Science - 06.12.2019

(singke) #1

3 min followed by a 5-min dissociation time.
Regeneration was accomplished using 3 M
magnesium chloride with a 180-s contact time
and injected four times per cycle. Raw senso-
grams were analyzed using ProteOn Manager
software (Bio-Rad), including interspot and
column double referencing, and either Equilib-
rium fits or Kinetic fits with Langmuir model,
or both, were used when applicable. For the
Biacore4000 instrument, we used similar con-
ditions but lower ligand capture levels. In the
case of Fab-antigen kinetic and affinity mea-
surements on ProteOn XPR36 or Biacore4000,
we used a similar ligand-capture technique
with several modifications. The capture re-
agent was His-tag Rabbit pAb (GenScript Cat.
Sensor Chip surface using the same protocol
from the GE Human Antibody Capture Kit
referenced above. Our regeneration solution
was phosphoric acid 0.85% with a 30-s con-
tact time, four injections per cycle. In the case
of the ferritin nanoparticle experiment, we
used the ProteOn XPR36 system and Human
Antibody Capture protocol described above
with one additional step. We captured PGT128
IgG at 1300 RU level in all channels, including
reference, followed by NP (as ligand) capture
at 1600 RU. All other steps were the same as
in the Human Antibody Capture protocol.
Analyte concentrations were measured on a
NanoDrop 2000c Spectrophotometer using an
absorption signal at 280 nm ( 8 ).

NGS dataset of human BCR HCs

This work utilized a large NGS dataset of 1.1 ×
109 amino acid sequences of BCR HCs from
14 healthy, HIV-uninfected donors. In this
dataset, 255 million sequences from 10 donors
were obtained from ( 21 ), which used the HiSeq
sequencing platform and an amplification
strategy including unique identifiers (UIDs)
to enable discrimination of unique mRNA
transcripts from PCR artifacts. These 10 do-
nors were evenly divided between males and
females and nearly evenly divided between
Caucasians and African Americans, and had
ages ranging from 18 to 30 ( 21 ). These se-
quences were collapsed by UID, assigned to
VDJ gene segments with Abstar ( 21 ), and
then rendered unique by clustering at the
99% amino acid identity level within each of
six biological replicates per donor. Thus the
255 million sequences were unique at the
amino acid level within biological replicates.
JSON output files from Abstar were con-
verted to parquet format and uploaded to the
Amazon S3 storage cloud. To query databases,
Amazon Elastic Map Reduce (EMR) 5.15.5
was used to configure a Spark cluster with
added PySpark and Zeppelin configurations.
Zeppelin was used to assemble PySpark scripts
to query the database with custom scripts. An
additional 858 million sequences from four

additional donors were obtained here by both
HiSeq and NextSeq sequencing platforms
without the use of UIDs, as described below.

BCR HC sequencing for four donors
Full leukopaks (three blood volumes) were
obtained from four human subjects (AllCells
LLC or Hemacare, Inc.) under a protocol ap-
proved by the Institutional Review Board of
the respective commercial provider. All subjects
were healthy, HIV-negative adults with no
reported acute illness in the 14 days prior to
leukapheresis, and samples were deidentified
prior to shipment. The Institutional Review
Board of The Scripps Research Institute deter-
mined that research with these samples did
not constitute human subjects research. Im-
mediately upon receipt of the leukopak, pe-
ripheral blood mononuclear cells (PBMCs)
were purified by gradient centrifugation and
cryopreserved in aliquots of approximately
5×10^8 PBMCs. The junctional regions of anti-
body heavy chain libraries were amplified as
in Williset al.( 48 ). SPRI-purified sequencing
libraries were initially quantified using fluo-
rometry (Qubit, Thermo Fisher Scientific)
before size determination using a bioanalyzer
(Agilent 2100). Libraries were requantified
using qPCR (KAPA Biosystems) before sequenc-
ing on either an Illumina HiSeq (2 × 150–bp
chemistry) or NextSeq (2 × 150–bp chemistry).
Sequences were merged with PANDAseq using
the default (symple_bayesian) merging algo-
rithm before annotation with Abstar ( 21 ). Iden-
tical amino acid sequences from the same
donor and biological replicate were collapsed
into a single unique amino acid sequence.

