Sex differences and mosaic loss of Y chromosome

Sex differences are prevalent in development and physiology in humans, and pathogeneses of various diseases, such as cancers, neurodevelopmental, neurodegenerative and cardiovascular diseases [1,2,3,4,5,6,7,8]. Such sex differences in diseases include incidence, onset age, progression, phenotypes and treatment responses. Although sex hormones, i.e. androgens and estrogens, and their receptors, i.e. androgen and estrogen receptors, could play important roles in such biological processes [1, 3], genes on the male-specific Y chromosome could also contribute at the genetic levels to such differences between the sexes [9,10,11]. Recent studies on large populations with well-defined health information suggest that mosaic loss of the Y chromosome (mLOY) in the peripheral white blood cells predisposes men to various diseases, including cancers, cardiovascular and Alzheimer’s diseases [12,13,14,15,16,17], suggesting that the Y chromosome could be essential in maintaining the homeostasis important for the health of men [11]. Despite such associations, it is uncertain how mLOY in small portion of the leukocytes could contribute to the genetic predisposition to diseases in men. One hypothesis suggests that such mLOY in peripheral white blood cells is an indicator of genome instability in general, affecting genes in lymphocytes and other tissues and/or various physiological processes, such as inflammation, immunosurveillance and oxidative stresses [12, 13, 18], with functional consequences across diverse biological systems. Indeed, various novel and known loci in cell cycle regulation and cancer susceptibility have been associated with mLOY [12, 13, 19], thereby supporting the essential nature of the Y chromosome genes in the well-being of men. Mosaic LOY disrupts such balances and predisposes men to pathogenesis, resulting in sex differences in the various diseases.

Aberrant activation of Y chromosome genes potentiates pathogeneses of human diseases

Studies on individual Y chromosome genes have provided information suggesting that they could exert positive actions on the pathogeneses of various human diseases, including cancers and neurodevelopmental diseases, thereby preferentially affecting males [6, 20]. For example, expression of the sex-determining region Y (SRY) gene is elevated in dopamine neurons in human and experimental Parkinson’s disease models and suppression of its expression could exert protective functions against the disease in these models [21]. Studies on the spontaneously hypertensive rat (SHR) indicated that the rat Sry up regulates genes in the renin-angiotensin system, resulting in higher blood pressure in the male SHRs [22]. The human SRY could upregulate the monoamine oxidase A (MAOA) gene, whose expression levels are associated with various neurological and psychological disorders [23]. Further, aberrant expression of SRY could compete against the proper functions of a family of related transcription factors, encoded by the SRY-box (SOX) genes, which play critical roles in numerous developmental, physiological and pathogenic processes [24,25,26]. Indeed, SRY could impair the SOX10 regulation of the RET gene, important for enteric nervous system (ENS) differentiation [6]. Such impairment results in haploinsufficiency of the RET protein and exacerbation of the pathogenesis of the Hirschsprung’s disease, a congenital disorder affecting the ENS differentiation with significantly high male preference [6]. Importantly, aberrant activation of a human SRY transgene during embryogenesis in transgenic mice impairs the normal development of various vital organs, resulting in postnatal growth retardation and lethality [27]. Hence, these studies suggest that aberrant activation of Y chromosome genes, in this case SRY, could disrupt normal development and exacerbate the disease processes, thereby contributing to sex differences in a positive manner(s). These findings are in contrast to those of mLOY studies, in which loss of genes on the Y chromosome potentiates the disease processes [13, 15, 18, 19]. To understand the roles of the Y chromosome in human health and diseases, it is crucial to discuss a few basic aspects of the genetics and biological functions of the genes on this male-specific chromosome.

