DOI: 10.5061/dryad.m905qfvdq
title: Dermal fibroblast cultures recapitulate differences between deermice and mice in responses to a Toll-like receptor agonist

description: The white-footed deermouse Peromyscus leucopus is a primary reservoir for
 the agents of Lyme disease and other zoonoses in North America. These and
 other species of Peromyscus are tolerant of the infection by the bacteria,
 protozoa, and viruses they host. This is mainly achieved by mitigating the
 damaging effects of the innate immune response. In previous studies, we
 demonstrated differences between P. leucopus and either inbred or outbred
 M. musculus in the degree of sickness and profiles of biomarkers after
 exposure to bacterial lipopolysaccharide, a TLR4 agonist. To develop a
 method for broadly assessing of innate immunity of capture-release mammals
 in nature, we evaluated using bulk and single-cell RNA-seq primary dermal
 fibroblast cultures of P. leucopus and M. musculus in their short-term
 responses to a lipopeptide that is a TLR2 agonist. As we had observed for
 experimental animals, the fibroblast cultures of the two species displayed
 both similarities and differences in their responses to the agonist. The
 notable differences included the greater magnitude of an anti-viral
 profile of cytokines and other effectors in the deermouse fibroblasts and
 the occurrence of an interleukin-11 response in the mouse cultures but not
 deermouse. We also observed in both species' cultures an increased
 transcription of several types of endogenous retrovirus (ERV) elements
 after exposure of the cells to the agonist. The P. leucopus cells were
 distinguished from M. musculus cells in the generally shorter retroviral
 open reading frames among the differentially expressed sequences. This was
 consistent with previous findings about ERV transcription in P. leucopus
 and M. musculus and suggests a greater suppression of ERV activity in P.
 leucopus. The results affirm the feasibility of this in vitro model for
 both laboratory- and field-based studies without need for euthanasia, and
 that inherent differences between deermice and mice in innate immune
 responses can be demonstrated in primary fibroblasts as well as the
 animals themselves.
description: # Dermal fibroblast cultures recapitulate differences between deermice and
 mice in responses to a Toll-like receptor agonist Dataset DOI:
 [10.5061/dryad.m905qfvdq](10.5061/dryad.m905qfvdq) ## Description of the
 data and file structure Peromyscus leucopus and Mus musculus RNA-seq data
 of coding sequences (CDS), endogenous retroviruses (ERVs) and species
 comparisons across treatment groups of control or 1 µg/ml or 10 µg/ml
 Pam3CSK4.  ### Files and variables #### File: TableD6_PM_ERV_100k_FC.xlsx
 **Description:** Table D6. ERV/TEs ≥500 bp of P. leucopus and M. musculus
 dermal fibroblasts without (control) or with 1 µg/ml Pam3CSK4 and by
 length, transcription, and fold change of treatment to control. Column
 names: ERV ≥500, genome location, length (bp), mean transcription control,
 mean transcription 1 µg/ml Pam3CSK4, log2 fold chain (FC).  #### File:
 TableD1_Peromyscus_CDS_22K.xlsx **Description:** Table D1. Peromyscus
 leucopus dermal fibroblast normalized RNA-seq reads per kb of genome-wide
 CDS by animal source, treatment (control or 1 µg/ml or 10 µg/ml Pam3CSK4),
 and comparison of 1 µg/ml treatment to control by paired t-test and mean
 paired fold-change, and mean transcription across all samples by gene
 Column names: gene, length in base pairs (bp), 25417 control, 25418
 control, 25459 control, 25510 control, 25558 control, 25417 1µg/ml, 25418
 1µg/ml, 25459 1µg/ml, 25510 1µg/ml, 25558 1µg/ml, 25417 10µg/ml, 25418
 10µg/ml, 25459 10µg/ml, 25510 10µg/ml, 25558 10µg/ml, paired t-test 1
