The Human Cell Atlas: An international effort

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In the Spotlight

The Human Cell Atlas: An international effort

by Sherry Ward, AltTox Contributing Editor
Posted: October 31, 2016

An international group of renowned researchers met in London on October 13-14, 2016 to discuss building the Human Cell Atlas. But, you might ask, what is the big deal about a new database to catalogue all of the types of cells in the human body? It is a big deal, and you can read on to find out why!

Human Cell Heterogeneity
human cell diagram

iStockphoto.com; used with permission

Cells are the basic building block of all organisms. Various types of human cells are the building blocks of all human tissues and organs. Beginning in the embryo, cells divide and begin to specialize into the different cell types that make up the human body. Human cells are microscopic, and range in size from an 8 µm red blood cell to the 30 µm skin cell to the “huge” 130 µm human egg cell. The total number of cells in the human body has been estimated to be 37.2 trillion (3.72 x 1013) cells (Bianconi et al., 2013).

The complexity of estimating the total number of cells in the human body (Bianconi et al., 2013), however, is dwarfed by the even greater complexity in identifying all of the different types of cells in the human body. General estimates typically seen are for 200-300 major cell types. Each organ and tissue contains a number of cell types, or sub-populations of cells that look and behave similarly. New methods of characterizing cells, however, show that even within what appears to be a homogenous population, there is great variability. For example, white adipose tissue, which “stores energy reserves as fat,” is no longer considered one type of tissue due to its different metabolic functions in different locations (Esteve-Ràfols, 2013). In addition to adipocyte cells, adipose tissue also contains stem cells, preadipocytes, macrophages, neutrophils, lymphocytes, and endothelial cells. Grouping the cells of the adipose tissue in this manner is still an overgeneralization. Recent studies on single cells show that “the assumption that all cells of a particular ‘type’ are identical” is incorrect. “Individual cells within the same population may differ dramatically, and these differences can have important consequences for the health and function of the entire population.”

Cell and tissue samples used to determine gene expression profiles in microarray experiments are usually composed of multiple cell types. As such, “changes detected by differential expression analysis may reflect differences in the proportions of the cell-types between samples rather than an important mechanistic change in gene-expression.” (Zuckerman et al., 2013). Solutions include: a) experimentally separating the cells before the microarray analysis, which is time consuming and not always effective; b) using computational methods to identify the gene expression profile of individual cell types in the mixture, but these methods typically require the identification of cell types present and their relative amounts, which are usually not known; and c) using the technique of single-cell messenger RNA sequencing (RNA-seq), which “uses next generation sequencing technology to sequence and identify every mRNA species in a sample.” RNA-seq is expensive, relatively new, and was not widely used prior to recent government funding initiatives for single cell analysis.

Grün, et al. (2015) explain that the characterization of all of the cell types of an organ is essential to fully understand the function of a tissue or organ. They found the traditional methods for identifying different cell types using messenger RNA or protein expression of a few marker genes to be ineffective for identifying rare or transient cell types. Using the technique of RNA-seq and a new computational algorithm, they identified rare intestinal cell types.

genomics diagram

Credit: Genome Research Limited

Single-cell transcriptomes (another term for RNA-seq) have also been reported for a number of other cell types, including endocrine cells in human pancreatic islets (Li et al., 2016), lung epithelium (Treutlein et al., 2014), and brain (Zeisel et al., 2015; La Manno et al, 2016). Moreover, with this cutting-edge technology cellular diversity is “approached through inference of variable and dynamic pathway activity rather than a fixed preprogrammed cell-type hierarchy” (Jaitin et al., 2014). Along with improved tools for single-cell RNA-seq, algorithms such as Mpath are emerging that use the gene expression information “to infer the progression of cells from their progenitor state…[to] construct both linear and branching differentiation pathways.”

“The field is in its infancy” according to the announcement for an upcoming 2017 Keystone Symposium on Single Cell Omics.

NIH Single Cell Analysis Program

Recent government funding initiatives have spurred innovation and progress in studying cells at the level of the single cell. In 2014, the US National Institutes of Health (NIH) awarded $7.9 million to 25 projects studying various aspects of single cell analysis as part of the Single Cell Analysis Program (SCAP).

Single Cell Analysis Graphic

SCAP was designed as a 5-year program funded through the NIH Common Fund, which supports programs expected to have exceptionally high impact. Common Fund programs are intended “to address key roadblocks in biomedical research that impede basic scientific discovery and its translation into improved human health…[and] are expected to transform the way a broad spectrum of health research is conducted.”