Genes on the human Y chromosome

In humans, men and women are genetically identical with 22 pairs of autosomes, except their sex chromosomes, i.e. X and Y chromosome. Men possess XY while women possess XX sex chromosome constitution. The gene dosage differences for the X chromosome is compensated by inactivation of the genes, with specific exceptions, on one of the X chromosomes during early development in females [28,29,30]. The mammalian X and Y chromosome originated from a pair of autosomes. One of them had acquired a male sex-determining gene, i.e. SRY, postulated to occur over 180 million years ago, and became the Y chromosome while the other homologue maintained the genetic content and structure of the ancestral chromosome and evolved to be the X chromosome [31]. Various evolutionary rearrangements and deterioration events resulted in a reduction in genetic content on the Y chromosome, which evolved to be the smallest and/or most gene-poor chromosome in most mammals, including humans [32]. The human Y chromosome is 57.23 MB in size and harbors two specific regions, generally referred to as the pseudoautosomal regions (i.e. PAR1 and PAR2) and male-specific region Y (MSY). PAR1 and PAR2 harbor ~ 2.6 MB and 320 kb of DNA and are located at the telomeric ends of the short and long arm of the Y chromosome respectively. The MSY is about 54 MB in size, consisting of approximately 24 MB of euchromatin and 30 MB of heterochromatin composed of mostly repetitive sequences (Genome Reference Consortium Human Build 38.p13). Cytogenetically, the heterochromatic long arm is highly variable, mostly involving either amplification or deletion of the heterochromatin and possibly the PAR2 at the telomere of the long arm [33, 34]. At present, there are 40 protein-coding genes/gene families on the human Y chromosome (Table 1) [35]. Fifteen genes are on the PAR1 and 3 genes are on the PAR2, which are also present in the PARs of the X chromosome. There is an obligatory crossover(s) between the X and Y chromosomes at their PARs during male meiosis [36], and hence genes on PARs behave similarly as those of the autosomes. The PAR genes escape X-inactivation and are mostly expressed in similar levels in both female and male tissues/cells [28] (Additional file 1: Figure S1A). Interestingly, there are 5 receptor genes, i.e. CRLF2, CSF2RA, IL3RA, P2RY8 and IL9R, among the PAR genes, involved in various cytokine and immune functions. Initial sequencing results suggested that there are 78 protein-coding genes on the MSY, corresponding to 27 distinct proteins [10]. This number varies due to microdeletions and copy number variations (CNV) of ampliconic genes among the general population [37]. There are 22 MSY genes, of which 17 are evolutionarily conserved with corresponding X homologues, widely expressed (Additional file 1: Figure S1B-C) and postulated to serve dosage-sensitive regulatory functions in chromatin modification, transcription, translation, RNA splicing and protein stability [9, 10], which likely exert global effects on gene expression and modification of protein functions. Gene ontology analysis of all 40 Y chromosome genes suggested that they could be associated with male fertility/infertility, autism, coronary and psychological/neurological diseases (Additional file 1: Table S1).

Table 1 Protein-coding genes and functions on the human Y chromosome
Full size table

Noticeably, several MSY genes, such as SRY, TSPY and RBMY, are exceptions to such dosage-sensitive functions. They are primarily expressed in the testis and serve vital functions in the differentiation and physiology of this male-specific organ [38,39,40]. Their counterparts on the X chromosome are expressed ubiquitously in numerous tissue/cell types and mostly at similar levels between the sexes (Additional file 1: Figure S1D) and are subjected to X-inactivation [28]. Further, the respective encoded proteins could possess structural divergence(s), suggesting that they might serve different functions in various biological systems [24, 25, 41]. Accordingly, expression of these testis-specific MSY genes in somatic tissues could exert male-specific effects on the respectively affected organs/cells. We surmise that low-level/spatiotemporal expression of these MSY gene(s) during development/physiology could produce normal differences between the sexes [5, 42, 43], and aberrant/high level expression could result in male biases in the pathogeneses of various human diseases [6, 27, 41]. In particular, TSPY and its X homologue TSPX (TSPYL2) evolved from the same ancestral gene but diverged structurally in their encoded proteins to process contrasting functions in cell cycle regulation and androgen receptor (AR) transactivation [44, 45]. They represent a pair of homologues on the sex chromosomes, which could oppose each other in various biological processes [41]. TSPY is specifically expressed in the testis (Additional file 1: Figure S1E) and could serve important functions in spermatogonia stem cell renewal and male meiosis [46]. It is located on and is the putative gene for the gonadoblastoma locus on the Y chromosome (GBY) [47, 48]. It is frequently and aberrantly activated in various cancers, including gonadoblastoma, testicular germ cell tumors, melanoma, liver, head and neck and prostate cancers and promotes cell proliferation [48, 49]. TSPY interacts with AR and stimulates the AR transactivation of its target genes [45]. Importantly, TSPY is an androgen-responsive gene, and hence TSPY and AR form a positive feedback loop in amplifying their respective biological functions in male-specific manners [41]. TSPX is widely expressed equally in both male and female tissues (Additional file 1: Figure S1D) and is subjected to X-inactivation [50]. It retards cell proliferation and suppresses AR transactivation activities [45]. Accordingly, TSPY is a Y-located proto-oncogene and TSPX is an X-located tumor suppressor at the two extremes of the human oncogenic spectrum respectively [41]. This peculiar situation raises some very interesting scenarios on the roles of the X–Y homologues in cancers. As a proto-oncogene, abnormal activation of TSPY in somatic tissues could promote oncogenesis while an inactivation/deletion of TSPX could impair its tumor suppression function(s) [51, 52] specifically for males with only one X chromosome. If under certain conditions, TSPX escapes X-inactivation, it could increase the tumor suppression functions in females [29, 50]. Collectively, such aberrations could disproportionally exacerbate cancer initiation and progression in males.

