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Supplementary Table 1. Control System M1 and M2 Significantly Expressed Genes Involved in Macrophage Differentiation and Polarization

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Supplementary Table 1. Control system M1 and M2 significantly expressed genes involved in macrophage differentiation and polarization. M1 Gene Name Entrez M2 Gene Name Entrez Gene ID Gene ID Interferon, gamma-inducible protein 16 3428 Cystinosis, nephropathic 1497 Hypothetical protein BC012330 116071 Protease, serine, 22 64063 Chemokine (C-C motif) ligand 2 6347 Niemann-Pick disease, type C1 4864 Poly (ADP-ribose) polymerase family, 83666 Phosphatidylinositol binding clathrin assembly 8301 member 9 protein Lipocalin-interacting membrane receptor 55716 Solute carrier family 38, member 6 145389 Epithelial stromal interaction 1 (breast) 94240 Homeobox C14 360030 2'-5'-oligoadenylate synthetase 3, 4940 Selenoprotein T 51714 100kDa Somatostatin receptor 2 6752 Angiopoietin-like 4 51129 Chemokine (C-X-C motif) ligand 16 58191 GRP1 (general receptor for phosphoinositides 160622 1)-associated scaffold protein GTPase, IMAP family member 8 155038 Nuclear receptor subfamily 4, group A, 8013 member 3 DR1-associated protein 1 (negative 10589 Chromosome 21 open reading frame 82 114036 cofactor 2 alpha) Interferon-induced protein 44 10964 Oviductal glycoprotein 1, 120kDa (mucin 9, 5016 oviductin) PTK2B protein tyrosine kinase 2 beta 2185 Chromosome 9 open reading frame 150 286343 Hypothetical protein BC012317 93082 30 kDa protein 55831 N-acetylglucosamine kinase 55577 Growth arrest-specific 2 like 3 283431 TPR domain containing STI2 199223 Serine protease inhibitor, Kunitz type 1 6692 Phosphodiesterase 4D interacting 9659 FK506 binding protein 1A, 12kDa 2280 protein (myomegalin) Baculoviral IAP repeat-containing 2 329 SH3 and cysteine rich domain 2 342667 2'-5'-oligoadenylate synthetase 2, 4939 ATPase, Na+/K+ transporting, beta 3 483 69/71kDa polypeptide V-yes-1 Yamaguchi sarcoma viral 4067 Annexin A1 301 related oncogene homolog Ras homolog gene family, member G 391 Chromosome 12 open reading frame 5 57103 (rho G) Caspase recruitment domain family, 84674 VGF nerve growth factor inducible 7425 member 6 Solute carrier organic anion transporter 28232 Solute carrier family 6 (neurotransmitter 6539 family, member 3A1 transporter, betaine/GABA), member 12 Interleukin 1 receptor, type II 7850 Tissue inhibitor of metalloproteinase 4 7079 Solute carrier family 25, member 27 9481 CD1C antigen, c polypeptide 911 V-src sarcoma (Schmidt-Ruppin A-2) 6714 KIAA1919 91749 viral oncogene homolog (avian) 5,10-methenyltetrahydrofolate 10588 Synuclein, beta 6620 synthetase (5-formyltetrahydrofolate cyclo-ligase) Ligand of numb-protein X 84708 Chromosome 20 open reading frame 139 140809 Discoidin domain receptor family, 4921 Transmembrane 7 superfamily member 1 7107 member 2 (upregulated in kidney) 2'-5'-oligoadenylate synthetase-like 8638 Translation factor sui1 homolog 10289 Hypothetical protein FLJ40722 285966 RCE1 homolog, prenyl protein protease (S. 9986 cerevisiae) Amyotrophic lateral sclerosis 4 23064 Solute carrier family 24 57419 (sodium/potassium/calcium exchanger), member 3 Normal mucosa of esophagus specific 1 84419 Sortilin-related VPS10 domain containing 114815 receptor 1 Ring finger protein (C3HC4 type) 159 84333 Dehydrogenase/reductase (SDR family) 51635 member 7 HEG homolog 57493 Interleukin 6 signal transducer (gp130, 3572 oncostatin M receptor) IBR domain containing 3 127544 Tumor necrosis factor receptor superfamily, 4982 member 11b (osteoprotegerin) Sialyltransferase 4B (beta-galactoside 6483 Stress-induced-phosphoprotein 1 10963 alpha-2,3-sialyltransferase) (Hsp70/Hsp90-organizing protein) CASP8 and FADD-like apoptosis 8837 NADPH oxidase organizer 1 124056 regulator Thyroid hormone receptor associated 9969 Epidermal growth factor receptor pathway 2059 protein 1 substrate 