David C. Page

Abstract

We talk to David C. Page, corresponding author of “The human Y and inactive X chromosomes similarly modulate autosomal gene expression” in this issue of Cell Genomics, about his paper, the most exciting findings in the paper, and his advice for other scientists.

We talk to David C. Page, corresponding author of “The human Y and inactive X chromosomes similarly modulate autosomal gene expression” in this issue of Cell Genomics, about his paper, the most exciting findings in the paper, and his advice for other scientists.

Main text

Can you tell us about your current lab and topic?

David C. Page

Whitehead Institute; photo by Gretchen Ertl/Whitehead Institute.

Our lab’s mission is to build an empirical and conceptual foundation for understanding male-female differences in health and disease across the human body. We assume that all biologically based sex differences—those not due to social or environmental cues—ultimately derive from the sex chromosomes, either directly or through chains of molecular events that begin with or are modified by genes on the X and Y chromosomes.

This motivates our lab’s ongoing efforts to understand the biology of the human X and Y chromosomes as deeply and thoroughly as we possibly can. Over the decades, our lab and collaborators near and far have worked tirelessly to rescue the Y chromosome from the dustbin of human genetics, and I believe we’ve succeeded in bringing it to a more prominent place in biology and medicine. In recent years, I’ve become convinced that the human X chromosome—historically the most intensely studied chromosome in all of genetics—is as misunderstood as the Y chromosome was when we began our studies.

The X chromosome exists in two epigenetic states, which have historically and unfortunately been referred to as “active” and “inactive,” or Xa and Xi. It has been known for decades that some genes are expressed on Xi—many more in humans than in mice—but the biological significance of Xi’s genetic activity in 46,XX cells, tissues, organs, and bodies has barely been explored. It is time for Xi to step out conceptually and scientifically from the long shadows cast by (1) the intensely studied Xa and (2) the equally intensely studied process of X chromosome inactivation, which of course gives rise to Xi. Our current paper represents an early, halting step toward revealing the wonders of Xi together with those of its counterpart in 46,XY cells—the Y chromosome.

Can you briefly explain what your Cell Genomics paper is about?

All euploid human somatic cells share 45 chromosomes: 22 pairs of autosomes plus one Xa. In females, the 46^th chromosome is an Xi, while in males, it is a Y chromosome. Our paper asks the question: does the presence of this 46^th chromosome—Xi or Y—change the expression of autosomal genes in cultured somatic cells from outside the reproductive tract? We addressed this question by studying cells cultured from individuals with naturally occurring variation in the number of sex chromosomes—specifically, cells with 0–3 Xi and 0–4 Y chromosomes. (Diploid human cells always have one Xa, and any additional X chromosomes are “inactivated.”) These naturally occurring copy-number series for Xi and Y set us up to employ linear modeling of Xi and Y’s effects on autosomal gene expression as assayed by RNA sequencing. I can’t overstate how important the copy-number series and linear models were in detecting and quantifying the impact of Xi and Y across the genome.

What was the most exciting finding in your paper?

The most exciting finding is that the Xi and Y chromosomes modulate the expression levels of thousands of autosomal genes in the two cultured cell types that we studied. The “inactive” X chromosome and the “gene-poor” Y chromosome have a big impact across the genome! The even more surprising finding—and not at all what we were looking for—is that the Xi and Y chromosomes have remarkably similar effects on autosomal gene expression. Biologists traditionally think of the X and Y chromosomes as driving differences between the sexes, but here we find them to be pushing autosomal genes in somatic cells in the same direction. This does not negate or contradict the understanding that the sex chromosomes drive all biologically based differences between males and females. Instead, what our findings show is that, in addition to their sex-differentiating roles, the X and Y chromosomes have shared effects that ripple across the genome in remarkably similar ways.

Did you encounter any particular difficulties during the project? How did you overcome them?

Sometimes in science it’s hard to see and hear what the data are trying to tell you, especially when the data are telling you something that you were not anticipating or even hoping for. That was very much the case here. Adrianna San Roman, our lab colleagues, and I were anticipating—perhaps hoping, if we are honest with ourselves—that the response of autosomal genes to Xi would be very different from the response of autosomal genes to Y. This could have provided a simple and straightforward answer to the question of how the identity of the 46^th chromosome—Xi or Y—leads to sex-differential outcomes in health and disease. Consequently, it took a while for us to acknowledge, embrace, and eventually highlight what the data were trying to tell us all along: that the autosomal responses to Xi and Y are more similar than dissimilar. In hindsight, this all makes sense given the shared autosomal ancestry of the X and Y chromosomes and the Xi and Y’s expression of homologous genes like ZFX and ZFY, whose actions in trans clearly drive shared responses on autosomes—and even on Xa. Also in hindsight, we might have anticipated these results given the long-standing observation that 99% of human fetuses with only one sex chromosome—45,X fetuses—abort spontaneously. Our present findings suggest that viability depends not only on gene expression from the 46^th chromosome—Xi or Y—but also on the impact this second sex chromosome has on autosomal gene expression.

What are the key implications of your research? And what are the open questions for future research?

Our findings provide a first, tentative glimpse of what I believe will be a new medical genetics of the sex chromosomes. The key lesson here is that closely related but nonidentical global regulators expressed by Xi and Y are influencing the expression of many, many genes across the genome, opening the door to a new and unfamiliar way of thinking about the roles of the Xi and Y chromosomes in health and disease. This is not the textbook X chromosome of X-linked recessive traits like colorblindness or hemophilia caused by mutations in genes that are expressed only by Xa, are silenced on Xi, and have no homologs on the Y chromosome. Similarly, this is not the textbook Y chromosome that functions only in testes and is otherwise of little direct consequence across the body.

The next step, and a crucial one, is to test whether this model of Xi and Y modulating autosomal gene expression in two types of cultured cells also applies in vivo and whether it generalizes to other human cell types.

Looking further ahead, a major task is to distinguish between the sex-shared and sex-differentiating roles of genes expressed from Xi or Y in human somatic cells. It will be challenging to find the sex-differentiating needles amid the sex-shared haystack. But our paper, together with an earlier one by Adrianna San Roman and colleagues, also published in Cell Genomics (in 2023), points to a small set of genes expressed from Xi and Y that merit special attention.

Why did you decide to submit your paper to Cell Genomics? How was your experience with the editorial team and reviewing process?

Cell Genomics is a new journal, but with great leadership, including the editors, advisory board, and staff, it’s off to a terrific start. Very appealing to my coauthors and me was Cell Genomics’ ensuring gold open access, which means that the final, fully edited versions of all published articles are freely available online for anyone to read. Our experience with the editorial team, staff, and reviewing process compared favorably with what we’ve encountered elsewhere. With a clear commitment to deep and rigorous genomic studies, Cell Genomics was and is an appealing place to publish our lab’s best work.

What advice would you give young scientists?

Stay true to your ideals: rigor and integrity are the foundation of everything in science. Master the intellectual history of your field and particularly of the issues that you think are most fundamental, and then prepare to shake them up. Bring lots of data, and quantitative analysis, to bear on questions that are invisible in plain sight.