BG18 precursor frequency estimate
The NGS dataset of human BCR HCs was
queried by bioinformatic searches to gain
information on the frequency of BG18-like
HCDR3s in the human B cell repertoire (fig.
S5). HCDR3s meeting the definition of BG18-
like feature set i in fig. S5A, constituting a
broad set of potential BG18-like HCDR3 pre-
cursors, were identified in 14 of 14 donors
(fig. S5C). The geomean frequency was 1 in
58,000 among the 10 donors sequenced by
Brineyet al.( 21 )usingUIDs.Torefinethis
frequency estimate, we considered that only
11 of 14 BG18 iGL variants with NGS-derived
HCDR3s differing in the HCDR3 junctions
(fig. S5B) exhibited binding to N332-GT2 (Fig.
1D). BG18-like feature set ii (HCDR3 junction
features) in fig. S5A characterized amino acids
present in the nontemplated junction regions
of BG18 and its somatic variants ( 17 )andinthe
11 precursors that bound to N332-GT2. The
frequency of HCDR3s meeting the definitions
for both feature sets i and ii was found to be
lower than those within set i by a factor of

  1. Because the VLgene plays an important
    role In the BG18 V1-loop straddling binding

mode, we incorporated VLgene usage into the
frequency estimate, as feature set iii (“VLgene
family”). We made the conservative assump-
tion that only VL3 LCs can support the BG18-
class binding mode, as all VL3LCstested
bound with high affinity to N332-GT2. The
frequency of all VL3-derived Abs in the HC-LC
paired sequences in DeKoskyet al.( 49 ) was
1in9(13845VL3s in 127701 sequences). We
also assumed that any VHgene can support
this binding mode, because when five of the
most common human VHgenes were substi-
tuted into BG18 iGL 1 , all five variants showed
low nanomolar binding to N332-GT2 (Fig. 1D).
Therefore, no frequency factor was imposed
for VHgene usage. Multiplying the frequencies
of all three feature sets together gave our best
estimate for the frequency in the human B cell
repertoire of BG18-like precursors that could
be targeted by N332-GT2: 1 in 54 million.

N332-GT–specific naïve human B cell sorting
and BCR sequencing
LRS (leukoreduction) tubes were obtained
from the San Diego Blood Bank from healthy,
HIV-seronegative human donors. These studies
do not constitute human subjects research,
as determined by the Institutional Review
Boards of both La Jolla Institute and The
Scripps Research Institute. More than 1 billion
peripheral blood mononuclear cells were reg-
ularly recovered from each donor. CD19+Bcells
were isolated using a positive-selection magnetic-
bead separation kit (Miltenyi Biotec) and resus-
pended in complete RPMI media with 10% FBS.
Avi-tagged protein immunogens were bio-
tinylated using the Bulk BirA kit (Avidity, LLC).
N332-GT5 and N332-GT5-KO probes were used
in N332-GT5 sorting experiments. N332-GT2
and N332-GT2-KO probes were used in N332-
GT2 sorting experiments. N332-GT1 and MD39
probes were used in N332-GT1 sorting experi-
ments. 11mutBand MD39 probes were used in
11mutBsorting experiments. Biotinylated pro-
tein immunogens were individually premixed
with fluorescently labeled streptavidin to form
tetramer probes. Multiple tactics were used
to avoid false positives: (i) used two“positive”
probes, (ii) each“positive”probe used a dif-
ferent protein tag (His-tag or Strep-tag) to
avoid tag specific B cells, (iii) used a“negative”
probe to identify N332-epitope specific B cells,
(iv) chose independent (no tandems) fluoro-
chromes for all probes to avoid fluorochrome
specific B cells ( 29 ). For example, N332-GT2
sorting experiments used the follow probes:
N332-GT2–StrepTag-biotin + streptavidin Alexa
Fluor 647 (“N332-GT2-S-A647”), N332-GT2–
HisTag-biotin + streptavidin Brilliant Violet
421 (“N332-GT2-H-BV421”), and N332-GT2-KO–
StrepTag-biotin + streptavidin phycoerythrin
Cells were incubated with N332-GT probes

Steichenet al.,Science 366 , eaax4380 (2019) 6 December 2019 11 of 13


on December 12, 2019^

Downloaded from
Free download pdf