8 Chemokine (C-C motif) receptor 7 1236 Hypothetical protein FLJ20753 55036 Glutamine-fructose-6-phosphate 9945 Tubulin, alpha 8 51807 transaminase 2 Histone 1, H2aj 8331 Myosin VI 4646 Chemokine (C-C motif) ligand 1 6346 Aryl hydrocarbon receptor nuclear 406 translocator-like Solute carrier family 43, member 2 124935 Hemicentin 83872 Cancer/testis antigen 1B 1485 RAS p21 protein activator (GTPase activating 5921 protein) 1 Histone 1, H2bg 8339 Visual system homeobox 1 homolog, CHX10- 30813 like (zebrafish) Histone 3, H2a 92815 Hypothetical protein MGC19780 199857 Histone 1, H2bl 8340 Glutaminase 2744 Histone 1, H2be 8344 Solute carrier family 16 (monocarboxylic acid 9120 transporters), member 6 Histone 1, H2bn 8341 Prion protein (p27-30) 5621 TNFAIP3 interacting protein 1 10318 Phosphatidylinositol glycan, class W 284098 TNFAIP3 interacting protein 3 79931 Serine protease inhibitor, Kazal type 6 404203 Serine (or cysteine) proteinase inhibitor, 8710 Chromodomain helicase DNA binding protein 55636 clade B (ovalbumin), member 7 7 Interferon-induced protein with 3434 Syntaxin binding protein 1 6812 tetratricopeptide repeats 1 Tumor protein p53 inducible nuclear 58476 Diacylglycerol O-acyltransferase homolog 2 84649 protein 2 (mouse) Superoxide dismutase 2, mitochondrial 6648 Protein kinase C, alpha 5578 Ankyrin repeat and BTB (POZ) domain 80325 Retinol dehydrogenase 10 (all-trans) 157506 containing 1 Secretogranin III 29106 Hypothetical protein LOC151146 79134 Interferon regulatory factor 7 3665 Hypothetical protein LOC55924 55924 Persephin 5623 Biliverdin reductase B (flavin reductase 645 (NADPH)) Poly (ADP-ribose) polymerase family, 84875 KIAA0802 23255 member 10 F-box protein 32 114907 Protein phosphatase 1 (formerly 2C)-like 151742 SP140 nuclear body protein 11262 HIV-1 induced protein HIN-1 54726 Chromosome 1 open reading frame 38 9473 Methionyl-tRNA formyltransferase, 123263 mitochondrial Myosin regulatory light chain MRLC2 103910 Ubiquitin-like 3 5412 Serine dehydratase 10993 DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 9188 KIAA1404 protein 57169 Phytoceramidase, alkaline 55331 Sidekick homolog 2 (chicken) 54549 ATP-binding cassette, sub-family G (WHITE), 9429 member 2 Rab geranylgeranyltransferase, alpha 5875 Glucose-fructose oxidoreductase domain 54438 subunit containing 1 Tumor necrosis factor receptor 8764 Collagen, type VI, alpha 2 1292 superfamily, member 14 (herpes virus entry mediator) Regulatory factor X, 3 (influences HLA 5991 Chromosome 9 open reading frame 55 55667 class II expression) HORMA domain containing protein 84072 Acid phosphatase-like 2 92370 Hypothetical protein FLJ11286 55337 Collagen, type VI, alpha 1 1291 Hyperparathyroidism 2 (with jaw tumor) 79577 Germ cell associated 1 83445 KIAA1970 protein 124454 Adaptor-related protein complex 2, alpha 2 161 subunit GRIP1 associated protein 1 56850 Sialytransferase 7 30815 Vascular endothelial growth factor C 7424 Solute carrier family 27 (fatty acid 10999 transporter), member 4 RasGEF domain family, member 1B 153020 Protease, serine, 23 11098 Hypothetical protein FLJ32009 220001 Hypothetical protein PP1665 81544 Hypothetical protein LOC348094 348094 Adenosine monophosphate deaminase 2 271 (isoform L) Zinc finger, MYND domain containing 15 84225 Nestin 10763 Hypothetical protein FLJ39575 286006 Protein kinase C and casein kinase substrate 29763 in neurons 3 Tumor necrosis factor receptor 8792 Collomin 342035 superfamily, member 11a, activator of NFKB ADP-ribosylation factor-like 8 221079 Chromodomain helicase DNA binding protein 80205 9 Acyl-Coenzyme A binding domain 91452 Hypothetical protein FLJ32954 151393 containing 5 Pellino homolog 1 (Drosophila) 57162 Adrenergic, alpha-1B-, receptor 147 Brain abundant, membrane attached 10409 Carbonyl reductase 3 874 signal protein 1 IQ motif containing GTPase activating 10788 Transmembrane 4 superfamily member 2 7102 protein 2 Hypothetical protein MGC4655 84752 ATP-binding