Mosaic loss of the Y chromosome in 5–15% of the leukocytes of men represents one of the most common genetic abnormalities in humans [13,14,15,16, 18]. Since the Y chromosome includes the pseudoautosomal and male-specific regions, the loss of the PAR genes and those on MSY with dosage-sensitive functions could result in gene dosage deficiency in various biological systems. On the other hand, the testis-specific MSY genes are important for male-specific functions, and their loss might be less critical in such mLOY-mediated disease predispositions, except those associated with reproductive tissues. However, the abnormal expression of these-testis specific MSY genes in non-gonadal cells could modify the normal differentiation and physiology as well as the pathogenesis of the affected cells/tissues in male biased manners. Accordingly, there are two general categories of Y chromosome genes, those on the PARs and MSY with dosage-sensitivity and MSY genes with male/testis-specific expression and functions. Understanding the biology and genetics of individual genes on the Y chromosome could provide some clues on which genes are likely to be important for the maintenance of homeostasis and their losses or aberrant activations could contribute to disease predisposition in men.

Of mice and men

The laboratory mouse has been widely used as experimental models for human diseases using transgenic means [53, 54], including male and female animals with different sex chromosome constitutions [55, 56]. Beside sex determination, the genetic contents of the human and mouse Y chromosome are quite distinct [10, 57]. The mouse Y chromosome is ~ 92 Mb in size, likely one of the largest and most gene-rich Y chromosomes in mammals. Its PAR is ~ only 700 kb, located at the telomere of the long arm, and harbors only 3 genes, i.e. Asmt, Sts (pseudogene) and Mid1. The mouse MSY is > 90 Mb in size and is entirely euchromatic. It harbors ~ 700 genes, but only 8 ancestral genes, i.e. Sry, Zfy1/Zfy2, Usp9y, Ddx3y, Uty, Kdm5d, Tspy (pseudogene), and Rbmy, are conserved on the human Y chromosome (Table 1). Other orthologues of the human Y chromosome genes are located on either the X chromosome or autosomes of the mouse. The remainder ~ 690 genes of the mouse MSY are acquired repetitive genes, some of which are embedded in a 500-kb repeat unit, likely to be important for mouse fertility, but are not conserved in any mammalian Y chromosome [57]. Significantly, only two MSY genes, i.e. Sry (the sex-determining gene) and Eif2s3y (absent on the human Y chromosome), are sufficient to generate male mice with spermatogenesis [58]. Further, these two MSY genes could be replaced by the activation of Sox9 (the Sry downstream gene [26]) and Eif2s3x (the X-homologue of Eif2s3y) to produce similarly functional male mice without a Y chromosome [59]. Although transgenic mouse studies have provided critical information on the functional aspects on some of those conserved MSY genes [54, 58,59,60,61], studies on the other MSY genes of the human Y chromosome with the laboratory mouse might require some retrofitting of the mouse Y chromosome. In particular, the mouse Tspy is a recently evolved pseudogene, harboring numerous in-frame mutations disrupting its open reading frame. Transgenic studies had generated a specific line, TgTSPY9, which harbors ~ 50 copies of the an 8.2-kb human TSPY structural gene tandemly integrated on the Y chromosome of the mouse [62]. Since TSPY is tandemly repeated 30–60 times on the human Y chromosome [40], such tandem integration of the human transgene on the mouse Y chromosome resembles the organization of the human endogenous gene. Characterization of animals from this transgenic line showed that the human TSPY transgene is expressed in similar patterns as those of the human endogenous gene, including normal expression in spermatogonia and spermatocytes in the testis [62] and aberrant activation during oncogenesis [63]. Hence, TgTSPY9 is a humanized mouse model for TSPY gene. Accordingly, with the recent advances of genome editing and transgenic technologies [64,65,66,67], targeting the integration of human MSY gene(s) onto the mouse Y chromosome could be viable strategies to model and study their functions in biological processes, involved in various aspects of development, physiology and disease pathogeneses.