The Program identified the major challenges in characterizing the extent of human cell heterogeneity, and targeted these areas for funding. Thus, the funded proposals were to “address significant challenges that currently exist with regard to systematically describing the given ‘state’ of a cell, defining normal cell-to-cell variation, measuring the impact of environmental perturbations, understanding cellular responses in the larger context of tissues and networks, and overcoming limitations in measurement approaches.” These research challenges are explained in greater detail in the Funding Opportunity Announcement, “Studies to evaluate cellular heterogeneity using transcriptional profiling of single cells.” Workshops and meetings were supported to develop a multidisciplinary single cell analysis research community.

Mapping the cellular phenotype, like mapping the human genome, is the next frontier in understanding the cellular basis of organism function.

“Initiatives that comprise Common Fund programs are intended to be catalytic in nature by providing limited term investments in strategic areas to stimulate further research through [other funding] mechanisms.” Although, new funding under SCAP has ended, NIH continues to fund single cell analysis research as a part of other programs, and within new projects such as the Kidney Precision Medicine Project to “create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways and targets for novel therapies.” A Request for Information earlier this year, asking for stakeholder input on “a proposal for a new Common Fund program aimed at characterizing and understanding organization of large numbers of primary cells in human tissues using high throughput approaches,” suggests more funding for single cells studies is under consideration.

The Human Cell Atlas

The launch of a new international collaboration to develop “comprehensive reference maps of all human cells” in the form of the Human Cell Atlas, is the latest news in single cell analysis. Technological advances, like described above, along with relevant funding programs such as SCAP, have made advancements in the development of a Human Cell Atlas feasible.

The Human Cell Atlas will be more than just a catalogue of static cell types. It involves addressing the same challenges in characterizing human cell heterogeneity as initiated by SCAP, explained as follows on their website:

At its core, a cell atlas would be a collection of cellular reference maps, characterizing each of the thousands of cell types in the human body and where they are found. It would be an extremely valuable resource to empower the global research community to systematically study the biological changes associated with different diseases, understand where genes associated with disease are active in our bodies, analyze the molecular mechanisms that govern the production and activity of different cell types, and sort out how different cell types combine and work together to form tissues. More specifically, a human cell atlas could:

  • catalog all cell types and sub-types in the human body,
  • map cell types to their location within tissues and within the body,
  • distinguish cell states,
  • capture the key characteristics of cells during transitions, and
  • trace the history of cells through a lineage.

The difference between SCAP and the Human Cell Atlas is primarily in scope and organization. SCAP research could be considered the pilot phase to the development of the Human Cell Atlas initiative, which proposes within 5 years “to generate a detailed first draft of a molecular atlas of cells in the human body” (Regev, 2016).

The October 13-14, 2016 meeting in London, organized by the Broad Institute of MIT and Harvard, the Wellcome Trust Sanger Institute, and the Wellcome Trust, rallied an international group of experts “to decide on the elements of the first phase of the Human Cell Atlas initiative.”

Their approach to developing a plan for the first phase of this initiative involved discussions to answer a number of questions “about the best way to generate a draft Human Cell Atlas.” Questions included:

  • What are the potential benefits of a human cell atlas?
  • What should the scope of a human cell atlas be?
  • Where and how should we source samples for the project?
  • Which technologies should we deploy to generate data, and which technologies must be developed further?
  • Which computational strategies will best enable data analysis?
  • How do we create and structure our scientific consortium?
  • What principles should underlie our activities?
  • How should data be shared and disseminated?

This was a planning meeting where the participants discussed how to address these questions, including how to structure the initiative’s consortium. Their goal was to define a framework for developing the human cell atlas as a collaborative international effort. As we eagerly await hearing about the outcomes of this meeting, we can consider some of the potential implications of its success.

Anticipated Impact

One of the questions addressed by participants at the October meeting was:
What are the potential benefits of a Human Cell Atlas? For example, what types of new science might a Human cell Atlas enable, and what new technologies might it launch?

Leaders of the initiative believe that “A human cell atlas would have immediate, tangible, and transformative benefits…[and] would likely impact almost every aspect of biology and medicine, leading to a richer understanding of life’s most fundamental units and principles.”

Aviv Regev of the Broad Institute described the anticipated impact of the Human Cell Atlas initiative by saying, “We believe that a successful description of all the cells in the healthy human body will impact almost every aspect of biology and medicine in the decades to come” (Kelland, 2016).

The Common Fund’s recent Request for Information provides this compelling synopsis:

Through the characterization of cell functional history, morphology, lineage mapping, and molecular characterization to develop more detailed maps, we have the opportunity to identify the foundational principles underlying cellular organization in human tissues that could lead to a new level of understanding in many scientific areas including developmental and aging processes, emergence of pathological states and how to engineer complex functional tissue.

Is it also time to begin to consider the potential impact of this initiative on our understanding of toxicology and ability to predict human toxicity? Will the research breakthroughs resulting from single cell analysis and the Human Cell Atlas provide the technological breakthrough(s) needed to transform the way we predict human toxicity?

We welcome your serious and substantive commentary.

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