cassette, sub-family B 5244 (MDR/TAP), member 4 KIAA1463 protein 57609 Solute carrier family 20 (phosphate 6575 transporter), member 2 Thyroid hormone receptor interactor 12 9320 KIAA0690 23223 Tight junction protein 1 (zona occludens 7082 Four and a half LIM domains 3 2275 1) Signal transducer and activator of 6774 Zinc finger CCCH type domain containing 8 84524 transcription 3 (acute-phase response factor) Chemokine (C-X-C motif) ligand 14 9547 Parathyroid hormone-like hormone 5744 Mannosidase, beta A, lysosomal 4126 Pleckstrin homology domain containing, 79156 family F (with FYVE domain) member 1 Hypothetical protein DKFZp761A052 55593 Mitochondrial ribosomal protein S6 64968 RAB43, member RAS oncogene family 339122 Diencephalon/mesencephalon homeobox 1 127343 Chromosome 9 open reading frame 95 54981 Six transmembrane epithelial antigen of the 26872 prostate ERO1-like beta (S. cerevisiae) 56605 Antigen p97 (melanoma associated) 4241 Myosin regulatory light chain MRCL3 10627 Plexin domain containing 2 84898 Butyrophilin, subfamily 2, member A3 54718 Integrin, alpha M (CD11b) 3684 Sialyltransferase 8D (alpha-2, 8- 7903 Tryptophan 2,3-dioxygenase 6999 polysialyltransferase) Cathepsin S 1520 Adenosine A3 receptor 140 FOS-like antigen 2 2355 Mitochondrial tumor suppressor 1 57509 General transcription factor IIF, 2962 Tumor necrosis factor receptor superfamily, 27242 polypeptide 1, 74kDa member 21 GCIP-interacting protein p29 25949 Chromosome 20 open reading frame 32 57091 Hypothetical protein LOC283680 283680 Hypothetical protein MGC34732 220047 Hypothetical protein MGC35194 93190 Hypothetical protein MGC40397 121053 Chemokine (C-C motif) ligand 5 6352 Peroxisome proliferative activated receptor, 5468 gamma Glucosamine (N-acetyl)-6-sulfatase 2799 FCH domain only 1 23149 (Sanfilippo disease IIID) Hypothetical protein LOC285216 285216 Abhydrolase domain containing 6 57406 Chromosome 10 open
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  • Novel Targets of Apparently Idiopathic Male Infertility

    Novel Targets of Apparently Idiopathic Male Infertility

    International Journal of Molecular Sciences Review Molecular Biology of Spermatogenesis: Novel Targets of Apparently Idiopathic Male Infertility Rossella Cannarella * , Rosita A. Condorelli , Laura M. Mongioì, Sandro La Vignera * and Aldo E. Calogero Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; [email protected] (R.A.C.); [email protected] (L.M.M.); [email protected] (A.E.C.) * Correspondence: [email protected] (R.C.); [email protected] (S.L.V.) Received: 8 February 2020; Accepted: 2 March 2020; Published: 3 March 2020 Abstract: Male infertility affects half of infertile couples and, currently, a relevant percentage of cases of male infertility is considered as idiopathic. Although the male contribution to human fertilization has traditionally been restricted to sperm DNA, current evidence suggest that a relevant number of sperm transcripts and proteins are involved in acrosome reactions, sperm-oocyte fusion and, once released into the oocyte, embryo growth and development. The aim of this review is to provide updated and comprehensive insight into the molecular biology of spermatogenesis, including evidence on spermatogenetic failure and underlining the role of the sperm-carried molecular factors involved in oocyte fertilization and embryo growth. This represents the first step in the identification of new possible diagnostic and, possibly, therapeutic markers in the field of apparently idiopathic male infertility. Keywords: spermatogenetic failure; embryo growth; male infertility; spermatogenesis; recurrent pregnancy loss; sperm proteome; DNA fragmentation; sperm transcriptome 1. Introduction Infertility is a widespread condition in industrialized countries, affecting up to 15% of couples of childbearing age [1]. It is defined as the inability to achieve conception after 1–2 years of unprotected sexual intercourse [2].