6473	GCFX, PHOG, SHOXY, SS	skeletal system development
SKI	6497	SGS, SKV	Schwann cell development, Schwann cell differentiation
SLC12A6	9990	ACCPN, KCC3, KCC3A, KCC3B	blood vessel development, synaptic transmission
SLC26A2	1836	D5S1708, DTD, DTDST, EDM4, MST153, MSTP157	regulation of membrane potential, ossification
SLC39A13	91252	LZT-Hs9	connective tissue development, tissue development
SLC3A1	6519	ATR1, CSNU1, D2H, NBAT, RBAT	carbohydrate metabolic process
SLC9A6	10479	MRSA, NHE6	regulation of cellular response to growth factor stimulus, developmental growth
SMN1	6606	BCD541, GEMIN1, SMA, SMA1, SMA2, SMA3, SMA4, SMA@, SMN, SMNT, T-BCD541, TDRD16A	I band, contractile fiber
SOD1	6647	ALS, ALS1, HEL-S-44, IPOA, SOD, hSod1, homodimer	muscle cell cellular homeostasis, Schwann cell development
SOX10	6663	DOM, PCWH, WS2E, WS4, WS4C	neuroblast proliferation, peripheral nervous system development
SOX9	6662	CMD1, CMPD1, SRA1, SRXX2, SRXY10	prostate gland epithelium morphogenesis, bone morphogenesis
SPG20	23111	SPARTIN, TAHCCP1	neuromuscular process, connective tissue development
SRD5A3	79644	CDG1P, CDG1Q, KRIZI, SRD5A2L, SRD5A2L1	glycoprotein biosynthetic process, glycoprotein metabolic process
STAC3	246329	NAM	neuromuscular synaptic transmission, skeletal muscle contraction
SULF1	23213	SULF-1	prostate gland epithelium morphogenesis, proteoglycan metabolic process
SYNE1	23345	8B, ARCA1, C6orf98, CPG2, EDMD4, MYNE1, Nesp1, SCAR8, dJ45H2.2	contractile fiber, synaptic membrane
TARP	445347	CD3G, TCRG, TCRGC1, TCRGC2, TCRGV	cell-type specific apoptotic process
TBX15	6913	TBX14	embryonic skeletal system development, skeletal system morphogenesis
TBX5	6910	HOS	embryonic limb morphogenesis, limb morphogenesis
TGFB3	7043	ARVD, ARVD1, RNHF, TGF-beta3	face development, body morphogenesis
TNNI2	7136	AMCD2B, DA2B, FSSV, fsTnI	striated muscle thin filament, muscle filament sliding
TNNT1	7138	ANM, NEM5, STNT, TNT, TNTS	striated muscle thin filament, muscle filament sliding
TNNT3	7140	TNTF	striated muscle thin filament, muscle filament sliding
TPM2	7169	AMCD1, DA1, DA2B, HEL-S-273, NEM4, TMSB	striated muscle thin filament, muscle filament sliding
TPM3	7170	CAPM1, CFTD, HEL-189, HEL-S-82p, NEM1, OK/SW-cl.5, TM-5, TM3, TM30, TM30nm, TM5, TPMsk3, TRK, hscp30	striated muscle thin filament, muscle filament sliding
TREX1	11277	AGS1, CRV, DRN3, HERNS	endoplasmic reticulum part
TSC1	7248	LAM, TSC	hippocampus development, limbic system development
TSC2	7249	LAM, PPP1R160, TSC4	protein import, morphogenesis of an epithelium
TWIST2	117581	AMS, BBRSAY, DERMO1, FFDD3, SETLSS, bHLHa39	face development, body morphogenesis
TYMP	1890	ECGF, ECGF1, MEDPS1, MNGIE, MTDPS1, PDECGF, TP, hPD-ECGF	blood vessel development, chemotaxis
UBA1	7317	A1S9, A1S9T, A1ST, AMCX1, CFAP124, GXP1, POC20, SMAX2, UBA1A, UBE1, UBE1X	endoplasmic reticulum part
UBE3A	7337	ANCR, AS, E6-AP, EPVE6AP, HPVE6A	developmental growth, brain development
UPK3A	7380	UP3A, UPIII, UPIIIA, UPK3	endoplasmic reticulum part, cellular component morphogenesis
UTRN	7402	DMDL, DRP, DRP1	sarcolemma, synaptic membrane
VPS33B	26276		bone development, organelle localization
WNT5A	7474	hWNT5A	prostate gland epithelium morphogenesis, face development
WNT7A	7476		chemical synaptic transmission, postsynaptic, chondrocyte differentiation
ZBTB42	100128927	LCCS6, ZNF925	muscle organ development, muscle structure development
ZC4H2	55906	HCA127, KIAA1166, WRWF, WWS	spinal cord development, central nervous system neuron differentiation
ZIC3	7547	HTX, HTX1, VACTERLX, ZNF203	digestive tract development, digestive system development
ZMPSTE24	10269	FACE-1, FACE1, HGPS, PRO1, STE24, Ste24p	endoplasmic reticulum part
ZNF335	63925	MCPH10, NIF-1, NIF1, NIF2	neuroblast proliferation, regulation of stem cell proliferation

