10.1021/acs.jproteome.5b00520.s001 Diba Ahmadi Rastegar Diba Ahmadi Rastegar Mehdi Sharifi Tabar Mehdi Sharifi Tabar Mehdi Alikhani Mehdi Alikhani Pouria Parsamatin Pouria Parsamatin Fazel Sahraneshin Samani Fazel Sahraneshin Samani Marjan Sabbaghian Marjan Sabbaghian Mohammad Ali Sadighi Gilani Mohammad Ali Sadighi Gilani Ali Mohammad Ahadi Ali Mohammad Ahadi Anahita Mohseni Meybodi Anahita Mohseni Meybodi Abbas Piryaei Abbas Piryaei Naser Ansari-Pour Naser Ansari-Pour Hamid Gourabi Hamid Gourabi Hossein Baharvand Hossein Baharvand Ghasem Hosseini Salekdeh Ghasem Hosseini Salekdeh Isoform-Level Gene Expression Profiles of Human Y Chromosome Azoospermia Factor Genes and Their X Chromosome Paralogs in the Testicular Tissue of Non-Obstructive Azoospermia Patients American Chemical Society 2015 WB 5D 5C 41 alternative transcripts PRY CDY USP 9Y DDX 3Y XKRY HSFY SCOS IHC PCR Human Y Chromosome Azoospermia Factor Genes NOA sperm retrieval 28 premiotic maturation arrest expression X Chromosome Paralogs AZFc region genes 1A RBMX KDM X chromosome homologue transcripts CYORF 12 MA patients Y chromosome genes TESE EIF BPY isoform level signature testicular sperm extraction RPS 15B 4Y spermatogenesi protein level X chromosome counterparts DAZL 1 transcripts 1AY testis cell types RBMY azoospermic men 15A 2015-09-04 00:00:00 Journal contribution https://acs.figshare.com/articles/journal_contribution/Isoform_Level_Gene_Expression_Profiles_of_Human_Y_Chromosome_Azoospermia_Factor_Genes_and_Their_X_Chromosome_Paralogs_in_the_Testicular_Tissue_of_Non_Obstructive_Azoospermia_Patients/2135281 The human Y chromosome has an inevitable role in male fertility because it contains many genes critical for spermatogenesis and the development of the male gonads. Any genetic variation or epigenetic modification affecting the expression pattern of Y chromosome genes may thus lead to male infertility. In this study, we performed isoform-level gene expression profiling of Y chromosome genes within the azoospermia factor (AZF) regions, their X chromosome counterparts, and few autosomal paralogues in testicular biopsies of 12 men with preserved spermatogenesis and 68 men with nonobstructive azoospermia (NOA) (40 Sertoli-cell-only syndrome (SCOS) and 28 premiotic maturation arrest (MA)). This was undertaken using quantitative real-time PCR (qPCR) at the transcript level and Western blotting (WB) and immunohistochemistry (IHC) at the protein level. We profiled the expression of 41 alternative transcripts encoded by 14 AZFa, AZFb, and AZFc region genes <i>(USP9Y</i>, <i>DDX3Y</i>, <i>XKRY</i>, <i>HSFY1</i>, <i>CYORF15A, CYORF15B, KDM5D, EIF1AY</i>, <i>RPS4Y2</i>, <i>RBMY1A1</i>, <i>PRY, BPY2, DAZ1</i>, and <i>CDY1</i>) as well as their X chromosome homologue transcripts and a few autosomal homologues. Of the 41 transcripts, 18 were significantly down-regulated in men with NOA when compared with those of men with complete spermatogenesis. In contrast, the expression of five transcripts increased significantly in NOA patients. Furthermore, to confirm the qPCR results at the protein level, we performed immunoblotting and IHC experiments (based on 24 commercial and homemade antibodies) that detected 10 AZF-encoded proteins. In addition, their localization in testis cell types and organelles was determined. Interestingly, the two missing proteins, XKRY and CYORF15A, were detected for the first time. Finally, we focused on the expression patterns of the significantly altered genes in 12 MA patients with successful sperm retrieval compared to those of 12 MA patients with failed sperm retrieval to predict the success of sperm retrieval in azoospermic men. We showed that <i>HSFY1-1</i>, <i>HSFY1-3</i>, <i>BPY2-1</i>, <i>KDM5C2</i>, <i>RBMX2, </i>and <i>DAZL1</i> transcripts could be used as potential molecular markers to predict the presence of spermatozoa in MA patients. In this study, we have identified isoform level signature that can be used to discriminate effectively between MA, SCOS, and normal testicular tissues and suggests the possibility of diagnosing the presence of mature sperm cell in azoospermic men to prevent additional testicular sperm extraction (TESE) surgery.