 µg/ml vs control, fold-change 1 µg/ml vs control, log10 mean transcription
 (n=15) #### File: TableD4_Peromyscus_ERV_1M.xlsx **Description:** Table
 D4. Endogenous retrovirus (ERV) /transposable element sequences by name,
 genome location, and length of Peromyscus leucopus LL stock Column names:
 ERV name, location, length in base pairs (bp).  #### File:
 TableD5_Mus_ERV__1M.xlsx **Description:** Table D5. Endogenous
 retrovirus/transposable element sequences by name, genome location, and
 length of Mus musculus C57BL/6. Column names: ERV name, location, length
 in base pairs (bp).  #### File: TableD2_Mus_CDS_22K.xlsx
 **Description:** Table D2. Mus musculus dermal fibroblast normalized
 RNA-seq reads per kb of genome-wide CDS by animal source, treatment
 (control or 1 µg/ml or 10 µg/ml Pam3CSK4), and comparison of 1 µg/ml
 treatment to control by paired t-test and mean paired fold-change, and
 mean transcription across all samples by gene. Column names: gene, length
 in base pairs (bp), MF1 control, MF2 control, MF3 control, MM1 control,
 MM2 control, MF1 1 µg/ml, MF2 1 µg/ml, MF3 1 µg/ml, MM1 1 µg/ml, MM2 1
 µg/ml, MF1 10 µg/ml, MM2 10 µg/ml, MF3 10 µg/ml, MM1 10 µg/ml, MF2 10
 µg/ml, paired t-test 1 µg/ml vs control, fold-change 1 µg/ml vs control,
 log10 mean transcription (n=15) #### File: TableD3_PM_paired_14K.xlsx
 **Description:**  Table D3.Paired treatment-to-control fold-change (FC)
 and paired t-tests of transcribed (TPM≥10) CDS (n= 14,979) in common for
 M. musculus (M) and P. leucopus (P) treated with Pam3CSK4 at 1 µg (01) or
 10 µg/ml (10).  Column names: gene, log2 FC M01, ttest p M01, log2 FC M10,
 ttest p M10, log2 FC P01, ttest p P01, log2 FC P10, ttest p P10, P01/M01
 FC #### File: Table_D7.xlsx **Description:**  Differential gene expression
 of dermal fibroblasts to TLR agonist by isoform for 13,786 genes of Mus
 musculus for which there are two isoforms for protein coding sequences
 Column names: gene name first_isoform, length_1 (bp), TPM mean 1, fold
 change (FC) 1, log₂ FC 1, FDR p-value 1, gene name second_isoform,
 length_2 (bp), TPM mean 2, fold change (FC) 2, log₂ FC 2, FDR p-value 2
 #### File: Table_D8.xlsx **Description:**  Differential experssion of
 ERV/TEs ≥500 bp of Mus musculus (Table D5) in low-passage dermal
 fibroblasts untreated or treated with 1 µg/ml Pam3CSK4 Column names: M.
 musculus ERV/TE, genome location, sequence length, log10 length, z_score
 length, MF2 1 µg/ml TPM, MF3 1 µg/ml TPM, MM2 1 µg/ml TPM, MM1 1 µg/ml
 TPM, MF1 1 µg/ml TPM, MF2 cont TPM, MF3 cont TPM, MM2 cont TPM, MM1 cont
 TPM, MF1 cont TPM, mean TPM, log10 MF2_1, log10 MF3_1, log10 MM2_1, log10
 MM1_1, log10 MF1_1, log10 MF2_C, log10 MF3_C, log10 MM2_C, log10 MM1_C,
 log10 MF1_C, paired t-test p, negative log10 p, fold change MF2, fold
 change MF3, fold change MM2, fold change MM1, fold change MF1, mean fold
 change, log2 mean fold change #### File: Table_D9.xlsx
 **Description:**  Differential experssion of ERV/TEs ≥500 bp of Peromyscus
 leucopus (Table D4) in low-passage dermal fibroblasts untreated or treated
 with 1 µg/ml Pam3CSK4 Column names: P. leucopus ERV/TE, genome location,
 sequence length, log10 length, z_score length, 25558M 1 µg/ml, 25417F 1
 µg/ml, 25459F 1 µg/ml, 25510M 1 µg/ml, 25418F 1 µg/ml, 25558M cont, 25417F
 cont, 25459F cont, 25510M cont, 25418F cont, mean TPM, log10 25558M_1,
 log10 25417F_1, log10 25459F_1, log10 25510M_1, log10 25418F_1, log10
 25558M_C, log10 25417F_C, log10 25459F_C, log10 25510M_C, log10 25418F_C,
 paired t-test p, negative log10 p, fold change 25558M, fold change 25417F,
 fold change 25459F, fold change 25510M, fold change 25418F, mean fold
 change, log2 mean fold change ## Code/software Microsoft Excel can be used
 to view the files