This table lists all the genes associated with arthrogryposis used in the ClueGO enrichment analysis. Entrez Gene ID: Entrez Gene unique ID; Aliases: additional gene names; Functions: GO terms that are associated with the specific gene.

Popular gene set libraries used for EA include manually curated gene sets representing canonical signaling pathways, such as Reactome [Croft et al., 2014], and structured gene sets based on the Gene Ontology (GO) resource [Gene Ontology Consortium, 2015]. The GO is a resource, in the form of a structured ontology, which describes and categorizes gene product functions in distinct categories and the relationships between them. The GO functional categories are classified in 3 general categories: biological process, molecular function, and cellular component. The biological process category contains individual GO terms that describe processes associated with molecular events and pathways representing multiprotein-dependent functions. The molecular function category, in contrast, describes basic gene functions at the molecular level. Lastly, the cellular component category describes the location, environment, or part of the cell, so that the gene product can be located.

The EA for this review was performed using the software tool ClueGO [Bindea et al., 2009]. ClueGO calculates enrichment scores for selected gene sets against a user-provided gene list. Our analysis was performed using the biological process and cellular component categories of the gene ontology. The biological process category was selected because it captures functional descriptions that provide a better biological interpretation based on multicomponent signaling and functional groupings. The cellular component category was selected as it provides details on not only intracellular locations, but also higher ordered structures such as the ‘synaptic membrane’. The other main benefit of performing EA with ClueGO is that it groups similar GO terms and provides a network-based view of the enriched GO terms. This is important in that it aides interpretation of results by grouping related GO terms, based on shared gene members, presenting the results as a network. Since GO has a hierarchical ontological-based structure, GO terms often have overlapping gene members. When results of enrichment are presented in tabular form, this could inhibit the interpretation and summary of the results. The network visualization groups similar GO terms as nodes in the network with edges representing a measure of shared gene membership (kappa score).

The ClueGo analysis identified 145 enriched GO terms with a corrected p < 0.001 (online suppl. table 1; see www.karger.com/doi/10.1159/000446617 for all online suppl. material). The automatic grouping of terms, performed by ClueGO, assigned them to 22 groups based on overlapping gene membership measured by the kappa score statistic (online suppl. table 2). The number of GO terms in the groups varied from a maximum of 57 to 8 groups with just 1 term each and 9 groups with shared GO terms. The network representation is displayed in figure 1. The network is composed of nodes representing enriched GO terms connected by kappa scores that are a measure of gene overlap between terms. The node color represents the membership in one of the ClueGO determined clusters. While ClueGo attempts to determine the most representative GO term to name the grouped terms, we have provided our own annotation grouping for greater clarity in interpretation and meaning (online suppl. table 3). This grouping is indicated by the shading overlaid on the network with an annotated group labeled with a summary title of the underlying GO terms in the group.

Fig. 1.

GO enrichment network. The nodes in the network represent a specific GO term. The edges connecting the nodes are based on the kappa statistic that measures the overlap of shared genes between terms. The node colors correspond to the ClueGO-determined GO term clusters. The shadings represent author-annotated groupings with a summary title.

The purpose of this paper is to highlight the genes in which mutations have been identified to be associated with arthrogryposis in order to emphasize the importance of defining the other genes in their developmental pathways. This is in order to (1) develop a logical diagnostic approach and (2) to begin to think about specific therapies for specific disorders. For instance, in the disorders of neuromuscular endplate related to fetal endplate receptor, they seem to respond to increased neurotransmitters (a readily available drug used to myasthenia gravis), which then seem to allow the normal adult endplate to be able to function [Michalk et al., 2008].

Perhaps the most puzzling aspect of arthrogryposis is why extra connective tissue/fibrosis is deposited around the immobile joint(s) in the fetus. Is the process related to immobilizing that occurs with a sprain or fracture, where pain leads to an individual immobilizing the surrounding joints which then develop contractures? This process would be magnified as the fetus grows. Or is there another unique developmental process of fibrosis in young individuals? Is the process similar to tendon and ligament formation? Are connective tissue stem cells overstimulated or more susceptible in the fetus? Is this excess of connective tissue an unusual scar of some type? Is one of the connective tissue growth factors a potential therapy for arthrogryposis contractures of the future?

In this molecular era, syndromes of congenital anomalies give insight into normal developmental processes and their secondary and tertiary effects. In the case of arthrogryposis, so many of the features are secondary deformations related to fetal non-movement [Hall, 2009]. Nevertheless, all of the features which are part of the natural history of the specific disorder are important for families to know about in order to plan effectively.

The specific gene mutation in a specific disorder is acting against the rest of the individual's genome, epigenetics, and environmental history. In the course of development, the embryo fetus goes through many physiological developmental stages. The vulnerabilities, timing of insults, involved polymorphisms along a pathway, and gene action also provide insights into the human normal and abnormal developmental processes.

The work up of affected individuals [Hall, 2012, 2014] as well as the known genes are covered elsewhere; the associated syndromes are found in OMIM (http://www.omim.org/) [Hall, 2012, 2014; Hunter et al., 2015; Bayram et al., 2016].

Table 1 outlines gene ontology categories and begins to suggest prime candidates for recognizing critical pathways involved in normal fetal movement. Interestingly, many candidate genes show up in several ontology categories. This may relate to different domains of the genes, to alternative splicing, or to the ‘recycling’ of pathways for different functions.

It is hoped that this exercise is useful to those reflecting on the many mechanisms and structures involved in the development of movement, and fetal movement in particular. The listing of all genes recognized to be involved in arthrogryposis at this time is obviously an incomplete list. Some genes are involved in several disorders which were clinically thought to be distinct (perhaps related to the specific nucleotide replacement or perhaps related to various modifiers). Once a group of families with a specific mutation has their whole genome analyzed, the variation in clinical phenotype can be elucidated and important modifiers identified.

Many specific single gene disorders have intra- and interfamilial variability as to how severe the contractures are at birth, what positioning they take, or whether contractures are even present. For instance, several forms of dominant distal arthrogryposis have completely unaffected carrier individuals [Kimber et al., 2012].

It is also hoped that this listing will point to other genes involved in ontological processes that may also result in arthrogryposis and be part of the pathways leading to normal fetal movement - thereby providing better diagnostic precision among the present quagmire of interpretation of the whole genome and even exome sequencing. Ultimately, specific therapies may involve alternative pathways and enhance the affected pathway.

Disclosure Statement

The authors declare no conflicts of interest.

Supplementary Material

Supplementary data

Supplementary data

Supplementary data